NZ741586B2 - New polypeptide having affinity to pd-l1 - Google Patents
New polypeptide having affinity to pd-l1 Download PDFInfo
- Publication number
- NZ741586B2 NZ741586B2 NZ741586A NZ74158616A NZ741586B2 NZ 741586 B2 NZ741586 B2 NZ 741586B2 NZ 741586 A NZ741586 A NZ 741586A NZ 74158616 A NZ74158616 A NZ 74158616A NZ 741586 B2 NZ741586 B2 NZ 741586B2
- Authority
- NZ
- New Zealand
- Prior art keywords
- binding
- seq
- sequence
- group
- binding polypeptide
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- A61K38/17—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
- A61K38/1703—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
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- A61K47/30—Macromolecular organic or inorganic compounds, e.g. inorganic polyphosphates
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- C07K14/195—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria
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Abstract
The present disclosure relates to a class of engineered polypeptides having a binding affinity for programmed death-ligand 1 (PD-L1), and provides a PD-L1 binding polypeptide comprising the sequence ERNX4AAX7EIL X11LPNLX16X17X18QX20WAFIWX26LX28D. The present disclosure also relates to the use of such a PD-L1 binding polypeptide as a therapeutic, prognostic and/or diagnostic agent. Wherein specific embodiments the PD-L1 binding motif is a binding polypeptide, antibody, fusion protein or conjugate. h a PD-L1 binding polypeptide as a therapeutic, prognostic and/or diagnostic agent. Wherein specific embodiments the PD-L1 binding motif is a binding polypeptide, antibody, fusion protein or conjugate.
Description
NEW POLYPEPTIDE HAVING AN AFFINITY TO PD-L1
Field of the invention
The t disclosure relates to a class of engineered polypeptides
having a binding affinity for programmed death-ligand 1(in the following referred
to as PD-L1). The present disclosure also relates to the use of such a PD-L1
binding polypeptide as a therapeutic, prognostic and/or diagnostic agent.
ound
Under normal physiologic conditions, the immune checkpoints are crucial
for ining self-tolerance (i.e. prevent autoimmunity) and for modulating the
immune response to protect against tissue damage when the immune system is
responding to pathogenic infections. At times, tumor cells can co-opt certain
immune checkpoint pathways to escape from immunesurveillance mechanisms.
Inhibition of immune oints has therefore emerged as a promising
ch in cancer immunotherapy. The two immune checkpoint ors that
have been most actively studied in this context are the cytotoxic T-lymphocyteassociated
antigen (CTLA-4; also known as CD152) and programmed cell death
protein 1 (PD-1; also known as CD279), which regulate the immune response at
different . CTLA-4 primarily regulates immune responses early in T-cell
activation, whereas PD-1 primarily limits the ty of T-cells in the effector
phase within tissues and tumors (Pardoll, 2012, Nat. Rev. Cancer, 12:252-64).
PD-1 has two known ligands: programmed death-ligand 1 (PD-L1; also
known as human B7 homolog 1, B7-H1, or cluster of differentiation 274, CD274)
and programmed ligand 2 ; also known as B7-DC and CD273).
Both ligands belong to the B7 immunoglobulin superfamily and are type I
transmembrane glycoproteins composed of IgC- and IgV-type extracellular
domains. r, it was recently reported that PD-L1 and PD-L2, as well as
PD-1, also exist in soluble forms in addition to being membrane bound. PD-L1
and PD-L2 share approximately 40 % amino acid residue identity. Whereas the
expression of PD-L2 is mainly limited to antigen
presenting cells, PD-L1 is expressed in both hematopoietic and non-
hematopoietic cells. High tumor expression of PD-L1 is associated with
increased aggressiveness and worse prognosis (Dai et al, 2014, Cellular
Immunology, 290:72-79).
The clinical significance of targeting immune checkpoint pathways has
been demonstrated with several monoclonal antibodies inhibiting ,
PD-1 and PD-L1, which work by restoring protective immune responses to
tumor cells. The anti—CTLA—4 antibody ipilimumab (Yervoy®, Bristol Myers
Squibb) was approved by FDA in 2011 for the treatment patients with
metastatic ma where a durable response was observed in 10-15 % of
the patients. However, ipilimumab is ated with -related
toxicities, potentially due to its role in the priming phase of the immune
se thereby also affecting normal tissues. A safer approach may be to
target the D-L1 pathway to restore umor immunity selectively
within the tumor microenvironment. Inhibition of the PD-1/PD-L1 pathway has
demonstrated durable response in 30-35 % of patients with advanced
melanoma, which in 2014 resulted in the FDA approval of the anti-PD-1
antibodies lizumab (formerly lambrolizumab; Keytruda®, Merck) and
nivolumab (Bristol Myers Squibb and Ono Pharmaceutical) (Shin and Ribas,
2015, Curr. Opin. |mmunol., 33:23-35; Philips and Atkins, 2015, International
Immunology, 27:39-46). The first PD-L1 targeting antibody investigated in
clinical trials was MDX-1105 which was evaluated in a Phase I study in
patients with advanced solid tumors including melanoma, non-small cell lung
cancer (NSCLC), colorectal cancer, renal cell carcinoma, n cancer,
pancreatic cancer, gastric cancer and breast cancer (Momtaz and Postow,
2014, Pharmgenomics Pers Med. 7:357-65). The results demonstrated
potential benefits of PD-L1 de. Other antibodies against PD—L1 that are
currently in Phase III al trials include atezolizumab (MDPL3280A,
Genentech), durvalumab (MEDI4736, Medlmmune/Astra Zeneca, Celgene),
and avelumab (MSBOO10718C, EMD Serono, Pfizer).
To e the efficacy and increase the number of patients that
d to immunotherapy, it may be beneficial to target the antitumor
immune response at multiple levels. This may be ed through
2016/076040
synergistic combinations. For instance, preclinical studies combining CTLA-4
and PD-1 blocking antibodies (ipilimumab and nivolumab) has demonstrated
or antitumor activity, but with a toxicity similar to TLA-4
monotherapy (Shin and Ribas, 2015, supra). Furthermore, PD-L1 is
speculated to be a potential biomarker, due to its abundance in the tumor
microenvironment and because tumor expression of PD-L1 has a strong
association with se to anti-PD-1/PD-L1 therapy.
The high prevalence of cancer and infectious diseases, together with a
high unmet medical need, warrants the development of new modes of
treatment. Since tissue penetration rate is negatively associated with the size
of the molecule, a relatively large antibody molecule inherently has poor
tissue distribution and ation capacity.
Thus, the use of monoclonal antibodies is not always optimal for
therapy and there is continued need for ion of agents with a high affinity
for PD-L1. Ofgreat st is also the provision of uses of such molecules in
the treatment, sis and prognosis of PD—L1 related disorders.
Summary of the invention
It is an object of the present disclosure to provide new PD-L1 binding
agents, which could for example be used for therapeutic, prognostic and
diagnostic applications.
It is an object of the present disclosure to e a new multispecific
agent, such as a bispecific agent, which has affinity for PD-L1 and at least
one additional antigen.
It is an object of the present disclosure to provide a molecule allowing
for efficient therapy of for example various forms of cancer and ious
disease, while alleviating the abovementioned and other drawbacks of current
therapies.
It is an object of the present disclosure to provide a molecule suitable
for prognostic and diagnostic applications, for example stic and
diagnostic application in relation to various forms of cancer and infectious
disease.
These and other s, which are evident to the skilled person from
the present disclosure, are met by the different aspects of the invention as
claimed in the appended claims and as generally disclosed herein.
Thus, in the first aspect of the disclosure, there is provided a PD-L1
binding ptide, comprising a PD-L1 binding motif BM, which motif
consists of an amino acid sequence selected from:
i) ERNX4AAX7E|L X11LPNLX16X17X1sQX20 WAFIWX25LX28D
wherein, independently from each other,
X4 is selected from A, D, E, F, H, I, K, L, N, Q, R, S, T, V and Y;
X7 is selected from A, E, F, H, N, Q, S, T, V, W and Y;
X11 is selected from A, D, E, F, H, K, L, N, Q, R, S, T, V, W and Y;
X16 is selected from N and T;
X17 is ed from A, H, K, N, Q, R and S;
X18 is selected from A, D, E, G, H, K, L, N, Q, R, S, T, V and Y;
X20 is selected from H, I, K, L, N, Q, R, T, V and Y;
X25 is selected from K and S; and
X28 is selected from A, D and E;
ii) an amino acid sequence which has at least 96 % identity to the
sequence defined in i).
The above definition of a class of sequence related, PD-L1 binding
polypeptides is based on a statistical analysis of a number of random
polypeptide ts of a parent scaffold, that were selected for their
interaction with PD-L1 in selection experiments. The identified PD-L1 binding
motif, or ’, corresponds to the target binding region of the parent scaffold,
which region constitutes two alpha helices within a three-helical bundle
protein domain. In the parent scaffold, the varied amino acid residues of the
two BM helices constitute a binding surface for ction with the nt
Fc part of antibodies. In the present sure, the random variation of
binding surface residues and subsequent selection of ts have replaced
the Fc interaction capacity with a capacity for interaction with PD-L1.
As the skilled person will realize, the function of any ptide, such
as the PD-L1 binding capacity of the polypeptide of the present disclosure, is
dependent on the tertiary structure of the polypeptide. It is therefore possible
to make minor s to the sequence of amino acids in a polypeptide
without affecting the function thereof. Thus, the disclosure encompasses
modified variants of the PD-L1 binding polypeptide, which have retained PD-
L1 binding characteristics.
In this way, encompassed by the present disclosure is a PD-L1 binding
polypeptide sing an amino acid sequence with 96 % or greater ty
to a polypeptide as defined in i). For e, it is possible that an amino acid
residue belonging to a certain functional grouping of amino acid residues (e.g.
hydrophobic, hydrophilic, polar etc) could be exchanged for another amino
acid residue from the same functional group.
In some embodiments, such changes may be made in any position of
the sequence of the PD-L1 g polypeptide as disclosed herein. In other
embodiments, such changes may be made only in the non-variable positions,
also denoted scaffold amino acid residues. In such cases, changes are not
d in the variable positions. In other embodiments, such changes may
be only in the variable positions. According to one definition of such “variable
positions”, these are positions denoted with an “X” in sequence i) as defined
above. According to another definition, “variable positions” are those positions
that are randomized in a selection library of Z variants prior to selection, and
may thus for example be positions 2, 3, 4, 6, 7, 10, 11, 17, 18, 20, 21, 25 and
28 in sequence i), as illustrated in Example 1.
The term ”% identity”, as used throughout the specification, may for
e be calculated as follows. The query sequence is aligned to the target
sequence using the L W algorithm (Thompson et al., (1994) Nucleic
Acids Research, 22: 4673-4680). A comparison is made over the window
corresponding to the shortest of the aligned sequences. The shortest of the
aligned sequences may in some instances be the target sequence. In other
instances, the query sequence may constitute the shortest of the aligned
sequences. The amino acid es at each position are compared and the
percentage of positions in the query sequence that have identical
correspondences in the target sequence is reported as % identity.
In another embodiment, there is provided a PD-L1 binding ptide
wherein in sequence i)
X4 is selected from A, D, E, F, H, I, K, L, N, Q, R, S, T, V and Y;
X7 is selected from E, F, H, N, Q, S, T, V, W and Y;
X11 is selected from A, D, H, L, Q, R, T, V, W and Y;
X15 is selected from N and T;
X17 is ed from A, H, K, N, Q, R and S;
X18 is selected from A, D, E, G, H, K, L, N, Q, R, S, T, V and Y;
X20 is selected from H, l, K, L, Q, R, T, V and Y;
X26 is selected from K and S; and
X28 is selected from A, D and E.
In r embodiment, there is provided a PD-L1 binding polypeptide,
wherein in sequence i)
X4 is selected from A, D, E, F, H, |, K, L, N, Q, R, S, T, V and Y;
X7 is selected from A, E, F, H, N, Q, S, T, V, W and Y;
X11 is selected from A, D, E, F, H, K, L, N, Q, R, S, T, V, W and Y;
X15 is selected from N and T;
X17 is selected from A, H, K, N, Q, R and S;
X18 is selected from A, D, E, G, H, K, L, N, Q, R, S, T, V and Y;
X20 is selected from H, l, K, L, N, Q, R, T, V and Y;
X25 is selected from K and S; and
X28 is ed from A, D and E.
In yet another embodiment, there is ed a PD-L1 binding
polypeptide, wherein in sequence i)
X4 is selected from A, D, E, F, H, I, K, L, N, Q, R, S, T and V;
X7 is ed from F, H, Q and Y;
X11 is ed from H, Q, W and Y;
X16 is selected from N and T;
X17 is selected from A, H, K, N, Q and S;
X18 is ed from A, E, G, H, K, L, N, Q, R, S, T, V and Y;
X20 is selected from H, l, K, Q, R and V;
X26 is selected from K and S; and
X28 is selected from A and D.
As used herein, “Xn” and “Xm” are used to indicate amino acids in
positions n and m in the sequence i) as defined above, wherein n and m are
integers which te the position of an amino acid within said sequence as
counted from the N-terminal end of said sequence. For example, X3 and X7
indicate the amino acid in position three and seven, respectively, from the N-
terminal end of sequence i).
In embodiments according to the first aspect, there are provided
polypeptides wherein Xn in sequence i) is independently selected from a
group of possible residues according to Table 1. The skilled person will
appreciate that Xn may be selected from any one of the listed groups of
possible residues and that this selection is independent from the selection of
amino acids in Xm, wherein n¢m. Thus, any of the listed le residues in
position Xn in Table 1 may be independently combined with any of the listed
possible residues any other variable position in Table 1.
The skilled person will appreciate that Table 1 is to be read as follows:
In one embodiment according to the first aspect, there is provided a
polypeptide wherein amino acid residue “Xn” in sequence i) is selected from
“Possible residues”. Thus, Table 1 discloses several ic and
individualized embodiments of the first aspect of the t disclosure. For
example, in one embodiment according to the first aspect, there is provided a
polypeptide wherein X4 in sequence i) is selected from A, D, E, l, K, L, N, Q, S
and T and in another embodiment according to the first aspect, there is
provided a polypeptide n X4 in sequence i) is selected from A, D, E, l,
K, Q, S and T. For avoidance of doubt, the listed embodiments may be freely
combined in yet other embodiments. For e, one such ed
embodiment is a polypeptide in which X4 is selected from A, D, E, l, K, Q, S
and T, while X7 is selected from F, H, Q and Y, and X18 is selected from A, L,
K and S.
Table 1
Xn Possible residues Xn Possible residues
X4 A, D, E, F, H, l, K, L, N, Q, X4 E
R, S, T and V X4 A
X4 A, D, E, F, H, l, K, L, N, Q, X4 D
R, S and T X4 K
X4 A, D, E, F, H, l, K, L, N, Q, X4 S
S and T X4 L
X4 A, D,E, K,L, N,Q,SandT X4 T
X4 A, D, E, l, K, L, N, Q, S and X7 E, F, H, N, Q, S, T, V, W
T and Y
X4 A, D, E, K, L, N, Q, and S X7 E, F, H, N, Q, S, V, W and
X4 A, D, E, l, K,Q,SandT Y
X4 A, E, K, L, N, Q, and S X7 E, F, H, N, Q, S, T, V and Y
X4 E, l, K, L, N, Q, S and T X7 E, F, H, N, Q, S, T, Wand
X4 A, D, K, L, N, and S Y
X4 A, K, L, N, and S X7 E, F, H, Q, S, T, V, W and Y
X4 A, D, E, Q and S X7 E, F, H, N, Q, S, V and Y
X4 A, D, E, K, and S X7 E, F, H, N, Q, S and Y
X4 A, K, L, and S X7 E, F, H, Q, S and Y
X4 A, D, E and S X7 E, F, H, Q and Y
X4 A, E,QandS X7 F,H,QandY
X4 A, E, K and S X7 F, Q and Y
X4 L, N,SandT X7 H,QandY
X4 L, S and T X7 F, Y
X4 A, D and K X7 F, Q
X4 A, E and S X7 Q, Y
X4 A, E and K X7 F
X4 A, D X7 Q
X4 A, K X7 Y
X4 D, K X7 H
X4 A, E X11 A, D, E, F, H, K, N, Q, R, S,
X4 A, S T, W a d Y
X4 E, S X11 D, E, F, H, K, N, Q, R, S, T,
X4 E, K Wand
X4 L,S X11 D, E, H, K,N,Q, R, S,T,W
X4 L, T and Y
x4 8, T X11 E, H, K, N, Q, R, S, T, W
Xn Possible residues Xn le residues
and Y X18 8
X11 E, H, K, N, Q, S, T, W and X18 H
Y X20 H, I, K, L, Q, R, T, V and Y
X11 E, H, K, N, Q, W and Y X20 H, I, K, L, Q, R, V and Y
X11 A, D, H, L, Q, R, T, V, W X20 H, I, K, Q, R and V
and Y X20 H, I, K an R
X11 H, O; W and Y X20 H, I and K
X11 Q, Y X20 H, K and R
X11 W, Y X20 K and R
X11 H, Y X20 I, K
X11 H X20 I, H
X11 Y X20 H: K
X16 N X20 H
X16 T X20 I
X17 A, H, K, N, Q and S X20 K
X17 A, K, N, Q, R and S X20 R
X17 A, K, N, Q and S X26 K
X17 A, N, Q and S X26 8
X17 K, N, Q and S X28 A, D
X17 N, Q and S X28 A, E
X17 N, Q X28 D, E
X17 N, S X28 A
X17 N X28 D
X17 Q X28 E
X17 S
X18 A, E, G, H, K, L, N, Q, R, S,
T, V and Y
X18 A, E, G, H, K, L, N, Q, R, S,
T and Y
X18 A, E, G, H, K, L, N, Q, R, S,
and Y
X18 A, E, G, H, K, L, N, Q, R
and S
X18 A, E, G, K, N, Q, R and S
X18 A, G, H, L, N, Q, S and Y
X18 A, G, N, Q and S
X18 A, H, Q and S
X18 A, H and Q
X18 A, L, K and S
X18 A, K, Q and S
X18 A, Q and S
X18 A, G
X18 A, Q
X18 A
X18 Q
X18 G
In one particular embodiment ing to the first aspect, there is
provided a polypeptide wherein sequence i) fulfills at least four of the seven
conditions l-Vll:
l. X7 is selected from F, H, Q and Y;
H. X11 is selected from H and Y;
lll. X16 is T;
IV. X17 is selected from N, Q and S;
V. X20 is ed from H, I, K and R;
VI. X26 is K; and
VII. X28 isAor D.
In one embodiment, sequence i) fulfills at least five of the seven
conditions l-Vll, such as least six of the seven conditions l-Vll. In one
particular embodiment, sequence i) fulfills all of the seven conditions l-Vll.
In some embodiments of a PD-L1 binding polypeptide according to the
first aspect, X7X11X20 is selected from FYK and WK. In some embodiments,
X11X17X20 is selected from YNK and YQK. In some embodiments, X11X18X20 is
YAK.
As described in detail in the experimental section to follow, the
selection of PD-L1 binding polypeptide variants has led to the identification of
a number of individual PD-L1 binding motif (BM) sequences. These
ces constitute individual embodiments of sequence i) according to this
aspect. The sequences of individual PD-L1 binding motifs correspond to
amino acid positions 8-36 in SEQ ID NO:1-808 presented in Figure 1. Hence,
in one ment of the PD-L1 binding polypeptide according to this aspect,
sequence i) ponds to the sequence from position 8 to position 36 in a
ce selected from the group consisting of SEQ ID NO:1-808. In one
embodiment, sequence i) corresponds to the sequence from on 8 to
position 36 in a sequence ed from the group consisting of SEQ ID
NO:1-93 and 774-796, such as the group consisting of SEQ ID NO:1-93 and
774-787. In one embodiment, sequence i) corresponds to the sequence from
position 8 to position 36 in a sequence selected from the group consisting of
SEQ ID NO:1-93, 775, 776, 779-781 and 784-786, such as the group
consisting of SEQ ID NO:1-93, 776, 780, 781, 784 and 786, such as the
group ting of SEQ ID NO:1—93, 776, 781 and 784, such as the group
ting of SEQ ID NO:1-93, 776 and 784 or the group consisting of SEQ
ID NO:1-93, 776 and 781, for example the group consisting of SEQ ID NO:1-
93 and 776 or the group consisting of SEQ ID NO:1-93 and 781 or the group
consisting of SEQ ID NO:1-93 and 784. In one embodiment, sequence i)
corresponds to the sequence from position 8 to on 36 in a sequence
selected from the group consisting of SEQ ID NO:1-93, 774, 775 and 780-
786, such as the group consisting of SEQ ID NO:1-93, 775, 780, 781, 784
and 786. In one embodiment, sequence i) corresponds to the sequence from
position 8 to on 36 in a sequence selected from the group consisting of
SEQ ID NO:1, 2, 17,776 and 781, such as the group consisting ofSEQ ID
NO: 1, 2 and 776. In one embodiment, sequence i) corresponds to the
sequence from on 8 to position 36 in SEQ ID NO:1, SEQ ID N02 or
SEQ ID NO:776. In one embodiment, sequence i) corresponds to the
sequence from position 8 to on 36 in a sequence selected from the
group ting of SEQ ID NO:1-93. In one embodiment, sequence i)
corresponds to the sequence from position 8 to position 36 in a sequence
selected from the group consisting of SEQ ID NO:1, 3-8, 11, 13, 16, 18, 20,
22, 23, 43 and 73. In one embodiment, sequence i) corresponds to the
sequence from position 8 to position 36 in a ce selected from the
group consisting of SEQ ID NO:1-24. For example, in one embodiment,
sequence i) corresponds to the sequence from position 8 to position 36 in a
ce selected from the group consisting of SEQ ID NO:1-16, such as the
group consisting of SEQ ID NO:1, 2, 4, 5, 7, 9 and 10. In another
embodiment, sequence i) corresponds to the sequence from position 8 to
position 36 in a sequence selected from the group consisting of SEQ ID
NO:1, 3-6, 9-10, 12-21, 23 and 24, such as the group consisting ofSEQ ID
NO:1, 4-6, 9, 14 and 18-21. In one embodiment, sequence i) corresponds to
WO 72280 2016/076040
the sequence from position 8 to position 36 in a sequence selected from the
group consisting of SEQ ID NO:1-12, 14 and 17-21. In one embodiment,
sequence i) corresponds to the sequence from position 8 to position 36 in a
sequence selected from the group consisting of SEQ ID NO:1-12 and 17,
such as the group consisting of SEQ ID NO:1-5 and 17, such as the group
consisting of SEQ ID NO:1, 2 and 17. In one embodiment, sequence i)
corresponds to the sequence from position 8 to position 36 in a sequence
selected from the group consisting of SEQ ID NO:1, 4, 5, 6, 9, 14 and 18-21,
such as the group consisting of SEQ ID NO:4, 5, 18 and 21, such as the
group consisting of SEQ ID NO:4, 5 and 21. In one embodiment, sequence i)
corresponds to the sequence from position 8 to position 36 in a sequence
selected from the group ting of SEQ ID NO:1, 2, 4, 5 and 21, such as
the group ting of SEQ ID NO:1 and 2. In one embodiment, sequence i)
corresponds to the sequence from position 8 to position 36 in SEQ ID NO:1,
SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:5 or SEQ ID NO:21.
In some ments of the present disclosure, the BM as defined
above “forms part of” a three-helix bundle protein domain. This is understood
to mean that the sequence of the BM is “inserted” into or “grafted” onto the
sequence of the al three-helix bundle domain, such that the BM
replaces a similar structural motif in the original . For example, without
wishing to be bound by , the BM is thought to constitute two of the three
helices of a three-helix bundle, and can therefore replace such a two-helix
motif within any three-helix bundle. As the skilled person will realize, the
replacement of two s of the three-helix bundle domain by the two BM
helices has to be performed so as not to affect the basic structure of the
polypeptide. That is, the overall folding of the Co backbone of the polypeptide
according to this embodiment of the invention is ntially the same as
that of the three-helix bundle protein domain of which it forms a part, e.g.
having the same elements of secondary structure in the same order etc.
Thus, a BM according to the present disclosure “forms part” of a three—helix
bundle domain if the polypeptide ing to this embodiment has the same
fold as the original domain, implying that the basic structural properties are
shared, those properties e.g. resulting in similar CD spectra. The skilled
person is aware of other parameters that are relevant.
In particular embodiments, the PD-L1 binding motif (BM) thus forms
part of a three-helix bundle protein domain. For example, the BM may
essentially constitute two alpha helices with an interconnecting loop, within
said helix bundle n domain. In particular embodiments, said three-
helix bundle protein domain is selected from domains of bacterial receptor
proteins. Non—limiting examples of such domains are the five ent three-
helical domains of Protein A from Staphylococcus aureus, such as domain B,
and derivatives thereof. In some embodiments, the three-helical bundle
protein domain is a variant of protein Z, which is derived from domain B of
staphylococcal Protein A (Wahlberg E eta], 2003, PNAS 100(6):3185-3190).
In some embodiments where the PD-L1 binding ptide as
disclosed herein forms part of a three-helix bundle protein domain, the PD-L1
binding polypeptide may comprise a binding module (BMod), the amino acid
sequence of which is selected from:
iii) K-[BM]—DPSQSXaXbLLXC dXeXfQ;
wherein
[BM] is a PD-L1 binding motif as defined ;
X3 is selected from A and S;
Xb is selected from N and E;
XC is selected from A, S and C;
Xd is ed from E, N and S;
X6 is selected from D, E and S; and
Xf is selected from A and S; and
iv) an amino acid sequence which has at least 93 % identity to a
sequence defined in iii).
In some embodiments, said polypeptide may beneficially exhibit a high
structural stability, such as resistance to chemical modifications, to s
in physical conditions and to proteolysis, during production and storage, as
well as in vivo.
As sed above, polypeptides comprising minor changes as
compared to the above amino acid sequences, which do not largely affect the
tertiary structure and the function of the polypeptide, are also within the scope
of the present disclosure. Thus, in some embodiments, sequence iv) has at
least 93 %, such as at least 95 %, such as at least 97 % identity to a
sequence defined by iii).
In one embodiment, Xa in sequence iii) is A.
In one embodiment, Xa in sequence iii) is S.
In one embodiment, Xb in sequence iii) is N.
In one embodiment, Xb in ce iii) is E.
In one embodiment, XC in ce iii) is A.
In one embodiment, XC in sequence iii) is S.
In one embodiment, XC in sequence iii) is C.
In one embodiment, Xd in sequence iii) is E.
In one embodiment, Xd in sequence iii) is N.
In one embodiment, Xd in sequence iii) is S.
In one embodiment, X6 in sequence iii) is D.
In one embodiment, X6 in sequence iii) is E.
In one ment, X6 in ce iii) is S.
In one embodiment, dee in sequence iii) is selected from EE, ES, SD, SE and SS.
In one embodiment, dee in sequence iii) is ES.
In one embodiment, dee in sequence iii) is SE.
In one embodiment, dee in sequence iii) is SD.
In one embodiment, Xf in sequence iii) is A.
In one embodiment, Xf in sequence iii) is S.
In one embodiment, in sequence iii), X8] is A; Xb is N; XC is A and Xf is A.
In one embodiment, in sequence iii), X8 is S; Xb is E; XC is A and Xf is A.
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In one embodiment, in sequence iii), Xa is A; Xb is N; XC is C and Xf is A.
In one embodiment, in sequence iii), Xa is S; Xb is E; XC is S and Xf is S.
In one embodiment, in sequence iii), X3 is S; Xb is E; XC is C and Xf is S.
In one embodiment, in sequence iii), Xa is A; Xb is N; XC is A; dee is ND and Xf is A.
In one embodiment, in sequence iii), Xa is S; Xb is E; XC is A; dee is ND and X is A.
In one embodiment, in sequence iii), Xa is A; Xb is N; XC is C; dee is ND and Xf is A.
In one ment, in sequence iii), Xa is S; Xb is E; XC is S; dee is ND and Xf is S.
In one ment, in sequence iii), Xal is S; Xb is E; Xc is C; XdXe is ND and X is S.
In one embodiment, in sequence iii), Xa is A; Xb is N; XC is A; dee is SE and Xf is A.
In one embodiment, in sequence iii), Xa is S; Xb is E; XC is A; dee is SE and X is A.
In one embodiment, in sequence iii), Xa is A; Xb is N; XC is C; dee is SE and Xf is A.
In one embodiment, in sequence iii), Xa is S; Xb is E; XC is S; dee is SE and X is S.
In one embodiment, in sequence iii), Xa is S; Xb is E; XC is C; dee is SE and Xf is S.
In one embodiment, in sequence iii), Xa is A; Xb is N; XC is A; dee is SD and Xf is A.
In one embodiment, in sequence iii), Xal is S; Xb is E; Xc is A; XdXe is SD and X is A.
In one embodiment, in sequence iii), Xa is A; Xb is N; XC is C; dee is SD and Xf is A.
In one embodiment, in sequence iii), Xa is S; Xb is E; XC is S; dee is SD and X is S.
In one embodiment, in sequence iii), Xa is S; Xb is E; XC is C; dee is SD and Xf is S.
In yet a further embodiment, sequence iii) corresponds to the
sequence from position 7 to position 55 in a sequence selected from the
group consisting of SEQ ID NO:1—808 presented in Figure 1. Hence, in one
embodiment of the PD-L1 binding polypeptide according to this aspect,
sequence iii) corresponds to the sequence from on 7 to position 55 in a
ce selected from the group ting of SEQ ID NO:1-808. In one
embodiment, sequence iii) corresponds to the sequence from on 7 to
position 55 in a sequence selected from the group consisting of SEQ ID
NO:1-93 and 774-796, such as the group consisting of SEQ ID NO:1-93 and
774-787. In one embodiment, sequence iii) corresponds to the ce from
position 7 to position 55 in a sequence selected from the group consisting of
SEQ ID NO:1-93, 775, 776, 779-781 and 784—786, such as the group
consisting of SEQ ID NO:1—93, 776, 780, 781, 784 and 786, such as the
group consisting of SEQ ID NO:1-93, 776, 781 and 784, such as the group
consisting of SEQ ID NO:1—93, 776 and 784 or the group consisting of SEQ
ID NO:1-93, 776 and 781, for example the group consisting of SEQ ID NO:1-
93 and 776 or the group consisting of SEQ ID NO:1—93 and 781 or the group
consisting of SEQ ID NO:1—93 and 784. In one ment, sequence iii)
corresponds to the sequence from position 7 to position 55 in a sequence
selected from the group consisting of SEQ ID NO:1-93, 774, 775 and 780—
786, such as the group consisting of SEQ ID NO:1-93, 775, 780, 781, 784
and 786. In one embodiment, sequence iii) corresponds to the sequence from
position 7 to position 55 in a sequence ed from the group consisting of
SEQ ID NO:1, 2, 17,776 and 781, such as the group consisting ofSEQ ID
NO: 1, 2 and 776. In one embodiment, sequence iii) corresponds to the
ce from position 7 to position 55 in SEQ ID NO:1, SEQ ID N02 or
SEQ ID NO:776. In one embodiment, sequence iii) corresponds to the
sequence from position 7 to position 55 in a ce selected from the
group consisting of SEQ ID NO:1—93. In one embodiment, sequence iii)
corresponds to the sequence from on 7 to position 55 in a sequence
selected from the group consisting of SEQ ID NO:1, 3-8, 11, 13, 16, 18, 20,
22, 23, 43 and 73. In one embodiment, sequence iii) corresponds to the
sequence from position 7 to position 55 in a sequence selected from the
group consisting of SEQ ID NO:1-24. For example, in one embodiment,
sequence iii) corresponds to the sequence from position 7 to position 55 in a
ce selected from the group consisting of SEQ ID NO:1-16, such as the
group consisting of SEQ ID NO:1, 2, 4, 5, 7, 9 and 10. In another
embodiment, sequence iii) corresponds to the sequence from position 7 to
on 55 in a sequence selected from the group consisting of SEQ ID
NO:1, 3-6, 9-10, 12-21, 23 and 24, such as the group consisting of SEQ ID
NO:1, 4-6, 9, 14 and 18-21. In one embodiment, sequence iii) corresponds to
the sequence from position 7 to position 55 in a sequence selected from the
group ting of SEQ ID NO:1—12, 14 and 17—21. In one embodiment,
sequence iii) corresponds to the sequence from position 7 to position 55 in a
sequence selected from the group consisting of SEQ ID 2 and 17,
such as the group consisting of SEQ ID NO:1-5 and 17, such as the group
ting of SEQ ID NO:1, 2 and 17. In one embodiment, sequence iii)
corresponds to the sequence from on 7 to position 55 in a sequence
selected from the group consisting of SEQ ID NO:1, 4, 5, 6, 9, 14 and 18-21,
such as the group consisting of SEQ ID NO:4, 5, 18 and 21, such as the
group consisting of SEQ ID NO:4, 5 and 21. In one embodiment, sequence iii)
corresponds to the sequence from position 8 to position 36 in a sequence
selected from the group consisting of SEQ ID NO:1, 2, 4, 5 and 21, such as
the group consisting of SEQ ID NO:1 and 2. In one embodiment, sequence iii)
corresponds to the sequence from position 7 to position 55 in SEQ ID NO:1,
SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:5 or SEQ ID NO:21.
Also, in a further embodiment, there is provided a PD—L1 binding
polypeptide, which comprises an amino acid sequence selected from:
v) YA-[BMod]—AP;
n [BMod] is a PD-L1 binding module as defined herein; and
vi) an amino acid sequence which has at least 90 % identity to a
sequence defined in v).
Alternatively, there is provided a PD-L1 binding polypeptide, which
comprises an amino acid sequence selected from:
vii) FN-[BMod]—AP;
n [BMod] is a PD-L1 g module as defined herein; and
viii) an amino acid sequence which has at least 90 % identity to a
sequence defined in vii).
For example, in one embodiment there is provided a PD-L1 binding
ptide ed from the group consisting of
ix) FNK-[BM]-DPSQS ANLLXC EAKKL NDAQA P;
wherein [BM] is a PD-L1 binding motif as defined above and XC is selected
from A and C; and
x) an amino acid sequence which has at least 90 % identity to a
sequence defined in ix).
In r embodiment, there is provided a PD-L1 binding polypeptide
ed from the group consisting of
xi) FAK-[BM]—DPSQS SELLXC EAKKL SESQA P;
wherein [BM] is a PD-L1 binding motif as defined above and XC is selected
from A, S and C; and
xii) an amino acid sequence which has at least 90 % identity to a
sequence defined in xi).
In another embodiment, there is provided a PD-L1 binding polypeptide
selected from the group consisting of
xiii) FAK-[BM]-DPSQS SELLXC EAKKL NDSQA P;
wherein [BM] is a PD-L1 binding motif as defined above and XC is selected
from A, S and C;
xiv) an amino acid sequence which has at least 90 % identity to a
sequence defined in xiii).
In yet another embodiment, there is provided a PD-L1 binding
polypeptide selected from the group consisting of
xv) YAK-[BM]-DPSQS SELLXC EAKKL NDSQA P;
wherein [BM] is a PD-L1 binding motif as defined above and XC is selected
from A, S and C;
xvi) and an amino acid ce which has at least 90 % identity to
a ce defined in xv).
As discussed above, polypeptides comprising minor s as
compared to the above amino acid sequences, which do not largely affect the
tertiary structure and the function of the polypeptide, also fall within the scope
of the present disclosure. Thus, in some embodiments, sequence vi), viii), x),
xii), xiv) or xvi) may for example be at least 90 %, such as at least 92 %, such
as at least 94 %, such as at least 96 %, such as at least 98 % identical to a
sequence defined by v, vii), ix), xi), xiii) and xv), tively.
In some embodiments, the PD-L1 binding motif may form part of a
polypeptide sing an amino acid sequence ed from
ADNNFNK-[BM]-DPSQSANLLSEAKKLNESQAPK;
ADNKFNK-[BM]-DPSQSANLLAEAKKLNDAQAPK;
ADNKFNK-[BM]-DPSVSKEILAEAKKLNDAQAPK;
ADAQQNNFNK-[BM]-DPSQSTNVLGEAKKLNESQAPK;
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AQHDE—[BM]—DPSQSANVLGEAQKLNDSQAPK;
VDNKFNK-[BM]—DPSQSANLLAEAKKLNDAQAPK;
K-[BM]—DPSESSELLSEAKKLNKSQAPK;
VDAKYAK-[BM]—DPSQSSELLAEAKKLNDAQAPK;
VDAKYAK-[BM]—DPSQSSELLAEAKKLNDSQAPK;
AEAKYAK-[BM]—DPSQSSELLSEAKKLNDSQAPK;
AEAKYAK-[BM]—DPSQSSELLSEAKKLNDSQAP;
AEAKFAK-[BMJ-DPSQSSELLSEAKKLNDSQAPK;
AEAKFAK-[BM]—DPSQSSELLSEAKKLNDSQAP;
AEAKYAK-[BM]—DPSQSSELLAEAKKLNDAQAPK;
AEAKYAK-[BM]—DPSQSSELLSEAKKLSESQAPK;
AEAKYAK-[BM]—DPSQSSELLSEAKKLSESQAP;
AEAKFAK-[BM]—DPSQSSELLSEAKKLSESQAPK;
AEAKFAK-[BM]—DPSQSSELLSEAKKLSESQAP;
AEAKYAK-[BM]—DPSQSSELLAEAKKLSEAQAPK;
AEAKYAK-[BMj-QPEQSSELLSEAKKLSESQAPK;
AEAKYAK-[BM]—DPSQSSELLSEAKKLESSQAPK;
AEAKYAK-[BM]—DPSQSSELLSEAKKLESSQAP;
AEAKYAK-[BM]—DPSQSSELLAEAKKLESAQAPK;
AEAKYAK-[BM]—QPEQSSELLSEAKKLESSQAPK;
AEAKYAK-[BMj-DPSQSSELLSEAKKLSDSQAPK;
AEAKYAK-[BM]—DPSQSSELLSEAKKLSDSQAP;
AEAKYAK-[BMj-DPSQSSELLAEAKKLSDSQAPK;
AEAKYAK-[BMj-DPSQSSELLAEAKKLSDAQAPK;
AEAKYAK-[BM]—QPEQSSELLSEAKKLSDSQAPK;
VDAKYAK-[BM]—DPSQSSELLSEAKKLNDSQAPK;
VDAKYAK-[BM]—DPSQSSELLAEAKKLNDAQAPK;
VDAKYAK-[BM]—DPSQSSELLSEAKKLSESQAPK;
VDAKYAK-[BM]—DPSQSSELLAEAKKLSEAQAPK;
VDAKYAK-[BM]—QPEQSSELLSEAKKLSESQAPK;
VDAKYAK-[BM]—DPSQSSELLSEAKKLESSQAPK;
K-[BM]—DPSQSSELLAEAKKLESAQAPK;
VDAKYAK-[BM]—QPEQSSELLSEAKKLESSQAPK;
VDAKYAK-[BM]—DPSQSSELLSEAKKLSDSQAPK;
VDAKYAK-[BM]—DPSQSSELLAEAKKLSDSQAPK;
VDAKYAK-[BM]—DPSQSSELLAEAKKLSDAQAPK;
VDAKYAK-[BM]—QPEQSSELLSEAKKLSDSQAPK;
VDAKYAK-[BM]—DPSQSSELLAEAKKLNKAQAPK;
K-[BMj-DPSQSSELLAEAKKLNKAQAPK; and
ADAKYAK-[BM]—DPSQSSELLSEAKKLNDSQAPK;
wherein [BM] is a PD—L1 binding motif as defined herein.
In one embodiment, the PD-L1 binding ptide comprises an
amino acid sequence selected from:
xvii) VDAKYAK-[BM]—DPSQSSELLSEAKKLNDSQAPK;
wherein [BM] is a PD—L1 binding motif as defined herein; and
xviii) an amino acid sequence which has at least 89 % identity to the
ce d in xvii).
In one embodiment, the PD-L1 binding polypeptide comprises an
amino acid sequence selected from:
xix) AEAKFAK-[BM]-DPSQSSELLSEAKKLSESQAPK;
wherein [BM] is a PD-L1 binding motif as defined herein; and
xx) an amino acid sequence which has at least 89 % identity to the
sequence defined in xix).
In one embodiment, the PD-L1 binding polypeptide comprises an
amino acid sequence selected from:
xxi) AEAKYAK-[BM]—DPSQSSELLSEAKKLNDSQAPK;
wherein [BM] is a PD-L1 binding motif as defined herein; and
xxii) an amino acid sequence which has at least 89 % identity to the
sequence defined in xxi).
In one embodiment, the PD-L1 g polypeptide comprises an
amino acid sequence selected from:
xxiii) AEAKFAK-[BM]—DPSQSSELLSEAKKLNDSQAPK;
wherein [BM] is a PD-L1 binding motif as d herein; and
xxiv) an amino acid sequence which has at least 89 % ty to the
sequence defined in xxiii).
Again, polypeptides comprising minor changes as compared to the
above amino acid sequences, which do not largely affect the tertiary structure
and the on of the polypeptide, also fall within the scope of the t
disclosure. Thus, in some embodiments, sequence xviii), xx), xxii) or xxiv)
may for example be at least 89 %, such as at least 91 %, such as at least 93
%, such as at least 94 %, such as at least 96 %, such as at least 98 %
identical to a sequence defined by xvii), xix), xxi) and xxiii), respectively.
Sequence xvii) or xxi) in such a ptide may be selected from the
group consisting of SEQ ID NO:1-814 presented in Figure 1. In one
embodiment of the PD-L1 binding polypeptide according to this aspect,
sequence xvii) or xxi) corresponds to the sequence from position 1 to position
58 in a ce selected from the group consisting of SEQ ID NO:1-808. In
one embodiment, sequence xvii) or xxi) ponds to the sequence from
position 1 to position 58 in a sequence selected from the group consisting of
SEQ ID NO:1-93, 774-796 and 4, such as the group consisting of SEQ
ID NO:1-93, 774-787 and 809-814. In one embodiment, sequence xvii) or xxi)
corresponds to the sequence from position 1 to position 58 in a sequence
selected from the group consisting of SEQ ID NO:1-93, 775, 776, 779-781,
784-786 and 809-814, such as the group consisting of SEQ ID NO:1-93, 776,
780, 781, 784, 786 and 809-814, such as the group consisting of SEQ ID
NO:1-93, 776,781,784 and 809-814, such as the group consisting of SEQ ID
NO:1-93, 776,784, 809 and 811-814 or the group consisting of SEQ ID NO:1-
93, 776, 781,809 and 811—814. In one embodiment, sequence xvii) or xxi)
corresponds to the sequence from position 1 to position 58 in a sequence
selected from the group consisting of SEQ ID NO:1-93, 776, 809 and 811-814
or the group consisting of SEQ ID NO:1-93, 781, 809 and 811-814 or the
group consisting of SEQ ID NO:1-93, 784 and 4. In one embodiment,
sequence xvii) or xxi) corresponds to the sequence from position 1 to on
58 in a sequence selected from the group consisting of SEQ ID NO:1-93, 774,
775, 780-786 and 810-814, such as the group ting of SEQ ID 3,
775, 780, 781, 784, 786 and 810-814. In one embodiment, ce xvii) or
xxi) corresponds to the sequence from position 1 to on 58 in a sequence
selected from the group consisting of SEQ ID NO:1-93, 776, 781 and 809—
813, such as the group consisting of SEQ ID NO:1-93, 781 and 810-813. In
one embodiment, sequence xvii) or xxi) corresponds to the sequence from
position 1 to on 58 in a sequence selected from the group consisting of
SEQ ID NO:1, 2, 17,776, 781, 809-812, such as the group consisting ofSEQ
ID NO: 1, 2, 776, 809, 811 and 812. In one embodiment, sequence xvii)
corresponds to the sequence from on 1 to position 58 in a sequence
selected from the group ting of SEQ ID 3, 776 and 781, such as
the group consisting of SEQ ID NO:1-93 and 781. In one embodiment,
sequence xvii) corresponds to the sequence from position 1 to position 58 in
a sequence selected from the group consisting of SEQ ID NO:1, 2, 17, 776
and 781, such as the group consisting of SEQ ID NO: 1, 2 and 776. In one
embodiment, sequence xvii) corresponds to the sequence from position 1 to
position 58 in SEQ ID NO:1, SEQ ID N02 or SEQ ID NO:776. In one
ment, sequence xvii) or xxi) corresponds to the sequence from
position 1 to position 58 in a sequence selected from the group consisting of
SEQ ID NO:1—93 and 811—813. In one embodiment, sequence xvii) or xxi)
corresponds to the sequence from position 1 to position 58 in a sequence
selected from the group consisting of SEQ ID NO:1, 3-8, 11, 13, 16, 18, 22,
23, 43, 73 and 811-813. In one embodiment, sequence xvii) or xxi)
corresponds to the sequence from position 1 to position 58 in a sequence
selected from the group consisting of SEQ ID NO:1-24 and 811-813. For
example, in one embodiment, ce xvii) or xxi) ponds to the
sequence from position 1 to position 58 in a sequence ed from the
group consisting of SEQ ID NO:1-16 and 811-813, such as the group
ting of SEQ ID NO:1, 2, 4, 5, 7, 9, 10, 811 and 812. In another
embodiment, ce xvii) or xxi) corresponds to the sequence from
position 1 to position 58 in a sequence selected from the group consisting of
SEQ ID NO:1,3-6, 9-10, 12-21, 23,24,811 and 812, such as the group
consisting of SEQ ID NO:1, 4-6, 9, 14,18-21,811 and 812. In one
embodiment, sequence xvii) or xxi) corresponds to the sequence from
position 1 to position 58 in a sequence selected from the group consisting of
SEQ ID NO:1-12, 14, 17-21 and 811-812. In one ment, sequence xvii)
or xxi) corresponds to the sequence from position 1 to position 58 in a
ce selected from the group consisting of SEQ ID NO:1-12, 17, 811
and 812, such as the group consisting of SEQ ID NO:1-5, 17,811 and 812,
such as the group consisting of SEQ ID NO:1, 2, 17,811 and 812. In one
embodiment, sequence xvii) or xxi) corresponds to the sequence from
position 1 to position 58 in a sequence selected from the group consisting of
SEQ ID NO:1, 4, 5, 6, 9, 14, 18, 19, 20, 21 and 811, such as the group
consisting of SEQ ID NO:4, 5, 18 and 21, such as the group consisting of
SEQ ID NO:4, 5 and 21. In one embodiment, sequence xvii)) corresponds to
the ce from position 8 to position 36 in a sequence selected from the
group consisting of SEQ ID NO:1, 2, 4, 5 and 21, such as the group
consisting of SEQ ID NO:1 and 2. In one embodiment, sequence xvii) or xxi)
corresponds to the sequence from position 1 to position 58 in SEQ ID NO:1 or
811. In one embodiment, sequence xvii) or xxi) corresponds to the sequence
from position 1 to position 58 in SEQ ID N02 or 812. In one embodiment,
sequence xvii) corresponds to the sequence from position 1 to position 58 in
SEQ ID NO:4, SEQ ID N05 or SEQ ID NO:21.
The terms “PD-L1 binding” and ng affinity for PD-L1” as used in
this specification refer to a property of a polypeptide which may be tested for
example by ELISA or by the use of surface plasmon resonance (SPR)
technology.
For example as described in the examples below, PD-L1 binding
ty may be tested in an experiment in which samples of the polypeptide
are captured on antibody-coated ELISA plates and biotinylated PD-L1 is
added followed by streptavidin-conjugated HRP. TMB substrate is added and
the absorbance at 450 nm is measured using a multi-well plate reader, such
as Victor3 (Perkin Elmer). The d person may then interpret the results
obtained by such ments to establish at least a qualitative measure of
the binding ty of the ptide for PD-L1. If a quantitative measure is
desired, for example to ine the EC50 value (the half maximal effective
concentration) for the interaction, ELISA may also be used. The response of
the polypeptide t a dilution series of biotinylated PD—L1 is measured
using ELISA as described above. The skilled person may then interpret the
results obtained by such experiments, and EC50 values may be calculated
from the s using for example GraphPad Prism 5 and non-linear
regression.
PD-L1 binding affinity may also be tested in an experiment in which
PD-L1, or a fragment thereof, is immobilized on a sensor chip of a surface
plasmon resonance (SPR) instrument, and the sample containing the
polypeptide to be tested is passed over the chip. Alternatively, the polypeptide
to be tested is immobilized on a sensor chip of the instrument, and a sample
containing PD-L1, or a fragment thereof, is passed over the chip. The skilled
person may then interpret the s obtained by such experiments to
establish at least a qualitative measure of the g affinity of the
polypeptide for PD-L1. If a quantitative measure is desired, for e to
determine a KD value for the interaction, surface plasmon resonance methods
may also be used. Binding values may for example be defined in a Biacore
(GE care) or ProteOn XPR 36 (Bio-Rad) instrument. PD-L1 is suitably
immobilized on a sensor chip of the instrument, and samples of the
polypeptide whose ty is to be determined are prepared by serial dilution
and injected in random order. KD values may then be calculated from the
results using for example the 1:1 Langmuir g model of the
BlAevaluation 4.1 software, or other suitable software, provided by the
instrument manufacturer.
The terms “albumin binding” and “binding affinity for n” as used
in this disclosure refer to a property of a polypeptide which may be tested for
example by the use of SPR technology in a e ment or ProteOn
XPR36 instrument, in an analogous way to the example described above for
PD-L1.
In one embodiment, the PD-L1 binding polypeptide is capable of
binding to PD-L1 such that the KD value of the interaction with PD-L1 is at
most 2 x10'8 M, such as at most 1 x10"8 M, such as at most 1 x10"9 M, such
as at most 5 x10'10 M, such as at most 3 x10'10 M.
2016/076040
In one embodiment, the PD-L1 g polypeptide is capable of
binding to PD-L1 such that the kd value of the interaction with PD-L1 is at
most 1 x10"3 s'1, such as at most 6 x104 s'1.
In one embodiment, there is provided a PD-L1 g polypeptide
according to any preceding item which is e of binding to PD-L1 such
that the E050 value of the interaction is at most 1 x 10'9 M, such as at most 1
x10'10 M, such as at most 7 X 10'11 M.
Binding of a polypeptide as defined herein to PD-L1 may interfere
either with signaling via PD-L1 in vivo or in vitro. When PD—L1 binds to PD-1,
the ligand/receptor interaction dampens the T-Iymphocyte response by e.g.
inhibiting kinases involved in T-lymphocyte activation. Thus, blocking the
binding of PD—L1 to PD-1 restores the hocyte response. ng
activity may for example be quantified by the half maximal inhibitory
concentration (ICSO), which is a measure of the effectiveness of a substance
in inhibiting a specific biological or biochemical function. This tative
measure indicates how much of a particular substance is needed to inhibit a
given biological process by half, and is ly used in the art.
Thus, in one embodiment, there is provided a PD-L1 binding
polypeptide as d herein which is capable of blocking PD-L1 dependent
signaling. In one embodiment, the half maximal inhibitory concentration
(IC50) of the blocking is at most 5 x 10'8 M, such as at most 1 x 10'8 M, such
as at most 5 x10'9 M, such as at most 3.5 x10'9 M, such as at most 1 x 10'9
M, such as at most 5 x10'10 M, such as at most 1 x10"10 M. In one
embodiment, the PD-L1 binding polypeptide is capable of blocking the
interaction of PD-L1 with PD-1.
In one embodiment, said PD-L1 is human PD-L1. In another
embodiment, said PD-L1 is rhesus monkey PD-L1.
The skilled person will understand that various modifications and/or
additions can be made to a PD—L1 binding polypeptide according to any
aspect disclosed herein in order to tailor the ptide to a specific
application without departing from the scope of the present disclosure.
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For example, in one embodiment, there is provided a PD-L1 binding
polypeptide as described herein, which polypeptide has been extended by
and/or comprises additional amino acids at the C terminus and/or N terminus.
Such a polypeptide should be understood as a polypeptide having one or
more additional amino acid residues at the very first and/or the very last
position in the polypeptide chain. Thus, a PD-L1 binding polypeptide may
se any suitable number of onal amino acid residues, for example
at least one additional amino acid residue. Each additional amino acid e
may individually or collectively be added in order to, for example, improve
and/or simplify production, purification, stabilization in vivo or in vitro, coupling
or detection of the polypeptide. Such additional amino acid residues may
comprise one or more amino acid residues added for the purpose of chemical
coupling. One example of this is the addition of a cysteine residue. Additional
amino acid residues may also provide a ”tag” for purification or detection of
the ptide, such as a Hise tag, a (HisGlu)3 tag (“HEHEHE” tag) or a
”myc” ) tag or a ”FLAG” tag for interaction with antibodies specific to
the tag or immobilized metal affinity chromatography (IMAC) in the case of a
Hise-tag.
In one embodiment, there is provided a PD-L1 binding polypeptide as
described herein which comprises additional amino acids at the C-terminal
and/or N-terminal end. For example, in one embodiment of the PD-L1 binding
polypeptide as disclosed herein, it consists of any one of the sequences
disclosed herein, having from 0 to 15 onal C-terminal and/or N-terminal
residues, such as from 0 to 7 additional inal and/or N-terminal
residues. In one embodiment, the PD-L1 binding polypeptide consists of any
one of the sequences disclosed herein, having from O to 15, such as from 0 to
4, such as 3 additional C-terminal residues. In one particular embodiment, the
PD-L1 binding polypeptide as described herein comprises the additional C-
terminal residues VDC or VEC.
The further amino acids as discussed above may be coupled to the
PD-L1 g polypeptide by means of chemical conjugation (using known
organic chemistry methods) or by any other means, such as expression of the
PD-L1 binding polypeptide as a fusion protein orjoined in any other fashion,
either directly or via a linker, for example an amino acid linker.
A further polypeptide domain may moreover provide another PD-L1
binding moiety. Thus, in a further embodiment, there is provided a PD-L1
g polypeptide in a multimeric form. Said multimer is understood to
comprise at least two PD-L1 binding polypeptides as disclosed herein as
monomer units, the amino acid sequences of which may be the same or
different. Multimeric forms of the polypeptides may se a suitable
number of domains, each having a PD—L1 g motif, and each forming a
monomer within the multimer. These domains may have the same amino acid
sequence, but alternatively, they may have ent amino acid sequences. In
other words, the PD—L1 binding polypeptide of the invention may form homo-
or heteromultimers, for example homo- or heterodimers. In one ment,
there is provided a PD-L1 binding ptide, wherein said monomer units
are covalently coupled together. In another ment, said PD-L1 binding
polypeptide monomer units are expressed as a fusion protein. In one
embodiment, there is provided a PD-L1 g polypeptide in dimeric form.
In one particular embodiment, said c form is a homodimeric form. In
another embodiment, said dimeric form is a heterodimeric form. For the sake
of clarity, throughout this disclosure, the term “PD-L1 binding ptide” is
used to encompass PD-L1 binding polypeptides in all forms, i.e. monomeric
and multimeric forms.
The further amino acids as discussed above may for example
comprise one or more further polypeptide (s). A further polypeptide
domain may provide the PD-L1 binding dimer with another function, such as
for example another binding function, or an enzymatic function, or a toxic
function or a fluorescent signaling function, or combinations thereof.
Furthermore, it may be beneficial that the PD—L1 binding polypeptide
as defined herein is part of a fusion protein or a ate comprising a
second or further moieties. Second and further moiety/moieties of the fusion
polypeptide or ate in such a protein may suitably have a desired
biological activity.
Thus, in a second aspect of the present disclosure, there is provided a
fusion protein or a conjugate, comprising a first moiety consisting of a PD-L1
binding polypeptide according to the first aspect, and a second moiety
ting of a polypeptide having a desired biological ty. In another
embodiment, said fusion n or conjugate may additionally comprise
further moieties, comprising desired biological activities that can be either the
same as or different from the biological activity of the second moiety.
Non-limiting examples of a d biological activity se a
therapeutic activity, a binding activity and an enzymatic activity. In one
embodiment, the second moiety having a desired biological activity is a
therapeutically active polypeptide. In one embodiment, said second moiety is
an immune response modifying agent. In another embodiment, said second
moiety is an anti-cancer agent.
In one embodiment of either the first or second aspect of the present
disclosure, there is provided a PD-L1 binding polypeptide, fusion protein or
ate which comprises an immune response ing agent. Non-
limiting examples of additional immune response modifying agents include
immunomodulating agents or other anti—inflammatory agents
In one embodiment of either the first or second aspect of the present
disclosure, there is provided a PD-L1 binding polypeptide, fusion protein or
conjugate which comprises an anti-cancer agent. Non-limiting examples of
anti-cancer agents include agents ed from the group consisting of
auristatin, anthracycline, calicheamycin, combretastatin, doxorubicin,
duocarmycin, the CC—1065 anti-tumor-antibiotic, ecteinsascidin,
geldanamycin, maytansinoid, methotrexate, xin, taxol, ricin, bouganin,
gelonin, pseudomonas exotoxin 38 (PE38), diphtheria toxin (OT), and their
analogues, and derivates thereof and combinations thereof. A d person
would appreciate that the non-limiting examples of anti-cancer agents include
all le variants of said agents, for example the agent auristatin is
ed to include for example auristatin E, auristatin F, auristatin PE, and
tives thereof.
Non-limiting examples of therapeutically active polypeptides are
biomolecules, such as molecules selected from the group consisting of
human endogenous enzymes, hormones, growth s, chemokines,
cytokines and lymphokines.
Non-limiting examples of binding activities are binding activities which
increase the in vivo half-life of the fusion protein or conjugate, and binding
activities which act to block a biological activity. One example of such a
binding activity is a binding activity, which ses the in vivo half-life of a
fusion protein or conjugate. In one embodiment of said fusion protein or
conjugate, the in vivo half—life of said fusion protein or conjugate is longer than
the in vivo half—life of the polypeptide having the desired biological activity per
so. In one embodiment, said in vivo half—life is sed at least 10 times,
such as at least 25 times, such as at least 50 times, such as at least 75 times,
such as at least 100 times compared the in vivo ife of the fusion protein
or conjugate per se.
The fusion n or conjugate may comprise at least one further
moiety. In one ular embodiment, said target is albumin, binding to which
increases the in vivo half-life of said fusion protein or conjugate. In one
embodiment, said albumin binding activity is provided by an albumin binding
domain (ABD) of streptococcal protein G or a derivative thereof. Thus, said
fusion protein may for example comprise a PD-L1 binding polypeptide in
ric or multimeric form (such as a homodimeric or heterodimeric form)
as defined herein and an albumin binding domain of streptococcal protein G
or a derivative f.
In another embodiment, said there is provided a fusion protein or a
ate wherein said second moiety having a desired binding ty is a
protein based on protein Z, derived from the B domain of protein A from
lococcus aureus, which has a binding affinity for a target other than
PD-L1.
For example, said fusion protein or conjugate, comprising at least one
further moiety, may comprise [PD-L1 binding polypeptide] — [albumin binding
moiety] — [moiety with affinity for selected target]. It is to be understood that
the three moieties in this e may be arranged in any order from the N-
to the inal of the ptide.
The d person is aware that the construction of a fusion protein
often involves the use of linkers between the functional moieties to be fused,
and there are different kinds of linkers with ent properties, such as
flexible amino acid linkers, rigid amino acid linkers and cleavable amino acid
linkers. s have been used to for example increase stability or improve
folding of fusion proteins, to increase expression, improve biological activity,
enable targeting and alter pharmacokinetics of fusion proteins. Thus, in one
embodiment, the polypeptide according to any aspect disclosed herein further
comprises at least one linker, such as at least one linker selected from flexible
amino acid s, rigid amino acid linkers and cleavable amino acid linkers.
In one embodiment, said linker is arranged between said PD—L1 binding
polypeptide and a further polypeptide domain, such as between a PD-L1
binding domain as disclosed herein and an antibody or n binding
fragment thereof (as described in further detail below). Flexible linkers are
often used in the art when the joined domains require a certain degree of
movement or interaction, and may be ularly useful in some
embodiments of the complex. Such linkers are generally composed of small,
non-polar (for example G) or polar (for example 8 or T) amino acids. Some
flexible linkers primarily consist of stretches of G and 8 residues, for example
(GGGGS)p. ing the copy number “p” allows for optimization of linker in
order to e appropriate separation between the functional moieties or to
maintain necessary moiety interaction. Apart from G and S linkers, other
flexible linkers are known in the art, such as G and S linkers containing
additional amino acid residues, such as T and A, to maintain flexibility, as well
as polar amino acid residues to improve solubility. Additional non-limiting
examples of linkers include GGGGSLVPRGSGGGGS, (GS)3, (GS)4, (GS)8,
GGSGGHMGSGG, GGSGGSGGSGG, GGSGG, GGSGGGGG,
GGSEGGGSEGGG, AAGAATAA, GGGGG, GGSSG,
GSGGGTGGGSG, GSGGGTGGGSG, GSGSGSGSGGSG,
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GSGGSGGSGGSGGS and GSGGSGSGGSGGSG, corresponding to SEQ
ID NO:820-836, respectively, and GT. The skilled person is aware of other
suitable linkers.
In one ment, said linker is a flexible linker comprising glycine
(G), serine (S) and/or threonine (T) residues. In one embodiment, said linker
has a general formula selected from p and (SnGm)p, wherein,
independently, n = 1-7, m = 0-7, n + m S 8 and p = 1-7. In one ment,
n = 1-5. In one embodiment, m = 0—5. In one embodiment, p = 1-5. In a more
specific embodiment, n = 4, m = 1 and p = 1-4. In one embodiment, said
linker is selected from the group ting of S4G, (S4G)3 and (S4G)4_ In one
ment, said linker is selected from the group consisting of G4S and
(G4S)3. In one particular embodiment, said linker is G48 and in another
embodiment said linker is (G4S)3.
With regard to the description above of fusion proteins or conjugates
incorporating a PD-L1 binding polypeptide according to the disclosure, it is to
be noted that the designation of first, second and further es is made for
clarity reasons to distinguish n PD-L1 binding polypeptide or
polypeptides according to the invention on the one hand, and moieties
exhibiting other functions on the other hand. These designations are not
intended to refer to the actual order of the different domains in the polypeptide
chain of the fusion protein or conjugate. Similarly, the designations first and
second monomer units are made for clarity reasons to distinguish between
said units. Thus, for example, said first moiety (or monomer unit) may without
restriction appear at the N-terminal end, in the middle, or at the C-terminal
end of the fusion protein or conjugate.
Recently, considerable progress has been made in the development of
multispecific , such as antibodies with the y to bind to more than
one antigen, for e through engineering of the complementarity
determining regions (CDRs) to address two antigens in a single antibody
combining site (Bostrom etal, 2009, Science 323(5921):1610-1614; Schaefer
et al, 2011, Cancer Cell 20(4):472—486), via construction of heterodimeric
antibodies using engineered Fc units (Carter, 2001, J Immunol Methods
248(1-2):7-15; Schaefer etal, 2011, Proc Natl Acad Sci USA ):11187-
11192) and via genetic fusion of auxiliary recognition units to N- or C-termini
of light or heavy chains of full-length antibodies (Kanakaraj et al, 2012, MAbs
4(5):600-613; LaFleur et al, 2013, MAbs 5(2):208—218). Thus, it may be
beneficial for a molecule incorporating an affinity for PD-L1 as disclosed
herein to also exhibit affinity for another factor, such as a factor associated
with cancer or an immune se associated factor.
Thus, in third aspect of the present disclosure, there is provided a
x comprising at least one PD-L1 binding polypeptide and at least one
antibody or an antigen binding fragment thereof, wherein the PD-L1 binding
polypeptide is as described .
When used herein, the term “complex” is intended to refer to two or
more associated polypeptide chains, at least one having an affinity for PD-L1
and at least one being an antibody or an antigen binding fragment thereof.
These polypeptide chains may each contain different n domains, and
the resulting multiprotein complex can have multiple functions. ex”
intends to refer to two or more polypeptides as defined herein, connected by
covalent bonds, for example two or more ptide chains ted by
covalent bonds through expression thereof as a inant fusion n,
or associated by chemical conjugation.
As is well known, antibodies are immunoglobulin molecules capable of
specific binding to a target (an antigen), such as a carbohydrate,
polynucleotide, lipid, polypeptide or other, through at least one antigen
recognition site d in the variable region of the immunoglobulin molecule.
As used herein, the term “antibody or an antigen binding fragment thereof’
encompasses not only full-length or intact polyclonal or monoclonal
antibodies, but also antigen-binding fragments thereof, such as Fab, Fab',
F(ab’)2, Fab3, Fv and variants thereof, fusion proteins comprising one or more
antibody portions, humanized antibodies, chimeric antibodies, minibodies,
diabodies, triabodies, tetrabodies, linear dies, single chain antibodies,
multispecific antibodies (e.g., bispecific antibodies) and any other modified
configuration of the immunoglobulin le that comprises an antigen
recognition site of the ed specificity, including glycosylation variants of
antibodies, amino acid sequence variants of antibodies and covalently
modified antibodies. Further examples of ed antibodies and antigen
binding fragments thereof include nanobodies, AlbudAbs, DARTs (dual
affinity re-targeting), BiTEs (bispecific T-cell engager), TandAbs (tandem
diabodies), DAFs (dual acting Fab), two—in-one antibodies, SMlPs (small
r immunopharmaceuticals), bs (fynomers fused to antibodies),
DVD-lgs (dual variable domain immunoglobulin), Con—bodies (peptide
modified antibodies), duobodies and triomAbs. This listing of variants of
antibodies and antigen binding nts thereof is not to be seen as limiting,
and the skilled person is aware of other suitable variants.
A full-length antibody comprises two heavy chains and two light chains.
Each heavy chain ns a heavy chain variable region (VH) and first,
second and third constant regions (CH1, CH2 and CH3). Each light chain
contains a light chain variable region (VL) and a light chain constant region
(CL). ing on the amino acid sequence of the nt domain of its
heavy , antibodies are assigned to different classes. There are six
major classes of antibodies: lgA, lgD, lgE, lgG, lgM and ng, and several of
these may be further divided into subclasses (isotypes), e.g., lgG1, lgG2,
lgG3, lgG4, lgA1 and lgA2. The term “full-length antibody” as used herein
refers to an antibody of any class, such as lgD, lgE, lgG, lgA, lgM or ng (or
any sub—class thereof). The subunit structures and three-dimensional
configurations of different classes of antibodies are well known.
An “antigen binding fragment” is a portion or region of an antibody
le, or a derivative thereof, that retains all or a significant part of the
n binding of the corresponding full-length antibody. An antigen g
fragment may comprise the heavy chain variable region (VH), the light chain
variable region (VL), or both. Each of the VH and VL typically contains three
complementarity determining regions CDR1, CDR2 and CDR3. The three
CDRs in VH or VL are flanked by framework regions (FR1, FR2, FR3 and
FR4). As briefly listed above, es of antigen binding fragments include,
but are not limited to: (1) a Fab fragment, which is a monovalent fragment
having a VL-CL chain and a VH-CH1 chain; (2) a Fab’ fragment, which is a Fab
fragment with the heavy chain hinge region, (3) a 2 fragment, which is a
dimer of Fab’ fragments joined by the heavy chain hinge , for e
linked by a disulfide bridge at the hinge region; (4) an Fc fragment; (5) an Fv
fragment, which is the minimum antibody fragment having the VL and VH
domains of a single arm of an antibody; (6) a single chain Fv (scFv) fragment,
which is a single polypeptide chain in which the VH and VL domains of an
scFv are linked by a peptide linker; (7) an (scFv)2, which comprises two VH
domains and two VL domains, which are associated through the two VH
domains via disulfide bridges and (8) domain antibodies, which can be
antibody single variable domain (VH or VL) polypeptides that ically bind
antigens.
Antigen g fragments can be prepared via e methods. For
example, 2 nts can be produced by pepsin digestion of a full-
length antibody molecule, and Fab nts can be generated by reducing
the disulfide bridges of F(ab’)2 fragments. Alternatively, fragments can be
prepared via recombinant technology by expressing the heavy and light chain
fragments in suitable host cells (e.g., E. coli, yeast, mammalian, plant or
insect cells) and having them led to form the desired antigen-binding
fragments either in vivo or in vitro. A single-chain antibody can be prepared
via recombinant technology by linking a nucleotide sequence coding for a
heavy chain variable region and a nucleotide sequence coding for a light
chain variable region. For example, a flexible linker may be incorporated
between the two variable regions. The skilled person is aware of methods for
the preparation of both ength antibodies and antigen binding fragments
thereof.
Thus, in one embodiment, this aspect of the disclosure es a
complex as defined herein, wherein said at least one antibody or antigen
binding fragment thereof is selected from the group consisting of full-length
antibodies, Fab fragments, Fab’ fragments, F(ab’)2 fragments, Fc fragments,
Fv fragments, single chain Fv fragments, (scFv)2 and domain antibodies. In
one ment, said at least one antibody or antigen binding fragment
thereof is selected from full—length antibodies, Fab fragments and scFv
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nts. In one particular embodiment, said at least one antibody or
antigen binding fragment thereof is a ength antibody.
In one embodiment of said complex as d herein, the antibody or
antigen binding fragment thereof is selected from the group consisting of
monoclonal antibodies, human antibodies, humanized antibodies, chimeric
antibodies, and antigen-binding fragments f.
The term “monoclonal antibodies” as used herein refers to antibodies
having monovalent ty, meaning that each antibody molecule in a sample
of the monoclonal antibody binds to the same epitope on the antigen,
whereas the term “polyclonal antibodies” as used herein refers to a collection
of antibodies that react against a specific antigen, but in which collection there
may be different dy molecules for example identifying different epitopes
on the antigen. Polyclonal antibodies are typically ed by inoculation of
a suitable mammal and are purified from the ’s serum. Monoclonal
antibodies are made by identical immune cells that are clones of a unique
parent cell (for example a hybridoma cell line). The term “human antibody” as
used herein refers to antibodies having variable and constant regions
corresponding substantially to, or derived from, antibodies obtained from
human subjects. The term “chimeric antibodies” as used herein, refers to
recombinant or genetically engineered antibodies, such as for example
mouse monoclonal antibodies, which contain polypeptides or domains from a
different species, for example human, introduced to reduce the antibodies’
immunogenicity. The term “humanized antibodies” refers to antibodies from
non—human species whose protein sequences have been modified to
se their similarity to antibody variants ed naturally in humans, in
order to reduce immunogenicity.
The complex as described herein may for example be present in the
form of a fusion n or a conjugate. Thus, said at least one PD-L1 binding
ptide and said at least one dy, or antigen binding fragment
thereof, may be coupled by means of chemical conjugation (using known
organic chemistry methods) or by any other means, such as expression of the
complex as a fusion protein orjoined in any other fashion, either directly or
via a linker, for example an amino acid linker. The skilled person will
appreciate that the above description of linker ces in relation to fusion
polypeptides is equally relevant for the complex as disclosed herein.
Thus in one embodiment, there is provided a complex as defined
herein, wherein said complex is a fusion protein or a conjugate. In one
embodiment, said complex is a fusion protein. In another embodiment, said
complex is a conjugate. In one embodiment of said x, said PD-L1
binding polypeptide is attached to the N—terminus or C—terminus of the heavy
chain of said antibody or antigen binding fragment thereof. In another
embodiment, said PD-L1 g ptide is ed to the N—terminus or
C-terminus of the light chain of said antibody or antigen binding fragment
thereof. In one ment, said PD-L1 binding polypeptide is attached to
the N-terminus and/or C-terminus of the light chain and heavy chain of said
antibody or antigen binding fragment thereof. For example, the PD-L1 binding
polypeptide may be attached to only the N-terminus of the heavy chain(s),
only the N-terminus of the light chain(s), only the C-terminus of the heavy
chain(s), only the C-terminus of the light chain(s), both the N-terminus and the
C-terminus of the heavy chain(s), both the inus and the C-terminus of
the light chain(s), only the C-terminus of the light chain(s) and the N-terminus
of the heavy chain(s), only the C-terminus of the heavy chain(s) and the N-
terminus of the light chain(s), of said antibody or antigen binding fragment
thereof.
In one embodiment there is provided a complex, wherein said PD-L1
binding polypeptide is attached either to the C-terminus or the inus of
the heavy chain or the light chain of said antibody or antigen binding fragment
thereof.
In one particular embodiment, there is provided a complex according to
any preceding item, wherein said antibody or antigen g fragment
thereof has affinity for an antigen, for example an antigen associated with an
ious e, or an antigen ated with cancer. For example, said
n may be PD—1 or CTLA—4.
In one embodiment there is provided a fusion protein, conjugate or
complex as bed herein, wherein the said second or further
moiety/moieties or dy or antigen binding fragment thereof is an inhibitor
selected from the group consisting of inhibitors of: PD-1, CTLA-4, T-cell
immunoglobulin and mucin containing protein—3 (TIM—3), galectin—9 (GAL—9),
cyte activation gene-3 (LAG-3), PD-L2, B7 homolog 3 (B7-H3), B7
homolog 4 (B7-H4), V-domain lg suppressor of T-cell tion (VISTA),
carcinoembryonic antigen-related cell on molecule 1 (CEACAMI), B
and T lymphocyte attenuator (BTLA), colony stimulating factor 1 receptor
(CSF1 R), herpes virus entry mediator (HVEM), killer immunoglobulin receptor
(KIR), adenosine, adenosine A2a receptor (A2aR), CD200-CD200R and T
cell lg and ITIM domain.
In one ment, said second moiety or antibody or antigen binding
fragment thereof is an inhibitor of PD-1, such as an inhibitor selected from the
group consisting of nivolumab, pidilizumab, BMS , MPDL328OA
(Roche) and pembrolizumab. In a specific embodiment, the inhibitor is
pembrolizumab.
In one embodiment, said second moiety or antibody or antigen g
fragment thereof is an inhibitor of CTLA—4, such as an inhibitor ed from
the group consisting of belatacept, abatacept, tremelimumab and ipilimumab.
In a specific embodiment, the tor is ipilimumab.
In one embodiment there is provide a fusion protein, conjugate or
complex as described herein, wherein said second moiety or antibody or
n binding fragment thereof is an agonist selected from the group
consisting of agonists of CD134, CD40, 4-1 BB and glucocorticoid-induced
TNFR—related protein (GITR).
The above aspects rmore encompass polypeptides in which the
PD-L1 binding polypeptide according to the first aspect, the PD-L1 binding
polypeptide as comprised in a fusion protein or conjugate according to the
second aspect or in a complex according to the third aspect, further
comprises a label, such as a label selected from the group consisting of
fluorescent dyes and metals, chromophoric dyes, chemiluminescent
compounds, bioluminescent proteins, enzymes, radionuclides, ctive
particles and pretargeting recognition tags. Such labels may for example be
used for detection of the polypeptide. For example, in some embodiments,
such labeled polypeptide may for example be used for labeling or targeting
tumors which have a high expression of PD—L1.
Indirect labeling of a Z variant polypeptide was ly shown using
pretargeting ition tags (Westerlund et al (2015), Bioconjugate Chem
4-1736). Similarly, the disclosure provides a PD-L1 binding polypeptide
as described herein labeled with a pretargeting moiety, which may then be
used for indirect labeling with a moiety complementary to the pretargeting
moiety. When comprising a pretargeting moiety, a PD-L1 binding agent of the
present disclosure is able to associate with a complementary pretargeting
moiety, and such complementary pretargeting moiety may then comprise or
be attached to a suitable radionuclide. The skilled person is aware of suitable
radionuclides for therapeutic, stic and/or prognostic purposes. Such a
radionuclide may be chelated to said complementary geting moiety via
a chelating nment as generally described for the PD-L1 binding agent
below.
In one embodiment, the complementary pair of pretargeting moieties
comprise stept(avidin)/biotin, oligonucleotide/complementary oligonucleotide
such as DNA/complementary DNA, RNA/complementary RNA,
phosphorothioate nucleic acid/ complementary phosphorothioate nucleic acid
and peptide nucleic acid (PNA)/complementary peptide nucleic acid (cPNA)
and morpholinos/ complementary morpholinos. In one ular embodiment,
said geting moiety is a PNA oligonucleotide, such as a 10mer PNA
ce, such as a 15—mer PNA sequence.
In ments in which the polypeptide, fusion protein, conjugate or
complex is labeled, directly or indirectly (e.g. via pretargeting as described
above), with an imaging agent (e.g. radioactive agent), measuring the amount
of labeled polypeptide present in a tumor may be done using imaging
ent, such as through acquiring radioactivity counts or images of
radiation density, or derivatives thereof such as ion concentration. Non—
limiting examples of radionuclides, suitable for either direct labeling of the PD-
L1 binding agent according to any aspect disclosed herein, or for indirect
labeling by ng of a complementary pretargeting moiety, include 686a,
110mm, 18F, 45-“, 4480, 61CU, 66GB, 64CU, 5500’ 72AS, 86Y, BQZF, 124', 768F, 111m,
gngc, 123', 131' and 67Ga-
In one embodiment, the imaging equipment used in such
measurements is positron emission tomography (PET) equipment, in which
case the radionuclide is selected such that it is suitable for PET. The skilled
person is aware of radionuclides suitable for use with PET. For example, a
PET radionuclide is selected from the group consisting of 686a, 110mIn, 18F,
45Ti, 44Sc, 61Cu, 666a, 64Cu, 550o, 72As, 86v, 892r, 124i and 76Br.
In another embodiment, the imaging equipment used is single-photon
emission computed tomography (SPECT) equipment, in which case the
uclide is selected such that it is suitable for SPECT. The skilled person
is aware of radionuclides suitable for use with SPECT. For example, a
SPECT uclide is selected from the group consisting ofmln, 9ngc, 123l,
131| and 676a.
Thus, in one embodiment there is provided a PD-L1 binding
ptide, fusion protein or x as bed herein, which comprises
a direct or indirect radionuclide label, such as a radionuclide selected from the
group consisting of 68Ga, “0min, 18F, 45Ti, 44Sc, 61Cu, 66Ga, 64Cu, 55Co, 72As,
86Y, 89Zr, 124l, 76Br, 111In, QQmTc, 123I, 131l and 676a, such as the group
consisting of 686a, “0min, 18F, 45Ti, 44Sc, 61Cu, 66Ga, 64Cu, 55Co, 72As, 86v,
89Zr, 124| and 76Br, such as 18F.
In some embodiments, the d PD—L1 binding polypeptide is
present as a moiety in a fusion protein, conjugate or complex also comprising
a second moiety having a d biological ty. The label may in some
instances be coupled only to the PD-L1 binding polypeptide, and in some
instances both to the PD-L1 binding polypeptide and to the second moiety of
the fusion protein or conjugate and/or the antibody or antigen binding
fragment thereof the complex. Furthermore, it is also possible that the label
may be coupled to a second moiety, or antibody or antigen binding fragment
thereof only and not to the PD-L1 binding moiety. Hence, in yet another
embodiment, there is provided a PD-L1 binding polypeptide comprising a
second moiety, n said label is coupled to the second moiety only. In
another embodiment, there is provided a complex as defined herein, n
said label is coupled to the antibody or antigen binding fragment thereof only.
When reference is made to a labeled polypeptide, this should be
understood as a reference to all aspects of polypeptides as described herein,
including PD-L1 binding polypeptides, fusion proteins, conjugates and
complexes comprising a PD-L1 binding polypeptide. Thus, a labeled
polypeptide may contain only the PD-L1 binding polypeptide and e.g. a
eutic radionuclide, which may be chelated or covalently coupled to the
PD-L1 binding ptide, or contain the PD—L1 binding polypeptide, a
therapeutic uclide and a second moiety such as a small molecule
having a desired biological activity, for example a therapeutic efficacy. A
labeled polypeptide may contain a PD-L1 binding polypeptide in
heterodimeric form and e.g. a therapeutic uclide, which may be
chelated or covalently coupled to the PD-L1 binding polypeptide, or contain
the PD-L1 binding polypeptide in dimeric form, a eutic
radionuclide and a second moiety such as a small molecule having a desired
biological activity, for example a therapeutic efficacy. Also envisioned is a
complex which contains a PD-L1 binding ptide as defined herein, an
antibody or antigen binding fragment thereof and a e.g. a therapeutic
radionuclide, which may be chelated or covalently coupled to the PD-L1
binding ptide or to the antibody or antigen binding fragment thereof.
The skilled person is aware of other possible variants.
ln embodiments where the PD—L1 binding polypeptide, fusion n,
ate or complex is radiolabeled, such a radiolabeled polypeptide may
se a uclide. A majority of radionuclides have a ic nature
and metals are typically incapable of forming stable covalent bonds with
elements presented in proteins and peptides. For this reason, labeling of
proteins and peptides with radioactive metals is performed with the use of
chelators, i.e. multidentate ligands, which form non-covalent compounds,
called chelates, with the metal ions. In an embodiment of the PD—L1 binding
polypeptide, fusion protein, conjugate or complex, the incorporation of a
radionuclide is enabled through the ion of a chelating environment,
through which the radionuclide may be coordinated, chelated or xed to
the polypeptide. One example of a chelator is the polyaminopolycarboxylate
type of chelator. Two classes of such polyaminopolycarboxylate chelators can
be distinguished: macrocyclic and acyclic chelators.
In one embodiment, the PD-L1 binding polypeptide, fusion n,
conjugate or complex ses a chelating environment provided by a
polyaminopolycarboxylate chelator conjugated to the PD-L1 binding
polypeptide via a thiol group of a cysteine residue or an epsilon amine group
of a lysine residue.
The most commonly used macrocyclic chelators for radioisotopes of
indium, gallium, yttrium, bismuth, radioactinides and radiolanthanides are
different derivatives of DOTA (1 ,4,7,10-tetraazacyclododecane-1 ,4,7,10-
tetraacetic acid). In one embodiment, a chelating environment of the PD-L1
g ptide, PD-L1 binding polypeptide in heterodimeric form, fusion
protein, ate or complex is provided by DOTA or a derivative thereof.
More specifically, in one embodiment, a chelating polypeptide encompassed
by the present disclosure is obtained by reacting the DOTA tive
1,4,7,10-tetraazacyclododecane-1,4,7-tris-acetic acid—10-
maleimidoethylacetamide (maleimidomonoamide-DOTA) with said
polypeptide. In one embodiment, a chelating polypeptide encompassed by
the present disclosure is obtained by reacting the DOTA derivative DOTAGA
(2,2’,2”—(10-(2,6-dioxotetrahydro-2H-pyranyl)—1 ,4,7,10-
tetraazacyclododecane-1,4,7-triyl)triacetic acid) with said ptide.
Additionally, triazacyclononane—1,4,7-triacetic acid (NOTA) and
derivatives thereof may be used as chelators. Hence, in one embodiment, a
chelating environment of the PD—L1 g polypeptide, PD-L1 binding
polypeptide in heterodimeric form, fusion protein, conjugate or x is
provided by NOTA or a derivative thereof. In one embodiment, a chelating
ptide encompassed by the present disclosure is obtained by reacting
the NOTA derivative NODAGA (2,2’-(7-(1-carboxy((2,5-dioxopyrrolidin
yl)oxy)oxobutyl)—1,4,7—triazonane-1,4-diyl)diacetic acid) with said
polypeptide. The most commonly used acyclic polyaminopolycarboxylate
chelators are different tives of DTPA (diethylenetriamine-pentaacetic
acid). Hence, polypeptides having a chelating nment provided by
diethylenetriaminepentaacetic acid or derivatives f are also
encompassed by the present disclosure.
In further aspects of the present disclosure, there is provided a
polynucleotide encoding a PD-L1 binding polypeptide, fusion protein or
complex as described herein; an expression vector comprising said
polynucleotide; and a host cell comprising said expression vector.
Also encompassed by this disclosure is a method of producing PD-L1
binding polypeptide, fusion protein or complex as described above,
comprising culturing said host cell under conditions permissive of expression
of said polypeptide from its expression vector, and isolating the polypeptide.
The PD—L1 g polypeptide, fusion protein or complex of the
present sure may atively be produced by non-biological peptide
synthesis using amino acids and/or amino acid derivatives having protected
ve side-chains, the non-biological peptide synthesis comprising
- step—wise coupling of the amino acids and/or the amino acid
derivatives to form a polypeptide, fusion protein or complex as bed
herein having protected reactive hains,
- removal of the protecting groups from the reactive side-chains of the
polypeptide fusion protein or x, and
- folding of the ptide in aqueous solution.
A complex as disclosed herein may also be produced by the
conjugation of at least one PD-L1 binding polypeptide or fusion protein as
described herein to at least one antibody or antigen binding fragment thereof.
The skilled person is aware of conjugation methods, such as conventional
chemical conjugation methods, for example using charged succinimidyl esters
or carbodiimides.
it should be understood that the PD-L1 binding polypeptide according
to the present disclosure may be useful as a therapeutic, stic and/or
prognostic agent in its own right or as a means for targeting other therapeutic
or diagnostic agents, with eg. direct or indirect effects on PD—L1 . A direct
eutic effect may for example be accomplished by inhibiting PD-L1
signaling. An indirect therapeutic effect may for example be accomplished by
pretargeting using PD-L1 binding polypeptides as described above.
Thus, in another aspect, there is provided a composition comprising a
PD-L1 g polypeptide, fusion protein, conjugate or complex as described
herein and at least one pharmaceutically acceptable excipient or carrier. In
one embodiment, said ition further comprises at least one additional
active agent, such as at least two additional active agents, such as at least
three additional active agents. Non-limiting examples of additional active
agents that may prove useful in such combination are immune response
modifying agents and anti-cancer agents as described herein.
The small size and robustness of the PD—L1 binding polypeptides of
the present disclosure confer l advantages over conventional
monoclonal antibody based therapies. Such advantages include advantages
in ation, modes of administration, such as alternative routes of
administration, stration at higher doses than antibodies and absence of
Fc-mediated side effects. The agents of the present disclosure are
contemplated for oral, topical, intravenous, intraperitoneal, subcutaneous,
ary, ermal, intramuscular, asal, buccal, sublingual or
suppository administration, such as for topical administration. Also, many
diseases and disorders, such as cancers and infectious disease, are
associated with more than one factor. Thus, a complex as defined herein
confers the advantage of targeting an additional antigen together with PD-L1.
In another aspect of the present sure, there is provided a PD-L1
binding polypeptide, fusion protein, conjugate, complex or ition as
described herein for use as a medicament, a prognostic agent and/or a
stic agent. In one embodiment, there is provided a PD-L1 binding
polypeptide, fusion protein, conjugate, complex or composition for use in the
treatment, diagnosis or prognosis of a PD-L1 related disorder.
In one embodiment, said PD-L1 binding polypeptide, fusion protein,
conjugate, x or composition is provided for use as a medicament. In a
2016/076040
more specific embodiment, there is provided a PD-L1 binding polypeptide,
fusion protein, conjugate, complex or composition as described herein, for
use as a ment to modulate PD—L1 function in vivo. As used herein, the
term “modulate” refers to changing the activity, such as rendering PD-L1
function hypomorph, partially inhibiting or fully inhibiting PD—L1 function.
In one embodiment, there is ed a PD-L1 binding polypeptide,
fusion protein, conjugate, complex or composition for use in the treatment of a
PD-L1 related disorder.
In one ment, there is provided a PD-L1 binding polypeptide,
fusion n, conjugate, complex or composition for use in the diagnosis of a
PD-L1 related disorder.
In one embodiment, there is provided a PD-L1 binding polypeptide,
fusion protein, conjugate, complex or composition for use in the prognosis of
a PD-L1 related disorder.
As used herein, the term “PD-L1 d disorder” refers to any
disorder, disease or condition in which PD-L1 signalling plays a regulatory
role. Examples of such PD-L1 related disorder include infectious diseases
and cancers.
It is to be understood that said PD-L1 binding polypeptide, fusion
protein, conjugate, complex or composition may be used as the sole
diagnostic or prognostic agent or as a companion diagnostic and/or
stic agent.
In one embodiment, said PD-L1 related disorder is selected from the
group consisting infectious diseases and cancers. Non-limiting es of
ious diseases include chronic viral infection, for example selected from
the group consisting of human immunodeficiency virus (HIV), hepatitis B virus
(HBV) and hepatitis C virus (HCV). The d person will appreciate that a
cancer suitable for treatment, diagnosis and/or sis using PD-L1 binding
polypeptide, fusion protein, conjugate, x or composition may be a solid
tumor cancer or a non-solid tumor cancer characterized by over—expression of
PD-L1. Non-limiting examples of such cancers include skin cancer; such as
melanoma and nonmelanoma skin cancer (NMSC); lung cancers such as
small cell lung cancer, non—small cell lung cancer (NSCLC); head and neck
cancer, renal cell carcinoma (RCC), r cancer, breast cancer, colorectal
cancer, gastric , ovarian cancer, pancreatic cancer, te cancer,
glioma, glioblastoma, liver carcinoma, gallbladder cancer, thyroid cancer,
bone cancer, cervical cancer, uterine cancer, vulval , endometrial
cancer, testicular , kidney cancer, esophageal carcinoma, brain/CNS
cancers, neuronal cancers, mesothelioma, as, small bowel
adenocarcinoma and pediatric malignancies; leukaemia, acute myeloid
leukaemia, acute lymphoblastic leukaemia and multiple myeloma.
In one particular embodiment, said cancer is selected from the group
consisting of melanoma, NSCLC, head and neck cancer, RCC, r
cancer, breast cancer, colorectal cancer, gastric cancer, n cancer,
pancreatic cancer and prostate cancer, such as a cancer selected from the
group consisting of melanoma, NSCLC, head and neck cancer, RCC and
bladder cancer.
In one ment, it may be beneficial to administer a therapeutically
effective amount of a PD—L1 binding polypeptide, fusion protein, conjugate,
complex or composition as described herein together with at least one second
drug substance, such as an anti—cancer agent or an immune response
modifying agent.
In one embodiment, there is provided a PD-L1 binding polypeptide,
fusion protein, conjugate, complex or ition for use in prognosis and/or
diagnosis together with at least one cell proliferation marker. Non-limiting
es of contemplated cell proliferation markers are those selected from
the group consisting of Ki-67, AgNOR, choline, claspin, cyclin A, CYR61,
Cdk1, histone H3, HsMCM2, IL-2, Ki-S‘I, Ki-SZ, LigI, MCM2, MCM6, MCM7,
mitosin, p120, PCNA, PDPK, PLK, STK1, TK-1, topoisomerase II alpha and
TPS.
In a related aspect, there is provided a method of treatment of a PD-L1
related disorder, sing stering to a subject in need thereof an
ive amount of a PD—L1 binding polypeptide, fusion protein, conjugate,
complex or composition as described . In a more specific embodiment
of said method, the PD-L1 binding polypeptide, fusion protein, conjugate,
complex or ition as described herein modulates PD-L1 function in
vivo. The skilled person will appreciate that any description in relation to the
use of PD-L1 g polypeptide, fusion protein, conjugate, complex or
ition as bed herein for treatment of a disease or disorder is
equally relevant for the related eutic method. For the sake of brevity,
such description will not be repeated here.
In one particular embodiment, said method of treatment, particularly
relevant for the treatment of PD-L1 related cancers, comprises the steps of
- contacting the subject with a PD-L1 binding polypeptide, fusion
protein, conjugate or complex comprising a pretargeting moiety as
described herein, or with a composition comprising said PD-L1
binding polypeptide, fusion protein, conjugate or complex
comprising a pretargeting moiety, and
- contacting the subject with a mentary pretargeting moiety
comprising a radionuclide.
In another aspect of the present disclosure, there is provided a method
of detecting PD-L1, comprising providing a sample ted to contain PD-
L1, contacting said sample with a PD-L1 binding polypeptide, fusion protein,
ate, complex or composition as described herein, and detecting the
binding of the PD-L1 binding polypeptide, fusion protein, ate, complex
or composition to indicate the presence of PD-L1 in the sample.
In one embodiment, said method further comprises an intermediate
washing step for removing non-bound polypeptide, fusion protein, conjugate,
complex or ition, after ting the sample.
In another embodiment, said method is a diagnostic or prognostic
method for determining the presence of PD-L1 in a subject, the method
comprising the steps:
a) contacting the subject, or a sample isolated from the t, with a
PD-L1 binding polypeptide, fusion protein, conjugate, complex or
composition as described herein, and
b) ing a value corresponding to the amount of the PD-L1 binding
ptide, fusion protein, conjugate, complex or composition that has
bound in said t or to said sample.
In one embodiment, said method further comprises an intermediate
washing step for removing non-bound polypeptide, fusion protein, conjugate
or composition, after contacting the subject or sample and before obtaining a
value.
In one embodiment of this diagnostic or prognostic , said PD—L1
binding ptide, fusion protein, conjugate or complex comprises a
pretargeting moiety as described herein, and the contacting step a) of the
method further comprises contacting the subject with a complementary
pretargeting moiety labeled with a detectable label, such as a radionuclide
label.
In one embodiment, said method further comprises a step of
comparing said value to a reference. Said reference may be by a numerical
value, a threshold or a visual indicator, for e based on a color on.
The skilled person will appreciate that different ways of comparison to a
reference are known in the art and may be suitable for use.
In one embodiment of such a method, said t is a mammalian
subject, such as a human subject. In one embodiment, said method is
performed in vivo. In another embodiment, said method is performed in vitro.
In one embodiment, the diagnostic or prognostic method is a method
for medical imaging in vivo as discussed above. Such a method comprises
the systemic stration of a PD-L1 binding entity as disclosed herein (i.e.
the polypeptide per se, or the fusion protein, conjugate, complex or
ition containing it) to a mammalian subject. The PD-L1 binding entity
is directly or ctly labelled, with a label comprising a uclide suitable
for medical imaging (see above for a list of contemplated radionuclides).
Furthermore, the method for medical imaging comprises obtaining one or
more images of at least a part of the subject’s body using a medical imaging
instrument, said image(s) indicating the presence of the radionuclide inside
the body.
While the invention has been described with reference to various
exemplary aspects and embodiments, it will be understood by those skilled in
the art that various changes may be made and equivalents may be
substituted for elements thereof without departing from the scope of the
ion. In addition, many modifications may be made to adapt a particular
situation or molecule to the teachings of the invention without departing from
the essential scope thereof. Therefore, it is intended that the invention not be
limited to any particular embodiment contemplated, but that the invention will
include all embodiments g within the scope of the appended claims.
Brief description of the figures
Figure 1 is a listing of the amino acid sequences of es of PD-L1
binding polypeptides of the present disclosure (SEQ ID NO:1-814), as well as
the heavy chain (HCLam; SEQ ID NO:815) and the light chain (LCLam; SEQ ID
NO:816) of the PD—1 binding monoclonal dy Lam and the heavy chain
(HCIpi; SEQ ID NO:817) and the light chain (LClpi; SEQ ID NO:818) of the
CTLA—4 binding monoclonal antibody lpi. In the PD-L1 binding polypeptides of
the present disclosure, the deduced PD-L1 binding motifs (BM) extend from
residue 8 to residue 36 in each ce. The amino acid sequences of the
49 amino acid residues long polypeptides (BMod) ted to constitute the
te three-helix bundle within each of these Z variants extend from
residue 7 to residue 55.
Figure 2 shows binding of two first tion polypeptides to human
PD-L1 analyzed by Biacore as described in Example 3. Z variants (A) 213091
(SEQ ID NO:776) and (B) 213156 (SEQ ID NO:781 were injected at
concentrations of 50 nM (black), 5 nM (dark grey) and 0.5 nM (light grey) over
a CM5 chip with immobilized hPD-L1.
Figure 3 shows e of SPR response against (A) hPD-L2, (B)
hB7—H3 and (C) hB7-H4, here illustrated with the PD—L1 binding polypeptides
213091 (SEQ ID NO:776) and 213156 (SEQ ID ) ed at
concentrations of 50 nM, 5 nM and 0.5 nM.
Figure 4 shows circular dichroism (CD) spectra of two first generation
PD-L1 binding ptides. The CD a at ngs ranging from 250
to 195 nm collected at 20 °C before (broken line) and after (solid line) variable
temperature measurement (VTM) are shown for (A) 215168—Cys (SEQ ID
NO:809) and (B) 215169-Cys (SEQ ID NO:810).
Figure 5 shows binding of two second generation polypeptides to
human PD-L1 analyzed by e as described in Example 7. Z variants (A)
217964 (SEQ ID N02) and (B) 218064 (SEQ ID NO:1) were injected at
trations of 135 nM (black), 45 nM (dark grey) and 15 nM (light grey)
over a CM5 chip with lized hPD—L1.
Figure 6 shows circular dichroism (CD) spectra of two second
generation PD-L1 binding polypeptides. The CD spectra at wavelengths
ranging from 250 to 195 nm ted at 20 °C before (broken line) and after
(solid line) the variable temperature measurement (VTM) are shown for (A)
218064 (SEQ ID NO:1) and (B) 218090 (SEQ ID NO:17).
Figure 7 is a schematic representation of the design of complexes
according to the disclosure, produced as described in Example 8. “Z” denotes
the PD—L1 targeting Z variant 215170 (SEQ ID NO:814), which was
genetically fused to the N—termini (7A and 7B) or the C-termini (7C and 7D) of
the heavy (7A and 7D) or the light (7B and 7C) chains of the D-1
monoclonal antibody Lam or the anti-CTLA-4 monoclonal antibody lpi via a 15
residue )3-linker.
Figure 8 shows dual binding specificity of complexes analyzed in a
Biacore capture assay as described in Example 8. (A) 215170-HCLam and (B)
215170-LCLam were injected for 5 min over chip surfaces immobilized with
PD-1, followed by ion of PD-L1 at a concentration of 100 andfor 500 nM,
respectively. (C) 215170-HClpi and (D) 215170—LClpi were injected for 5 min
over chip surfaces immobilized with CTLA-4, followed by injection of PD-L1 at
a concentration of 100 and 500 nM, respectively.
Figure 9 shows the result of inhibition of PD-L1 and CTLA-4 by Ipi—
based complexes, ed in a mixed lymphocyte assay as described in
Example 8. (A) Reduction in the number of MDA-MB231 cells and (B)
increasing number of CD3+ T-cells with increasing concentrations of the Ipi-
based complexes HCipi-Z15170, LCipi-Z15170, Z15170-Hcipi and 215170-
LCipi.
Figure 10 shows PET maximum intensity projection (MIP) images of
aft mice. (A) MIPs of mice with LOX tumor (left) and SUDHL6 tumor
(right) afts, 30-90 min after administration of [18F]AlF—NOTA-Z15168.
(B) MIPs of mice with LOX tumor xenografts, 30-90 min after administration of
[18F]AlF-NOTA-Z15168 (left) at baseline and (right) following pre-block with
400 pg NOTA—Z15168.
Figure 11 shows ex vivo biodistribution results for LOX and SUDHL6
mouse aft models, as analyzed directly after PET data acquisition. The
results are displayed in units of (A) Standard Uptake Value (SUV) and (B)
blood ratio. Error bars represent standard deviation.
Figure 12 shows the result of whole body scan of rhesus monkeys.
MIPs d over 90-180 min; colour inverted images) of rhesus monkeys
administered with (A) [18F]AlF-NOTA-Z15168 and (B) [18F]AlF—NOTA-Z18609.
(C) Average tracer uptake over z 120-180 min in different organs displayed in
the units of SUV. Error bars represent standard deviation.
Examples
Summary
The following Examples disclose the development of novel 2 variant
molecules targeted to human programmed death-ligand 1 (PD-L1), also
known as human B? homolog 1 (B7-H1) and cluster of differentiation 274
(CD274), based on phage display technology. The PD-L1 binding
polypeptides described herein were sequenced, and their amino acid
sequences are listed in Figure 1 with the sequence identifiers SEQ ID NO:1-
808. The Examples further describe the characterization of PD-L1 binding
polypeptides and trate in vitro functionality of said polypeptides.
Example 1
Selection and screening of PD-L1 binding Z variants
In this e, human PD-L1 (hPD-L1)was used as target in phage
display ions using a phage library of Z variants. Selected clones were
DNA sequenced, produced in E. coli periplasmic fractions and assayed
against PD-L1 in ELISA (enzyme-linked sorbent assay).
Materials and methods
ylation of target protein: hPD-L1 (human PD-L1 Fc a, R&D
Systems, cat. no. 156-B7-100) was biotinylated using No-Weigh EZ-Link
NHS-LC-Biotin (Thermo Scentific, cat. no. 21327) at a 10x molar
excess, according to the manufacturer’s recommendations. The reaction was
performed at room temperature (RT) for 40 min. Subsequent buffer exchange
to PBS (10 mM phosphate, 137 mM NaCl, 2.68 mM KCI, pH 7.4) was
performed using a Slide-a-Iyzer dialysis cassette (10000 MWCO, Thermo
Scientific, cat. no. 66383) according to the manufacturer’s instructions.
Phage display selection of PD-L1 binding Z variants: A library of
random ts of protein Z displayed on bacteriophage, constructed in
phagemid pAY02592 essentially as described in Grénwall etal. (2007) J
hnol, 128:162-183, was used to select PD-L1 binding Z variants. In this
library, an albumin binding domain (ABD, GA3 of protein G from
Streptococcus strain G148) is used as fusion partner to the Z variants. The
library is denoted Zlib006Naive.ll and has a size of 1.5 x 1010 library members
(Z variants). E. coli RRIAM15 cells (RUther et a/., (1982) Nucleic Acids Res
:5765-5772) from a glycerol stock ning the phagemid library
Zlib006Naive.ll were inoculated in 20 l of a defined proline free medium [3 g/l
KH2PO4, 2 g/l K2HPO4, 0.02 g/l uracil, 6.7 g/l YNB (DifcoTM Yeast Nitrogen
Base w/o amino acids, Becton Dickinson), 5.5 g/l glucose monohydrate, 0.3
g/l ine, 0.24 g/l L-arginine monohydrochloride, 0.11 g/l L-asparagine
drate, 0.1 g/l L-cysteine, 0.3 g/l L-glutamic acid, 0.1 g/l L—glutamine,
0.2 g/l glycine, 0.05 g/l L-histidine, 0.1 g/l L-isoleucine, 0.1 g/l L-leucine, 0.25
g/l L-lysine monohydrochloride, 0.1 g/l L-methionine, 0.2 g/l L-phenylalanine,
0.3 g/l L—serine, 0.2 g/l L-threonine, 0.1 g/l L-tryptophane, 0.05 g/l L—tyrosine,
0.1 g/l ne], supplemented with 100 ug/ml ampicillin. The cultivations
were grown at 37 °C in a fermenter (Belach nik, BR20). When the cells
d an optical density at 600 nm (ODeoo) of 0.75, approximately 2.6 l of
the cultivation was infected using a 10 x molar excess of M13K07 helper
phage (New England Biolabs, cat. no. N0315S). The cells were incubated for
min, whereupon the fermenter was filled up to 20 l with cultivation medium
(2.5 g/l (NH4)2SO4; 5.0 g/l Yeast Extract (Merck 1037530500); 25 g/l
Peptone lau 07-119); 2 g/l K2HPO4; 3 g/l ; 1.25 g/l Na3C5H507 -
2 H20; 0.1 ml/l Breox FMT30 aming agent) supplemented with 100 uM
isopropyl-B-Dthiogalactopyranoside (IPTG) for induction of expression and
with 50 ug/ml llin, 12.5 ug/ml carbenicillin, 25 ug/ml kanamycin, 35 ml/l
of 1.217 M MgSO4 and 10 ml of a trace element solution [129 mM FeCI3; 36.7
mM ZnSO4; 10.6 mM CuSO4; 78.1 mM MnSO4; 94.1 mM 08012, dissolved in
1.2 M HCI]. A glucose-limited fed-batch cultivation was started where a 600
g/l glucose solution was fed to the reactor (15 g/h in the start, 40 g/h at the
end of the tation after 17 h). pH was controlled at 7 through the
automatic addition of 25 % NH4OH, air was supplemented (10 l/min), and the
stirrer was set to keep the dissolved oxygen level above 30 %. The cells in
the cultivation were removed by tangential flow filtration.
The phage particles were itated from the supernatant twice in
PEG/NaCl (polyethylene glycol/sodium chloride), filtered and dissolved in
PBS and glycerol as described in Grénwall et al., supra. Phage stocks were
stored at -80 °C before use.
Selections against biotinylated hPD-L1 were performed in four cycles
initially divided in two different tracks (1 and 2). As selection proceeded, the
tracks were further divided according to target concentration and number
and/or time of washes to finally end up in nine tracks in cycle 4. More
precisely, the first track (1) was divided in the second to the fourth cycles,
resulting in a total of two tracks (1-1 to 1-2) in cycle 2, four tracks (11 to 1-
2-2) in cycle 3 and six tracks (1—11 to 1-2—2—1) in cycle 4. The second track
(2) was divided in the third to the fourth cycles, resulting in a total of two
tracks (21 to 2-1—2) in cycle 3, three tracks —1 to 2—11) in cycle 4.
In track 1 with dants, Dynabeads® M-280 Streptavidin (SA-beads,
ogen, cat. no. 11206D) were used to catch the hPD-L1:Z variant
complexes. In track 2, Dynabeads® Protein A (SPA—beads, Invitrogen, cat.
no. 10002D) were used instead to catch the hPD-L1:Z variant complexes by
g to the Fc part of the hPD—L1 Fc chimeric protein.
Phage stock ation, selection procedure and amplification of
phage between selection cycles were performed essentially as described for
selection against another biotinylated target in W02009/077175 with the
following exception: the selection buffer consisted of PBS supplemented with
10 % Fetal Bovine Serum (FBS, Gibco, cat. no. 10108-165) and 0.1%
Tween20 (Acros Organics, cat. no. 233362500).
In order to reduce the amount of background binders, a pre—selection
was performed in each cycle. In the pre-selection, the same types of beads
were used as during the selection, i.e. ds in track 1 and SPA-beads in
track 2. In all tracks of cycle 1-4, pre-selections were performed using SA— or
SPA-beads coated with biotinylated human lgG-Fc (Jackson
ImmunoResearch Lab, cat. no. 009-060—008). Furthermore in cycle 1, track 1,
the pre—selection was performed using SA-beads coated with a mix of hPD-L2
(human PD-L2 Fc Chimera; R&D Systems, cat. no. 1224-PL-100), hB7-H3
(human B7-H3 Fc Chimera; R&D s, cat. no. 1027-B3—100), hB7-H4
(human B7-H4; R&D s, cat. no. 6576-B7-50), ylated previously
as described for hPD—L1. In cycle 1, track 2, the pre-selection was performed
using SPA-beads coated with a mix of biotinylated PD-L2 and biotinylated B7-
H3. During pre-selection the phage stock was incubated with coated beads
er end for 30-90 min at RT. A|| tubes and beads used in the pre-
selections or selection were pre—blocked with PBS supplemented with 3%
Bovine Serum Albumin (BSA, Sigma A3059-100G) and 0.1 % 0.
Selection was performed in solution at RT and the time for selection was
approximately 120 min followed by wash with PBS + 0.1 % Tween20 and
catch of target-phage complexes on ds or SPA-beads using 1 mg
beads per 1.6 or 8.5 pg biotinylated hPD-L1, respectively.
For amplification of phage particles between selection cycle 1 and 2,
E. coli strain ER2738 cells (Lucigen, Middleton, WI, USA) were used for
infection and grown in medium supplemented with 20 ug/ml tetracycline. A 5 x
excess of M13K07 helper phage compared to bacteria were allowed to infect
log phase bacteria.
Table 2: Selection against biotinyiated hPD-L1 Fc a
Cycle Selection Phage stock Proteins used Target Number on
track from library in pre-selection conc. of of last
or selection (nM) washes wash
track (h)
lgG—Fc, hPD—L2,
1 1
Zlib006Naive.ll_ . hB7-H3, hB7-H4 100 2
1 2 lgG-Fc, hPD-L2,
Zlib006Naive.l|_ . hB7-H3 100 2
2 1-1 1 lgG-Fc 66 4
2 1-2 1 lgG—Fc 10 4
2 2-1 2 lgG-Fc 66 4
3 1—1-1 1-1 IgG-Fc 44 6
3 12 1—1 lgG-Fc 10 6
3 1—2-1 1-2 lgG-Fc 1 6
3 12 1—2 IgG-Fc 0.5 10
3 21 2-1 lgG-Fc 44 6
3 22 2—1 IgG-Fc 10 6
4 11-1 11 lgG-Fc 30 10
4 11—2 1—1-1 IgG—Fc 10 31 1
4 12-1 12 lgG-Fc 10 31 15
4 1—21 1-2—1 lgG-Fc 0.5 10
4 11-2 1—2-1 lgG-Fc 0.2 31 64 [4 °C]
4 1—21 1-2—2 lgG-Fc 0.05 31 15
4 1 2—1-1 IgG-Fc 30 10
4 21-2 21 lgG-Fc 10 31 1
4 22—1 2—1-2 IgG-Fc 10 31 15
The amplification of phage particles between selection cycles 2 and 4
was done by performing ion of bacteria in solution as follows. After
infection of log phase E. coli ER2738 with phage particles, T88
supplemented with 2 % glucose, 10 ug/ml tetracycline and 100 ug/ml
ampicillin was added, followed by incubation with rotation for 30 min at 37 °C.
Thereafter, the bacteria were infected with M13K07 helper phage in 5 x
excess. The ed bacteria were pelleted by centrifugation, re-suspended
in TSB—YE medium mented with 100 uM IPTG, 25 ug/ml kanamycin
and 100 ug/ml ampicillin, and grown overnight at 30 °C. The overnight
cultures were centrifuged, and phage particles in the supernatant were
precipitated twice with PEG/NaCl buffer. Finally, the phage particles were re-
suspended in selection buffer before entering the next selection cycle.
In the final selection cycle, log phase ia were infected with eluate
and diluted before ing onto TBAB plates (30 g/l tryptose blood agar
base, Oxoid, cat. no. B) supplemented with 0.2 g/l ampicillin in order
to form single colonies to be used in ELISA screening.
An overview of the selection strategy, describing an increased stringency in
subsequent cycles, using a lowered target concentration and an increased
number of washes, is shown in Table 2. Washes were performed for 1 min, if
nothing else is stated in Table 2, using PBST 0.1 % (PBS supplemented with
0.1 % Tween-20) and elution was carried out as described in
WO2009/077175.
Production of Z variants for ELISA: Z variants were ed by
inoculating single colonies from the selections into 1 ml TSB-YE medium
supplemented with 100 ug/ml ampicillin and 1 mM IPTG in deep-well plates
(Nunc, cat. no. 278752). The plates were incubated with rotation for 24 h at
37 °C. Cells were pelleted by centrifugation, re-suspended in 200 pl PBST
0.05 % and frozen at -80 °C to release the periplasmic fraction of the cells.
Frozen samples were thawed in a water bath and the freeze-thawing
procedure was repeated eight times. 600 pl PBST 0.05 % was added to the
thawed samples and cells were pelleted by centrifugation.
The final supernatant of the periplasmic extract contained the Z
variants as fusions to ABD, expressed as LE-[Z#####]—VDYV-
[ABD]-YVPG (Gronwall et al., supra). Z##### refers to dual, 58 amino
acid residue Z variants.
ELISA screening of Z variants: The binding of Z variants to hPD-L1
was analyzed in ELISA assays. Half-area 96-well ELISA plates (Costar, cat.
no. 3690) were coated at 4 °C overnight with 2 ug/ml of an BD goat
antibody (produced in-house) diluted in g buffer (50 mM sodium
ate, pH 9.6; Sigma, cat. no. . The antibody solution was poured
off and the wells were washed in water and blocked with 100 pl of PBSC
(PBS supplemented with 0.5 % casein; Sigma, cat. no. C8654) for 1 to 3 h at
RT. The blocking solution was discarded and 50 pl periplasmic solutions,
diluted 1:1 with PBST 0.05%, were added to the wells and incubated for 1.5
to 2.5 h at RT under slow agitation. As a blank control, PBST 0.05 % was
added instead of a asmic sample. The supernatants were poured off
and the wells were washed 4 times with PBST 0.05 %. Then, 50 pl of
biotinylated hPD-L1 at a concentration of 0.32 nM in PBSC was added to
each well. The plates were incubated for 1 h at RT followed by washes as
described above. Streptavidin conjugated HRP (Thermo ific, cat. no.
N100) diluted 1:30,000 in PBSC, was added to the wells and the plates were
incubated for approximately 1 h. After washing as described above, 50 pl
lmmunoPure TMB ate (Thermo Scientific, cat. no. 34021 ) was added to
the wells and the plates were treated according to the cturer’s
recommendations. The absorbance at 450 nm was measured using a multi-
well plate reader, 3 (Perkin Elmer).
cing: In parallel with the ELISA screening, all clones were
sequenced. PCR fragments were amplified from single colonies, sequenced
and analyzed essentially as described in WO2009/077175.
EC50 analysis of Z variants: A selection of PD—L1 binding Z variants
was subjected to an analysis of the response against a on series of
biotinylated hPD-L1 ing the procedure described above. The Z variants
were diluted 1:1 in PBST 0.05 %. Biotinylated hPD-L1 was added at a
concentration of 40 nM and diluted stepwise 1:4 down to 32 pM. As a
background control, all Z variants were also assayed with no target protein
added. Periplasm samples containing the PD-L1 binding Z variant Z131 12
(SEQ |D.NO:777) were included on each plate and analyzed as positive
control. Periplasm containing the ABD moiety only was used as negative
control. In the same assay, the icity of the Z variants was tested by
incubating periplasm samples with the four ent biotinylated control
proteins hPD-L2, hB7-H3, hB7-H4 and IgGFc, respectively, added at a
concentration of 8 nM. Data were analyzed using ad Prism 5 and non—
linear regression, and EC50 values (the half maximal effective concentration)
were calculated.
Results
Phage display selection of PD—L1 binding Z variants: Individual clones
were obtained after four cycles of phage display selections against
biotinylated hPD-L1.
ELISA screening of Z variants: The clones obtained after four cycles of
selection were ed in 96-well plates and screened for hPD-L1 binding
activity in ELISA. Several unique Z variants were found to give a response of
0.3 AU or higher (corresponding to at least 3 X the blank control) t hPD-
L1 at a concentration of 0.32 nM. The average response of the blank controls
was 0.067 AU.
Seguencing: Sequencing was med for clones obtained after four
cycles of selection. Each variant was given a unique identification number
#####, and individual variants are referred to as Z#####. The amino acid
sequences of the 58 amino acid residues long Z variants are listed in Figure 1
and in the sequence listing as SEQ ID NO:774-808. The deduced PD-L1
binding motifs extend from residue 8 to residue 36 in each ce. The
amino acid sequences of the 49 amino acid residues long polypeptides
predicted to constitute the complete three-helix bundle within each of these Z
variants extend from e 7 to residue 55.
EC50 analysis of Z variants: A subset of Z variants having the highest
ELISA values in the ELISA screening experiment described above was
selected and subjected to a target titration in ELISA format. Periplasm
samples were incubated with a serial dilution of biotinylated hPD—L1 . A
asm sample containing 213112 (SEQ ID NO:777), confirmed to bind
PD-L1 in the ELISA screen, was selected as a positive l and used to
normalize different plates to each other. Obtained values were analyzed and
their respective EC50 values were calculated (Table 3).
No icant g was detected to any of the included l
proteins of the B7-family (hPD-L2, hB7-H3 and hB7-H4), nor to the control
protein lgGFc (included here because Fc chimeric proteins were used in the
ion and screening). These results indicate that the selected Z variants
are specific to PD-L1.
Table 3: Calculated E050 values from ELISA titration analysis
Z variant SEQ ID NO: EC50 (M) Z variant SEQ ID NO: EC50 (M)
213080 774 2.8 x 10'10 213184 783 2.2 x 10'10
213088 775 3.8 x 10‘10 213185 784 2.4 x 10'10
213091 778 2.2 x 10'10 213189 785 1.5 x 10‘10
213104 788 4.1 x10'10 213188 792 4.7 x10'10
213112 777 2.2 x10"10 213190 793 2.8 x10'10
213115 789 4.0 x10'10 213198 788 1.8 x10'10
213117 790 2.9 x10‘10 213210 794 3.5 x10'10
213134 791 4.5 x 10'10 213304 787 3.2 x 10-10
213147 779 2.8 x 10‘10 213388 795 4.8 x 10'10
213154 780 1.1 x 10'10 213447 798 2.9 x 10'10
213158 782 2.5 x10‘10
Example 2
Subcloning and tion of a subset of primary PD-L1 binding Z variants
Materials and methods
Subcloning of Z variants with a Hise-tag: The DNA of 14 PD—L1 binding
Z variants, Z13080 (SEQ ID ), 213088 (SEQ ID NO:775), 213091
(SEQ ID NO:776), Z13112 (SEQ ID NO:777), Z13120 (SEQ ID NO:778),
Z13147 (SEQ ID NO:779), Z13154 (SEQ ID NO:780), 213156 (SEQ ID
NO:781), Z13158 (SEQ ID NO:782), 213164 (SEQ ID ), Z13165 (SEQ
ID NO:784), 213169 (SEQ ID NO:785), Z13198 (SEQ ID ) and
213304 (SEQ ID NO:787) were amplified from the library vector pAY02592. A
subcloning strategy for uction of monomeric Z variant molecules with N-
terminal Hiss-tag was applied using standard molecular biology techniques
(essentially as described in detail in WO2009/O77175 for Z variants binding
another target). The Z gene fragments were subcloned into the sion
vector pAY01448 resulting in the encoded ce MGSSHHHHHHLQ—
[Z#####]—VD.
Subcloning of Z variants with a C-terminal Cys: Two Z variants,
Z13091 (SEQ ID NO:776) and 213156 (SEQ ID NO:781)were mutated to
WO 72280
start with the N-terminal amino acids AE instead of VD and further subcloned
with the C-terminal addition of the amino acids VDC (incorporating a unique
cysteine in the polypeptide) using rd molecular biology techniques. The
resulting encoding sequences are referred to as Z15168—Cys (SEQ ID
NO:809) and Z15169-Cys (SEQ ID NO:810), respectively.
Cultivation: E. coli T7E2 cells (GeneBridges) were transformed with
plasmids containing the gene fragments of each respective PD-L1 binding Z
variant and cultivated at 37 °C in 940 ml of TSB—YE medium supplemented
with 50 ug/ml kanamycin. In order to induce n expression, IPTG was
added to a final concentration of 0.2 mM at OD600 = 2 and the cultivation was
incubated at 37 °C for r 5 h. The cells were harvested by
centrifugation.
Purification of PD-L1 binding Z ts with a Hise-tag: Approximately
1-2 g of each cell pellet was resuspended in 30 ml of binding buffer (20 mM
sodium phosphate, 0.5 M NaCl, 20 mM imidazole, pH 7.4) supplemented with
Benzonase® (Merck, cat. no. 1016540001) to a concentration of 15 U/ml.
After cell disruption by tion, cell debris was d by centrifugation
and each supernatant was applied on a 1 ml His GraviTrap IMAC column (GE
Healthcare, cat. no. 1199). Contaminants were removed by washing
with wash buffer (20 mM sodium phosphate, 0.5 M NaCl, 60 mM imidazole,
pH 7.4) and the PD—L1 binding Z variants were subsequently eluted with
elution buffer (20 mM sodium phosphate, 0.5 M NaCl, 500 mM imidazole, pH
7.4). After the IMAC purification, the protein buffer was exchanged to PBS
using PD-10 columns (GE Healthcare, cat. no. 1701).
Purification of PD-L1 binding Z variants with a C-terminal Cys: The
respective cell pellet was resuspended in 20 mM Tris-HCI, pH 8 (10 ml buffer
/g cell pellet) and lysed by heat ent in a water bath at 90 °C for 10 min,
ed by cooling on ice to approximately 20 °C. Benzonase® was added (1
ul/g cell ) and each cell lysate was incubated at RT for 30 min, before
cell debris was removed by centrifugation. For reduction of disulfides,
dithiothreitol (DTT; Acros organics, cat. no. 165680250) was added to a final
concentration of 20 mM followed by incubation at RT for 1 h. Purification was
performed by anion ge followed by reverse phase chromatography
(RPC). Buffer exchange to 20 mM HEPES, 1 mM EDTA, pH 7.2 was carried
out using HiPrep 26/10 columns (GE care, cat. no. 1701).
Finally, each Z variant was purified on EndoTrap® red columns (Hyglos, cat.
no. 321063) to ensure low xin t.
For each protein purified by any method described above, the
concentration was determined by ing the absorbance at 280 nm, using
a NanoDrop® ND-1000 spectrophotometer and the extinction coefficient of
the n. The purity was analyzed by SDS-PAGE stained with Coomassie
Blue and the identity of each purified Z variant was confirmed using HPLC-
MS analysis (HPLC—MS 1100; Agilent Technologies).
Results
Cultivation and purification: The PD-L1 binding Z variants with a Hiss-
tag or a inal Cys were sed as soluble gene products in E. coli.
GE analysis of each final protein preparation showed that these
predominantly contained the PD-L1 binding Z variant. The correct identity and
molecular weight of each Z variant were confirmed by HPLC-MS analysis.
Example 3
Characterization of primary PD-L1 binding Z variants
In this Example, a subset of Z variants was characterized in terms of
stability and in vitro binding properties. The specificity and affinity for human
PD-L1 of the Z variants were analyzed by SPR and binding to PD-L1
expressing cells was analyzed using Fluorescence Activated Cell Sorting
. Furthermore, the ability of Z variants to block the binding of PD-L1 to
its receptor PD1 was investigated using AlphaLlSA.
Materials and methods
Biacore kinetic and specificity is: Kinetic constants (ka and kd)
and affinities (KD) for hPD-L1 were determined for 14 Hiss-tagged Z variants
using a Biacore 2000 instrument (GE Healthcare). Some of the Z variants
WO 72280
were also tested for binding against the sequence-related proteins hPD-L2,
hB7-H3, hB7-H4 and mPD-L1 (mouse PD-L1 Fc Chimera, R&D Systems, cat.
no. 1019-B7).
hPD-L1, hPD-L2, hB7-H3, hB7-H4 and mPD-L1 were immobilized in
separate flow cells on the carboxylated dextran layer of different CM5 chip
es (GE Healthcare, cat. no. BR100012). The lization was
performed using amine coupling chemistry according to the manufacturer’s
protocol and using HBS-EP as running buffer (0.01 M HEPES pH 7.4, 0.15 M
NaCl, 3 mM EDTA, 0.005 % v/v Surfactant P20, GE Healthcare, cat. no.
BR100188). The ligand immobilization levels on the surfaces were 4
RU for , 537-742 RU for hPD-L2, 383 RU for hB7-H3, 538-659 RU for
hB7-H4 and 482 RU for mPD-L1. One flow cell e on each chip was
activated and deactivated for use as blank during analyte injections. In the
kinetic experiment, HBS-EP was used as running buffer and the flow rate was
50 ul/min. The analytes, i.e. the Z variants, were each diluted in HBS-EP
buffer within a concentration range of 1000 to 0.01 nM and injected for 5 min,
followed by dissociation in running buffer for 15-25 min. After dissociation, the
surfaces were rated with one or two injections of 0.1 % SDS. Kinetic
constants were calculated from the sensorgrams using the Langmuir 1 :1
model of BiaEvaluation software 4.1 (GE Healthcare).
AlphaLlSA blocking assay: The potential of Z variants to t g
of PD-L1 to PD—1 was analyzed by AlphaLlSA and recordings in an EnSpire
multiplate reader 2300 (Perkin Elmer). hPD-1 (human PD-1 Fc-chimera; R&D
Systems, cat. no. 1086-PD-050) was immobilized on AlphaLlSA Acceptor
beads (Perkin Elmer, cat. no. 6772002) according to the manufacturer’s
recommendations. Stepwise serial dilutions 1:3 of agged Z variants to
final concentrations of 250 nM to 12 pM were made in a 384 plate (Perkin
Elmer, cat. no. 6005350) and incubated for 1 h with 10 nM ylated hPD-
L1 in AlphaLlSA buffer (Perkin Elmer, cat. no. AL000F). hPD—1-coated
Acceptor beads were added to a final concentration of 10 ug/ml and
incubated for 1 h. Finally, streptavidin coated Donor beads (Perkin Elmer, cat.
no. 6772002) were added to a final concentration of 40 ug/ml and incubated
for 30 min. All incubations were performed at RT in the dark. The plate was
analyzed in the EnSpire instrument and the |C50 values were ated
using GraphPad Prism 5.
Cell binding analysis by FACS: The potential on variants to bind PD-
L1 expressing cells was igated using Fluorescence Activated Cell
Sorting (FACS). THP-1 cells, cultivated in RPMI , cat. no. BE12-702F)
containing 10 % FBS were stimulated with 10 ng/ml lFNg (R&D Systems, cat.
no. 285-lF-100) overnight which results in up-regulation of PD-L1. 150,000
stimulated and unstimulated cells were pipetted per well of a v-bottomed 96
well plate (Nunc, cat. no. 277143) and the cells in the plate were
subsequently pelleted at 400 g for 3 min at RT. The supernatants were
removed and the cells were resuspended in 100 pl PBS plus 2.5 % FBS
(staining buffer) containing 10 ug/ml of the different His-tagged Z variants. A
mouse anti-PD-L1 antibody (R&D Systems, cat. no. MAB1561) at 1 ug/ml
was used as a positive control. Cells incubated with buffer alone were used
as negative controls. The cells were incubated for 1 h at 8 °C in the dark,
washed twice with 100 pl staining buffer and resuspended in 100 pl of
ng buffer containing a goat anti-Z antibody (produced in house) at a
concentration of 5 ug/ml. Cells stained with the positive control were treated
with buffer only. The cells were incubated for 1 h at 8 °C in the dark, washed
twice with 100 pl staining buffer and resuspended in 100 pl of staining buffer
containing an Alexa Fluor 647 chicken anti-goat lgG antibody (Life
technologies, cat. no. A21469) or an Alexa Fluor 647 goat anti-mouse lgG
antibody (Life technologies cat. no. A21236). The cells were once again
incubated for 1 h at 8 °C in the dark, washed twice with 100 pl staining buffer
and ended in 200 pl of staining buffer. Data from 10,000 cells were
obtained using a FACS Calibur (Beckman Coulter) and the data was
analyzed using Flowing software 2.5.0 (Turku University). Mean scence
intensity (MFI) was used as a read out of g capacity.
Circular ism (CD) spectroscopy analysis: Two purified Z ts
with a C-terminal cysteine, Z15168—Cys (SEQ ID NO:809) and Z15169-Cys
(SEQ ID NO:810), were diluted to 0.5 mg/ml in 20 mM HEPES, 1 mM EDTA,
pH 7.2. For each diluted Z variant, a CD spectrum at 250-195 nm was
obtained at 20 °C. In addition, a le temperature measurement (VTM)
was performed to determine the melting temperature (Tm). In the VTM, the
absorbance was measured at 221 nm while the temperature was raised from
to 90 °C, with a ature slope of 5 °C/min. A new CD spectrum was
obtained at 20 °C after the heating procedure in order to study the refolding
ability of the Z variants. The CD measurements were performed on a Jasco J-
810 opolarimeter (Jasco Scandinavia AB) using a cell with an optical
path length of1 mm.
Results
Biacore kinetic and specificity analysis: The interactions of 14 Hise—
tagged PD-L1-binding Z variants with hPD-L1 were analyzed in a e
instrument by injecting various concentrations of the Z variants over a surface
containing immobilized hPD-L1. All tested Z variants showed binding to hPD-
L1. A summary of the kinetic parameters (KD, ka and kd) for binding of the Z
variants to hPD—L1 obtained using a 1:1 interaction model is given in Table 4.
Typical resulting curves, where responses from a blank surface were
acted, are displayed in Figure 2 for two selected Z variants, 213091
(SEQ ID ) and 213156 (SEQ ID NO:781).
Table 4: Kinetic parameters for binding of Z ts to hPD-L1
z variant SEQ ID NO: hPD-L1
ka (1lMs) k... (1ls) KD (M)
213080 774 1.4 x106 9.2 x10"3 6.6 x10“9
213088 775 1.4 x106 3.7 x10'3 2.6 x10'9
213091 776 3.1 x106 1.4 x10‘3 4.6 x10'10
213112 777 6.1 x105 1.5 x10'3 2.5 x10'9
213120 778 2.0 x106 1.2 x10‘2 6.0 x10'9
213147 779 6 1.7x10'3 1.6x10'9
213154 780 2.3 x106 3.1x10'3 1.4 x10'9
213156 781 1.7x 108 2.5x 10-3 1.5x10'9
213158 782 6.7 x105 5.6 x10'3 8.3 x10'9
213164 783 7.9 x105 8.7 x10‘3 1.1x10'8
213165 784 2.0 x106 1.3 x10'3 6.4 x10'10
213169 785 2.4 x106 3.5 x10‘3 1.5 x10'9
213198 786 5.8 x106 5.6 x10'3 9.7 x10'10
213304 787 1.6 x106 6.4 x10‘3 4.1 x10'9
A subset of the Z variants was also tested for binding against four
lized, sequence-related proteins: hPD-L2, hB7-H3, hB7-H4 and mPD-
L1. No binding against hPD-L2, hB7-H3, hB7-H4 or mPD—L1 was detected at
Z variant concentrations up to 50 nM. When injecting 1000 nM of a few
selected Z ts (213088, 213091, 213112, , 213154, 213156,
213165, 213169, 213198) some response against B7—H4 was observed for
213156 and 213165. The result of the g specificity analysis is
summarized in Table 5. Typical non-interacting traces from the SPR analysis
against hPD-L2, hB7-H3 and hB7-H4 are shown in Figure 3.
Table 5: Binding specificity against , hPD-L2, hB7—H3 and hB7—H4
Z variant SEQ ID NO: mPD-L1 hPD-L2 hB7-H3 hB7-H4
213080 774 n.a. n.d. n.d. n.a.
213088 775 n.d. n.d. n.d. n.d.
213091 776 n.d. n.d. n.d. n.d.
213112 777 n.a. n.d. n.a. n.d.
213120 778 n.a. n.d. n.d. n.a.
213147 779 n.d. n.d. n.a. n.d.
213154 780 n.d. n.d. n.d. n.d.
213156 781 n.d. n.d. n.d. KD > 5 pM
213158 782 n.a. n.d. n.d. n.a.
213164 783 n.a. n.d. n.d. n.a.
213165 784 n.d. n.d. n.d. KD > 5 pM
213169 785 n.d. n.d. n.d. n.d.
213198 786 n.d. n.d. n.d. n.d.
213304 787 n.a. n.d. n.a. n.d.
n.a. not d; n.d. no binding detected
AlphaLlSA blocking assay: The y of 14 Hise-tagged 2 variants to
inhibit hPD—L1 binding to hPD-1 was tested in an AlphaLlSA blocking assay.
Serial dilutions of the 2 variants were incubated with biotinylated hPD-L1 and
the blocking ability of each respective variant was measured after addition of
hPD-1 coated Acceptor beads and subsequently streptavidin coated Donor
beads. Inhibition could be measured as a decrease in AlphaLlSA counts for
positive Z variants. The calculated ICSO values for the 14 variants that were
all shown to block PD-L1 binding to PD-1 in this assay are shown in Table 6.
Table 6: IC50 values forZ variants inhibiting binding of PD-L1 to PD-1
Z variant SEQ ID NO: |C50
213080 774 2.7 x10'9
213088 775 8.8 x10'10
213091 776 6.9 x10'9
213112 777 3.9 x10“9
213120 778 4.2 x10'9
213147 779 5.6 x10‘9
213154 780 '9
213156 781 1.4 x10'9
213158 782 2.4 x10'9
213164 783 2.3 x10'9
213165 784 1.3 x10'9
213169 785 2.2 x10'9
213198 786 1.3 x10'9
213304 787 4.2 x10'8
Table 7: Normalized MFI for binding of Z variants to THP-1 cells
Z variant SEQ ID NO: MFI (normalized)
Z13080 774 1.06
213088 775 1.00
Z13091 776 1.00
Z13112 777 0.76
Z13120 778 0.71
Z13147 779 0.56
Z13154 780 1.04
Z13156 781 1.09
Z13158 782 0.91
Z13164 783 0.81
213165 784 1.24
Z13169 785 0.91
213198 786 0.89
Z13304 787 0.75
anti-PD—L1 antibody - 0.40
2016/076040
Cell binding analysis by FACS: This experiment confirmed binding of
the PD-L1 specific Z variants to PD-L1 expressing cells. THP-1 cells
stimulated with lFNy overnight, which increases the PD-L1 sion, were
stained with 10 pg/ml of each of the agged Z variants. The analyses
were performed at two different occasions and the MFI values, normalized
against 213091 included in both assays, are presented in Table 7.
CD analysis: The CD spectra determined for two selected PD-L1
binding Z variants with a C—terminal cysteine, Z15168—Cys (SEQ ID NO:809)
and Z15169-Cys (SEQ ID NO:810) showed that both variants had an o-helical
structure at 20 °C based on the typical minima at 208 and 222 nm. Reversible
folding was seen for both Z variants when ying spectra measured
before and after heating to 90 °C (Figure 4). The noisy signal observed in the
far UV region is expected to result from buffer effects (HEPES, which was
used as analysis buffer, absorbs strongly at 200 nM and below).The melting
atures (Tm) were determined to 50 °C and 58 °C for Z15168—Cys and
Z15169-Cys, respectively (Table 8).
Table 8: g temperatures (Tm)
z variant SEQ ID NO: Tm (°C)
Z15168—Cys 809 50
Z15169-Cys 810 58
Example 4
Design and construction of a maturated library of PD-L1 binding Z variants
In this Example, a maturated library was ucted. The library was
used for selections of PD-L1 binding Z variants. Selections from ted
libraries may result in binders with increased affinity (Orlova et a/., (2006)
Cancer Res 4339-48). In this study, randomized single stranded
oligonucleotides are generated, using split-pool DNA synthesis enabling
incorporation of defined codons in desired positions in the synthesis.
Materials and methods
Library design: The library was based on the sequences of the PD-L1
binding Z variants identified and characterized as described in Example 1 and
Example 3. In the new library, 13 variable positions in the Z molecule scaffold
were biased towards certain amino acid residues, according to a strategy
based on the Z variant sequences defined in SEQ ID NO:774-808. Two
ucleotides, one forward and one reverse complementary, with
complementary 3’-ends were generated using split-pool synthesis. The two
ucleotides were ed and extended by PCR, using outer primers,
to yield one gene fragment covering 147 bp corresponding to partially
ized helix 1 and 2 of the amino acid sequence: 5’- AA ATA AAT CTC
GAG GTA GAT GCC AAA TAC GCC AAA GAA CGT AAC NNN GCG GCT
NNN GAG ATC CTG NNN CTG CCT AAC CTC ACC NNN NNN CAA NNN
TGG GCC TTC ATC TGG AAA TTA NNN GAT GAC CCA AGC CAG AGC
TCA TTA TTT A -3’ (SEQ ID NO:819; randomized codons are illustrated as
NNN) flanked by restriction sites Xhol and Sacl. The oligonucleotides were
ordered from Ella Biotech GmbH (Martinsried Germany).
Table 9: Design of maturated librar
Amino acid Randomization (amino acid No of tion
position in the Z abbreviations) amino
t molecule acids
50% D, 30% A, 20% E 3 1/2 (D), 3/10
(A), 1/5 (E)
The theoretical distributions of amino acid residues in the new library
including 7 variable positions (11, 14, 18, 24, 25, 27 and 35) in the Z molecule
scaffold are given in Table 9. The resulting theoretical library size is 5.3 x 107
variants.
Library construction: The library was amplified using AmpliTaq Gold
polymerase (Life Technologies, cat. no. 4311816) during 12 cycles of PCR
and pooled products were ed with QlAquick PCR Purification Kit
(QIAGEN, cat. no. 28106) ing to the supplier’s recommendations. The
purified pool of randomized library fragments was digested with restriction
s Xhol and Sacl-HF (New England Biolabs, cat. no. R0146L, and cat.
no. R3156M, respectively) and concentrated using a PCR Purification Kit.
Subsequently, the product was run on a preparative 2.5 % agarose (NuSieve
GTG ® Agarose, Lonza, cat. no. 50080) gel electrophoresis and purified
using QIAGEN Gel Extraction Kit (QIAGEN, cat. no. 28706) according to the
er’s recommendations.
The phagemid vector pAY02592 (essentially as pAffi1 described in
Gronwall et a/., supra) was restricted with the same enzymes and ed
using phenol/chloroform extraction and ethanol precipitation. The restricted
fragments and the restricted vector were ligated in a molar ratio of 5:1 with T4
DNA ligase (Thermo Scientific, cat. no. EL0011) for 2 h at RT, ed by
overnight incubation at 4 °C. The ligated DNA was recovered by
phenol/chloroform tion and ethanol itation, followed by dissolution
in 10 mM Tris-HCI, pH 8.5. Thus, the resulting library in vector pAY02592
d Z variants each fused to an albumin binding domain (ABD) derived
from streptococcal protein G.
The ligation ons (approximately 160 ng DNA/transformation) were
electroporated into electrocompetent E. coli ER2738 cells (Lucigen,
Middleton, WI, USA, 50 pl). Immediately after electroporation, approximately
1 ml of recovery medium (supplied with E. coli ER2738 cells) was added. The
ormed cells were incubated at 37 °C for 60 min. Samples were taken for
titration and for determination of the number of transformants. The cells were
thereafter pooled and cultivated overnight at 37 °C in 1 l of TSB-YE medium,
supplemented with 2 % e, 10 ug/ml tetracycline and 100 ug/ml
ampicillin. The cells were pelleted for 15 min at 4,000 g and resuspended in a
PBS/glycerol solution (approximately 40 % glycerol). The cells were aliquoted
and stored at —80 °C. Clones from the library of Z variants were sequenced in
order to verify the content and to evaluate the outcome of the constructed
library vis-a-vis the library design. Sequencing was performed as described in
Example 1 and the amino acid bution was verified.
Preparation of phage stock: Cells from a glycerol stock containing the
phagemid y were inoculated in 3.5 l of TSB-YE supplemented with 1 g/l
glucose, 100 mg/l ampicillin and 10 mg/l tetracycline. The cells were
cultivated at 37 °C with orbital shaking (100 RPM). When the cells d an
optical density at 600 nm (OD600) of 0.59, approximately 620 ml of the
cultivation was infected using a 5 x molar excess of M13K07 helper phage.
The cells were incubated for 30 min, whereupon the cells were pelleted by
centrifugation at 3,000 g and resuspended in 3 | fresh TSB-YE supplemented
with 100 mg/l ampicillin, 25 mg/l kanamycin, and 0.1 mM IPTG. The
cultivation was split into 6 x 5 l shaker flasks at and incubated at 30 °C with
orbital g and after ~18 h the cells were pelleted by centrifugation at
4,700 g. The phage particles were precipitated from the supernatant twice in
PEG/NaCl, filtered and ved in PBS and ol as described in
Example 1. Phage stocks were stored at -80 °C until use in selection.
Results
Library construction: The new library was designed based on a set of
PD-L1 binding Z variants with verified binding properties (Example 1 and 3).
The theoretical size of the designed library was 5.3 x 107 Z variants. The
actual size of the library, determined by titration after transformation to E. coli.
ER2738 cells, was 2.8 x 109 transformants.
The library quality was tested by sequencing of 116 transformants and
by comparing their actual sequences with the theoretical design. The contents
of the actual library ed to the designed library were shown to be
actory. A maturated library of potential s to PD-L1 was thus
successfully constructed.
Selection, screening and characterization of Z variants from a maturated
library
als and methods
Phage display selection of PD-L1 binding Z variants: The target n
PD-L1 was biotinylated as described in Example 1. Phage display selections,
using the new library of Z variant molecules constructed as described in
Example 4, were performed in four cycles against hPD-L1 ially as
described in e 1, with the following exceptions: Exception 1: SA-beads
were used to catch the PD-L1:Z variant complexes in all selection tracks.
Exception 2: pre-selection was performed against SA—beads coated with
biotinylated human lgG-Fc only before cycle 1 and 2. Furthermore in cycle 1,
another pre-selection was performed against SA—beads coated with a mix of
PD-L2, B7-H3, and B7-H4 as previously described in Example 1. Exception 3:
selections t biotinylated human PD-L1 was performed in four cycles
initially divided in two different tracks (1 and 2). As selection proceeded, the
tracks were further divided according to target concentration and number
and/or time of washes to finally end up in 11 tracks in cycle four. More
precisely, the first track (1) was divided in the second to the fourth cycles,
resulting in a total of2 tracks (1-1 to 1-2) in cycle 2, fourtracks (1-1—1 to 1—2-
2) in cycle 3 and seven tracks (11-1 to 12-2) in cycle 4. The second
track (2) was d in the second to the fourth cycles, resulting in a total of 2
tracks (2-1 to 2-2) in cycle 2, four tracks (21 to 22) in cycle 3 and four
tracks (21—1 to 2—21) in cycle four. ion 4: during the 19 h washing
step in selection cycle 12-3 a 20-fold molecular excess of non-biotinylated
hPD-L1 was added to the wash buffer. An overview of the selection strategy,
describing an increased stringency in subsequent cycles ed by using a
lowered target concentration and an increased number of washes, is shown
in Table 10.
Table 10. Selection against biotiny/ated hPD-L1 Fc using a ted library
Cycle ion Phage Proteins Target Number Duration Addition
track stock from used in conc. of of last to last
library or pre- (nM) washes wash (h) wash
selection selection buffer
track
ZIib006PD- | G-Fc, PD-L2,
1 1 50 2
L1 .l Bg7-H3, B7-H4
Zlib006PD- | -F
1 2 gfiHsc, B7-H4, PD-L2, 25 2
L1 .l
2 1-1 1 lgG-Fc 25 8
2 1-2 1 lgG-Fc 10 12
2 2-1 2 lgG-Fc 2.5 12
2 2-2 2 lgG-Fc 0.5 12
3 11 1-1 no pre-selection 5 20
3 12 1-1 no pre-selection 5 20
3 1-2—1 1-2 no pre-selection 2.5 20
3 12 1-2 no pre-selection 1 20
3 21 2-1 no lection 0.5 20
3 22 2-1 no pre-selection 0.1 20
3 21 2-2 no pre-selection 0.05 20
3 22 2-2 no pre-selection 0.005 20
4 11—1 1—1-1 no pre-selection 2.5 20
4 1 12 no pre-selection 2.5 20
4 12—2 12 no pre-selection 2.5 20
4 12-3 12 no pre-selectlon 2.5 20 22351—1
4 11-1 11 no pre-selection 0.1 20
4 12-1 22 no pre-selection 0.5 20
4 12—2 1—2-2 no pre-selection 0.5 20
4 2-1—1-1 21 no pre-selection 0.05 20
4 1 22 no pre-selection 0.1 30
4 21-1 21 no pre-selection 0.01 30
4 22-1 22 no pre-selection 0.05 20
Production of Z variants for ELISA: The Z variants were produced by
inoculating single colonies from the selections into 1.2 ml TSB-YE medium
supplemented with 100 pgiml ampicillin and 1 mM IPTG in deep-well plates
(Nunc, cat. no. 278752). The plates were incubated with rotation for 24 h at
37 °C. Cells were pelleted by centrifugation at 3300 g and re-suspended in
150 pl PBST 0.05 % and frozen at -80 °C to release the periplasmic fraction
of the cells. Frozen samples were thawed in a water bath and the freeze-
thawing procedure was repeated eight times before the periplasmic fraction
was isolated in deep-well plates (Axygen, cat. no. 391101) by filtration
using filter plates (EMD Millipore, cat. no. MSNANLY50). The final
supernatant of the periplasmic extract contained the Z variants as fusions to
ABD, expressed as AQHDEALE-[Z#####]-VDYV-[ABD]-YVPG (Grc'jnwall et
al., supra). Z##### refers to individual, 58 amino acid residue Z variants.
ELISA screening of Z variants: The binding of Z variants to human PD-
L1 was analyzed in ELISA assays as described previously in e 1 with
the following exceptions. Exception 1: The periplasmic fraction was d
1:8 with PBST 0.05% before added to the wells and incubated for 1.7 h.
Exception 2: d of a blank control a negative l of a periplasmic
fraction containing the fusion protein ABD with no Z—fusion partner was used.
Exception 3: periplasm s containing the primary PD-L1 binding Z
variant 213091 (SEQ ID.NO:776) was included in ates on each plate
and analyzed as ve controls. Exception 4: 50 ul of biotinylated hPD-L1 at
a concentration of 40 pM in PBSC was added to each well and the plates
were incubated for 1.8 h at RT.
Seguencing: In parallel with the ELISA screening, all clones were
sequenced as described in Example 1.
ELISA EC50 analysis: A selection of PD—L1 binding Z variants was
subjected to an is of the response against a dilution series of
biotinylated human PD-L1 as bed in Example 1 with the following
exceptions. Exception 1: the Z variants were diluted 1:8 in PBST 0.05 %
before added to the wells. Exception 2: ylated human PD-L1 was added
at a concentration of 15 nM and diluted stepwise 1:3 down to 0.25 pM.
Exception 3: a asm sample containing the primary PD—L1 binding Z
variant 213091 (SEQ ID.NO:776) was included for comparison and analyzed
together with the maturated Z variants.
Results
Phage display selection of PD-L1 binding Z ts: Individual clones
were obtained after four cycles of phage display selection t biotinylated
hPD-L1.
ELISA screening of Z variants: The clones obtained after four cycles of
selection were produced in 96-well plates and screened for hPD-L1 g
activity in ELISA. A majority of the unique Z variants were found to give a
higher response than average response of the positive control Z13091
ge 0.264 AU) against hPD-L1 at a concentration of 40 pM. The average
response of the negative controls was 0.051 AU.
Seguencing: Sequencing was performed for clones obtained after four
cycles of selection. Each variant was given a unique identification number,
Z#####, as described in e 1. The amino acid sequences of the 58
amino acid residues long Z ts are listed in Figure 1 and in the sequence
listing as SEQ ID NO:1-773. The deduced PD-L1 binding motifs extend from
position 8 to on 36 in each sequence. The amino acid sequences of the
49 amino acid residues long polypeptides predicted to constitute the complete
three-helix bundle within each of these Z variants extend from residue 7 to
residue 55.
EC50 analysis of Z ts: A subset of Z variants having the highest
ELISA values in the ELISA screening experiment described above was
selected and subjected to a target titration in ELISA format. Periplasm
samples were ted with a serial dilution of biotinylated hPD-L1. A
periplasm sample containing Z13091 (SEQ ID NO:776), the isolated primary
Z variant that showed the highest binding affinity to hPD-L1, was included as
a positive control. Obtained values were analyzed and their respective EC50
values were calculated using GraphPad Prism 5 (Table 11). All maturated Z
variants showed lower EC50 values than the top primary Z variant Z13091.
Table 11: ated EC50 values of Z-ABD variants from maturation
Z variant SEQ EC50 Z variant SEQ EC50 Z variant SEQ EC50
ID (M) ID (M) ID (M)
217746 218054 218135
217748 218060 218137
217756 218064 218138
217758 218065 218140
217772 218066 218143
217825 218069 218144
217843 218070 218148
217911 218074 218149
217928 218078 218150
217950 218090 218152
217964 218092 218153
217968 218095 218156
217972 218096 218158
217975 218099 218164
217978 218101 218167
217990 218104 218172
217995 218106 218174
217997 218108 218176
217999 218110 218179
218000 218111 218185
218005 218115 218220
218008 218116 218228
218021 218117 218233
218022 218118 218240
218027 218119 218243
218038 41 7.8 x10' 218124 82 8.4 x10' 218252 90 8.5 x10'
218037 42 7.7 x10'11 218128 83 7.7 x10'11 218288 91 8.9 x1011
218038 43 8.9 x10"11 218129 18 8.2 x10"11 218353 15 7.7 x10'fi
218039 20 8.9 x10'11 218130 84 7.4 x10'11 218374 92 1.0 x1010
218048 4 8.5 x10‘11 218131 85 8.7 x10'11 218377 93 7.8 x10'11
218052 14 7.1 x1011 218133 88 7.7x10'11 218418 24 8.0x 10'11
213091 778 1.2 x1010
Example 6
ning and production of a subset of maturated PD-L1 binding Z ts
Materials and methods
Subcloning of 2 variants with a Hise-tag: The DNA of 24 maturated PD-
L1 binding Z variants, (217746 (SEQ ID NO:8), 217748 (SEQ ID ,
217756 (SEQ ID NO:7), 217825 (SEQ ID NO:5), 217911 (SEQ ID NO:3),
217964 (SEQ ID NO:2), 217972 (SEQ ID NO:19), 217978 (SEQ ID NO:13),
218022 (SEQ ID NO:9), 218039 (SEQ ID NO:20), 218048 (SEQ ID NO:4),
218052 (SEQ ID NO:14), 218054 (SEQ ID NO:22), 218064 (SEQ ID N011),
218066 (SEQ ID NO:12), 218070 (SEQ ID NO:10), 218074 (SEQ ID NO:6),
218090 (SEQ ID NO:17), 218101 (SEQ ID NO:23), 218129 (SEQ ID NO:16),
218149 (SEQ ID NO:18), 218233 (SEQ ID , 218353 (SEQ ID NO:15)
and 218418 (SEQ ID NO:24)) were amplified from the library vector
pAY02592 and subcloned with a Hise-tag as described in e 2 above.
ning of 2 variants with a C-terminal Cys: Three 2 variants,
218064 (SEQ ID N021), 217964 (SEQ ID N02) and 218090 (SEQ ID NO:17)
were mutated to start with the N-terminal amino acids AE instead of VD and
further subcloned with the C-terminal addition of the amino acids VDC
(incorporating a unique cysteine in the polypeptide) using standard molecular
biology techniques. The resulting sequences are referred to as 218608-Cys
(SEQ ID NO:811), 218609-Cys (SEQ ID NO:812) and -Cys (SEQ ID
), respectively.
Cultivation: Generally, E. coliT7E2 cells (GeneBridges) were
transformed with plasmids containing the gene fragments of each respective
PD-L1 binding 2 variant and cultivated at 37 °C in approximately 940 ml of
TSB-YE medium supplemented with 50 pg/ml kanamycin. In order to induce
protein expression, IPTG was added to a final concentration of 0.2 mM at
ODGOO = 2 and the cultivation was incubated at 37 °C for another 5 h. The
cells were harvested by centrifugation. Specifically, 218608—Cys and 218609-
Cys were fed-batch cultivated at 37 °C in approximately 700 ml of defined
l medium supplemented with 50 ug/ml kanamycin. In order to induce
protein sion, IPTG was added to a final concentration of 0.5 mM at
ODeoo =75 and the cultivation was incubated for another 7 h. The cells were
harvested by centrifugation.
Purification of PD—L1 binding Z variants with a Hise—tag: IMAC
purifications, buffer exchange to PBS and concentration inations were
performed essentially as described in Example 2.
Purification of PD-L1 binding Z variants with a C-terminal Cys: The
respective cell pellet was re-suspended in 20 mM Tris-HCI, 0.5 mM EDTA,
0.1 % Tween 80, pH 7.5 (10 ml buffer / g cell pellet) and lysed by heat
treatment in a water bath at 80 °C for 10 min, followed by cooling on ice to
approximately 20 °C. Benzonase® was added (1 pl/g cell pellet) and each cell
lysate was incubated at RT for 30 min, before cell debris was removed by
centrifugation. For reduction of disulfides, dithiothreitol (DTT; Acros Organics,
cat. no. 250) was added to a final concentration of 10 mM followed by
incubation at RT for 20 min. Thereafter, the lysate was filtered through a 0.45
pm syringe filter pore). Purification was performed by anion exchange
followed by reverse phase chromatography (RPC). Buffer ge to 20 mM
HEPES, 1 mM EDTA, pH 7.2 was carried out using Sephadex G—25 medium
(GE Healthcare) packed in an XK-50 column.
For any protein purified by either method described above, the
concentration was ined by measuring the absorbance at 280 nm, using
a NanoDrop® ND-1000 spectrophotometer and the extinction coefficient of
the protein. The purity was analyzed by SDS-PAGE d with Coomassie
Blue, and the identity of each purified Z t was confirmed using HPLC-
MS analysis (HPLC—MS 1100; Agilent logies).
Results
Cultivation and purification: The PD-L1 binding Z variants were
expressed as soluble gene ts in E. coli. The amount of purified protein
from imately 2.0-2.4 g bacterial pellet was determined
spectrophotometrically by measuring the absorbance at 280 nm and ranged
from imately 18 mg to 29 mg for the different Hise-tagged PD-L1
binding Z variants. SDS—PAGE analysis of each final protein preparation
showed that these predominantly contained the PD-L1 binding Z variant. The
correct identity and molecular weight of each Z variant were confirmed by
HPLC-MS analysis.
Example 7
Additional characterization of a subset of primary PD-L1 binding Z ts
In this e, a subset of Z variants was characterized in terms of
stability and various binding properties. The specificity and affinity for PD-L1
of the Z variants were analyzed by Biacore and the ability of Z variants to
block the binding of PD-L1 to its receptor PD-1 was investigated using
AlphaLlSA.
Materials and methods
Biacore kinetic and specificity analysis: Kinetic constants (ka and kd)
and affinities (KD) for human PD—L1 and rhesus monkey PD-L1 (RhPD—L1;
rhesus PD-L1/Fc Chimera, Sino Biological |nc., cat. no. 90251-C02H) were
determined for 24 matured Hiss-tagged Z variants (specified in Example 6).
The Z variants were also tested for binding against the sequence-related
proteins , hB7-H3 and hB7-H4. The Biacore analyses were performed
essentially as described in Example 3, however a flow rate of 30 ul/min was
used. The ligand immobilization levels on the surfaces were 1030 RU for
hPD-L1, 1060 RU for RhPD-L1, 1070 RU for hPD-L2, 1090 RU for hBT-H3,
and 770 RU for hB7-H4. In a first binding kinetic analysis, the 24 Z variants
were ed at concentrations of 5 and 50 nM over chips immobilized with
hPD-L1 and 1, respectively. The 12 maturated PD-L1 binding Z
variants that showed the t affinity to hPD-L1 in the first ment
were analyzed in more detail and injected at concentrations of 135, 45, 15, 5
and 1.67 nM over lized hPD-L1 and RhPD-L1. In the icity test,
i.e. the binding analysis against hPD-L2, hBY—H3 and hBT—H4, the 24 Z
ts were injected at a concentration of 500 nM.
AlphaLlSA blocking assay: The potential of the Z variants to inhibit
binding of PD-L1 to its natural ligand PD-1 was analyzed in an AlphaLlSA
assay as described in Example 3 with the following exceptions: Exception 1:
stepwise serial ons 1:3 of Hise-tagged Z variants to final concentrations
of 250 nM to 4 pM were made in a 384SW plate (Perkin Elmer, cat. no.
6008350) and incubated for 45 min with 8 nM biotinylated hPD-L1 (R&D
Systems) in lSA buffer (Perkin Elmer, cat. no. AL000F). Exception 2:
hPDcoated Acceptor beads were added to a final concentration of 10 ug/ml
and incubated for 50 min.
Circular dichroism (CD) spectroscopy analysis: A subset of the purified
Hiss-tagged Z variants were ed by CD spectroscopy as described in
Example 3, but with the exceptions that the analysis buffer was PBS and that
the temperature was raised to 80 °C in the VTM.
s
Biacore c and icity analysis: The interactions of 24
maturated Hise-tagged Z variants with human and rhesus monkey PD-L1,
were analyzed in a e instrument by injecting various concentrations of
the Z variants over surfaces containing immobilized hPD-L1 and RhPD-L1,
tively. A first kinetic is was performed in order to rank the Z
variants in terms of their affinity for hPD—L1 and RhPD-L1, as well as to
e their binding kinetics with the primary PD-L1 binding Z variant
213091. A summary of the approximate affinity constants from the ranking
experiment, which were obtained by using a 1:1 interaction model, is given in
Table 12.
The 12 maturated Z variants that showed the highest binding affinity to
hPD-L1 were further analyzed and the more precisely determined kinetic
parameters for these 12 Z variants are given in Table 13. l resulting
curves, where responses from a blank surface were subtracted, are displayed
for two selected variants in Figure 5.
Table 12: Approximate affinity constants for binding of Z variants to hPD-L1
and RhPD-L1
z variant SEQ ID NO hPD-L1 1
of Z variant KD (M) KD (M)
213091 776 7.4 x10'10 5.2 x10‘9
217746 8 3.8 x10'10 5.2 x10'10
217748 11 4.5 x10'10 7.4 x1010
217756 7 2.4 x10'10 2.1 x10'9
217825 5 2.5 x10'10 1.2 x10‘9
217911 3 3.6 x10'10 2.2 x10'9
217964 2 3.0 x10'10 2.0 x10'9
217972 19 5.4 x10'10 2.7 x10'9
217978 13 4.5 x10'10 1.0 x10'9
218022 9 3.4 x10'10 1.4 x10‘9
218039 20 6.3 x10'10 1.9 x10'9
218048 4 3.5 x10'10 1.8 x10‘9
218052 14 4.5 x10'10 1.2 x10'9
218054 22 7.6 x10'10 1.2 x10‘9
218064 1 1.3 x10'10 1.5 x10'9
218066 12 4.3 x10'10 2.1 x10'9
218070 10 3.1 x10'10 2.5 x10"9
218074 6 3.6 x10'10 2.9 x10'9
218090 17 5.1 x10'10 2.3 x10‘9
218101 23 9.3 x10'10 2.4 x10'9
218129 16 4.8 x10'10 1.2 x10‘9
218149 18 5.3 x10'10 9.6 x10'10
218233 21 7.2 x10'10 4.4 x10'9
218353 15 4.6 x10'10 1.6 x10'9
218418 24 1.9x10'9 4.1 x10'9
Furthermore, all 24 maturated Hise-tagged Z ts were also tested
for binding against the three sequence-related proteins, hPD-L2, hB7-H3, and
hB7-H4. In line with the results in Example 3, no binding to either of the
control proteins were ed at a Z variant concentration of 500 nM.
Table 13: Kinetic ters for binding of Z variants to hPD-L1 and RhPD-
ID hPD-L1 RhPD-L1
Zvariant NO:
ka (1/Ms) kd (1ls) KD (M) ka (1/Ms) kd (1ls) KD (M)
213091 776 1.8x106 '3 6.3x10'10 1.9x106 1.0x10'3 5.4x10'10
217746 8 1.6 x106 4.6 x10'4 2.8 x10'10 1.4 x106 4.0 x104 2.8 x10'10
217748 11 1.7x106 5.7x104 3.4x10'10 1.8x106 5.1x104 2.9x10'10
217756 7 2.0 x106 5.4 x10'4 2.8 x10'10 2.7 x106 4.5 x104 1.7 x10'10
217825 5 2.0 x106 4.7 x 10*1 2.4 x10'10 1.9 x106 3.9 x10'4 2.1 x10'10
217911 3 6 4.9x10'4 2.1 x1010 2.1 x106 4.2x104 '10
217964 2 2.1 x106 4.3x 10'4 2.1 x10'10 3.4x106 3.8x 10'4 1.1x10'10
218022 9 1.7 x106 4.9 x10'4 2.8 x10'10 1.6 x106 4.6 x104 2.8 x10'10
218048 4 1.9 x106 4.4 x10'4 2.3 x10'10 1.6 x106 3.8 x10“1 2.4 x10'10
218064 1 3.5x106 4.3x104 1.3x10'10 3.5x106 3.4x104 9.6x10'11
218066 12 1.5x106 5.4x10'4 3.7x10'10 1.4x106 4.7x104 3.5x10'10
218070 10 2.0 x106 5.7 x 10*1 2.9 x10'10 1.7 x106 4.7 x10'4 2.8 x10'10
218074 6 2.0 x106 5.4 x10'4 2.7 x10'10 1.7 x106 4.6 x104 2.7 x10'10
AlphaLlSA blocking assay: The ability of 24 maturated Hiss—tagged
monomeric Z ts to inhibit hPD-L1 binding to hPD-1 was tested in an
AlphaLlSA blocking assay. The primary Z variant 213091 was included as a
reference. Serial ons of the Z ts were incubated with biotinylated
hPD-L1 and the blocking ability of each respective variant was measured
after addition of hPD-1 coated Acceptor beads and subsequently streptavidin
coated Donor beads. Inhibition could be measured as a decrease in
AlphaLlSA counts for positive Z variants. The calculated IC5O values for the
variants that were shown to block PD-L1 binding to PD-1 in this assay are
shown in Table 14.
2016/076040
Table 14: IC50 values for Z variants blocking the PD-1/PD-L1 interaction
Z variant SEQ ID NO: IC50 AlphaLlSA
213091 776 1.1 x10'9
217746 8 1.3 x10'9
217748 11 1.1x10'9
217756 7 1.5 x10'9
217825 5 1.6 x10'10
217911 3 5.7 x 1010
217964 2 8.9 x10'9
217972 19 2.9 x10‘10
217978 13 6.2 x10‘10
218022 9 3.1 x10'10
218039 20 2.9 x10'10
218048 4 1.5 x10'10
218052 14 3.4 x10'10
218054 22 1.1 x10'9
218064 1 3.9 x 1010
218066 12 8.3 x10'10
218070 10 8.6 x10‘10
218074 6 3.1 x10‘10
218090 17 6.7 x10'10
218101 23 6.2 x10'10
218129 16 6.0 x10'10
218149 18 1.9x10'10
218233 21 1.5 x10'10
218353 15 7.2 x10'10
218418 24 5.7 x10'10
CD analysis: The CD spectra determined for 24 maturated PD-L1
binding 2 variants with a Hise tag showed that each had an d—helical structure
at 20 °C. The melting temperatures (Tm) were determined using variable
temperature measurements (Table 15). Reversible folding was observed for
all PD-L1 g Z variants when overlaying spectra measured at 20 °C
before and after heating to 80 °C, as shown for two ed Z variants in
Figure 6.
Table 15: Melting temperatures of maturated PD-L1 binding Z variants
Z variant SEQ ID NO: Tm
(°C)
217746 8 59
217748 11 63
217756 7 63
217825 5 60
217911 3 59
217964 2 62
217978 13 59
218022 9 59
218039 20 55
218048 4 60
218064 1 62
218066 12 58
218070 10 60
218074 6 62
218090 17 68
218129 16 63
218233 21 57
Characterization of anti-PD-L1/PD-1 and anti-PD-L1/CTLA-4 complexes
als and methods
Production of complexes and control dies: Four different
complexes targeting PD-L1 and PD-1, and four ent complexes targeting
PD-L1 and CTLA-4 were constructed, as well as a control antibody targeting
PD-1. An antibody denoted “Lam”, having the same CDR sequences and
icity as the commercially available, PD-1 ing monoclonal antibody
pembrolizumab (formerly lambrolizumab), was constructed using the heavy
chain (HC) and light chain (LC) sequences HCLam (SEQ ID NO:815) and
LCLam (SEQ ID NO:816). An antibody denoted “Ipi”, having the same CDR
sequences and specificity as the commercially available, CTLA-4 targeting
monoclonal antibody ipilimumab, was constructed using the heavy chain (HC)
and light chain (LC) sequences HClpi (SEQ ID NO:817) and LCIpi (SEQ ID
NO:818). The PD-L1 targeting Z variant 215170 (SEQ ID NO:814; identical to
213165 (SEQ ID ) but starting with the amino acid residues AE
d of VD) with a C-terminal VD sequence was genetically fused, via a
flexible 15 residue (GGGGS)3 linker, to the ini of HCLam‘ LCLam, HCIpiand
LCIpi, respectively, resulting in the complexes 215170—HCLam, 215170-LCLam,
215170-HCIpi and -LCIpi, respectively; or to the C-termini of the same
chains, resulting in the complexes HCLam—215170, LCLam-215170, HCIpi-
215170 and LCM-215170, respectively. Gene synthesis, cloning, production
by transient gene expression in CHO cells as well as purification by Protein A
chromatography and verification of constructs by gel electrophoresis were
med by Evitria AG (Switzerland).
Biacore kinetic analyses: Kinetic constants (ka and kd) and affinities
(KD) for hPD-L1, human PD-1 (hPD-1; R&D Systems cat. no. 1086-PD-050)
and human CTLA-4 (hCTLA—4; R&D Systems cat. no. 325-CT-200) were
determined for all eight complexes ed and using a Biacore 2000
instrument (GE Healthcare). The control antibody Lam was also analyzed for
binding against PD-1. 5 ug/ml solutions of each of the proteins hPD-L1,
hPD-1 and hCTLA—4 were prepared in 10 mM NaAc buffer (pH 5.0 for PD-L1,
and pH 4.5 for PD-1 and CTLA-4) and used for immobilization in separate
flow cells on the carboxylated dextran layer of different CM5 chip surfaces
(GE Healthcare, cat. no. BR100012). The immobilization was performed
using amine coupling chemistry according to the manufacturer’s protocol and
using HBS—EP with 500 mM NaCI as g buffer. Immobilization levels
obtained were ~110-140 RU. A series of 3.33, 10, 30, 90, 270 nM
concentrations of the respective complex and Lam were injected and the
responses recorded, except for analysis of binding to PD-L1 for constructs
with 215170 positioned on the C-terminus of the respective antibody, for
which a concentration series of 30, 90, 270 and 900 nM was used.
In a separate ment, the dual binding specificity was evaluated by
a e assay using the Biacore 2000 instrument. The complexes 215170-
HCLam, 215170-LCLam, 215170-HCIpi and 215170-LCIpi, Lam and ipilimumab
y®, l-Myers Squibb/Astra Zeneca via Apoteket AB, cat. no.
065544, lot no. 4A85968), at a concentration of 300 nM, were injected over
chip surfaces lized with PD-1 or CTLA-4 as described above. In all
cases, the duration of the injection was 5 min at a flow rate of 30 ul/min with a
wait/dissociation step of 5 min before a second injection (5 min) of 100 or 500
nM PD-L1 was made. HBS—EP with 500 mM NaCl was used as a running
buffer and for protein dilutions.
Cell binding analysis by FACS: The potential of the complexes to bind
PD-L1 expressing cells was investigated using FACS. 150 000 cells of the
breast cancer cell line MDA-MB-231, cultivated in DMEM (ATCC cat. no. 30-
2002) containing 10 % FBS, were pipetted per well of a v—bottomed l
plate (Nunc, cat. no. 277143) and the cells in the plate were subsequently
pelleted at 400 g for 3 min at RT. The supernatants were removed and the
cells were resuspended in 100 pl PBS plus 2.5 % FBS (staining buffer)
containing 0.625 ug/ml of the complexes Z15170-HCLam, Z15170-LCLam,
HCLam-Z15170, LCLam-Z15170, Z15170-HCIpi, Z15170—LCIpi, HCIpi-Z15170 and
LCIpi-Z15170, respectively, or 0.625 ug/ml of the antibodies Lam or
ipilimumab. A mouse anti-PD-L1 antibody (RnD Systems, cat. no. MAB1561)
at a concentration of 1 ug/ml was used as a ve control. Cells incubated
with buffer alone were used as negative controls. The cells were incubated for
1 h at 8 °C in the dark, washed twice with 100 pl staining buffer, and
resuspended in 100 pl of staining buffer containing 2.5 ug/ml of a goat-anti-
human lgG-Alexa488 ular Probes, cat. no. A11013) or, for cells stained
with the ve control antibody, goat anti-mouse lgG-Alexa647 antibody
(Life Technologies, cat. No. A21236). The cells were incubated for 1 h at 8 °C
in the dark, washed twice with 100 pl staining buffer and resuspended in 300
pl of staining . Data from 10,000 cells were ed using a FACS
Calibur (Beckman r) and the data was analyzed using g software
2.5.0 (Turku University). Mean fluorescence intensity (MFI) was used as a
read out of g capacity.
Co-culture of MDA-MB-231 and PBMC: A mixed lymphocyte assay
was used to analyze if the sed complexes could affect proliferation or
the cytotoxic effect of T-cells and thereby increase the elimination of cancer
cells. Herein, peripheral blood mononuclear cells (PBMC) and MDA-MB—231
cells were co-cultivated for six days and the number of T-cells and cancer
cells were assessed. 20000 MDA-MB-231 cells, cultivated in DMEM
containing 10 % FBS, were pipetted per well of a ottomed 96—well plate
and were left to adhere to the bottom of the well by incubation at 37 °C in a
humidified 5 % C02 atmosphere. Day 2 of the experiment, serial ons
(200-0064 nM) of the lpi-based complexes were prepared in a separate plate
using RPM|1640 with L-glut (Lonza) supplemented with 10 % FCS, and 1 %
Pen-Strep (Lonza, cat. no. DE17-603E). The DMEM medium was discarded
from the MDA—MB-231 cells and 100 pl of the diluted complexes were added.
PBMC were prepared form a buffy coat using Ficoll Paque PLUS (GE
Healthcare, cat no.1702). In brief, the buffy coat was d 2X in PBS.
ml of the diluted buffy coat were layered on the top of 5 ml Ficoll in 15 ml
falcon tubes and centrifuged at RT for 30 min at 400 g. The lymphocyte layer
was collected and the cells were washed twice in the supplemented
RPM|1640 medium described above. The cells were counted and adjusted to
1 million cells per ml in supplemented RPMI medium. 100 pl of the cell
suspension were added to the plate with the MDA-MB-231 cells. The plates
were incubated for 6 days at 37 °C in a humidified 5 % C02 atmosphere. At
day 7 of the experiment, the number of MDA-MD-231 cells and CD3+ T-cells
were counted by FACS. The PBMC were transferred to a v-bottom plate,
washed two times with PBS containing 2 % FBS (also used as staining buffer)
and d with a mouse anti-CD3 antibody (EXBIO Praha, cat no. 12
M001) at a concentration of 2 ug/ml for 1 h at 4 °C. The MDA-MB231 cells
were nated (20 ul/well) and transferred to another v—bottom shaped plate
washed two times with PBS containing 2 % FBS and stained with a rabbit
anti-EGFR antibody (Abcam, cat no. -1) at a concentration of 2 ug/ml
for 1 h at 4 °C. The cells were washed two times with PBS ning 2 %
FBS and an Alexa-fluor 488-goat-anti-rabbit antibody (lnvitrogen, cat no.
A11008) and Alexa-fluor 647-goat—anti-mouse antibody (Life technologies, cat
no. A21236) were used as detection antibodies at a concentration of 1 ug/ml
and incubated for 1 h at 4 °C.
Results
Production of complex constructs: A schematic representation of the
design of each of the four types of produced complexes is shown in Figure 7.
e kinetic analyses: The affinity to the target proteins PD-L1, PD-
1 and CTLA—4, respectively, were determined for each relevant complex. The
control antibody Lam was also analyzed against its target PD-1. The kinetic
ters for the ctions with PD—L1 are summarized in Table 16. The
capability of the Z moiety of the complex to interact with PD—L1 was
maintained, although the affinity was reduced as well as affected by the
positioning of the Z moiety on the dy. For comparison, the KB of the
Hiss-Z13165 interaction with PD-L1 was 0.64 nM (as presented in Example 3)
whereas the KD for xes with inally oned Z moieties was
1.5-2.6 nM and the KO for C-terminally positioned Z es was 12-41 nM.
Thus, N-terminal positioning of the Z moiety was superior to the C-terminal
positioning, with approximately 10 times higher affinity. This effect was
evident with both Lam- and |pi-based constructs. Whether the fusions were
made to the heavy or light chains of the antibodies were of less importance
for the N-terminally positioned Z moiety, but had major impact on the C-
terminally positioned Z moiety, where the light chain fusions had a KB of 12-
18 nM compared to a KB of 29-41 nM for the heavy chain fusions.
Table 16: Kinetic parameters for binding of indicated complexes to hPD-L1
Analyte ka (1lMs) k,| (1ls) KD (M)
HCLam-Z15170 2.44 x104 7.17 x10‘4 2.9 x10‘8
LCLam-Z15170 3.06 x 104 3.58 x 10'4 1.2 x 10'8
z1517o-HcLam 1.16 x105 2.84 x10'4 2.4 x10'9
Z15170—LCLam 2.33 x 105 6.01 x10'4 2.6 x10'9
Hopi-215170 1.78x104 7.27x10'4 4.1 x10'8
Low-215170 3.07 x 104 5.63 x 10'4 1.8 x10‘8
-Hclpi 2.05 x 105 4.83 x10'4 2.4 x10'9
z1517o-LcIpi 2.30 x 105 3.49 x 10'4 1.5 x10'9
The interactions of the complexes with PD-1 and , respectively,
followed a bivalent model. The K91, K92, ka1, kaz, km and kdz are summarized
in Table 17 and Table 18 for PD—1 and CTLA—4, tively. The affinity
nt Km for the interaction of PD-1 with the produced Lam control
antibody was determined to 18.6 nM. The affinity was stronger for all the Lam
based xes, with a K01 range of 0.8-2.7 nM. A somewhat slower
association and rate, ka1, was seen for Z15170-HCLam, but generally the
differences between the complexes were small, i.e. the positioning of the Z
moiety on the antibody seems to have minor impact on the interaction
between the antibody and PD-1.
Table 17: Parameters for binding of indicated complexes and Lam to hPD-1
Analyte ka1 kd1 Km kaz kdz K02
(1lMs) (1ls) (M) (1lRUs) (1ls) (RU)
Lam 4.35x104 8.10x10'4 1.9x 10‘8 1.88x10'3 1.83x10'3 0.97
Z15170 1.17 x105 1.64 x10'4 1.4 x10'9 3.35 x 100 1.65 x101 4.9
LCLam-Z1517O 1.78 x105 1.34 x10'4 7.5 x 10-10 2.92 x10'1 7.89 x10'1 2.7
z15170—HcLam 4.27 x104 1.17 x10'4 2.7 x10'9 1.93 x10"2 7.87 x10'2 4.1
215170-LcLam 05 1.56x10'4 1.4x 10'9 2.22x10‘2 1.72x 10-1 7.7
Table 18: Kinetic parameters for binding of indicated complexes to hCTLA-4
Analyte ka1 kd1 Km kaZ kdz K132
(1lMs) (1ls) (M) (1/RUs) (1ls) (RU)
Hopi-215170 6.79 x104 5.40 x10'4 8.0 x10'9 6.76 x10‘2 4.10 x 10-1 6.1
Low-215170 5.48 x104 4.41 x10'4 8.0 x10‘9 4.04 x10"2 2.88 x10'1 7.1
215170—HcIpi 3.33 x104 2.79 x10'4 8.4 x10'9 1.38 x10‘2 8.20 x10'2 5.9
z15170-LcIpi 4.55 x104 4.49 x10'4 9.9 x10‘9 9.74 x10'3 4.22 x10'2 4.3
The affinity constant Km for the interaction of complexes with CTLA-4
was in the range of 8-10 nM and this is in line with the reported KD for
ipilimumab (5.25 1r 3.62 nM; an Medicines Agency’s assessment
report 2011: EMA/CHMP/557664/2011). The kinetic profiles were similar for
all lpi-based constructs, but with somewhat slower association and
dissociation rates for Z15170-HCIpi.
The Biacore capture assay confirmed the dual binding specificity of all
complexes included in the assay, i.e. Z15170-HCLam, Z15170-LCLam, Z15170-
HCIpi and -LCIpi. Figure 8 shows that the complexes first bind to
immobilized PD-1 or CTLA—4 and that PD-L1 subsequently binds to the
respective captured complex. In separate control experiments, it was shown
that PD—L1 does not bind to CTLA—4 or lpi and that no additional binding by
PD-L1 was seen ing injection of PD-L1 to Lam captured on PD-1.
Cell binding analysis by FACS: This experiment was performed to
analyze whether the complexes could bind to PD-L1 expressing cells. MDA-
MB-231 cells that naturally express PD—L1 were stained with 0.625 pg/ml of
the respective complex. The MFI values are presented in Table 19 and shows
that the xes had the y to bind PD-L1 expressing cells. For both
the lpi- and Lam-based complexes, the highest MFI values were obtained for
N-terminal positioning of the Z moiety on the light chain of the antibody.
Table 19: MFI for binding of complexes to PD-L1 expressing cells
e MFI
Lam 62
Z15170-HCLam 161
HCLam‘Z15170 274
Z15170-LCLam 327
LCLam-Z1517O 145
umab 64
-HCIpi 488
HCIpi-Z1517O 264
Z15170-LCIpi 582
LCIPi-Z15170 192
Negative control 69
Anti-PD-L1 antibody 610
WO 72280
Co-culture of MDA-MB-231 and PBMC: To assess whether the lpi—
based xes could affect the inhibitory mechanisms caused by CTLA-4
and PD-L1, a mixed lymphocyte assay was used. Breast cancer cells MDA-
MB-231 were co-cultivated with PBMC for six days and the number of cancer
cells and T-cells were ted. The analysis revealed a concentration
dependent effect of the complexes, with an increased amount of T—cells and a
lowered number of cancer cells. Figure 9A shows the reduction in number of
MDA-MB231 cells with increasing concentration of the xes. This
reduction was evident for all complexes with the best effect achieved with the
uct in which the Z moiety is situated at the N—terminus of the light chain
of the antibody. In contrast, the ipilimumab control antibody did not induce a
concentration dependent decrease of the cancer cells. Thus, blocking of the
interaction PD-1/PD-L1 appears essential to reduce the amount of cancer
cells. Figure QB shows the increase in the number of T-cells with an
increasing tration of the complexes. Again, the effect is most
prominent with the construct in which the Z moiety is situated at the N-
terminus of the light chain of the antibody.
Example 9
ation and radiolabeling of PD-L1 binding Z variants
This Example describes the conjugation and radiolabeling of 215168-
Cys (SEQ ID NO:809), Z18608—Cys (SEQ ID NO:811), Z18609-Cys (SEQ ID
NO:812) and Z18610-Cys (SEQ ID NO:813), cloned and produced as
described in Example 2 and Example 6, and further used for the in vivo
imaging studies described in Example 10 and 11.
Materials and methods
Reduction and NOTA coniugation: To 5 mg on t in [20 mM
HEPES, 1 mM EDTA, pH 7.2] was added three molar equivalents of tris(2—
carboxyethyl)phosphine (TCEP) in 0.5 ml of degassed 0.2 M ammonium
e buffer (pH 7.0). The reaction was kept at RT for 60 min before being
transferred to an Ultracel 3K Centrifugal Filter and centrifuged at 4000 rpm for
90 min. The flow-through was discarded and an additional 1 ml of0.2 M
um acetate buffer added, and the process repeated. The reduced Z
variant was then transferred to a second reaction vessel in 2 ml of oxygen
free 0.2 M ammonium acetate buffer (pH 7.0). 4 mg of NOTA-maleimide
(Macrocyclics) in 0.5 ml of0.2 M ammonium acetate buffer (pH 7.0) was then
added, and the reaction vessel purged with argon before heating to 40 °C for
3 h, at which point the reaction mixture was transferred to an Ultracel 3K
Centrifugal Filter and centrifuged for 90 min at 4000 rpm. The flow-through
was discarded and 2 ml milIiQ water added. fugation was performed for
an additional 90 min and the flow-through ded. Purified NOTA-
conjugated Z variant was collected in 1 ml miIIiQ water, lyophilized and stored
at -70 °C prior to use. Purity of the final t was determined by LC/MS.
abeling: A cartridge containing [18F]-f|uoride was first washed
with 1.5 ml of ultrapure water, then f|uoride was eluted with 1.0 ml of 0.4
M KHCOg. 100 pl of the eluted [18F]-f|uoride solution was added to a stem vial
charged with 10 ul acetic acid, 50 pl AlCl3 (2 mM in 0.1 M NaOAc buffer, pH
4) and 125 pl 0.1 M NaOAc pH 4. The solution was incubated for 2 min at RT
before 1 mg of NOTA-conjugated Z variant in 400 pl of a 1:1 solution of
acetrontrile and 0.1 M NaOAc pH 4 was added, then heated to 100 °C for 15
min. After g was complete, the sample was transferred to a vial
containing 0.7 ml of 0.1 % formic acid, mixed and purified by HPLC [Waters
Xselect CSH C18 column (250><10 mm, 130 um)] using a gradient of 10-30 %
MeCN over 15 min at a flow rate of 5 ml/min, the balance being 0.1 % formic
acid. The peak corresponding to [18F]AIF-NOTA-Z##### was collected, the
MeCN was removed in vacuo, and transferred to a sterile vial using
physiologic saline as a rinse to give [18F]AIF-NOTA-Z#####. ic ty
and radiochemical purity was determined via a Waters Acquity LC/MS system
(Milford, MA, USA) and a B—RAM Model 4 Radio—HPLC detector (IN/US
Systems, Brandon, FL, USA).
Results
The PD-L1 g 2 variants, —Cys (SEQ ID ), 218608-
Cys (SEQ ID NO:811), Z18609—Cys (SEQ ID NO:812) and Z18610-Cys (SEQ
ID NO:813), were site specifically conjugated with NOTA at their respective
unique C-terminal cysteine residue. Subsequent radiolabeling with [18F]AIF
typically resulted in radiochemical purities of 97—100 % and specific activities
of 14.6 1r 6.5 GBq/mmol. The radiolabeled Z ts will be referred to as
[18F]AlF—NOTA—Z[#####].
Example 10
In vivo imaging and biodistribution in tumor bearing mice
Materials and methods
Animal models: Female SCID Beige mice (6-8 week old, Charles River
Laboratories) were housed in a temperature and humidity controlled room
and kept on a r diet. LOXIMVI (human melanoma cell line; PD-L1
positive) or SUDHL-6 (PD-L1 negative) cells were cultured in complete
growth medium containing RPMI 1640 medium with 10 % fetal bovine serum
at 37°C with 5 % 002. The growth medium was changed 2 or 3 times per
week and the cells subcultured at a ratio of 1 :10 when . Tumors were
implanted at the right shoulder by subcutaneous injection of 1 X 106 LOXIMVI
cells in 100 pl PBS or 10 x106 SUDHL-6 cells in 100 pl PBS + Growth Factor
Reduced Matrigel (1 :1). The mice were used for micro—PET and ex vivo
studies about 5-7 days and 3 weeks after the injection of LOXIMVI and
SUDHL-6 cells, respectively, when tumors reached a mass of 100-400 mg.
PET data acguisition: Mice were anesthetized with isoflurane (4-5 %
ion, 1-3 % maintenance), prepared with tail vein catheters, and placed
in a dedicated small animal PET scanner (microPET Focus220, Siemens
Preclinical Solutions). A 20 min transmission scan with 57Co was obtained to
correct for photon attenuation and r. Then, 0.2-0.6 MBq of the
respective labe||ed Z variant was administered via the tail vein catheters,
and PET data were ted for 90 min. In a separate pre-blocking
WO 72280
experiment, 400 pg non-labelled NOTA-conjugated Z15168—Cys was
administered prior to administration of [18F]AlF-NOTA-Z15168.
Ex vivo biodistribution measurements: Immediately after PET
acquisition, mice were ized. Tumor, heart, lung, spleen, liver, kidneys,
blood, plasma and muscle were collected and measured using a gamma
counter (PerkinElmer). For each mouse, biodistribution measurements were
ted into units of Standard Uptake Value (SUV). Regions of Interest
(ROI) were drawn on all tumors that could be identified in PET , and
time activity curves (TACs) were calculated.
Representative PET images following injection of [18F]-labelled Z
variants into tumor-bearing mice showed the highest uptake in kidney and
bladder. PD-L1 positive LOX tumors could be clearly seen in images, while
PD-L1 negative SUDHL6 tumors were not e. Representative PET
images are shown in Figure 10A for [18F]AlF-NOTA-Z15168. Ex vivo
biodistribution measurements at 90 min post—injection were in agreement with
PET images. The uptake of [18F]-labelled z variants Z15168—Cys (SEQ ID
NO:809), Z‘l8608—Cys (SEQ ID NO:811), Z18609-Cys (SEQ ID NO:812) and
—Cys (SEQ ID NO:813) was icantly higher in LOX tumors than in
SUDHL6 tumors and the tumor uptake increased with the PD-L1 binding
affinity of the Z variants (Figure 11A-B). Target specificity was confirmed in a
pre-blocking experiment in which pre-administration of 400 ug NOTA-Z15168
caused a reduction in [18F]AlF-NOTA—215168 uptake in LOX tumors (Figure
108). Changes in distibution, including faster clearance as ted by
reduced blood uptake at 90 min, was also seen. The kidney tracer retention
(average SUV ranged between 57 to 84 in LOX tumor xenographs) is likely
due to tubular reuptake of proteins, where [18F]AIF label is trapped after
cleavage of the Z variants. To summarize, the results show that Z variant
ligands are effective in targeting PD-L1 positive tumors in vivo, exhibiting
specific binding and a rapid clearance.
Example 11
In vivo imaging in rhesus monkey
Materials and methods
Fasted rhesus monkeys were sedated with Ketamine (10 mg/kg,
intramuscular). An intrevenous catheter was inserted into the right and left
saphenous veins and the animals were maintained on propofol esia
(5 mg/kg for ion and 0.45 mg/kg/min throughout the scanning
procedure). Following the initial induction with propofol, the animal was
intubated and maintained on ventilated oxygen/air gas mixture at
approximately 10 cm3/kg/breath, and 23 respirations per minute. s
were instrumented with a temperature probe, a pulse er and an end
tidal 002 monitor. Body temperature was maintained using K-module heating
pads. General fluid y was maintained with Lactated ’s solution
(10 ml/kg/h i.v.) throughout the scanning procedure. 84-138 MBq of [18F]AIF-
NOTA-Z15168 and 147-227 MBq of [18F]AlF-NOTA-Z18609, respectively,
were stered as a 2 min infusion. Whole body dynamic scan was
initiated at the start of the tracer injection and aquired for 180 min using a
Siemens Biograph 64 TPTV PET/CT scanner. Whole body reconstruction
was performed using the PET/CT scanner vendor supplied re. PET
image analysis was performed using customized Matlab based software.
Results
Representative maximum ity projection images of rhesus
monkeys administered with[18F]AIF-NOTA-Z15168 and [18F]AIF-NOTA-
218609, respectively, are shown in Figure 12A—B and graphs of the average
tracer uptake (~120—180 min) are shown in Figure 120. As in mice, the
highest uptake was seen in kidney (SUV z 100—112) and bladder, but also
lymph node and spleen targeting was observed, which is consistent with PD-
L1 expression.
2016/076040
ITEMIZED LIST OF EMBODIMENTS
1. PD—L1 binding polypeptide, comprising a PD-L1 g motif BM, which
motif consists of an amino acid sequence selected from:
i) ERNX4AAX7E|L X11LPNLX15X17X1aQX20 WAFIWX26LX28D
wherein, independently from each other,
X4 is selected from A, D, E, F, H, l, K, L, N, Q, R, S, T, V and Y;
X7 is selected from A, E, F, H, N, Q, S, T, V, W and Y;
X11 is selected from A, D, E, F, H, K, L, N, Q, R, S, T, V, W and Y;
X16 is selected from N and T;
X17 is selected from A, H, K, N, Q, R and S;
X18 is selected from A, D, E, G, H, K, L, N, Q, R, S, T, V and Y;
X20 is selected from H, l, K, L, N, Q, R, T, V and Y;
X26 is selected from K and S; and
X28 is selected from A, D and E;
and
ii) an amino acid sequence which has at least 96 % identity to the
sequence defined in i).
2. PD-L1 g polypeptide according to item 1, wherein in sequence i)
X4 is selected from A, D, E, F, H, I, K, L, N, Q, R, S, T, V and Y;
X7 is selected from E, F, H, N, Q, S, T, V, W and Y;
X11 is ed from A, D, H, L, Q, R, T, V, W and Y;
X15 is selected from N and T;
X17 is selected from A, H, K, N, Q, R and S;
X18 is selected from A, D, E, G, H, K, L, N, Q, R, S, T, V and Y;
X20 is selected from H, l, K, L, Q, R, T, V and Y;
X25 is selected from K and S; and
X28 is selected from A, D and E.
3. PD-L1 binding polypeptide according to item 1, n in ce i)
X4 is selected from A, D, E, F, H, I, K, L, N, Q, R, S, T, V and Y;
X7 is selected from A, E, F, H, N, Q, S, T, V, W and Y;
X11 is selected from A, D, E, F, H, K, L, N, Q, R, S, T, V, W and Y;
X15 is selected from N and T;
X17 is selected from A, H, K, N, Q, R and S;
X18 is selected from A, D, E, G, H, K, L, N, Q, R, S, T, V and Y;
X20 is selected from H, l, K, L, N, Q, R, T, V and Y;
X26 is selected from K and S; and
X28 is selected from A, D and E.
4. PD-L1 binding polypeptide according to item 2 or 3, wherein in sequence i)
X4 is ed from A, D, E, F, H, I, K, L, N, Q, R, S, T and V;
X7 is selected from F, H, Q and Y;
X11 is selected from H, Q, W and Y;
X15 is selected from N and T;
X17 is selected from A, H, K, N, Q and S;
X18 is selected from A, E, G, H, K, L, N, Q, R, S, T, V and Y;
X20 is selected from H, l, K, Q, R and V;
X25 is selected from K and S; and
X28 is selected from A and D.
. PD-L1 binding polypeptide according to any one of item 1-4, wherein
sequence i) fulfills at least four of the seven conditions l-VII:
l. X7 is selected from F, H, Q and Y;
H. X11 is selected from H and Y;
lll. X16 is T;
IV. X17 is selected from N, Q and S;
V. X20 is selected from H, I, K and R;
VI. X26 is K; and
VII. X28 isAor D.
6. PD-L1 binding ptide according to item 5, wherein sequence i)
fulfills at least five of the seven ions I-VII.
7. PD-L1 binding polypeptide according to item 6, wherein sequence i)
fulfills at least six of the seven conditions I-VII.
8. PD—L1 binding polypeptide according to item 7, wherein sequence i)
fulfills all of the seven conditions I—VII.
9. PD-L1 g polypeptide according to any one of items 1-8,
wherein X7X11X20 is selected from FYK and YYK.
. PD-L1 binding polypeptide according to any one of items 1-9,
wherein X11X17X20 is selected from YNK and YQK.
11. PD-L1 binding polypeptide according to any one of items 1-10,
n X11X18X20 is YAK.
12. PD-L1 binding ptide according to any preceding item,
wherein sequence i) corresponds to the sequence from position 8 to position
36 in a sequence selected from the group consisting of SEQ ID NO:1-808.
13. PD-L1 binding polypeptide according to item 12, wherein sequence
i) corresponds to the sequence from position 8 to position 36 in a sequence
selected from the group consisting of SEQ ID NO:1-93 and 774-796.
14. PD-L1 binding polypeptide according to item 13, wherein ce
i) corresponds to the sequence from position 8 to position 36 in a sequence
selected from the group ting of SEQ ID NO:1-93 and 774-787.
. PD-L1 binding polypeptide according to item 14, wherein sequence
i) corresponds to the sequence from position 8 to position 36 in a sequence
selected from the group ting of SEQ ID NO:1-93, 775, 776, 779-781
and 784-786, such as the group consisting of SEQ ID NO:1-93, 776, 780,
781, 784 and 786, such as the group consisting of SEQ ID NO:1—93, 776,781
and 784, such as the group consisting of SEQ ID NO:1-93, 776 and 784 or
the group consisting of SEQ ID NO:1-93, 776 and 781, for example the group
consisting of SEQ ID NO:1—93 and 776 or the group consisting of SEQ ID
NO:1-93 and 781 or the group consisting of SEQ ID NO:1-93 and 784.
16. PD-L1 binding polypeptide according to item 15, wherein sequence
i) corresponds to the sequence from on 8 to position 36 in a sequence
selected from the group consisting of SEQ ID NO:1-93, 774, 775, 6,
such as the group consisting of SEQ ID NO:1-93, 775, 780, 781, 784 and
786.
17. PD—L1 binding polypeptide according to any one of items 14-16,
n sequence i) corresponds to the sequence from on 8 to position
36 in a sequence selected from the group consisting of SEQ ID NO:1-93.
18. PD-L1 g polypeptide according to item 17, wherein sequence
i) corresponds to the sequence from position 8 to position 36 in a sequence
selected from the group consisting of SEQ ID NO:1-24.
19. PD-L1 binding polypeptide according to item 18, wherein ce
i) corresponds to the sequence from position 8 to on 36 in a sequence
selected from the group consisting of SEQ ID NO:1-12, 14 and 17-21.
. PD-L1 binding polypeptide according to item 19, wherein sequence
i) corresponds to the sequence from on 8 to position 36 in a sequence
selected from the group consisting of SEQ ID NO:1-12 and 17, such as the
group consisting of SEQ ID NO:1—5 and 17, such as the group consisting of
SEQ ID NO:1, 2 and 17.
21. PD-L1 binding polypeptide according to item 19, wherein sequence
i) corresponds to the sequence from position 8 to position 36 in a sequence
selected from the group consisting of SEQ ID NO:1, 4, 5, 6, 9, 14 and 18-21,
such as the group consisting of SEQ ID NO:4, 5, 18 and 21, such as the
group consisting of SEQ ID NO:4, 5 and 21.
22. PD—L1 binding polypeptide according to item 20 or 21, wherein
sequence i) corresponds to the sequence from position 8 to position 36 in
SEQ ID NO:1.
23. PD-L1 binding polypeptide according to item 20 or 21, wherein
ce i) corresponds to the sequence from position 8 to position 36 in
SEQ ID NO:4.
24. PD—L1 binding polypeptide according to item 20 or 21, wherein
sequence i) corresponds to the sequence from position 8 to position 36 in
SEQ ID NO:5.
. PD-L1 binding polypeptide according to item 21, wherein sequence
i) corresponds to the sequence from position 8 to on 36 in SEQ ID
NO:21.
26. PD-L1 binding polypeptide according to any preceding item,
wherein said PD-L1 binding motif forms part of a three—helix bundle protein
domain.
27. PD—L1 binding polypeptide according to item 26, wherein said PD-
L1 binding motif essentially forms part of two helices with an interconnecting
loop, within said three-helix bundle protein domain.
28. PD—L1 g polypeptide according to item 27, wherein said
three-helix bundle n domain is selected from ial receptor domains.
29. PD—L1 binding polypeptide according to item 28, wherein said
three-helix bundle protein domain is selected from domains of n A from
Staphylococcus aureus or derivatives f.
. PD—L1 binding polypeptide according to any preceding item, which
comprises a binding module BMod, the amino acid ce of which is
selected from:
iii) K—[BM]—DPSQSXaXbLLXC EAKKLXdXeXfQ;
wherein
[BM] is a PD-L1 binding motif as defined in any one of items 1-25;
X2! is selected from A and S;
Xb is selected from N and E;
XC is selected from A, S and C;
Xd is ed from E, N and S;
X9 is selected from D, E and S; and
Xf is selected from A and S; and
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iv) an amino acid sequence which has at least 93 % identity to a
sequence defined in iii).
31. PD-L1 binding polypeptide according to any preceding item,
n sequence iii) corresponds to the sequence from position 7 to position
55 in a sequence selected from the group consisting of SEQ ID NO:1-808.
32. PD-L1 binding polypeptide according to item 31, wherein sequence
iii) corresponds to the sequence from position 7 to position 55 in a sequence
selected from the group consisting of SEQ ID NO:1-93 and 774-796.
33. PD-L1 binding polypeptide according to item 32, wherein sequence
iii) corresponds to the sequence from position 7 to position 55 in a sequence
selected from the group consisting of SEQ ID 3 and 774-787.
34. PD-L1 binding polypeptide according to item 33, wherein sequence
iii) ponds to the ce from on 7 to position 55 in a sequence
selected from the group consisting of SEQ ID NO:1-93, 775, 776, 779-781
and 784-786, such as the group consisting of SEQ ID NO:1-93, 776, 780,
781, 784 and 786, such as the group consisting of SEQ ID NO:1—93, 776,781
and 784, such as the group consisting of SEQ ID NO:1-93, 776 and 784 or
the group consisting of SEQ ID NO:1-93, 776 and 781, for example the group
consisting of SEQ ID NO:1—93 and 776 or the group consisting of SEQ ID
NO:1-93 and 781 or the group consisting of SEQ ID NO:1-93 and 784.
. PD-L1 binding polypeptide according to item 33, wherein sequence
iii) corresponds to the sequence from position 7 to position 55 in a sequence
selected from the group consisting of SEQ ID 3, 774, 775 and 780-
786, such as the group consisting of SEQ ID NO:1-93, 775, 780, 781, 784
and 786.
36. PD-L1 g polypeptide according to any one of items 33-35,
wherein sequence iii) corresponds to the sequence from position 7 to position
55 in a sequence selected from the group consisting of SEQ ID NO:1-93.
37. PD-L1 binding polypeptide according to item 36, wherein sequence
iii) corresponds to the sequence from position 7 to position 55 in a sequence
selected from the group consisting of SEQ ID NO:1-24.
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38. PD-L1 binding polypeptide ing to item 37, wherein sequence
iii) corresponds to the sequence from position 7 to position 55 in a sequence
selected from the group consisting of SEQ ID NO:1—12, 14 and 17—21.
39. PD-L1 binding polypeptide according to item 38, wherein sequence
iii) corresponds to the sequence from position 7 to position 55 in a sequence
selected from the group consisting of SEQ ID NO:1-12 and 17, such as the
group consisting of SEQ ID NO:1—5 and 17, such as the group consisting of
SEQ ID NO:1, 2 and 17.
40. PD-L1 binding polypeptide according to item 38, wherein sequence
iii) corresponds to the ce from position 7 to position 55 in a sequence
selected from the group ting of SEQ ID NO:1, 4, 5, 6, 9, 14 and 18-21,
such as the group consisting of SEQ ID NO:4, 5, 18 and 21, such as the
group consisting of SEQ ID NO:4, 5 and 21.
41. PD-L1 binding polypeptide according to item 40 or 41, n
sequence iii) corresponds to the sequence from position 7 to position 55 in
SEQ ID NO:1.
42. PD—L1 g polypeptide according to item 40 or 41, wherein
sequence iii) corresponds to the sequence from position 7 to position 55 in
SEQ ID NO:4.
43. PD—L1 binding polypeptide according to item 40 or 41, wherein
sequence iii) corresponds to the sequence from position 7 to position 55 in
SEQ ID NO:5.
44. PD-L1 binding polypeptide according to item 41, wherein sequence
iii) corresponds to the sequence from position 7 to position 55 in SEQ ID
NO:21.
45. PD-L1 binding polypeptide according to any preceding item, which
comprises an amino acid sequence ed from:
v) YA-[BMod]—AP;
wherein [BMod] is a PD-L1 binding module as defined in any one of items 30-
44;and
vi) an amino acid sequence which has at least 90 % identity to a
sequence defined in v).
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46. PD—L1 binding ptide according to any one of items 1-44,
which comprises an amino acid sequence selected from:
vii) FN-[BMod]—AP;
wherein [BMod] is a PD-L1 binding module as defined in any one of items 30-
44;and
viii) an amino acid sequence which has at least 90 % identity to a
sequence defined in vii).
47. PD—L1 binding polypeptide according to any preceding item, which
comprises an amino acid sequence selected from:
ADNNFNK-[BM]—DPSQSANLLSEAKKLNESQAPK;
ADNKFNK-[BM]-DPSQSANLLAEAKKLNDAQAPK;
ADNKFNK-[BM]—DPSVSKEILAEAKKLNDAQAPK;
NFNK-[BM]—DPSQSTNVLGEAKKLNESQAPK;
AQHDE-[BM]-DPSQSANVLGEAQKLNDSQAPK;
VDNKFNK-[BMJ-DPSQSANLLAEAKKLNDAQAPK;
AEAKYAK-[BM]—DPSESSELLSEAKKLNKSQAPK;
VDAKYAK-[BM]—DPSQSSELLAEAKKLNDAQAPK;
VDAKYAK-[BM]—DPSQSSELLAEAKKLNDSQAPK;
AEAKYAK-[BMj-DPSQSSELLSEAKKLNDSQAPK;
AEAKYAK-[BMj-DPSQSSELLSEAKKLNDSQAP;
AEAKFAK-[BM]—DPSQSSELLSEAKKLNDSQAPK;
AEAKFAK-[BMJ-DPSQSSELLSEAKKLNDSQAP;
AEAKYAK-[BM]—DPSQSSELLAEAKKLNDAQAPK;
AEAKYAK-[BM]—DPSQSSELLSEAKKLSESQAPK;
AEAKYAK-[BM]—DPSQSSELLSEAKKLSESQAP;
AEAKFAK-[BMj-DPSQSSELLSEAKKLSESQAPK;
K-[BMj-DPSQSSELLSEAKKLSESQAP;
AEAKYAK-[BM]—DPSQSSELLAEAKKLSEAQAPK;
AEAKYAK-[BMJ-QPEQSSELLSEAKKLSESQAPK;
AEAKYAK-[BM]—DPSQSSELLSEAKKLESSQAPK;
AEAKYAK-[BM]—DPSQSSELLSEAKKLESSQAP;
AEAKYAK-[BM]—DPSQSSELLAEAKKLESAQAPK;
AEAKYAK-[BMj-QPEQSSELLSEAKKLESSQAPK;
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AEAKYAK-[BM]—DPSQSSELLSEAKKLSDSQAPK;
AEAKYAK-[BM]—DPSQSSELLSEAKKLSDSQAP;
AEAKYAK-[BM]—DPSQSSELLAEAKKLSDSQAPK;
AEAKYAK-[BM]—DPSQSSELLAEAKKLSDAQAPK;
AEAKYAK-[BM]—QPEQSSELLSEAKKLSDSQAPK;
VDAKYAK-[BMj-DPSQSSELLSEAKKLNDSQAPK;
VDAKYAK-[BM]—DPSQSSELLAEAKKLNDAQAPK;
VDAKYAK-[BM]—DPSQSSELLSEAKKLSESQAPK;
VDAKYAK-[BM]—DPSQSSELLAEAKKLSEAQAPK;
VDAKYAK-[BM]—QPEQSSELLSEAKKLSESQAPK;
VDAKYAK-[BM]—DPSQSSELLSEAKKLESSQAPK;
VDAKYAK-[BM]—DPSQSSELLAEAKKLESAQAPK;
VDAKYAK-[BMj-QPEQSSELLSEAKKLESSQAPK;
VDAKYAK-[BM]—DPSQSSELLSEAKKLSDSQAPK;
VDAKYAK-[BMJ-DPSQSSELLAEAKKLSDSQAPK;
VDAKYAK-[BM]—DPSQSSELLAEAKKLSDAQAPK;
VDAKYAK-[BM]—QPEQSSELLSEAKKLSDSQAPK;
VDAKYAK-[BM]—DPSQSSELLAEAKKLNKAQAPK;
AEAKYAK-[BM]—DPSQSSELLAEAKKLNKAQAPK; and
ADAKYAK-[BMj-DPSQSSELLSEAKKLNDSQAPK;
wherein [BM] is a PD-L1 binding motif as defined in any one of items 1-25.
48. PD—L1 binding polypeptide according to any one of items 1-47,
which comprises an amino acid sequence selected from:
xvii) VDAKYAK-[BM]—DPSQSSELLSEAKKLNDSQAPK;
wherein [BM] is a PD-L1 binding motif as defined in any one of items 1-25;
xviii) an amino acid sequence which has at least 89 % identity to the
sequence defined in xvii).
49. PD—L1 binding ptide according to any one of items 1-47,
which comprises an amino acid sequence selected from:
xix) AEAKFAK-[BM]—DPSQSSELLSEAKKLSESQAPK;
wherein [BM] is a PD-L1 g motif as defined in any one of items 1-25;
xx) an amino acid sequence which has at least 89 % identity to the
sequence defined in xix).
50. PD—L1 binding ptide according to any one of items 1-47,
which comprises an amino acid sequence selected from:
xxi) AEAKYAK-[BMj-DPSQSSELLSEAKKLNDSQAPK;
wherein [BM] is a PD—L1 binding motif as defined in any one of items 1-25;
xxii) an amino acid sequence which has at least 89 % identity to the
sequence defined in xxi).
51. PD—L1 binding polypeptide according to any one of items 1-47,
which comprises an amino acid sequence selected from:
xxiii) AEAKFAK-[BMj-DPSQSSELLSEAKKLNDSQAPK;
wherein [BM] is a PD—L1 binding motif as defined in any one of items 1-25;
xxiv) an amino acid ce which has at least 89 % identity to the
sequence defined in xxiii).
52. PD-L1 binding polypeptide according to any preceding item,
wherein sequence xvii) or xxi) corresponds to the sequence from position 1 to
position 58 in a sequence selected from the group consisting of SEQ ID
NO:1-814.
53. PD-L1 binding ptide according to item 52, wherein sequence
xvii) or xxi) corresponds to the sequence from position 1 to position 58 in a
sequence ed from the group ting of SEQ ID NO:1-93, 774-796
and 809-814.
54. PD-L1 binding polypeptide according to item 53, wherein sequence
xvii) or xxi) corresponds to the ce from position 1 to position 58 in a
sequence selected from the group consisting of SEQ ID NO:1-93, 774-787
and 809-814.
55. PD-L1 binding polypeptide according to item 54, wherein sequence
xvii) or xxi) ponds to the sequence from position 1 to position 58 in a
sequence selected from the group consisting of SEQ ID NO:1-93, 775, 776,
779-781, 784-786 and 4, such as the group consisting of SEQ ID
3, 776, 780, 781, 784, 786 and 809-814, such as the group consisting
of SEQ ID NO:1-93, 776, 781, 784 and 809-814, such as the group consisting
of SEQ ID NO:1-93, 776, 784, 809 and 811-814 or the group ting of
SEQ ID NO:1—93, 776, 781, 809 and 811-814, for e the group
consisting of SEQ ID 3, 776, 809 and 811-814 or the group consisting
of SEQ ID NO:1-93, 781, 809 and 811—814 or the group consisting of SEQ ID
NO:1-93, 784 and 811-814.
56. PD-L1 binding polypeptide according to item 55, wherein sequence
xvii) or xxi) corresponds to the sequence from position 1 to position 58 in a
sequence selected from the group consisting of SEQ ID NO:1-93, 774, 775,
780—786 and 810—814, such as the group consisting of SEQ ID NO:1-93, SEQ
ID , 780, 781, 784,786 and 810-814.
57. PD-L1 binding polypeptide according to any one of items 54-56,
wherein ce xvii) or xxi) corresponds to the sequence from position 1 to
position 58 in a sequence selected from the group consisting of SEQ ID
NO:1-93 and 811-813.
58. PD-L1 binding polypeptide according to item 57, wherein sequence
xvii) or xxi) corresponds to the sequence from position 1 to position 58 in a
sequence selected from the group consisting of SEQ ID NO:1-24 and 811-
813.
59. PD-L1 binding polypeptide according to item 58, wherein sequence
xvii) or xxi) corresponds to the sequence from position 1 to position 58 in a
sequence selected from the group consisting of SEQ ID NO:1-12, 14, 17-21
and SEQ ID NO:811-812.
60. PD-L1 binding polypeptide according to item 59, wherein ce
xvii) or xxi) corresponds to the sequence from position 1 to position 58 in a
ce selected from the group ting of SEQ ID NO:1-12, 17, 811
and 812, such as the group consisting of SEQ ID NO:1-5, 17,811 and 812,
such as the group consisting of SEQ ID NO:1, 2, 17,811 and 812.
61. PD-L1 binding polypeptide according to item 58, wherein sequence
xvii) or xxi) corresponds to the ce from position 1 to position 58 in a
sequence selected from the group consisting of SEQ ID NO:1, 4, 5, 6, 9, 14,
18, 19, 20, 21 and 811, such as the group consisting of SEQ ID NO:4, 5, 18
and 21, such as the group consisting of SEQ ID NO:4, 5 and 21.
62. PD—L1 binding polypeptide according to item 60 or 61, wherein
sequence xvii) or xxi) corresponds to the ce from position 1 to position
58 in SEQ ID NO:1 or 811.
63. PD-L1 g polypeptide according to item 60, wherein sequence
xvii) or xxi) corresponds to the sequence from position 1 to position 58 in SEQ
ID N02 or 812.
64. PD-L1 binding polypeptide according to item 60 or 61, wherein
sequence xvii) corresponds to the sequence from position 1 to on 58 in
SEQ ID NO:4.
65. PD—L1 binding polypeptide according to item 60 or 61, wherein
sequence xvii) corresponds to the sequence from position 1 to position 58 in
SEQ ID NO:5.
66. PD-L1 binding ptide according to item 61, wherein sequence
xvii) corresponds to the sequence from position 1 to position 58 in SEQ ID
NO:21.
67. PD-L1 binding ptide according to any preceding item, which
is capable of blocking PD—L1 dependent signaling.
68. PD—L1 binding polypeptide according to item 67, wherein the half
maximal inhibitory concentration (ICSO) of the ng is at most 5 x 10'8 M,
such as at most 1 x10'8 M, such as at most 5 x10'9 M, such as at most 3.5 x
'9 M, such as at most 1 x10'9 M, such as at most 5 x10'10 M, such as at
most 1 x 10-10 M.
69. PD-L1 binding polypeptide ing to any preceding item, which
is capable of blocking the interaction of PD-L1 with PD-1.
70. PD—L1 binding polypeptide according to any preceding item, which
is capable of binding to PD-L1 such that the KB value of the interaction is at
most 2 x10'8 M, such as at most 1 x10'8 M, such as at most 1 x10'9 M, such
as at most 5 x10'10 M, such as at most 3 x10'10 M.
71. PD—L1 binding polypeptide according to any preceding item, which
is capable of binding to PD-L1 such that the kd value of the interaction is at
most 1 x10"3 s'1, such as at most 6 x104 s'1.
72. PD—L1 binding polypeptide according to any preceding item, which
is e of binding to PD-L1 such that the E050 value of the interaction is
at most 1 X 10'9 M, such as at most 1 x10"10 M, such as at most 7 x10'11 M.
73. PD-L1 binding polypeptide according to any preceding item,
wherein said PD-L1 is human PD-L1.
74. PD—L1 binding polypeptide according to any preceding item which
comprises additional amino acids at the C-terminal and/or N-terminal end.
75. PD—L1 binding polypeptide according to item 74, wherein said
additional amino ) improve(s) production, purification, stabilization in
vivo or in vitro, coupling or detection of the polypeptide.
76. PD—L1 binding polypeptide according to any preceding item in
multimeric form, comprising at least two PD-L1 binding ptide monomer
units, whose amino acid sequences may be the same or different.
77. PD-L1 binding polypeptide according to item 76, wherein said PD-
L1 binding polypeptide monomer units are covalently coupled together.
78. PD-L1 binding polypeptide according to item 77, wherein the PD-L1
g polypeptide monomer units are expressed as a fusion protein.
79. PD—L1 binding polypeptide according to any one of items 76-78, in
dimeric form.
80. Fusion protein or conjugate comprising
- a first moiety consisting of a PD-L1 binding ptide according to any
preceding item; and
- a second moiety consisting of a polypeptide having a desired biological
activity.
81. Fusion protein or conjugate according to item 80, n said
d biological activity is a therapeutic activity.
82. Fusion protein or conjugate ing to item 80, wherein said
desired biological activity is a binding activity.
83. Fusion protein or conjugate according to item 80, wherein said
desired biological activity is an tic activity.
84. Fusion n or ate according to item 82, wherein said
binding ty is albumin binding activity which increases in vivo half-life of
the fusion protein or conjugate.
85. Fusion protein or conjugate according to item 84, wherein said
second moiety comprises the albumin g domain of streptococcal protein
G or a derivative thereof.
86. Fusion protein or ate according to item 82, wherein said
g activity acts to block a biological activity.
87. Fusion protein or conjugate ing to item 81, wherein the
second moiety is a therapeutically active polypeptide.
88. Fusion protein or conjugate according to item 87, wherein the
second moiety is an immune response modifying agent.
89. Fusion protein or conjugate according to item 87, wherein the
second moiety is an anti-cancer agent.
90. Fusion protein or conjugate according to any one of items 80—83
and 86—89, wherein the second moiety is selected from the group consisting
of human endogenous enzymes, hormones, growth factors, chemokines,
cytokines and lymphokines.
91. Fusion protein according to any one of items 80-91, wherein the
second moiety further comprises a linker.
92. Complex, comprising at least one PD-L1 binding ptide
according to any one of the ing items and at least one antibody or an
antigen g fragment thereof.
93. x according to item 92, wherein said at least one antibody
or antigen binding fragment f is selected from the group consisting of
full-length antibodies, Fab fragments, Fab’ fragments, F(ab’)2 fragments, Fc
fragments, Fv fragments, single chain Fv (scFv) fragments, (scFv)2 and
domain antibodies.
94. Complex according to item 93, wherein said at least one antibody
or antigen binding fragment thereof is selected from the group ting of
full-length antibodies, Fab fragments and scFv fragments.
95. x according to item 94, wherein said at least one antibody
or antigen binding fragment thereof is a ength antibody.
96. Complex according to any one of items 92—95, wherein said
antibody or antigen binding fragment thereof is a monoclonal antibody or an
antigen binding fragment thereof.
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97. Complex according to any one of items 92-96, wherein said
antibody or antigen binding fragment thereof is selected from the group
consisting of human antibodies, humanized antibodies and chimeric
antibodies, and antigen binding fragments thereof.
98. Complex according to item 97, wherein said antibody or antigen
binding fragment f is a human or humanized antibody, or an antigen
binding fragment thereof.
99. Complex ing to any one of items 92-98, wherein said PD-L1
binding polypeptide is attached at either the inus or the N-terminus of
the heavy chain or the light chain of said antibody or antigen binding fragment
thereof.
100. Complex ing to any one of items 92-99, further comprising
101. Complex according to any one of items , wherein said
antibody or antigen binding fragment thereof has affinity for an antigen, for
example an n associated with an infectious disease, or an antigen
associated with cancer.
102. Fusion protein or conjugate according to any one of items 79-90
or complex ing to any one of items 92-101, wherein said second
moiety or said antibody or antigen binding fragment thereof is an inhibitor
selected from the group consisting of inhibitors of: PD-1, CTLA-4, T-cell
immunoglobulin and mucin containing protein-3 (TIM-3), galectin-9 (GAL-9),
lymphocyte activation gene-3 (LAG-3), PD-L2, B7 homolog 3 (B7-H3), B?
homolog 4 ), V-domain lg suppressor of T-cell activation (VISTA),
carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1), B
and T lymphocyte attenuator (BTLA), colony stimulating factor 1 receptor
(CSF1 R), herpes virus entry or (HVEM), killer immunoglobulin receptor
(KIR), adenosine, adenosine A2a receptor (A2aR), CD200R and T
cell lg and ITIM domain.
103. Fusion protein, ate or complex according to item 102,
wherein said second moiety, antibody or antigen binding fragment thereof is
an inhibitor of PD-1, such as an inhibitor selected from the group consisting of
nivolumab, zumab, BMS 936559, MPDL328OA and pembrolizumab,
such as pembrolizumab.
104. Fusion protein, conjugate or complex according to item 102,
wherein said second moiety, antibody or antigen binding fragment thereof is
an inhibitor of CTLA—4, such as an inhibitor ed from the group consisting
of belatacept, abatacept and ipilimumab, such as ipilimumab.
105. Fusion protein or conjugate according to any one of items 80-91
or complex according to any one of items 92-101, wherein said second
moiety or antibody or antigen g fragment thereof is an agonist selected
from the group consisting of ts of CD134, CD40, 4—1 BB and
glucocorticoid—induced TNFR-related protein (GITR).
106. PD-L1 binding polypeptide, fusion protein, conjugate or complex
according to any one of items 1-105, further comprising a label.
107. PD-L1 binding polypeptide, fusion protein, conjugate or complex
according to item 106, n said label is selected from the group
consisting of fluorescent dyes and metals, chromophoric dyes,
chemiluminescent nds and inescent proteins, enzymes,
uclides, radioactive particles and pretargeting recognition tags.
108. PD-L1 binding polypeptide, fusion protein, conjugate or complex
according to item 107, comprising a chelating nment provided by a
polyaminopolycarboxylate chelator ated to the PD-L1 binding
polypeptide via a thiol group of a cysteine residue or an amine group of a
lysine residue.
109. PD-L1 binding polypeptide, fusion n, conjugate or complex
according to item 106, which comprises a pretargeting recognition tag forming
part of a complementary pair of pretargeting moieties, for example selected
from stept(avidin)/biotin, oligonucleotide/complementary oligonucleotide such
as DNA/complementary DNA, RNA/complementary RNA, phosphorothioate
nucleic acid/ complementary phosphorothioate nucleic acid and peptide
nucleic acid/complementary peptide nucleic acid and
morpholinos/complementary morpholinos.
110. PD-L1 binding polypeptide, fusion protein, conjugate or complex
according to item 109, wherein said pretargeting recognition tag is a peptide
nucleic acid tag.
111. PD-L1 binding polypeptide, fusion protein, conjugate or x
according to any one of item 110, wherein said pretargeting recognition tag is
a 10-20—mer peptide c acid sequence, such as a 15-mer peptide nucleic
acid sequence.
112. A polynucleotide encoding a polypeptide according to any one of
items 1-105.
113. Expression vector comprising a polynucleotide according to item
112.
114. Host cell comprising an sion vector according to item 113.
115. Method of producing a polypeptide according to any one of items
1-105, comprising
— ing a host cell according to item 114 under conditions
permissive of expression of said polypeptide from said expression vector, and
- isolating said polypeptide.
116. Composition comprising a PD-L1 binding polypeptide, fusion
protein, conjugate or x according to any one of items 1-111 and at
least one pharmaceutically acceptable excipient or carrier.
117. Composition according to item 116, further comprising at least
one additional active agent, such as an agent selected from an immune
response modifying agent and an anti-cancer agent.
118. PD-L1 binding polypeptide, fusion n, conjugate or complex
according to any one of items 1-111 or a composition according to any one of
items 116-1 17 for oral, topical, enous, intraperitoneal, subcutaneous,
pulmonary, transdermal, intramuscular, intranasal, buccal, sublingual or
suppository administration, such as for topical stration.
119. PD-L1 binding polypeptide, fusion protein, conjugate or complex
according to any one of items 1-111 or a composition according to any one of
items 116-1 17 for use as a medicament, a diagnostic agent and/or a
prognostic agent.
WO 72280
120. PD-L1 binding polypeptide, fusion protein, conjugate, complex or
composition for use according to item 119 as a ment.
121. PD-L1 binding polypeptide, fusion protein, conjugate, complex or
composition for use according to item 119 as a diagnostic agent and/or a
prognostic agent.
122. PD-L1 binding polypeptide, fusion protein, conjugate, complex or
composition for use as a medicament according to item 120, wherein said
polypeptide, fusion protein, conjugate or composition modulates PD-L1
function in vivo.
123. PD-L1 binding polypeptide, fusion protein, conjugate, complex or
composition for use according to any one of items 119-121 in the treatment,
prognosis or diagnosis of a PD-L1 related disorder.
124. PD-L1 binding polypeptide, fusion protein, conjugate, x or
composition for use ing to item 122, wherein said PD-L1 related
disorder is selected from the group consisting of infectious diseases and
cancers.
125. PD-L1 binding polypeptide, fusion protein, conjugate, complex or
composition for use according to item 124, n said PD-L1 related
disorder is an ious disease, such as a chronic viral infection, for example
selected from the group consisting of human immunodeficiency virus (HIV),
hepatitis B virus (HBV) and hepatitis C virus (HCV).
126. PD-L1 binding polypeptide, fusion protein, ate, complex or
ition for use according to item 124, wherein said PD-L1 related
disorder is cancer, such as a cancer selected from the group consisting of:
- s manifesting solid tumors, for example selected from the
group consisting of skin cancer, such as melanoma and nonmelanoma skin
cancer (NMSC); lung cancers, such as small cell lung cancer, non-small cell
lung cancer (NSCLC); head and neck cancer; renal cell carcinoma (RCC);
bladder cancer; breast cancer; colorectal cancer; gastric cancer; ovarian
cancer; pancreatic cancer; prostate cancer; glioma; astoma; liver
carcinoma; gallbladder cancer; thyroid ; bone cancer; al ;
uterine cancer; vulval cancer; endometrial cancer; testicular ; kidney
cancer; esophageal carcinoma; brain/CNS cancers; neuronal cancers;
mesothelioma; sarcomas; small bowel adenocarcinoma; and pediatric
ancies; and
- cancers manifesting non—solid tumors, for example mia, acute
myeloid leukaemia, acute lymphoblastic leukaemia and le myeloma.
127. PD-L1 g polypeptide, fusion protein, conjugate, complex or
composition for use according to item 126, wherein said cancer is selected
from the group consisting of melanoma, NSCLC, head and neck cancer,
RCC, bladder cancer, breast cancer, colorectal cancer, gastric cancer,
ovarian cancer, pancreatic cancer and prostate cancer, such as selected from
the group consisting of melanoma, NSCLC, head and neck cancer, RCC and
bladder .
128. Method of treatment of a PD-L1 related er, sing
administering to a subject in need thereof an effective amount of a PD-L1
binding polypeptide, fusion protein, conjugate or complex according to any
one of items 1—1 11 or a composition ing to any one of items 116-117.
129. Method according to item 128, wherein said PD—L1 d
disorder is selected from the group consisting of infectious disease and
cancen
130. Method according to item 129, wherein said PD—L1 related
disorder is an infectious disease, such as a chronic viral infection, for example
selected from the group consisting of human immunodeficiency virus (HIV),
hepatitis B virus (HBV) and hepatitis C virus (HCV).
131. Method according to item 129, wherein said PD—L1 related
disorder is cancer, such as a cancer ed from the group consisting of:
- cancers manifesting solid tumors, for example selected from the
group ting of skin cancer, such as melanoma and nonmelanoma skin
cancer (NMSC); lung cancers, such as small cell lung cancer, non-small cell
lung cancer (NSCLC); head and neck cancer; renal cell carcinoma (RCC);
bladder cancer; breast cancer; colorectal cancer; gastric cancer; ovarian
cancer; pancreatic cancer; prostate cancer; glioma; glioblastoma; liver
carcinoma; gallbladder cancer; d cancer; bone cancer; al cancer;
uterine ; vulval cancer; endometrial cancer; testicular cancer; kidney
cancer; esophageal carcinoma; brain/CNS cancers; neuronal cancers;
mesothelioma; sarcomas; small bowel arcinoma; and pediatric
malignancies; and
- cancers manifesting non—solid tumors, for e leukaemia, acute
myeloid leukaemia, acute lymphoblastic leukaemia and multiple myeloma.
132. Method according to item 131, in which said cancer is selected
from the group consisting of melanoma, NSCLC, head and neck cancer,
RCC, bladder cancer, breast cancer, colorectal cancer, gastric cancer,
ovarian cancer, pancreatic cancer and prostate cancer, such as selected from
the group consisting of melanoma, NSCLC, head and neck cancer, RCC and
bladder cancer.
133. Method according to any one of items 131-132, comprising the
steps of:
- contacting the subject with a PD-L1 binding polypeptide, fusion
protein, conjugate or complex ing to any one of items 109-
111 comprising a pretargeting ition tag, or with a composition
comprising such a PD-L1 binding polypeptide, fusion protein,
conjugate or complex, and
- contacting the subject with a complementary pretargeting moiety,
comprising a radionuclide.
134. Method of ing PD-L1, sing providing a sample
suspected to contain PD-L1, contacting said sample with a PD-L1 binding
polypeptide, fusion n, conjugate or complex according to any one of
items 1-111 or a composition according to any one of items 116-117, and
detecting the binding of the PD—L1 binding polypeptide, fusion protein,
conjugate, complex or ition to indicate the presence of PD-L1 in the
sample.
135. Method for determining the presence PD-L1 in a subject,
comprising the steps of:
a) contacting the subject, or a sample isolated from the subject, with a
PD-L1 binding polypeptide, fusion n, ate or complex
according to any one of items 1—1 11 or a composition according to any
one of items 116-117, and
b) ing a value corresponding to the amount of the PD-L1 binding
polypeptide, fusion protein, conjugate or ition that has bound in
said t or to said sample.
136. Method according to item 135, in which said PD-L1 binding
polypeptide, fusion protein, conjugate or complex is according to any one of
items 109-111, or said composition comprises such a PD-L1 binding
polypeptide, fusion protein, conjugate or complex, and step a) further
comprises contacting the subject with a complementary pretargeting moiety
labeled with a detectable label, such as a radionuclide label.
137. Method according to item 135 or 136, further comprising a step of
comparing said value to a reference.
138. Method according to any one of items 134-137, wherein said
subject is a mammalian subject, such as a human subject.
139. Method according to any one of items 134-138, wherein the
method is performed in vivo.
140. Method ing to item 139, which is a method for medical
imaging in which
- step a) comprises the systemic administration of said PD-L1 binding
polypeptide, fusion n, conjugate, x or composition to a
ian subject;
- said PD-L1 binding polypeptide, fusion protein, conjugate, complex,
composition or pretargeting moiety comprises a radionuclide label suitable for
medical imaging; and
- step b) comprises obtaining one or more images of at least a part of
the subject’s body using a medical imaging instrument, said image(s)
indicating the presence of the radionuclide inside the body.
Claims (18)
1. PD-L1 binding polypeptide, comprising a PD-L1 binding motif BM, which motif consists of an amino acid sequence selected from: i) ERNX4AAX7EIL X11LPNLX16X17X18QX20 26LX28D wherein, independently from each other, X4 is selected from A, D, E, F, H, I, K, L, N, Q, R, S, T, V and Y; X7 is selected from A, E, F, H, N, Q, S, T, V, W and Y; X11 is selected from A, D, E, F, H, K, L, N, Q, R, S, T, V, W and Y; X16 is selected from N and T; X17 is selected from A, H, K, N, Q, R and S; X18 is selected from A, D, E, G, H, K, L, N, Q, R, S, T, V and Y; X20 is selected from H, I, K, L, N, Q, R, T, V and Y; X26 is selected from K and S; and X28 is selected from A, D and E; ii) an amino acid sequence which has at least 96 % identity to any one of the ces d in i).
2. PD-L1 binding ptide according to claim 1, wherein sequence i) corresponds to the sequence from position 8 to position 36 in a sequence selected from the group consisting of SEQ ID NO:1-808, such as the group consisting of SEQ ID NO:1-93, such as the group consisting of SEQ ID NO:1-24, such as the group consisting of SEQ ID NO:1, 2, 4, 5 and 21, such as the group consisting of SEQ ID NO:1 and 2.
3. PD-L1 binding polypeptide according to any preceding claim, wherein said PD-L1 binding motif forms part of a three-helix bundle n domain.
4. PD-L1 binding polypeptide according to any preceding claim, which comprises a binding module BMod, the amino acid sequence of which is ed from: iii) K-[BM]-DPSQSXaXbLLXc EAKKLXdXeXfQ; wherein Xa is selected from A and S; Xb is selected from N and E; Xc is selected from A, S and C; Xd is selected from E, N and S; Xe is selected from D, E and S; and Xf is ed from A and S; iv) an amino acid sequence which has at least 93 % ty to any one of the sequences d in iii); wherein [BM] is a PD-L1 binding motif as defined in any one of claims 1-2.
5. PD-L1 binding polypeptide according to any preceding claim, which comprises an amino acid sequence selected from: xvii) VDAKYAK-[BM]-DPSQSSELLSEAKKLNDSQAPK; xviii) an amino acid sequence which has at least 89 % identity to any one of the sequences defined in xvii); wherein [BM] is a PD-L1 binding motif as defined in any one of claims 1-2.
6. PD-L1 binding polypeptide according to any one of claims 1-4, which comprises an amino acid sequence selected from: xxi) AEAKYAK-[BM]-DPSQSSELLSEAKKLNDSQAPK; xxii) an amino acid sequence which has at least 89 % ty to any one of the sequences defined in xxi); wherein [BM] is a PD-L1 binding motif as defined in any one of claims 1-2.
7. PD-L1 binding polypeptide according to claim 5 or 6, wherein sequence xvii) or xxi) corresponds to the sequence from position 1 to position 58 in a sequence selected from the group ting of SEQ ID NO:1-814, such as the group consisting of SEQ ID NO:1-93 and 811-813, such as the group consisting of SEQ ID NO:1-24 and 3, such as the group consisting of SEQ ID NO:1, 2, 4, 5, 21, 811 and 812, such as the group consisting of SEQ ID NO:1 and 2 or SEQ ID NO:811 and 812.
8. PD-L1 binding ptide according to any preceding claim, which is capable of blocking PD-L1 dependent signaling.
9. PD-L1 binding polypeptide according to claim 8, wherein the half maximal tory concentration (IC50) of the blocking is at most 5 x 10-8 M, such as at most 1 x 10-8 M, such as at most 5 x 10-9 M, such as at most 3.5 x 10-9 M, such as at most 1 x 10-9 M, such as at most 5 x 10-10 M, such as at most 1 x 10-10
10. PD-L1 binding polypeptide ing to any preceding claim, which is capable of blocking the interaction of PD-L1 with PD-1.
11. PD-L1 binding polypeptide according to any preceding claim, which is capable of binding to PD-L1 such that the KD value of the interaction is at most 2 x 10-8 M, such as at most 1 x 10-8 M, such as at most 1 x 10-9 M, such as at most 5 x 10-10 M, such as at most 3 x 10-10 M.
12. Fusion protein or conjugate comprising - a first moiety ting of a PD-L1 binding polypeptide according to any preceding claim; and - a second moiety consisting of a polypeptide having a desired biological activity.
13. Complex, comprising at least one PD-L1 binding polypeptide, fusion n or conjugate according to any one of the preceding claims and at least one dy or an antigen binding fragment thereof.
14. A polynucleotide encoding a polypeptide, fusion protein, conjugate or complex ing to any one of claims 1-13.
15. Composition comprising a PD-L1 binding ptide, fusion protein, conjugate or x according to any one of claims 1-13 and at least one pharmaceutically acceptable excipient or carrier.
16. Use of a PD-L1 binding polypeptide, fusion protein, conjugate or complex according to any one of claims 1-13 in the manufacture of a medicament for the treatment, prognosis and/or diagnosis of a PD-L1 related disorder.
17. Use according to claim 16, wherein said medicament modulates PDL1 function in vivo.
18. Use according to any one of claims 16-17, wherein the PD-L1 related disorder is selected from the group consisting of infectious diseases and cancers. H N m \ I \ : I m.“ ! hm !I!I!! 959; ! -mmmwqqmmmommannnmgl_u¢zmomnen4mqqumwgmmmmmwmdmm mumHEmmommn H H H Lmzmom {mzimzmom ngwfiEo¢ ngmom hflEMOQZB. O; .5 .5 Emgmzn Cmfimmm Cmfinm H hmgmoomB_ngmgkmo¢<ommeg mmgkoooeg oeg EImmzmomoeg 8:82me Q) OW Q) OO OW OW Q) ‘_ LI) k0 OW C) (*7 k0 OW C) \ I OW OW C) C) C) C) \—I H \—I [\ [\ CO CO Q) CO Q) 00 (I) I I I I I | I \ | \ N N EmmaIChLO IE!!!!!!I[\LO !!!III!!!I!!IE!!!!!!I00 QM QM QM QM QM QM QM mmmmqqmmmammm Mmmmggmmmommm Mmmmggmwmommn‘ Mfimmggzmmommmw M cozmcgmwo [\ O LO 8:82me 0 l\ LO O (V) m W <1“ l\ (\1 ('7 (V) ('7 <14 (\1 (’7 l\ l\ l\ l\ l\ CO CO [\ [\ [\ [\ [\ I I I | \ | | \ I 5/42 I\ C) (\I <14 [\ CO m LO C) \—I mm W LO \ I (\I (\I (\I (\I (\I m (Y) <14 8:82me <1” (\I O W (Y) [\ Lr) LO [\ [\ 0:) w I.\ l\ I.\ I.\ I.\ I.\ [\ [\ [\ [\ [\ [\ I I I \ I I \ I N N I\ CO N cozmcgmwo MN LO [\ (I) HN (‘0 cozmcgmwo OW m Q) LO (\l [\ 0 C\] m (‘0 <1” Lr) L0 k0 03 w w 03 w 03 OD [\ [\ [\ [\ [\ [\ [\ I I I I \ I I \ | 8/42 wow mom mom Pom mom mom O HNMWDLO 03 CD \ : \:\|x:\:\|\: i \ E (\1 I\ NN N QMMflmeQmmemmflflflQMEI M cozmcgmwo w (Y) LO N LO O (Y) KO [\ [\ 0:) w OW m 0) w w w w OD w [\ [\ [\ [\ [\ [\ [\ I | I | \ I I \ I N N
Applications Claiming Priority (5)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| EP15192364.6 | 2015-10-30 | ||
| EP15192364 | 2015-10-30 | ||
| EP16157154.2 | 2016-02-24 | ||
| EP16157154 | 2016-02-24 | ||
| PCT/EP2016/076040 WO2017072280A1 (en) | 2015-10-30 | 2016-10-28 | New polypeptide having affinity to pd-l1 |
Publications (2)
| Publication Number | Publication Date |
|---|---|
| NZ741586A NZ741586A (en) | 2021-11-26 |
| NZ741586B2 true NZ741586B2 (en) | 2022-03-01 |
Family
ID=
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