US20180339043A1

US20180339043A1 - Modified antibodies

Info

Publication number: US20180339043A1
Application number: US15/988,944
Authority: US
Inventors: David Campbell; Ramesh Bhatt; William J. Dower; Steven E. Cwirla; Blake M. Williams
Original assignee: Janux Therapeutics Inc
Current assignee: Janux Therapeutics Inc
Priority date: 2017-05-26
Filing date: 2018-05-24
Publication date: 2018-11-29
Also published as: US20230270854A1; WO2018218076A1

Abstract

Provided herein are modified antibodies, pharmaceutical compositions thereof, as well as nucleic acids, and methods for making and discovering the same. The modified antibodies described herein are modified with a peptide. The peptide binds at or near the antigen binding site of the antibody at physiological pH, thus reducing binding affinity of the antibody for a target antigen. At acidic pH, the binding interaction of the peptide at or near the antigen binding site is disrupted, thus enabling binding with a target antigen.

Description

CROSS-REFERENCE

This application claims the benefit of U.S. Provisional Application No. 62/511,771 filed May 26, 2017 which is incorporated by reference herein in its entirety.

REFERENCE TO A SEQUENCE LISTING

The instant application contains a Sequence Listing which has been filed electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on May 24, 2018, is named 52426-701_201_SL.txt and is 73,393bytes in size.

SUMMARY OF THE INVENTION

Disclosed herein, in some embodiments, are modified antibodies comprising a formula: A-L-P wherein A is an antibody or antibody fragment that binds to a target antigen, P is a peptide that reduces binding of A to the target antigen at physiological pH and that does not reduce binding of A to the target antigen at acidic pH, and L is a linking moiety that connects A to P at physiological pH and in a tumor microenvironment and L is bound to A outside an antigen binding site. In some instances, at physiological pH P is reversibly bound to A through ionic, electrostatic, hydrophobic, Pi-stacking, and H-bonding interactions, or a combination thereof. In some instances, at physiological pH P is reversibly bound to A at or near the antigen binding site. In some instances, P inhibits the binding of A to the target antigen at physiological pH and P does not inhibit the binding of A to the target antigen at acidic pH. In some instances, in tissue other than the tumor microenvironment, P sterically blocks A from binding to the target antigen. In some instances, at the tumor microenvironment, P is removed from the antigen binding site, and the antigen binding site of A is exposed. In some instances, the modified antibody has an increased binding affinity for the target antigen in the tumor microenvironment compared to the binding affinity of the modified antibody for the target antigen in a non-tumor microenvironment. In some instances, P comprises a peptide sequence with at least one histidine. In some instances, the histidine forms a binding interaction at or near the antigen binding site of A at physiological pH. In some instances, at acidic pH P is reversibly bound to A in a region of A that is not the antigen binding site. In some instances, at acidic pH P is reversibly bound to A in a region of A that is not the antigen binding site through ionic, electrostatic, hydrophobic, Pi-stacking and H-bonding interactions, or a combination thereof. In some instances, P is resistant to cleavage by a protease. In some instances, physiological pH is about pH 7.4. In some instances, acidic pH is about pH 6.0 to about pH 7.0. In some instances, P comprises a peptide sequence of at least 6 amino acids in length. In some instances, P comprises a peptide sequence of at least 10 amino acids in length. In some instances, P comprises a peptide sequence of at least 6 to 20 amino acids in length. In some instances, P comprises a modified amino acid, a non-natural amino acid, or a modified non-natural amino acids, or combination thereof. In some instances, the modified amino acid or modified non-natural amino acid comprises a post-translational modification. In some instances, at acidic pH P is reversibly bound to L. In some instances, L comprises a peptide sequence with at least one aspartic acid or glutamic acid, or a combination thereof. In some instances, the histidine of P forms an interaction with the aspartic acid or glutamic acid of L. In some instances, L is a peptide sequence having at least 5 to no more than 50 amino acids. In some instances, L has a formula selected from the group consisting of: (GS)_n, wherein n is an integer from 6 to 20 (SEQ ID NO: 1); (G₂S)_n, wherein n is an integer from 4 to 13 (SEQ ID NO: 2); (G₃S)_n, wherein n is an integer from 3 to 10 (SEQ ID NO: 3); and (G₄S)_n, wherein n is an integer from 2 to 8 (SEQ ID NO: 4); and (G)_n, wherein n is an integer from 12 to 40 (SEQ ID NO: 5). In some instances, L has a formula comprising (GGSGGD)_n, wherein n is an integer from 2 to 6 (SEQ ID NO: 8). In some instances, L has a formula comprising (GGSGGE)_n, wherein n is an integer from 2 to 6 (SEQ ID NO: 9). In some instances, L has a formula comprising (GGGSGSGGGGS)_n, wherein n is an integer from 1 to 3 (SEQ ID NO: 6). In some instances, L has a formula comprising (GGGGGPGGGGP) _n, wherein n is an integer from 1 to 3 (SEQ ID NO: 7). In some instances, L has a formula selected from (GX)_n, wherein X is serine, aspartic acid, glutamic acid, threonine, or proline and n is at least 20 (SEQ ID NO: 24); (GGX)_n, wherein X is serine, aspartic acid, glutamic acid, threonine, or proline and n is at least 13 (SEQ ID NO: 25); (GGGX)_n, wherein X is serine, aspartic acid, glutamic acid, threonine, or proline and n is at least 10 (SEQ ID NO: 26); (GGGGX)_n, wherein X is serine, aspartic acid, glutamic acid, threonine, or proline and n is at least 8 (SEQ ID NO: 27); (G_zX)_n, wherein X is serine, aspartic acid, glutamic acid, threonine, or proline and n is at least 15, and z is between 1 and 20 (SEQ ID NO: 28). In some instances, L is resistant to cleavage by a protease. In some instances, L comprises a modified amino acid. In some instances, the modified amino acid comprises a post-translational modification. In some instances, L comprises a non-natural amino acid or a modified non-natural amino acid, or combination thereof. In some instances, the modified non-natural amino acid comprises a post-translational modification. In some instances, the target antigen is selected from the group consisting of: 4-1BB, CTLA4, PD-1, and PD-L1. In some instances, the target antigen is 4-1BB. In some instances, the target antigen is CTLA4. In some instances, the target antigen is PD-1. In some instances, the target antigen is PD-L1. In some instances, A is a full length antibody, a single-chain antibody, an Fab fragment, an Fab′ fragment, an (Fab′)2 fragment, an Fv fragment, a divalent single chain antibody, bispecific antibody, a trispecific antibody, a tetraspecific antibody, or an antibody drug conjugate. In some instances, A is selected from the group consisting of utomilumab, urelumab, ipilimumab, tremelimumab, pembrolizumab, nivolumab, and atezolizumab. In some instances, A is utomilumab. In some instances, A is urelumab. In some instances, A is ipilimumab. In some instances, A is tremelimumab. In some instances, A is pembrolizumab. In some instances, A is nivolumab. In some instances, A is atezolizumab. In some instances, P comprises an amino acid sequence selected from the group consisting of Peptide 1, Peptide 2, Peptide 5, Peptide 6, Peptide 10, Peptide 13, Peptide 26, Peptide 14, Peptide 15, Peptide 20, Peptide 27, Peptide 21, Peptide 22, Peptide 23, Peptide 28, Peptide 29, Peptide 30, Peptide 31, and Peptide 24. In some instances, the target antigen is CTLA4 and P comprises an amino acid sequence selected from the group consisting of Peptide 1, Peptide 2, Peptide 5, Peptide 6, Peptide 10, Peptide 13, Peptide 26, Peptide 14, and Peptide 15. In some instances, the target antigen is CTLA4 and P comprises an amino acid sequence according to Peptide 1. In some instances, the target antigen is CTLA4 and P comprises an amino acid sequence according to Peptide 2. In some instances, the target antigen is CTLA4 and P comprises an amino acid sequence according to Peptide 5. In some instances, the target antigen is CTLA4 and P comprises an amino acid sequence according to Peptide 6. In some instances, the target antigen is CTLA4 and P comprises an amino acid sequence according to Peptide 10. In some instances, the target antigen is CTLA4 and P comprises an amino acid sequence according to Peptide 13. In some instances, the target antigen is CTLA4 and P comprises an amino acid sequence according to Peptide 26. In some instances, the target antigen is CTLA4 and P comprises an amino acid sequence according to Peptide 14. In some instances, the target antigen is CTLA4 and P comprises an amino acid sequence according to Peptide 15. In some instances, the target antigen is CTLA4 and P comprises an amino acid sequence selected from the group consisting of Peptide 10, Peptide 13, Peptide 26, Peptide 14, and Peptide 15. In some instances, the target antigen is PD-L1 and P comprises an amino acid sequence selected from the group consisting of Peptide 20, Peptide 27, Peptide 21, Peptide 22, Peptide 23, Peptide 28, Peptide 29, Peptide 30, Peptide 31, and Peptide 24. In some instances, the target antigen is PD-L1 and P comprises an amino acid sequence according to Peptide 20. In some instances, the target antigen is PD-L1 and P comprises an amino acid sequence according to Peptide 27. In some instances, the target antigen is PD-L1 and P comprises an amino acid sequence according to Peptide 21. In some instances, the target antigen is PD-L1 and P comprises an amino acid sequence according to Peptide 22. In some instances, the target antigen is PD-L1 and P comprises an amino acid sequence according to Peptide 23. In some instances, the target antigen is PD-L1 and P comprises an amino acid sequence according to Peptide 28. In some instances, the target antigen is PD-L1 and P comprises an amino acid sequence according to Peptide 29. In some instances, the target antigen is PD-L1 and P comprises an amino acid sequence according to Peptide 30. In some instances, the target antigen is PD-L1 and P comprises an amino acid sequence according to Peptide 31. In some instances, the target antigen is PD-L1 and P comprises an amino acid sequence according to Peptide 24. In some instances, the target antigen is PD-L1 and P comprises an amino acid sequence selected from the group consisting of Peptide 27, Peptide 22, Peptide 23, and Peptide 31. In some instances, A comprises a kappa light chain amino acid sequence according to SEQ ID NO: 68. In some instances, A comprises a heavy chain amino acid sequence according to SEQ ID NO: 70. In some instances, the modified antibody comprises an amino acid sequence according to SEQ ID NO: 69. In some instances, P comprises an amino acid sequence selected from the group consisting of Peptide 1, Peptide 2, Peptide 5, Peptide 6, Peptide 10, Peptide 13, Peptide 26, Peptide 14, Peptide 15, Peptide 20, Peptide 21, Peptide 22, Peptide 23, Peptide 31, and Peptide 24. In some instances, P comprises a peptide sequence with at least two histidines. In some instances, P comprises an amino acid sequence selected from the group consisting of Peptide 5, Peptide 13, Peptide 26, Peptide 14, Peptide 15, Peptide 31, and Peptide 24. In some instances, P comprises a peptide sequence with at least two histidines and at least two cysteines. In some instances, P comprises a peptide sequence with at least two charged amino acid residues wherein the charged amino acid residues are selected from the group consisting of aspartate, glutamate, and histidine. In some instances, P comprises an amino acid sequence selected from the group consisting of Peptide 1, Peptide 2, Peptide 5, Peptide 6, Peptide 10, Peptide 13, Peptide 26, Peptide 14, Peptide 15, Peptide 20, Peptide 27, Peptide 21, Peptide 22, Peptide 23, Peptide 28, Peptide 29, Peptide 30, Peptide 31, and Peptide 24. In some instances, P comprises a peptide sequence with at least three charged amino acid residues wherein the charged amino acid residues are selected from the group consisting of aspartate, glutamate, and histidine. In some instances, P comprises an amino acid sequence selected from the group consisting of Peptide 1, Peptide 2, Peptide 5, Peptide 10, Peptide 13, Peptide 26, Peptide 14, Peptide 15, Peptide 21, Peptide 23, Peptide 28, Peptide 31, and Peptide 24. In some instances, P comprises a peptide sequence with at least one histidine and at least two aspartates. In some instances, P comprises a peptide sequence with at least one cysteine. In some instances, P comprises an amino acid sequence selected from the group consisting of Peptide 5, Peptide 6, Peptide 10, Peptide 13, Peptide 26, Peptide 14, Peptide 15, Peptide 22, Peptide 23, Peptide 29, Peptide 30, Peptide 31, and Peptide 24. In some instances, P comprises a peptide sequence with at least two cysteine amino acid residues. In some instances, P comprises an amino acid sequence selected from the group consisting of Peptide 6, Peptide 10, Peptide 13, Peptide 26, Peptide 14, Peptide 22, Peptide 23, Peptide 29, Peptide 30, Peptide 31, and Peptide 24. In some instances, P comprises a peptide sequence with at least two cysteines and at least three charged amino acid residues wherein the charged amino acid residues are selected from the group consisting of aspartate, glutamate, and histidine. In some instances, P comprises an amino acid sequence of formula GGX, wherein X is cysteine, alanine, proline, methionine, histidine, or leucine. In some instances, P comprises an amino acid sequence selected from the group consisting of Peptide 5, Peptide 6, Peptide 10, Peptide 13, Peptide 26, Peptide 14, Peptide 15, Peptide 22, Peptide 23, Peptide 29, Peptide 31, and Peptide 24. In some instances, P comprises an amino acid sequence of GGC. In some instances, P comprises an amino acid sequence selected from the group consisting of Peptide 5, Peptide 6, Peptide 13, Peptide 26, Peptide 14, Peptide 31, and Peptide 24. In some instances, P does not comprise a lysine or arginine. In some instances, P comprises at least one histidine and at least one aspartate. In some instances, P comprises at least one histidine and at least one glutamate. In some instances, P comprises at least one histidine and at least two glutamates. In some instances, P comprises at least two histidines and at least one aspartate or at least one glutamate. In some instances, P comprises at least one histidine, wherein at least one hydrogen bonding amino acid residue is within two amino acid positions to the histidine, wherein the hydrogen bonding amino acid residue is selected from the group consisting of serine, threonine, tyrosine, asparagine, and glutamine. In some instances, the hydrogen bonding amino acid residue is within one amino acid position to the histidine. In some instances, the hydrogen bonding amino acid residue is serine. In some instances, the hydrogen bonding amino acid residue is threonine. In some instances, the hydrogen bonding amino acid residue is tyrosine. In some instances, the hydrogen bonding amino acid residue is asparagine. In some instances, the hydrogen bonding amino acid residue is glutamine. In some instances, A-L-P does not comprise a protease cleavage site that releases A from P in a tumor microenvironment. In some instances, L comprises a peptide sequence with at least one histidine. In some instances, at acidic pH L is reversibly bound to P. In some instances, P comprises a peptide sequence with at least one aspartic acid or glutamic acid, or a combination thereof. In some instances, the histidine of L forms an interaction with the aspartic acid or glutamic acid of P.
Disclosed herein, in some embodiments, are pharmaceutical compositions, comprising: (a) a modified antibody according to any of the disclosures herein; and (b) a pharmaceutically acceptable excipient.

BRIEF DESCRIPTION OF THE DRAWINGS

The novel features of the invention are set forth with particularity in the appended claims. A better understanding of the features and advantages of the present invention will be obtained by reference to the following detailed description that sets forth illustrative embodiments, in which the principles of the invention are utilized, and the accompanying drawings of which:

FIG. 1 exemplifies an antibody that does not comprise a peptide modification. Such antibodies bind to unique antigens that exist in abundance in tumor tissue. But, the unique antigens are also found in some healthy tissues, which can trigger systemic immune activation in a subject, and cause toxicity.

FIG. 2 shows an exemplary modified antibody. In this example, the modified antibody is linked to a peptide which binds at or near the antigen binding site of the modified antibody at pH 7.4. This reduces binding of the modified antibody to its target antigen in healthy tissue. In tumor tissue, the acidic tumor microenvironment disrupts the interaction of the peptide with the modified antibody. The antigen binding site of the modified antibody is exposed, and the modified antibody selectively binds to its target antigen in tumor tissue.

FIG. 3 shows an exemplary modified antibody. The peptide is linked to the antibody via a linking moiety. The linking moiety creates a stable link between the antibody and peptide. The peptide prevents the antibody from binding to its target antigen in physiological pH, non-diseased tissue. A pH switch in tumor microenvironments modulates the peptide/antibody affinity. The peptide is released in tumor tissue, and enables the antibody to bind to its target antigen.

FIG. 4 shows an exemplary modified antibody. In this example, the peptide is engineered to contain a histidine. At physiological pH, the histidine of the peptide interacts with the antibody binding site. At acidic pH, such as in a tumor microenvironment, the interaction between the peptide and the antibody binding site is disfavored because the histidine is protonated. The antibody binding site is available for binding to its target antigen in a tumor microenvironment.

FIG. 5 is an exemplary schematic of phage panning screening platform to identify pH responsive peptide candidates.

FIG. 6 illustrates a phagemid ELISA of a collection of enriched clones resulting from three rounds of biopanning against anti-mouse CTLA-4 (clone 9D9).

FIG. 7 is an exemplary phagemid competition ELISA from a collection of enriched clones isolated after three rounds of biopanning against anti-mouse CTLA-4 (clone 9D9).

FIG. 8 is an exemplary pH-dependent “binding” assay of a collection of enriched clones isolated after three rounds of biopanning against anti-mouse CTLA-4 (clone 9D9).

FIG. 9 illustrates a pH-dependent “dissociation” assay of a collection of enriched clones isolated after three rounds of biopanning against anti-mouse CTLA-4 (clone 9D9).

FIG. 10A-FIG. 10B illustrate pH responsive anti-CTLA4 peptide candidates identified with phage panning screening platform. FIG. 10A illustrates peptide candidates identified that exhibit pH dependent binding to anti-CTLA4. FIG. 10B illustrates peptide candidates identified that exhibit pH dependent dissociation to anti-CTLA4.

FIG. 11A-FIG. 11C illustrate significant pH responsiveness of unoptimized peptide candidates Peptide 5 (FIG. 11A), Peptide 6 (FIG. 11B) and Peptide 10 (FIG. 11C).

FIG. 12 illustrates multiple pH response anti-CTLA4 peptide candidates with pH dependent dissociation identified from biased library.

FIG. 13A-FIG. 13B illustrate pH biased library generated peptide candidates Peptide 14 (FIG. 13A) and Peptide 15 (FIG. 13B).

FIG. 14 illustrates a Peptide 10 ELISA to anti-mouse antibody (clone 9D9).

FIG. 15 illustrates a Peptide 10 competition ELISA.

FIG. 16A-FIG. 16C illustrate octet binding curve of Peptide 15 (FIG. 16A), Peptide 17 (FIG. 16C) and Peptide 18 (FIG. 16C).

FIG. 17 illustrates pH-dependent binding of a-mCTLA-4 Fab to Peptide 15 by ELISA.

FIG. 18 illustrates CTLA4 antibody/ligand competition ELISA.

FIG. 19 illustrates a phagemid ELISA of a collection of enriched clones resulting from biopanning against PD-L1 antibody.

FIG. 20 illustrates anti-PD-L1 phage competition ELISA.

FIG. 21 illustrates pH-dependent phagemid PD-L1 antibody binding ELISA.

FIG. 22 illustrates pH-dependent phagemid PD-L1 antibody dissociation ELISA.

FIG. 23 illustrates Peptide 23 PD-L1 antibody binding.

FIG. 24 illustrates Peptide 23 PD-L1 competition ELISA.

FIG. 25 illustrates PD-L1 antibody/ligand competition ELISA.

DETAILED DESCRIPTION OF THE INVENTION

Protein-based therapies, including antibody therapies, are effective treatments for a variety of diseases. A strategy to improve toxicity and side effects of such treatments is to engineer a peptide that binds to the protein-based therapy at physiological pH, but does not bind to the protein-based therapy at acidic pH. While peptides have been shown to bind to antibodies with varying affinities, peptides which bind to antibodies in a pH dependent manner are not known. These pH-dependent peptides enable the protein-based therapy to be activated in certain acidic microenvironments while not affecting healthy tissues.

Certain Definitions

The terminology used herein is for the purpose of describing particular cases only and is not intended to be limiting. As used herein, the singular forms “a”, “an” and “the” are intended to include the plural forms as well, unless the context clearly indicates otherwise. Furthermore, to the extent that the terms “including”, “includes”, “having”, “has”, “with”, or variants thereof are used in either the detailed description and/or the claims, such terms are intended to be inclusive in a manner similar to the term “comprising.”
The term “about” or “approximately” means within an acceptable error range for the particular value as determined by one of ordinary skill in the art, which will depend in part on how the value is measured or determined, e.g., the limitations of the measurement system. For example, “about” can mean within 1 or more than 1 standard deviation, per the practice in the given value. Where particular values are described in the application and claims, unless otherwise stated the term “about” should be assumed to mean an acceptable error range for the particular value.
As used herein, “physiological pH” is used to refer to the pH of a non-diseased state cellular environment. In some embodiments, physiological pH is greater than pH 6.9. In some embodiments, physiological pH is about pH 7.0 to about pH 8.0. In some embodiments, physiological pH is about 7.4.
Described herein are modified antibodies, pharmaceutical compositions thereof, as well as nucleic acids, and methods for discovering the same.
The modified antibodies described herein are connected by a linking moiety to a peptide. The peptide is designed to reduce binding of the modified antibody to its target antigen when at physiological pH. At acidic pH, for example at a tumor microenvironment, the peptide does not reduce binding of the modified antibody to its target antigen. The peptide is designed to activate the modified antibody at tumor microenvironments, thus improving the safety profile of such therapies. While antibody-based therapies have proven effective for some diseases in some cases, there is a need for increased targeting of antibodies to the disease site to reduce systemic-based toxicities.
Disclosed herein, in certain embodiments, are modified antibodies comprising a formula:
A-L-P
wherein A is an antibody or antibody fragment that binds to a target antigen, P is a peptide that reduces binding of A to the target antigen at physiological pH, and that does not reduce binding of A to the target antigen at acidic pH, and L is a linking moiety that connects A to P at physiological pH and in a tumor microenvironment and L is bound to A outside an antigen binding site.

Peptide (P)

The peptide of the modified antibodies, in some embodiments, reversibly binds to A in such a way that P sterically blocks, inhibits, or reduces the binding of affinity of A for its target antigen at physiological pH. In some embodiments, P reversibly binds to A through ionic, electrostatic, hydrophobic, Pi-stacking, or H-bonding interactions, or a combination thereof. In some embodiments, P binds to the antigen binding site of A at physiological pH. In some embodiments, P binds to A at amino acid residues which are near the antigen binding site of A. In some embodiments, P binds to amino acid residues within the antigen binding site.
In some embodiments, at acidic pH, P is not reversibly bound to the antigen binding site of A. In some embodiments, at acidic pH, P is not reversibly bound to amino acid residues near the antigen binding site of A. The peptide activates the modified antibody at acidic pH by exposing the antigen binding site of A for engagement with its respective target antigen. In some cases, P has a different conformation at acidic pH, compared to the conformation of P at physiological pH. In some embodiments, at acidic pH, P does not form any interactions with A. In some embodiments, at acidic pH, P does not form any interactions with the linking moiety (L). In some embodiments, at acidic pH, P forms an interaction with L. In some embodiments, P and L reversibly bind through ionic, electrostatic, hydrophobic, Pi-stacking, or H-bonding interactions, or a combination thereof.
In some cases, P comprises a peptide sequence. In some cases, P comprises a peptide sequence disclosed in Table 1. In some cases, P comprises a peptide sequence at least 80% identical to a peptide sequence disclosed in Table 1. In some cases, P comprises a peptide sequence at least 90% identical to a peptide sequence disclosed in Table 1. In some cases, P comprises a peptide sequence at least 95% identical to a peptide sequence disclosed in Table 1. In some cases, the peptides disclosed herein are linear peptides. In some cases, the peptides disclosed herein are cyclic peptides.

TABLE 1

Peptide Sequences (P)

		SEQ
Peptide ID	Sequence	ID NO

CTLA4 peptides

Peptide

1	TLDDMSHVILYA	29

Peptide 2	VISDNHQIVWDL	30

Peptide 3	LTTQDHPLTILL	31

Peptide 4	GGWICHWLEPQEACTY	32

Peptide 5	GGCFEEHEQLVFQTHC	33

Peptide 6	GGCILPGQHESQAIAC	34

Peptide 7	GGCLSQMDFHDWLQYC	35

Peptide 8	GGTDCYLWDYKASCHQ	36

Peptide 9	GGKCDSLSYWQEIECS	37

Peptide 10	GGADCLLHDWDSACQI	38

Peptide 11	MQNVDEAPPLLL	39

Peptide 12	TNDWQGLLLNVF	40

Peptide 13	GGCQDSMFHHPNHC	41

Peptide 26	GGCGMHQHPLFVDC	42

Peptide 14	GGCSLSQHPNHSDC	43

Peptide 15	GGPCNQVECHHQFT	44

Peptide 16	GGCPSLHPQWIHVC	45

Peptide 17	GGCFDSANQHPNIVIC	46

Peptide 18	GGCHQDIEMPIYWC	47

Peptide 19	GGCQIHDPHTWHLC	48

PD-L1 peptides

Peptide

20	QLFYPSTYHIID	49

Peptide 27	QVSPLYFYEELA	50

Peptide 21	HQALLDFYGDY	51

Peptide 22	GGMCHELFYSNLNWCQ	52

Peptide 23	GGHCVDMVDFYQQTCQ	53

Peptide 28	VDLLDGSLQDFY	54

Peptide 29	GGLCSTFYEPQVDICY	55

Peptide 30	SDFSGLLFYDYQ	56

Peptide 31	GGCVHFFHHQRPDC	57

Peptide 24	GGCHNKSGLFYHYC	58

Peptide 25	GGCFYPGHHHQLLC	59

In some embodiments, P comprises an amino acid sequence selected from the group consisting of Peptide 1, Peptide 2, Peptide 5, Peptide 6, Peptide 10, Peptide 13, Peptide 26, Peptide 14, Peptide 15, Peptide 20, Peptide 27, Peptide 21, Peptide 22, Peptide 23, Peptide 28, Peptide 29, Peptide 30, Peptide 31, and Peptide 24. In some embodiments, P comprises an amino acid sequence selected from the group consisting of Peptide 10, Peptide 13, Peptide 26, Peptide 14, Peptide 15, Peptide 27, Peptide 22, Peptide 23, and Peptide 31. In some embodiments, P comprises an amino acid sequence selected from the group consisting of Peptide 15 and Peptide 23. In some embodiments, P comprises an amino acid sequence of Peptide 15. In some embodiments, P comprises an amino acid sequence of Peptide 23.
In some embodiments, P is designed to incorporate amino acid residues which cause a conformational change when triggered by an environmental change. In some cases, the environmental change is the difference in pH from normal, healthy tissue to an acidic pH that is found at tumor microenvironments.
Cancer cells in a solid tumor are able to form a tumor microenvironment in their surroundings to support the growth and metastasis of the cancer cells. A tumor microenvironment is often hypoxic. As the tumor mass increases, the interior of the tumor grows farther away from existing blood supply, which leads to difficulties in fully supplying oxygen to the tumor microenvironment. As a result, the tumor cells tend to rely on energy generated from lactic acid fermentation, which does not require oxygen. As a consequence of using lactic acid fermentation is that the tumor microenvironment is acidic (approximately pH 6.0-6.9) in contrast to other parts of the body which are typically either neutral or slightly basic. For example, human blood plasma has a pH of about 7.4.
In some embodiments, P contains at least one histidine residue. In some embodiments, at physiological pH, at least one histidine residue of P forms a binding interaction with at least one amino acid residue of the antigen binding site of A. In some embodiments, at physiological pH, at least one histidine residue of P forms a binding interaction with at least one amino acid residue that is near the antigen binding site of A. In some embodiments, at acidic pH, at least one histidine residue of P forms a binding interaction with a glutamic acid or aspartic acid located on L.
In some embodiments, P contains more than one histidine residue. In some embodiments, P contains at least two histidine residues. In some embodiments, at physiological pH, at least two histidine residues of P form a binding interaction with an amino acid residue of the antigen binding site of A. In some embodiments, at physiological pH, at least two histidine residues of P form a binding interaction with an amino acid residue that is near the antigen binding site of A. In some embodiments, at physiological pH, at least two histidine residues of P form binding interactions with amino acid residues that are at or near the antigen binding site of A. In some embodiments, at acidic pH, at least two histidine residues of P form a binding interaction with a glutamic acid or aspartic acid located on L.
In some embodiments, P contains at least two charged amino acid residues. In some embodiments, P contains at least three charged amino acid residues. In some embodiments, the charged amino acid residues are selected from the group consisting of lysine, arginine, histidine, aspartate, and glutamate. In some embodiments, the charged amino acid residues are selected from the group consisting of glutamate, histidine, and aspartate. In some embodiments, P contains at least glutamate and histidine. In some embodiments, P contains histidine and aspartate. In some embodiments, P contains aspartate and glutamate. In some embodiments, P contains at least one histidine and at least two aspartate residues. In some embodiments, P contains at least two histidine and at least one glutamate residues. In some embodiments, P contains at least one histidine and at least two glutamate residues. In some embodiments, P contains at least two histidine and at least one aspartate residues.
In some embodiments, P contains at least two polar amino acid residues. In some embodiments, P contains at least three polar amino acids. In some embodiments, P contains at least four polar amino acids. In some embodiments, the polar amino acid residues are selected from the group consisting of serine, threonine, cysteine, asparagine, glutamine, and tyrosine. In some embodiments, P contains at least one glutamine. In some embodiments, P contains at least two glutamines. In some embodiments, P contains at least one glutamine and at least one serine. In some embodiments, P contains at least one glutamine and at least one cysteine. In some embodiments, P contains at least one glutamine and at least one asparagine. In some embodiments, P contains at least two glutamines and at least one threonine. In some embodiments, P contains at least two glutamines, and at least one asparagine. In some embodiments, P contains at least two glutamines, at least one asparagine, and at least one cysteine. In some embodiments, P contains at least two glutamines, at least one asparagine, at least one cysteine, and at least one threonine.
In some embodiments, P contains at least one cysteine. In some embodiments, P contains at least two cysteines. In some embodiments, P contains at least three cysteines.
In some embodiments, P contains at least one glutamine and at least one methionine. In some embodiments, P contains at least two glutamines and at least one methionine. In some embodiments, P contains at least two glutamines at least one methionine, and at least one threonine.
In some embodiments, P contains at least one charged amino acid residue and at least one polar amino acid residue. In some embodiments, P contains at least one charged amino acid residue and at least two polar amino acid residues. In some embodiments, P contains at least one charged amino acid residue and at least three polar amino acid residues. In some embodiments, P contains at least two charged amino acid residues and at least one polar amino acid residues. In some embodiments, P contains at least two charged amino acid residues and at least two polar amino acid residues. In some embodiments, P contains at least two charged amino acid residues and at least three polar amino acid residues. In some embodiments, P contains at least two charged amino acid residues and at least four polar amino acid residues. In some embodiments, P contains at least three charged amino acid residues and at least one polar amino acid residues. In some embodiments, P contains at least three charged amino acid residues and at least two polar amino acid residues. In some embodiments, P contains at least three charged amino acid residues and at least three polar amino acid residues. In some embodiments, P contains at least two histidine and at least two cysteine residues. In some embodiments, P contains at least three charged amino acid residues and at least two cysteines. In some embodiments, P contains at least one histidine, at least one serine, and at least one glutamine. In some embodiments, P contains at least one histidine, at least one asparagine, and at least one glutamine.
In some embodiments, P comprises the sequence of GGX, wherein X is cysteine, alanine, proline, methionine, histidine, or leucine. In some embodiments, P comprises the sequence GGC. In some embodiments, P comprises the sequence GGP. In some embodiments, P comprises the sequence GGA. In some embodiments, P comprises the sequence GGP. In some embodiments, P comprises the sequence GGM. In some embodiments, P comprises the sequence GGH. In some embodiments, P comprises the sequence GGL.
In some embodiments, P does not contain a tryptophan residue. In some embodiments, P does not contain an arginine residue. In some embodiments, P does not contain a lysine residue. In some embodiments, P does not contain a lysine residue or an arginine residue. In some embodiments, P does not contain a lysine residue, an arginine residue, or a tryptophan residue.
In some embodiments, P comprises at least one histidine, wherein at least one hydrogen bonding amino acid residue is within two amino acid positions to the histidine. In some embodiments, the hydrogen bonding amino acid residue is serine, threonine, tyrosine, asparagine, glutamine or a combination thereof.
In some embodiments, the hydrogen bonding amino acid residue is within one amino acid position to the histidine. In some embodiments, serine is within one amino acid position to the histidine. In some embodiments, threonine is within one amino acid position to the histidine. In some embodiments, tyrosine is within one amino acid position to the histidine. In some embodiments, asparagine is within one amino acid position to the histidine. In some embodiments, glutamine is within one amino acid position to the histidine.
In some embodiments, the hydrogen bonding amino acid residue is two amino acid positions away from the histidine. In some embodiments, serine is two amino acid positions away from the histidine. In some embodiments, threonine is two amino acid positions away from the histidine. In some embodiments, tyrosine is two amino acid positions away from the histidine. In some embodiments, asparagine is two amino acid positions away from the histidine. In some embodiments, glutamine is two amino acid positions away from the histidine.
In some embodiments, P contains at least one aromatic amino acid residue. In some embodiments, P contains at least two aromatic amino acid residues. In some embodiments, P contains phenylalanine and tyrosine. In some embodiments, the phenylalanine and the tyrosine are next to each other in the amino acid sequence of P. In some embodiments, P contains two phenylalanines. In some embodiments, the phenylalanines are next to each other in the amino acid sequence of P.
In some embodiments, P is a peptide sequence at least 5 amino acids in length. In some embodiments, P is a peptide sequence at least 6 amino acids in length. In some embodiments, P is a peptide sequence at least 10 amino acids in length. In some embodiments, P is a peptide sequence at least 20 amino acids in length. In some embodiments, P is resistant to cleavage by a protease.
In some embodiments, P is not a natural binding partner of A. In some embodiments, P does not comprise a mimotope. In some embodiments, P contains a random amino acid sequence that does not share any sequence homology to the natural binding partner of A. It is advantageous to use sequences that do not share any sequence homology to the natural binding partner of A to allow for greater flexibility in the peptide design. This allows for building a larger library of candidate peptide sequences for screening. In some instances, P is a modified binding partner for A which contains amino acid changes that at least slightly decrease affinity and/or avidity of binding to A. In some embodiments, P contains no or substantially no homology to A's natural binding partner. In some embodiments, P is no more than 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, or 80% similar to the natural binding partner of A.
In some embodiments, P comprises a modified amino acid or non-natural amino acid, or a modified non-natural amino acid, or a combination thereof. In some embodiments, the modified amino acid or a modified non-natural amino acid comprises a post-translational modification. In some embodiments P comprises a modification including, but not limited to acetylation, acylation, ADP-ribosylation, amidation, covalent attachment of flavin, covalent attachment of a heme moiety, covalent attachment of a nucleotide or nucleotide derivative, covalent attachment of a lipid or lipid derivative, covalent attachment of phosphatidylinositol, cross-linking, cyclization, disulfide bond formation, demethylation, formation of covalent crosslinks, formation of cystine, formation of pyroglutamate, formylation, gamma carboxylation, glycosylation, GPI anchor formation, hydroxylation, iodination, methylation, myristoylation, oxidation, proteolytic processing, phosphorylation, prenylation, racemization, selenoylation, sulfation, transfer-RNA mediated addition of amino acids to proteins such as arginylation, and ubiquitination. Modifications are made anywhere to P including the peptide backbone, the amino acid side chains, and the terminus.

Linking Moiety (L)

In some embodiments, L is a peptide sequence of at least 5 amino acid residues. In some embodiments, L is a peptide sequence of no more than 50 amino acids. Regarding the amino acid composition of L, peptides are selected with properties that confer flexibility and facilitate a conformational change of P during a change in pH.
In some embodiments, L comprises a peptide sequence with at least one histidine. In some embodiments, at acidic pH L is reversibly bound to P. In some embodiments, P comprises a peptide sequence with at least one aspartic acid or glutamic acid, or a combination thereof. In some embodiments, the histidine of L forms an interaction with the aspartic acid or glutamic acid of P.
In some embodiments, L is resistant to protease cleavage. For example, glycine and serine residues generally provide protease resistance. Examples of suitable linking moieties for connecting A or C to P include, but are not limited to (GS)_n, wherein n is an integer from 6 to 20 (SEQ ID NO: 1); (G₂S)_n, wherein n is an integer from 4 to 13 (SEQ ID NO: 2); (G₃S)_n, wherein n is an integer from 3 to 10 (SEQ ID NO: 3); and (G₄S)_n, wherein n is an integer from 2 to 8 (SEQ ID NO: 4); and (G)_n, wherein n is an integer from 12 to 40 (SEQ ID NO: 5). Additional examples include, but are not limited to, (GGGSGSGGGGS)_n, wherein n is an integer from 1 to 3 (SEQ ID NO: 6), or (GGGGGPGGGGP)_n, wherein n is an integer from 1 to 3 (SEQ ID NO: 7).
In some embodiments, L binds to P at acidic pH, for example, at a tumor microenvironment. In some embodiments, at acidic pH, L is reversibly bound to P. In some embodiments, the interaction of L and P at acidic pH is mediated through a histidine residue on P and a glutamic acid or aspartic acid residue on L. Examples of such linking moieties include, but are not limited to, (GGSGGD)_n, wherein n is an integer from 2 to 6 (SEQ ID NO: 8); or (GGSGGE)_n, wherein n is an integer from 2 to 6 (SEQ ID NO: 9).
In some embodiments, L has a formula comprising, (GS)_x(GGSGGD)_y(GS)_z, wherein x is an integer from 0 to 20, y is an integer from 2 to 6, and z is an integer from 0 to 20 (SEQ ID NO: 10). In some embodiments, L has a formula comprising, (G₂S)_x(GGSGGD)_y(G₂S)_z, wherein x is an integer from 0 to 13, y is an integer from 2 to 6, and z is an integer from 0 to 13 (SEQ ID NO: 11). In some embodiments, L has a formula comprising, (G₃S)_x(GGSGGD)_y(G₃S)_z, wherein x is an integer from 0 to 10, y is an integer from 2 to 6, and z is an integer from 0 to 10 (SEQ ID NO: 12). In some embodiments, L has a formula comprising, (G₄S)_x(GGSGGD)_y(G₄S)_z, wherein x is an integer from 0 to 8, y is an integer from 2 to 6, and z is an integer from 0 to 8 (SEQ ID NO: 13). In some embodiments, L has a formula comprising, (G)_x(GGSGGD)_y(G)_z, wherein x is an integer from 0 to 40, y is an integer from 2 to 6, and z is an integer from 0 to 40 (SEQ ID NO: 14). In some embodiments, L has a formula comprising, (GGGSGSGGGGS)_x(GGSGGD)_y(GGGSGSGGGGS)_z, wherein x is an integer from 0 to 3, y is an integer from 2 to 6, and z is an integer from 0 to 3 (SEQ ID NO: 15). In some embodiments, L has a formula comprising, (GGGSGSGGGGP)_x(GGSGGD)_y(GGGSGSGGGGP)_z, wherein x is an integer from 0 to 3, y is an integer from 2 to 6, and z is an integer from 0 to 3 (SEQ ID NO: 16).
In some embodiments, L has a formula comprising, (GS)_x(GGSGGE)_y(GS)_z, wherein x is an integer from 0 to 20, y is an integer from 2 to 6, and z is an integer from 0 to 20 (SEQ ID NO: 17). In some embodiments, L has a formula comprising, (G₂S)_x(GGSGGE)_y(G₂S)_z, wherein x is an integer from 0 to 13, y is an integer from 2 to 6, and z is an integer from 0 to 13 (SEQ ID NO: 18). In some embodiments, L has a formula comprising, (G₃S)_x(GGSGGE)_y(G₃S)_z, wherein x is an integer from 0 to 10, y is an integer from 2 to 6, and z is an integer from 0 to 10 (SEQ ID NO: 19). In some embodiments, L has a formula comprising, (G₄S)_x(GGSGGE)_y(G₄S)_z, wherein x is an integer from 0 to 8, y is an integer from 2 to 6, and z is an integer from 0 to 8 (SEQ ID NO: 20). In some embodiments, L has a formula comprising, (G)_x(GGSGGE)_y(G)_z, wherein x is an integer from 0 to 40, y is an integer from 2 to 6, and z is an integer from 0 to 40 (SEQ ID NO: 21). In some embodiments, L has a formula comprising, (GGGSGSGGGGS)_x(GGSGGE)_y(GGGSGSGGGGS)_z, wherein x is an integer from 0 to 3, y is an integer from 2 to 6, and z is an integer from 0 to 3 (SEQ ID NO: 22). In some embodiments, L has a formula comprising, (GGGSGSGGGGP)_x(GGSGGE)_y(GGGSGSGGGGP)_z, wherein x is an integer from 0 to 3, y is an integer from 2 to 6, and z is an integer from 0 to 3 (SEQ ID NO: 23).
Additional examples of linking moieties include, but are not limited to wherein L has a formula selected from (GX)_n, wherein X is serine, aspartic acid, glutamic acid, threonine, or proline and n is at least 20 (SEQ ID NO: 24); (GGX)_n, wherein X is serine, aspartic acid, glutamic acid, threonine, or proline and n is at least 13 (SEQ ID NO: 25); (GGGX)_n, wherein X is serine, aspartic acid, glutamic acid, threonine, or proline and n is at least 10 (SEQ ID NO: 26); (GGGGX)_n, wherein X is serine, aspartic acid, glutamic acid, threonine, or proline and n is at least 8 (SEQ ID NO: 27); (G_zX)_n, wherein X is serine, aspartic acid, glutamic acid, threonine, or proline and n is at least 15, and z is between 1 and 20 (SEQ ID NO: 28).
In some embodiments, L comprises a modified amino acid or non-natural amino acid, or a modified non-natural amino acid, or a combination thereof. In some embodiments, the modified amino acid or a modified non-natural amino acid comprises a post-translational modification. In some embodiments L comprises a modification including, but not limited, to acetylation, acylation, ADP-ribosylation, amidation, covalent attachment of flavin, covalent attachment of a heme moiety, covalent attachment of a nucleotide or nucleotide derivative, covalent attachment of a lipid or lipid derivative, covalent attachment of phosphatidylinositol, cross-linking, cyclization, disulfide bond formation, demethylation, formation of covalent crosslinks, formation of cystine, formation of pyroglutamate, formylation, gamma carboxylation, glycosylation, GPI anchor formation, hydroxylation, iodination, methylation, myristoylation, oxidation, proteolytic processing, phosphorylation, prenylation, racemization, selenoylation, sulfation, transfer-RNA mediated addition of amino acids to proteins such as arginylation, and ubiquitination. Modifications are made anywhere to L including the peptide backbone, or the amino acid side chains.

Antibody or Antibody Fragments (A)

In some embodiments, A is a full length antibody, a single-chain antibody, a Fab Fragment, an Fab′ fragment, an (Fab′)2 fragment, an Fv fragment, a divalent single chain antibody, a bispecific antibody, trispecific antibody, tetraspecific antibody, or an antibody drug conjugate.
In some embodiments A is an antagonist, agonist, conditionally active antibody, or a sweeping body.
In some embodiments, A is an antibody or antibody fragment including, but not limited to, utomilumab, urelumab, ipilimumab, tremelimumab, pembrolizumab, nivolumab, and atezolizumab. In some embodiments, A is utomilumab. In some embodiments, A is urelumab. In some embodiments, A is ipilimumab. In some embodiments, A is tremelimumab. In some embodiments, A is pembrolizumab. In some embodiments, A is nivolumab. In some embodiments, A is atezolizumab.
In some embodiments, A binds to a target antigen. In some embodiments, the target antigen includes, but is not limited to, 4-1BB, CTLA4, PD-1, and PD-L1. In some embodiments, the target antigen is 4-1BB. In some embodiments, the target antigen is CTLA4. In some embodiments, the target antigen is PD-1. In some embodiments, the target antigen is PD-L1.
In some embodiments, A contains a modification so as to increase the bioavailability, improve stability, or solubility of the modified antibody. In some embodiments, A is conjugated to polyethylene glycol, polysialic acid (PSA), HPMA copolymer, dextran, albumin, a glycosyl group or a combination thereof.
In some embodiments, A comprises a modified amino acid or non-natural amino acid, or a modified non-natural amino acid, or a combination thereof. In some embodiments, the modified amino acid or a modified non-natural amino acid comprises a post-translational modification. In some embodiments A comprises a modification including, but not limited to acetylation, acylation, ADP-ribosylation, amidation, covalent attachment of flavin, covalent attachment of a heme moiety, covalent attachment of a nucleotide or nucleotide derivative, covalent attachment of a lipid or lipid derivative, covalent attachment of phosphatidylinositol, cross-linking, cyclization, disulfide bond formation, demethylation, formation of covalent crosslinks, formation of cystine, formation of pyroglutamate, formylation, gamma carboxylation, glycosylation, GPI anchor formation, hydroxylation, iodination, methylation, myristoylation, oxidation, proteolytic processing, phosphorylation, prenylation, racemization, selenoylation, sulfation, transfer-RNA mediated addition of amino acids to proteins such as arginylation, and ubiquitination. Modifications are made anywhere to A including the peptide backbone, the amino acid side chains, or the termini or terminus.

Modified Antibodies (A-L-P)

Disclosed herein, in certain embodiments, are modified antibodies comprising a formula:
A-L-P
wherein A is an antibody or antibody fragment that binds to a target antigen, P is a peptide that reduces binding of A to the target antigen at physiological pH, and that does not reduce binding of A to the target antigen at acidic pH, and L is a linking moiety that connects A to P at physiological pH and in a tumor microenvironment, and L is bound to A outside an antigen binding site.
In some embodiments, A-L-P does not comprise a protease cleavage site that releases A from P in a tumor microenvironment. It is advantageous that L and P are not cleaved from the molecule so that P can bind and re-bind to A depending upon the microenvironment. For example, in a tumor microenvironment, P is not bound to A thereby exposing the antigen binding site of A to its target antigen. However, because P is not cleaved from the molecule in the tumor microenvironment, if A-L-P were to then diffuse into a non-tumor microenvironment, P can then resume binding interactions with A, thereby preventing A from interacting with its target antigen in the non-tumor microenvironment.
In some embodiments, the modified antibodies disclosed herein comprise more than one P, one for each region of the antibody that contains the antigen binding site, connected to A by L. In some instances, L for each of the Ps is the same. In some instances, L for each of the P is different. In some embodiments, the Ps for each region of the antibody that contains the antigen binding site is the same. In some embodiments, the Ps for each region of the antibody that contains the antigen binding site is different. In some embodiments, the modified antibodies disclosed herein comprise one P.
In some embodiments, P is not a natural binding partner of A. In some embodiments, P does not comprise a mimotope. In some embodiments, P contains a random amino acid sequence that does not share any sequence homology to the natural binding partner of A. It is advantageous to use sequences that do not share any sequence homology to the natural binding part of A to allow for greater flexibility in the peptide design. This allows for building a larger library of candidate peptide sequences for screening.
In some embodiments, the target antigen to which the antibody or antibody fragment (A) binds is CTLA4, peptide (P) is Peptide 15, and linking moiety (L) is GSSGGSGGSGGSGGGSGGGSGGSSGT (SEQ ID NO: 60). In some embodiments, the target antigen to which the antibody or antibody fragment (A) binds is CTLA4, peptide (P) is Peptide 10, and linking moiety (L) is GSSGGSGGSGGSGGGSGGGSGGSSGT (SEQ ID NO: 60). In some embodiments, the target antigen to which the antibody or antibody fragment (A) binds is CTLA4, peptide (P) is Peptide 13, and linking moiety (L) is GSSGGSGGSGGSGGGSGGGSGGSSGT (SEQ ID NO: 60). In some embodiments, the target antigen to which the antibody or antibody fragment (A) binds is CTLA4, peptide (P) is Peptide 26, and linking moiety (L) is GSSGGSGGSGGSGGGSGGGSGGSSGT (SEQ ID NO: 60). In some embodiments, the target antigen to which the antibody or antibody fragment (A) binds is CTLA4, peptide (P) is Peptide 14, and linking moiety (L) is GSSGGSGGSGGSGGGSGGGSGGSSGT (SEQ ID NO: 60). In some embodiments, the target antigen to which the antibody or antibody fragment (A) binds is CTLA4, peptide (P) is Peptide 1, and linking moiety (L) is GSSGGSGGSGGSGGGSGGGSGGSSGT (SEQ ID NO: 60). In some embodiments, the target antigen to which the antibody or antibody fragment (A) binds is CTLA4, peptide (P) is Peptide 2, and linking moiety (L) is GSSGGSGGSGGSGGGSGGGSGGSSGT (SEQ ID NO: 60). In some embodiments, the target antigen to which the antibody or antibody fragment (A) binds is CTLA4, peptide (P) is Peptide 5, and linking moiety (L) is GSSGGSGGSGGSGGGSGGGSGGSSGT (SEQ ID NO: 60). In some embodiments, the target antigen to which the antibody or antibody fragment (A) binds is CTLA4, peptide (P) is Peptide 6, and linking moiety (L) is GSSGGSGGSGGSGGGSGGGSGGSSGT (SEQ ID NO: 60).
In some embodiments, the antibody or antibody fragment (A) that binds to a target antigen is Atezolizumab, peptide (P) is Peptide 23, and linking moiety (L) is GSSGGSGGSGGSGGGSGGGSGGSSGT (SEQ ID NO: 60). In some embodiments, the antibody or antibody fragment (A) that binds to a target antigen is Atezolizumab, peptide (P) is Peptide 27, and linking moiety (L) is GSSGGSGGSGGSGGGSGGGSGGSSGT (SEQ ID NO: 60). In some embodiments, the antibody or antibody fragment (A) that binds to a target antigen is Atezolizumab, peptide (P) is Peptide 22, and linking moiety (L) is GSSGGSGGSGGSGGGSGGGSGGSSGT (SEQ ID NO: 60). In some embodiments, the antibody or antibody fragment (A) that binds to a target antigen is Atezolizumab, peptide (P) is Peptide 31, and linking moiety (L) is GSSGGSGGSGGSGGGSGGGSGGSSGT (SEQ ID NO: 60). In some embodiments, the antibody or antibody fragment (A) that binds to a target antigen is Atezolizumab, peptide (P) is Peptide 20, and linking moiety (L) is GSSGGSGGSGGSGGGSGGGSGGSSGT (SEQ ID NO: 60). In some embodiments, the antibody or antibody fragment (A) that binds to a target antigen is Atezolizumab, peptide (P) is Peptide 21, and linking moiety (L) is GSSGGSGGSGGSGGGSGGGSGGSSGT (SEQ ID NO: 60). In some embodiments, the antibody or antibody fragment (A) that binds to a target antigen is Atezolizumab, peptide (P) is Peptide 28, and linking moiety (L) is GSSGGSGGSGGSGGGSGGGSGGSSGT (SEQ ID NO: 60). In some embodiments, the antibody or antibody fragment (A) that binds to a target antigen is Atezolizumab, peptide (P) is Peptide 29, and linking moiety (L) is GSSGGSGGSGGSGGGSGGGSGGSSGT (SEQ ID NO: 60). In some embodiments, the antibody or antibody fragment (A) that binds to a target antigen is Atezolizumab, peptide (P) is Peptide 30, and linking moiety (L) is GSSGGSGGSGGSGGGSGGGSGGSSGT (SEQ ID NO: 60). In some embodiments, the antibody or antibody fragment (A) that binds to a target antigen is Atezolizumab, peptide (P) is Peptide 24, and linking moiety (L) is GSSGGSGGSGGSGGGSGGGSGGSSGT (SEQ ID NO: 60).
In some embodiments, the target antigen to which the antibody or antibody fragment (A) binds is PD-L1, peptide (P) is Peptide 23, and linking moiety (L) is GSSGGSGGSGGSGGGSGGGSGGSSGT (SEQ ID NO: 60). In some embodiments, the target antigen to which the antibody or antibody fragment (A) binds is PD-L1, peptide (P) is Peptide 27, and linking moiety (L) is GSSGGSGGSGGSGGGSGGGSGGSSGT (SEQ ID NO: 60). In some embodiments, the target antigen to which the antibody or antibody fragment (A) binds is PD-L1, peptide (P) is Peptide 22, and linking moiety (L) is GSSGGSGGSGGSGGGSGGGSGGSSGT (SEQ ID NO: 60). In some embodiments, the target antigen to which the antibody or antibody fragment (A) binds is PD-L1, peptide (P) is Peptide 31, and linking moiety (L) is GSSGGSGGSGGSGGGSGGGSGGSSGT (SEQ ID NO: 60). In some embodiments, the target antigen to which the antibody or antibody fragment (A) binds is PD-L1, peptide (P) is Peptide 20, and linking moiety (L) is GSSGGSGGSGGSGGGSGGGSGGSSGT (SEQ ID NO: 60). In some embodiments, the target antigen to which the antibody or antibody fragment (A) binds is PD-L1, peptide (P) is Peptide 21, and linking moiety (L) is GSSGGSGGSGGSGGGSGGGSGGSSGT (SEQ ID NO: 60). In some embodiments, the target antigen to which the antibody or antibody fragment (A) binds is PD-L1, peptide (P) is Peptide 28, and linking moiety (L) is GSSGGSGGSGGSGGGSGGGSGGSSGT (SEQ ID NO: 60). In some embodiments, the target antigen to which the antibody or antibody fragment (A) binds is PD-L1, peptide (P) is Peptide 29, and linking moiety (L) is GSSGGSGGSGGSGGGSGGGSGGSSGT (SEQ ID NO: 60). In some embodiments, the target antigen to which the antibody or antibody fragment (A) binds is PD-L1, peptide (P) is Peptide 30, and linking moiety (L) is GSSGGSGGSGGSGGGSGGGSGGSSGT (SEQ ID NO: 60). In some embodiments, the target antigen to which the antibody or antibody fragment (A) binds is PD-L1, peptide (P) is Peptide 24, and linking moiety (L) is GSSGGSGGSGGSGGGSGGGSGGSSGT (SEQ ID NO: 60).

Polynucleotides Encoding Modified Antibodies

Also provided, in some embodiments, are polynucleotide molecules encoding a modified antibody described herein. In some embodiments, the polynucleotide molecules are provided as a DNA construct. In other embodiments, the polynucleotide molecules are provided as a messenger RNA transcript.
The polynucleotide molecules are constructed by known methods such as by combining the genes encoding the domains either separated by peptide linkers or, in other embodiments, directly linked by a peptide bond, into a single genetic construct operably linked to a suitable promoter, and optionally a suitable transcription terminator, and expressing it in bacteria or other appropriate expression system such as, for example CHO cells. Depending on the vector system and host utilized, any number of suitable transcription and translation elements, including constitutive and inducible promoters, may be used. The promoter is selected such that it drives the expression of the polynucleotide in the respective host cell.
In some embodiments, the polynucleotide is inserted into a vector, preferably an expression vector, which represents a further embodiment. This recombinant vector can be constructed according to known methods. Vectors of particular interest include plasmids, phagemids, phage derivatives, virii (e.g., retroviruses, adenoviruses, adeno-associated viruses, herpes viruses, lentiviruses, and the like), and cosmids.
A variety of expression vector/host systems may be utilized to contain and express the polynucleotide encoding the polypeptide of the described antigen-binding protein. Examples of expression vectors for expression in E. coli are pSKK (Le Gall et al., J Immunol Methods. (2004) 285(1):111-27) or pcDNA5 (Invitrogen) for expression in mammalian cells.
Thus, the modified antibodies as described herein, in some embodiments, are produced by introducing a vector encoding the protein as described above into a host cell and culturing said host cell under conditions whereby the protein domains are expressed, may be isolated and, optionally, further purified.

Pharmaceutical Compositions

Also provided, in some embodiments, are pharmaceutical compositions comprising a modified antibody described herein, a vector comprising the polynucleotide encoding the polypeptide of the modified antibody or a host cell transformed by this vector and at least one pharmaceutically acceptable carrier. The term “pharmaceutically acceptable carrier” includes, but is not limited to, any carrier that does not interfere with the effectiveness of the biological activity of the ingredients and that is not toxic to the patient to whom it is administered. Examples of suitable pharmaceutical carriers include phosphate buffered saline solutions, water, emulsions, such as oil/water emulsions, various types of wetting agents, sterile solutions etc. Such carriers can be formulated by conventional methods and can be administered to the subject at a suitable dose. Preferably, the compositions are sterile. These compositions may also contain adjuvants such as preservative, emulsifying agents and dispersing agents. Prevention of the action of microorganisms may be ensured by the inclusion of various antibacterial and antifungal agents.
In some embodiments of the pharmaceutical compositions, the modified antibody described herein is encapsulated in nanoparticles. In some embodiments, the nanoparticles are fullerenes, liquid crystals, liposome, quantum dots, superparamagnetic nanoparticles, dendrimers, or nanorods. In other embodiments of the pharmaceutical compositions, the modified antibody, is attached to liposomes. In some instances, the modified antibody is conjugated to the surface of liposomes. In some instances, the modified antibody is encapsulated within the shell of a liposome. In some instances, the liposome is a cationic liposome.
The modified antibodies described herein are contemplated for use as a medicament. Administration is effected by different ways, e.g. by intravenous, intraperitoneal, subcutaneous, intramuscular, topical or intradermal administration. In some embodiments, the route of administration depends on the kind of therapy and the kind of compound contained in the pharmaceutical composition. The dosage regimen will be determined by the attending physician and other clinical factors. Dosages for any one patient depends on many factors, including the patient's size, body surface area, age, sex, the particular compound to be administered, time and route of administration, the kind of therapy, general health and other drugs being administered concurrently. An “effective dose” refers to amounts of the active ingredient that are sufficient to affect the course and the severity of the disease, leading to the reduction or remission of such pathology and may be determined using known methods.
Methods for Discovering Modified Antibodies that are Conditionally Active at Tumor Microenvironments
Disclosed herein, in some embodiments, are methods for identifying peptides which reduce binding of the modified antibody to its target antigen when at physiological pH but do not affect target antigen binding at acidic pH.
In some embodiments, a modified antibody is tested for binding to a target antigen at a range of pH, from about pH 3 to about pH 12. In a further aspect, the testing step further includes testing for antigen binding within a pH range from about pH 5 to pH 10. In a further aspect, the testing step includes testing for antigen binding within a pH range from about pH 6 to pH 8. In a further aspect, the testing step further includes testing for antigen binding within a pH range from about pH 6.7 to pH 7.5.
In additional embodiments, P is identified by directed evolution techniques. In some embodiments, P is engineered to introduce one, two, or more ionizable groups which interact at protein-protein interfaces. Such ionizable groups, for example, interact with A at the antigen binding site or near the antigen binding site at physiological pH to block binding of A to its target antigen. Such ionizable groups, for example, are engineered into P using a histidine scanning library approach.

Methods for Generating Modified Antibodies

Methods for generating an antibody (or fragment thereof) for a given target are known in the art. The structure of antibodies and fragments thereof, variable regions of heavy and light chains of an antibody (VH and VL) Fv, F(ab′)2, Fab fragments, single chain antibodies (scAb), single chain variable regions (scFv), complementarity determining regions (CDR), and domain antibodies (dAbs) are well understood. Methods for generating a polypeptide having a desired antigen-binding domain of a target antigen are known in the art.
Methods for modifying antibodies or antibody fragments to couple additional polypeptides are known in the art. For example, peptides and linking moieties are coupled to modify antibodies to generate the modified antibodies of the disclosure.
In some embodiments, A, L, and P are expressed in a nucleic acid construct. In some embodiments, A, L, and P are expressed in the same nucleic acid construct. In some instances, the nucleic acid constructs include, but are not limited to, constructs which are capable of expression in a prokaryotic or eukaryotic cell.
In some embodiments, P is coupled to L and A through covalent binding. For example, A and L are expressed as a single transcript, and the terminal residue of L is a cysteine. P is then coupled to L and A by a cysteine-cysteine disulfide bridge.

EXAMPLES

Example 1

Screening of Candidate Peptides

To identify peptides for conjugation to or expression with an antibody of interest, a library of candidate peptides are generated. The candidate peptides have variable amino acid sequences and variable amino acid lengths. The candidate peptides are then screened for their ability to bind to the antibody of interest at pH 7.4 and at pH 6.0. Those candidate peptides that bind to the antibody of interest at pH 6.0 are eliminated. Candidate peptides that bind to the antibody of interest at pH 7.4, but not at pH 6.0, are sequenced and motifs are analyzed.

Example 2

Screening of Modified Antibody Libraries

Libraries of candidate modified antibodies having different amino acid sequences in the peptide and linker lengths and various points of attachment to the antibody are generated.
The libraries are introduced via expression vectors resulting in display of the modified antibodies on the surface of bacterial cells. After expansion of the libraries by culture, cells displaying the modified antibodies are tested for their abilities to bind to target antigens at pH 7.4 and at pH 6.0. Cells are contacted with fluorescently labeled target antigen and the cells are sorted by FACs to isolate those cells which can bind to the fluorescently labeled target antigen at pH 6.0, but not at pH 7.4. The cells can be subjected to additional cycles by expansion by growth in culture and again by subjecting the culture to all or part of the screening steps.

Example 3

In Vitro Screening of a Modified Antibody for pH Dependent Binding Affinity for its Target Antigen

An immunoabsorbant target displacement assay (TDA) is described herein for discovery and validation of a modified antibody for selective binding to its target antigen at an acidic pH. In the TDA assay, the ability of a modified antibody to bind to its target antigen is measured. The assay is conducted at pH 7.4, and then repeated at pH 6.0.
Briefly, the target antigen is adsorbed to the wells of an ELISA plate overnight at 4° C. The plate is blocked by addition of 2% non-fat dry milk in PBS, about 0.5% (v/v) Tween20 (PBST), and incubation at room temperature for about 1 hour. The plate is then washed about three times with PBST. About 50 μl of superblock is added. About 50 μl of the modified antibody is dissolved in superblock and incubated at about 37° C. for different periods of time. The plate is washed about three times with PBST. About 100 ml of anti-huIgG-HRP is added in about 2% NEM/PBST and incubated at room temperature for about 1 hour. The plate is washed about four times with PBST and about twice with PBS. The assay is developed using TMB (Thermo Scientific) as per manufacturer's instructions.

Example 4

Cytotoxicity Assay for Assessing pH Dependent Selectivity of Modified Antibodies

Modified antibodies are selected which demonstrate binding to its target antigen at pH 6.0, but with minimal or no binding to its target antigen at pH 7.4 conditions. A candidate antibody, and a peptide-modified candidate antibody validated in Example 3, is tested in a cell based cytotoxicity assay.
Cell Culture: A549 (human epithelial cell line derived from a lung carcinoma tissue), or an alternative cancer cell line (DU145, LNCaP, or PC-3 cells) can be obtained from, for example, the ATCC. Human umbilical vein endothelial cells (HUVEC) can be isolated from human umbilical veins as described. (Grant et al., “Matrigel induces thymosin h 4 gene in differentiating endothelial cells”, J Cell Sci 1995; 108:3685-94). HUVEC cells can be used as a positive control as a cell line that express ATP synthase on the cell surface. Cells can be cultured in DMEM (Life Technologies, Carlsbad, Calif.) with 1% penicillin streptomycin and 10% serum replacement medium 3 (Sigma, St. Louis, Mo.) to minimize the presence of plasminogen. Low-pH (6.7) medium can be prepared by reducing bicarbonate to 10 mmol/L at 5% CO2 and supplementing with 34 mmol/L NaCl to maintain osmolality or incubation of 22 mmol/L bicarbonate medium under 17% CO2 conditions. The method of lowering pH used can be varied by experimental constraints and assay.
Flow cytometry: To assure ATP synthase is functional on the cell surface of the tumor cell line, flow cytometry experiments can be performed. For example, A549 Cell lines can be cultured in varying pH medium (10, 22, and 44 mmol/L bicarbonate DMEM), under hypoxia (0.5% 02, 5% CO2, N2 balanced) versus normoxia (21% O2, 5% CO2) for 0, 12, 24, 48, and 72 hours. Live cells can be blocked, incubated with anti-β-subunit antibody, washed, blocked, incubated with a secondary goat anti-rabbit antibody-FITC (Southern Biotech, Birmingham, Ala.), and again washed, with all steps performed at 4 degrees C. Propidium iodide (BD Biosciences, San Jose, Calif.) can be included with all samples to discriminate cells with compromised membranes. The mean fluorescent intensity of FITC in 10,000 cells can be quantified by FACSCalibur flow cytometer (Becton Dickinson, Franklin Lakes, N.J.) and cells with propidium iodide uptake can be excluded to eliminate detection of mitochondrial ATP synthase on CELLQuest software (BD Biosciences).
Cell surface ATP generation assay: A549 or 1-LN cells (60,000 per well) in 96-well plates can be refreshed with medium and treated with a candidate antibody, a peptide-modified candidate antibody, anti-beta-subunit antibody, rabbit IgG raised to bovine serum albumin (Organon Teknika, West Chester, Pa.), piceatannol (a known inhibitor of ATP synthase F1 used as a positive control, Sigma), or medium alone for 30 minutes at 37 degrees C., 5% CO2. Cells can be then incubated with 0.05 mmol/L ADP for 20 seconds. Supernatants can be removed and assayed for ATP production by CellTiterGlo luminescence assay (Promega, Madison, Wis.) as described (23). Cell lysates can be similarly analyzed to confirm that intracellular pools of ATP did not vary under any conditions. Recordings can be made on the Luminoskan Ascent (Thermo Labsystems, Helsinki, Finland). Data are expressed in moles of ATP per cell based on standards determined for each independent experiment.
Cell proliferation assay: The effect of the candidate modified antibody on cancer cell lines can be assessed with a 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium, inner salt (MTS) proliferation assay in serum-free medium. Relative cell numbers in each well of a 96-well microplate after incubation for 20 hours, 37 degrees C., and 5% CO₂in the presence or absence of the candidate antibody can be determined using the AQueous One Cell Proliferation Assay (Promega) per protocol of the manufacturer. Medium pH can be regulated at 5% CO₂through bicarbonate concentration.
Assessment of cellular cytotoxicity: To quantify cell death and cell lysis, the activity of lactate dehydrogenase (LDH) released from the cytosol into supernatant can be measured with the Cytotoxicity Detection kit (Roche, Indianapolis, Ind.). Cancer cells (e.g. A549 cells) (5,000 per well) treated with a candidate antibody, a peptide-modified candidate antibody, anti-beta-subunit antibody, rabbit IgG, cariporide, and Triton X (a detergent used to permeabilize cells as a positive control) can be incubated at 37 degrees C. and 5% CO₂or 17% CO₂for 15 hours at neutral and low pH conditions, respectively. An index of cytotoxicity can be calculated by dividing the average absorbance from treated samples in quadruplicate by the average absorbance from untreated samples in quadruplicate corresponding to the same pH medium.
Assessment of cellular necrosis and apoptosis: To determine the mode of candidate antibody induced cell death a histone-DNA ELISA can be performed. The effects of a candidate antibody, a peptide-modified candidate antibody, anti-beta-subunit antibody, rabbit IgG, and cariporide on A549 cells (5,000 per well) can be determined using an ELISA apoptosis and necrosis assay (Roche) that is dependent on detection of extranuclear histone-DNA fragments. Apoptosis or necrosis can be determined from, respectively, the cell lysates or supernatants of quadruplicate samples after 15 hours of incubation at 37 degrees C., in the presence or absence of agents. The apoptotic or necrotic indices can be calculated by dividing the average absorbance from treated samples in quadruplicate by the average absorbance from untreated samples in quadruplicate corresponding to the same pH medium. Medium pH can be regulated by incubation at 5% CO2 or 17% CO₂.

Example 5

Biopanning

Biopanning with m13 phagemid p8 or p3 displayed peptide libraries was either performed with Fc immobilized anti-mouse CTLA-4 antibody (clone 9D9) on 96-well ELISA plates or with biotin-conjugated antibody immobilized on streptavidin coated paramagnetic beads. Following binding to target and washing steps, specifically bound phage were recovered by elution at pH 2.2 and in some instances recovery occurred through the use of acidic buffers of higher pH levels. Enrichment of specific binding clones was accomplished by 3-4 rounds of successive biopanning and amplification. After 3 or 4 rounds of biopanning phage pools were infected into TG1 cells and plated out on LB-ampicillin/agar plates for clonal isolation and subsequent characterization.

Example 6

Phagemid Hit Identification ELISA

For hit identification, individual colonies were grown in 96-deep well plates for 2-4 hours and infected with helper phage to produce peptide displayed phagemid following an overnight growth. The next day the deep well plates were centrifuged to separate the soluble phagemid from the E. coli cells. The phagemid containing supernatants were then combined with PBS-Tween 20 (0.05%)+BSA (1%) pH neutral blocking buffer and incubated in previously antibody (anti-mouse CTLA-4, clone 9D9) coated and blocked wells. After binding at 4 degrees the plates were washed and specifically bound phage were detected by anti-m13 HRP conjugated antibodies using standard TMB-based chromogenic ELISA procedures. Daughter plates or individual wells were subjected to standard DNA sequencing for peptide identification.

Example 7

Phagemid Competition ELISA Assay

Phagemid peptide clones were next tested to determine whether they bound within the antigen binding space of the antibody, by target-based competition assay. Antibody (anti-mouse CTLA-4, clone 9D9) immobilized and blocked 96-well ELISA plates similar to above were prepared. Mouse CTLA-4 was added to the well to block the antigen binding site. After a brief incubation period phagemid supernatants were added to the wells. Following an incubation at 4 degrees the plates were washed and specifically bound phage were detected by anti-m13 HRP conjugated antibodies using standard TMB-based chromogenic ELISA procedures. Phagemid clones binding within the antigenic binding pocket would be blocked and be identified by a decreased ELISA signal, compared to a well lacking previous antigen blockade.

Example 8

Phagemid pH “Binding” ELISA

To assess the pH dependent binding attributes of each of the individual clones, an ELISA similar to that described above was performed, but instead of combining the supernatants into pH neutral buffers they were combined with acidic pH buffered blocking buffer to achieve acidic pH levels such as pH 5.4 and then transferred into antibody (anti-mouse CTLA-4, clone 9D9) coated and blocked wells. Following incubation at 4 degrees the plates were washed and then all subsequent steps buffers used were neutral pH. As before, the specifically bound phage were similarly detected by anti-m13 HRP conjugated antibodies using standard TMB-based chromogenic ELISA procedures.
Table 2 below shows the ELISA results for pH-dependent phagemid 9D9 Antibody binding.

TABLE 2

pH-dependent phagemid 9D9 Antibody binding ELISA.

			ELISA
	Plate	ELISA signal	signal Ratio

	wells	pH 7.2	pH 5.4	5.4:7.2

A07	2.173	1.546	0.712
B07	0.567	0.177	0.312
C07	1.700	0.799	0.470
D07	1.753	1.136	0.648
E07	0.501	0.219	0.436
F07	0.477	0.054	0.113
G07	0.738	0.062	0.084
H07	1.687	1.096	0.650
A08	1.616	0.215	0.133
B08	0.125	0.045	0.359
C08	1.956	1.222	0.625
D08	1.004	0.278	0.276
E08	1.153	0.119	0.103
F08	2.415	1.651	0.684
G08	2.291	2.037	0.889
H08	1.099	0.539	0.491
A09	0.837	0.329	0.392
B09	2.283	1.836	0.804
C09	1.352	0.220	0.162
D09	1.055	0.260	0.247
E09	0.538	0.059	0.110
F09	0.949	0.264	0.278
G09	1.266	0.516	0.408
H09	0.422	0.066	0.156
A10	1.088	0.304	0.279
B10	1.147	0.495	0.431
C10	1.530	0.234	0.153
D10	1.842	1.105	0.600
E10	0.844	0.276	0.327
F10	2.154	1.645	0.764
G10	1.034	0.375	0.363
H10	0.425	0.174	0.409
A11	0.626	0.217	0.347
B11	0.851	0.306	0.360
C11	0.861	0.181	0.211
D11	1.358	0.570	0.420
E11	0.990	0.430	0.434
F11	1.699	0.958	0.564
G11	0.053	0.049	0.915
H11	2.369	2.110	0.891
A12	0.518	0.257	0.496
B12	0.331	0.148	0.447
C12	0.295	0.049	0.168
D12	1.103	0.208	0.189
E12	1.263	0.246	0.195
F12	0.593	0.283	0.478
G12	1.064	0.432	0.406
H12	3.031	1.749	0.577

Example 9

Phagemid “Dissociation” Assay

To determine pH dependent dissociation attributes of the individual phagemid displayed peptides, an ELISA similar to that described above was performed. Phagemid supernatants were combined with neutral pH PBS-Tween 20, BSA containing blocking buffer and then transferred into antibody (anti-mouse CTLA-4, clone 9D9) coated and blocked wells. After binding at 4 degrees the plates were washed extensively. In the next step the phage were incubated with either neutral or acidic pH buffers, such as pH 5.4 for approximately 30 minutes and then washed again at neutral pH. As described previously the specifically bound phage were similarly detected by anti-m13 HRP conjugated antibodies using standard TMB-based chromogenic ELISA procedures.
Table 3 below shows the ELISA results for pH-dependent phagemid 9D9 Antibody dissociation.

TABLE 3

pH-dependent phagemid 9D9 Antibody dissociation ELISA.

ELISA signal

	Plate wells	pH 7.2	pH 5.4	Ratio 5.4:7.2

A07	1.996	2.054	1.029
B07	0.578	0.377	0.652
C07	1.681	1.487	0.885
D07	1.851	1.775	0.959
E07	0.474	0.444	0.937
F07	0.400	0.063	0.156
G07	0.633	0.072	0.113
H07	1.611	1.541	0.956
A08	1.449	0.494	0.341
B08	0.113	0.043	0.386
C08	1.948	1.818	0.933
D08	0.947	0.575	0.607
E08	1.068	0.182	0.170
F08	2.421	1.986	0.820
G08	2.305	2.250	0.976
H08	1.007	0.980	0.974
A09	0.747	0.689	0.922
B09	2.372	2.129	0.897
C09	1.302	0.388	0.298
D09	0.987	0.617	0.625
E09	0.477	0.072	0.150
F09	0.866	0.556	0.642
G09	1.169	1.022	0.874
H09	0.302	0.054	0.179
A10	0.964	0.542	0.562
B10	1.250	0.833	0.666
C10	1.507	0.346	0.230
D10	1.896	1.815	0.957
E10	0.755	0.524	0.694
F10	2.184	2.180	0.998
G10	0.984	0.918	0.933
H10	0.371	0.354	0.955
A11	0.562	0.468	0.831
B11	0.928	0.714	0.770
C11	0.651	0.467	0.717
D11	1.383	0.978	0.707
E11	0.912	0.919	1.008
F11	1.581	1.595	1.009
G11	0.049	0.042	0.862
H11	2.382	2.320	0.974
A12	0.474	0.457	0.964
B12	0.380	0.278	0.732
C12	0.283	0.048	0.169
D12	1.055	0.266	0.252
E12	1.159	0.363	0.313
F12	0.505	0.490	0.969
G12	0.857	0.745	0.870
H12	2.366	0.184	0.078

Example 10

Peptide Antibody Dissociation

To determine pH dependent antibody dissociation attributes of the individual peptides identified through biopanning described above, the corresponding biotinylated peptides were chemically synthesized an ELISA similar to the phagemid antibody binding example described above was performed. To begin, peptides were immobilized on neutravidin coated and blocked wells. After unbound peptides were washed away, dilution series of anti-mouse CTLA-4 antibody (clone 9D9) were added to corresponding wells of peptides. After binding at 4 degrees the plates were washed extensively as before. Next the peptides were incubated with either neutral or acidic pH buffers for approximately 30 minutes and then washed again. The specifically peptide bound antibodies were detected by either anti-mouse Fc or anti-mouse kappa chain HRP conjugated antibodies using standard TMB-based chromogenic ELISA procedures. The effects of pH upon affinity were determined by standard EC50 analysis of each of the distinct pH dilution series binding curves and comparison of their respective EC50 values.
Similar approach was taken to determine pH-dependent antibody dissociation attributes of the individual peptides to PD-L1 antibody.

TABLE 4

pH-dependent CTLA-4 antibody-peptide dissociation.

SEQ

		ID	EC50 [M]	EC50 [M]	pH 6.0: pH 7.2
Peptide	sequence	NO	pH 7.2	pH 6.0	EC 50 ratio

1	TLDDMSHVILYA	29	2.9E-09	1.9E-08	6.7

2	VISDNHQIVWDL	30	1.8E-09	9.5E-09	5.2

3	LTTQDHPLTILL	31	2.2E-09	7.9E-09	3.5

4	GGWICHWLEPQEACTY	32	1.9E-09	4.1E-09	2.1

5	GGCFEEHEQLVFQTHC	33	2.5E-10	2.5E-09	9.6

6	GGCILPGQHESQAIAC	34	1.2E-10	1.7E-09	15.0

7	GGCLSQMDFHDWLQYC	35	7.8E-09	2.5E-08	3.2

8	GGTDCYLWDYKASCHQ	36	2.4E-09	5.3E-09	2.2

9	GGKCDSLSYWQEIECS	37	5.9E-09	1.4E-08	2.4

10	GGADCLLHDWDSACQI	38	5.5E-11	8.7E-10	15.8

11	MQNVDEAPPLLL	39	7.0E-09	1.1E-08	1.5

12	TNDWQGLLLNVF	40	4.0E-09	5.1E-09	1.3

13	GGCQDSMFHHPNHC	41	7.4E-09	3.6E-08	4.9

26	GGCGMHQHPLFVDC	42	1.6E-10	3.3E-09	20.9

14	GGCSLSQHPNHSDC	43	4.6E-10	4.1E-09	8.9

15	PCNQVECHHQFT	61	4.3E-10	5.4E-09	12.4

23	GGHCVDMVDFYQQTCQ	53	Inactive	—	—
(Control)

TABLE 5

pH-dependent PD-L1 antibody-peptide dissociation.

		SEQ				pH 6.0: pH	pH 5.4: pH
		ID	EC50 [M]	EC50 [M]	EC50 [M]	7.2 EC 50	7.2 EC 50
Peptide	sequence	NO	pH 7.2	pH 6.0	pH 5.4	ratio	ratio

20	QLFYPSTYHIID	49	1.3E-10	2.1E-10	8.4E-10	1.7	6.7

27	QVSPLYFYEELA	50	4.2E-10	9.0E-10	3.3E-09	2.2	7.8

21	HQALLDFYGDY	51	7.5E-10	1.8E-09	4.8E-09	2.5	6.4

22	GGMCHELFYSNLNWCQ	52	4.5E-11	7.0E-11	3.5E-10	1.5	7.8

23	GGHCVDMVDFYQQTCQ	53	3.0E-10	1.3E-09	3.9E-09	4.3	12.9

28	VDLLDGSLQDFY	54	1.8E-09	4.7E-09	9.1E-09	2.6	5.0

29	GGLCSTFYEPQVDICY	55	2.3E-10	4.9E-10	1.5E-09	2.1	6.5

30	SDFSGLLFYDYQ	56	9.5E-10	2.2E-09	5.6E-09	2.3	5.9

31	GGCVHFFEIHQRPDC	57	1.6E-10	3.6E-10	1.5E-09	2.3	9.4

24	GGCHNKSGLFYHYC	58	2.0E-10	5.6E-10	1.3E-09	2.8	6.6

10	GGADCLLHDWDSACQI	38	Inactive	—	—	—	—
(Control)

Example 11

Peptide Antibody Competition

To determine whether the peptides could inhibit mouse CTLA-4 from binding the 9D9 antibody a competition binding assay was utilized. Briefly, 9D9 antibody was preincubated against a dilution series of peptides. Following this incubation the peptide-antibody complexes were transferred to mouse CTLA-4 coated and blocked ELISA plates and incubated further. Following a brief binding period the plates were washed and target bound antibody was detected by either anti-mouse Fc or anti-mouse kappa chain HRP conjugated antibodies using standard TMB-based chromogenic ELISA procedures. The effects of competition were determined by standard IC50 analysis.

Example 12

pH-dependent Binding Analysis by ForteBio Octet Bio-Layer Interferometry (BLI)

To determine pH-dependent binding properties of peptides to mouse anti-CTLA-4 antibody, clone 9D9, monovalent antibody Fab fragment (mCTLA-4 Fab) was used on a ForteBio Octet Red96 System. Peptides with C-terminal biotinylation were captured on ForteBio High Precision Streptavidin (SAX) biosensors at 0.4 μg/ml in 50 mM sodium phosphate buffer, pH 7.4 with 150 mM NaCl, 0.1% BSA and 0.02% Tween-20 (pH 7.4 Assay Buffer).
For analysis of neutral pH binding, after loading, sensors were base-lined in pH 7.4 Assay Buffer followed by association with mCTLA-4 Fab (2-fold dilution series starting at 2.5 μM) in pH 7.4 Assay Buffer and dissociation in pH 7.4 Assay Buffer.
For analysis of acidic pH binding, after loading, sensors were base-lined in 50 mM sodium phosphate buffer, pH 6.0 with 150 mM NaCl, 0.1% BSA and 0.02% Tween-20 (pH 6.0 Assay Buffer) followed by association with mCTLA-4 Fab (2-fold dilution series starting at 2.5 μM) in pH 6.0 Assay Buffer and dissociation in pH 6.0 Assay Buffer.
Affinity measurements were determined by ForteBio Octet analysis software using global fitting.

Example 13

Anti-mCTLA-4 (Clone 9D9) Fab Binding to Peptide 15 by ELISA

Binding of anti-mouse CTLA-4 (clone 9D9) (Bio X Cell, Cat #BE0164) Fab fragment to Peptide 15 was determined by ELISA in 96-well plate. Briefly, 100 nM Peptide 15 with C-terminal biotin was captured on Neutravidin coated plates for 1 hour in PBS-T (50 mM phosphate buffered saline pH 7.4+0.05% Tween-20)+0.5% BSA. After washing in PBS-T, mCTLA-4 Fab diluted in either pH 7.4 Binding Buffer (50 mM sodium phosphate+150 mM NaCl+0.5% BSA+0.05% Tween-20, pH 7.4) or pH 6.0 Binding Buffer (50 mM sodium phosphate+150 mM NaCl+0.5% BSA+0.05% Tween-20, pH 6.0) was captured for 1 hour. After capture, wells were washed with either pH 7.4 Binding Buffer or pH 6.0 Binding Buffer, followed by additional 5-minute incubation with the appropriate pH Binding Buffer. Detection was performed with HRP conjugated goat anti-mouse IgG H+L (Southern Biotech.) for 1 hour at 1/2000 dilution in PBS-T+0.5% BSA followed by TMB (3-minute development) with acid stop. Absorbance at 450 nm was determined and data analysis was performed in GraphPad Prism by nonlinear regression with 4-parameter logistic curve. Data is expressed as mean+SD. All ELISA steps were performed at room temperature.

Example 14

Mammalian Expression of Reformatted Antibody Peptide Fusions

This example outlines a way to reformat peptides found above into recombinant antibody fusions. Antibodies are comprised of a full length heavy chain framework complexed with an antibody light chain. The heavy chain used is either a mouse Fc gamma 2a or mouse Fc gamma 2b isotype. The full length heavy chain and light chain sequences for 9D9 (anti-CTLA-4, clone 9D9, Curran et. al) are synthesized for expression in mammalian cells. Additional light chain constructs with 9D9 binding peptides fused by flexible linkers are similarly synthesized. The individual antibody light chain constructs are co-transfected along with the heavy chain expression vector in mammalian cells. Specifically the proteins are transiently produced in HEK293 suspension cell-based systems. The resulting proteins are harvested from the media after 5-7 days and FPLC purified to >95% purity via Protein A chromatography. Proteins are dialyzed and exchanged into pH 7.4 PBS, sterile filtered, quantitated by A280 absorbance, and stored either at 4 degrees or −80 degrees for longer term storage.
Listed below are exemplary antibody sequences comprising light chain with the peptide and heavy chain sequences.


Antibody-peptide fusion	Isotype	Light Chain + peptide	Heavy Chain

9D9 + peptide 10	Mouse IgG2b	Peptide 10-9D9 light chain	9D9 heavy chain (mouse
		fusion (mouse kappa)	IgG2b)
9D9 + peptide 13	Mouse IgG2b	Peptide 13-9D9 light chain	9D9 heavy chain (mouse
		fusion (mouse kappa)	IgG2b)
9D9 + peptide 14	Mouse IgG2b	Peptide 14-9D9 light chain	9D9 heavy chain (mouse
		fusion (mouse kappa)	IgG2b)
9D9 + peptide 15	Mouse IgG2b	Peptide 15-9D9 light chain	9D9 heavy chain (mouse
		fusion (mouse kappa)	IgG2b)
9D9 + peptide 10	Mouse IgG2a	Peptide 10-9D9 light chain	9D9 heavy chain (mouse
		fusion (mouse kappa)	IgG2a)
9D9 + peptide 13	Mouse IgG2a	Peptide 13-9D9 light chain	9D9 heavy chain (mouse
		fusion (mouse kappa)	IgG2a)
9D9 + peptide 14	Mouse IgG2a	Peptide 14-9D9 light chain	9D9 heavy chain (mouse
		fusion (mouse kappa)	IgG2a)
9D9 + peptide 15	Mouse IgG2a	Peptide 15-9D9 light chain	9D9 heavy chain (mouse
		fusion (mouse kappa)	IgG2a)
Atezolizumab + peptide 23	Human IgG1	Peptide 23-Atezolizumab light	Atezolizumab heavy chain
		chain fusion (human kappa)	(human IgG1)

9D9 light chain (mouse kappa)
(SEQ ID NO: 62)
DIVMTQTTLSLPVSLGDQASISCRSSQSIVHSNGNTYLEWYLQKPGQSPKLLIYKVSNRFSGV

PDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPYTFGGGTKLEIKRADAAPTVSIFPPS

SEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLT

KDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Peptide 10-9D9 light chain fusion (mouse kappa)
(SEQ ID NO: 63)
GGADCLLHDWDSACQI GSSGGSGGSGGSGGGSGGGSGGSSGTDIVMTQTTLSLPVSLGDQ

ASISCRSSQSIVHSNGNTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISR

VEAEDLGVYYCFQGSHVPYTEGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNE

YPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHK

TSTSPIVKSFNRNEC

Peptide 13-9D9 light chain fusion (mouse kappa)
(SEQ ID NO: 64)
GGCQDSMFHHPNHC GSSGGSGGSGGSGGGSGGGSGGSSGTDIVMTQTTLSLPVSLGDQAS

ISCRSSQSIVHSNGNTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRV

EAEDLGVYYCFQGSHVPYTEGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNEY

PKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTS

TSPIVKSFNRNEC

Peptide 14-9D9 light chain fusion (mouse kappa)
(SEQ ID NO: 65)
GGCSLSQHPNHSDC GSSGGSGGSGGSGGGSGGGSGGSSGTDIVMTQTTLSLPVSLGDQASI

SCRSSQSIVHSNGNTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVE

AEDLGVYYCFQGSHVPYTEGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNEYP

KDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTST

SPIVKSFNRNEC

Peptide 15-9D9 light chain fusion (mouse kappa)
(SEQ ID NO: 66)
GGPCNQVECHHQFT GSSGGSGGSGGSGGGSGGGSGGSSGTDIVMTQTTLSLPVSLGDQAS

ISCRSSQSIVHSNGNTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRV

EAEDLGVYYCFQGSHVPYTEGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNEY

PKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTS

TSPIVKSFNRNEC

9D9 heavy chain (mouse IgG2b)
(SEQ ID NO: 67)
EAKLQESGPVLVKPGASVKMSCKASGYTFTDYYMNWVKQSHGKSLEWIGVINPYNGDTSY

NQKFKGKATLTVDKSSSTAYMELNSLTSEDSAVYYCARYYGSWFAYWGQGTLITVSTAKT

TPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLY

TMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEPSGPISTINPCPPCKECHKCPAPN

LEGGPSVFIFPPNIKDVLMISLTPKVTCVVVDVSEDDPDVRISWFVNNVEVHTAQTQTH

REDYNSTIRVVSALPIQHQDWMSGKEFKCKVNNKDLPSPIERTISKIKGLVRAPQVYIL

PPPAEQLSRKDVSLTCLVVGFNPGDISVEWTSNGHTEENYKDTAPVLDSDGSYFIYSKL

DIKTSKWEKTDSFSCNVRHEGLKNYYLKKTISRSPGK

Atezolizumab light chain (human kappa)
(SEQ ID NO: 68)
DIQMTQSPSSLSASVGDRVTITCRASQDVSTAVAWYQQKPGKAPKWYSASFLYSGVPSRF

SGSGSGTDFTLTISSLQPEDFATYYCQQYLYHPATEGQGTKVEIKRTVAAPSVFIFPPSDEQL

KSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADY

EKHKVYACEVTHQGLSSPVTKSFNRGEC

Peptide 23-Atezolizumab light chain fusion (human kappa)
(SEQ ID NO: 69)
GGHCVDMVDFYQQTCQ GSSGGSGGSGGSGGGSGGGSGGSSGTDIQMTQSPSSLSASVGD

RVTITCRASQDVSTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSGSGTDFTLTISSLQP

EDFATYYCQQYLYHPATFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPR

EAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLS

SPVTKSFNRGEC

Atezolizumab heavy chain (human IgG1)
(SEQ ID NO: 70)
EVQLVESGGGLVQPGGSLRLSCAASGFTFSDSWIHWVRQAPGKGLEWVAWISPYGGSTYY

ADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARRHWPGGFDYWGQGTLVTVSSA

STKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSS

GLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPELLG

GPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREE

QYASTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLP

PSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLT

VDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK

Example 15

In Vitro Cell Based pH Dependent Binding of Masked 9D9 Antibodies

Masked 9D9 antibody binding is evaluated in isogenic 293 cells that stably express mouse CTLA-4 (mCTLA-4). Briefly, parent Flp-In 293 cells that harbor a single FRT recombination site are expanded in complete culture medium (DMEM GlutaMax 10% FBS) prior to transfection. Once sufficient parent cells are grown, cells are transfected with two vectors, one encoded the Flp recombinase and the other encoded mCTLA-4 plus a hygromycin B resistance gene. Cells successfully transfected are selected using hygromycin B. After several days of growth in the presence of hygromycin B, cellular foci are picked and expanded. Expanded foci are tested for mCTLA-4 expression via flow cytometry using the unmasked 9D9 antibody. Cells that express mCTLA-4 (mCTLA-4 293) are expanded further and cryopreserved.
mCTLA-4_293 cells are then used to evaluate pH dependent binding of masked 9D9 antibodies. mCTLA-4_293 cells are grown to 50%-75% confluence, washed, incubated in buffered EDTA, and gently scraped from the culture dish surface. Parent 293 cells are expanded in parallel and used as controls. Cells are transferred to a 15 mL falcon tube, spun down, and washed 3 times. Cells are washed with complete culture medium in the absence of bicarb, supplemented with MES and adjusted to pH 6.0, or supplemented with HEPES and adjusted to pH 7.4. Cell are concentrated then incubated with unmasked or masked 9D9 antibodies for 1 h at RT in complete culture medium plus MES pH 6.0 or HEPES pH 7.4. Cells are washed 3 times in complete culture medium plus MES pH 6.0 or HEPES pH 7.4. Cells are then fixed in buffered formalin for 15 min RT and washed 3 times in PBS pH 7.4. Cells are concentrated then incubated with secondary AlexaFluor 555 anti-mouse antibody for 1 hr at RT in PBS 5% BSA 0.1% tween. Cells are washed 3 times with PBS 0.1% tween and analyzed by flow cytometry.

Example 16

In Vivo Efficacy Evaluation of Masked 9D9 Antibodies

Efficacy of masked 9D9 antibodies is evaluated relative to parent 9D9 in C57BL/6 or BALB/c mice bearing syngeneic MC38 tumor xenografts. Briefly, mice are subcutaneously injected with 2 million MC38 tumor cells, respectively. Tumor volumes are recorded 3 times weekly. Mice bearing palpable tumors (50-75 mm³) are randomized into treatment groups with comparable mean tumor volumes. Antibodies formulated in PBS pH 7.4 are administered twice weekly intraperitoneally (IP) 200 μg per dose in a volume of 200 μL (10 mg/kg IP b.i.w). Matched isotype antibodies are used as negative controls. Percent tumor growth inhibition (TGI %) is determined after two weeks of dosing for antibody treatment groups relative to isotype controls.

Example 17

Tumor Actuated Binding of Masked 9D9 Antibodies Using In Vivo Near Infrared Imaging

Selective tumor binding of masked near infrared (NIR) labeled 9D9 antibodies is evaluated relative to parent NIR 9D9 in mice bearing MC38 or CT26 tumor xenografts. Antibodies are labeled with the NIR imaging probe, IRDye-800CW-NHS (IRDye 800CW-N-hydroxysuccinimide ester) according to manufacturer's instructions. Briefly, they are incubated in the dark at room temperature with IRDye800CW in 1.0 M potassium phosphate buffer (pH 9.0) for 2 hours. The unconjugated dye is removed by desalting spin columns and purified according to manufacturer's instructions. NIR masked 9D9, NIR 9D9, or NIR labeled isotype control are administered intravenously to MC38 bearing C57Bl/6 mice via the tail vein. Forty-eight hours after administration of the NIR labeled antibodies, probe uptake and tissue distribution in the tumor bearing mice is measured using a small-animal NIR scanner (IVIS Spectrum In Vivo Imaging System). During imaging, the mice are anesthetized with isoflurane gas and placed in the prone position.

Example 18

In Vivo Efficacy Evaluation of Masked anti-CTLA-4 Antibodies

Efficacy of masked anti-CTLA-4 antibodies is evaluated relative to parent anti-CTLA-4 antibody in C57BL/6 or BALB/c mice bearing syngeneic MC38 or CT26 tumor xenografts, respectively. Mice are subcutaneously injected with 1 million CT26 or 2 million MC38 tumor cells. Tumor volumes are recorded 3 times weekly for four weeks. Mice bearing palpable tumors (50-100 mm³) are randomized into treatment groups with comparable mean tumor volumes. Antibodies formulated in PBS pH 7.4 are administered twice weekly intraperitoneally (IP) 200 m per dose in a volume of 200 μL (10 mg/kg IP b.i.w). Matched isotype antibodies are used as negative controls. Percent tumor growth inhibition (TGI %) is determined after three weeks from first dose for antibody treatment groups relative to isotype controls.

Example 19

In Vivo Safety Evaluation of Masked anti-CTLA-4 Antibodies in Combination with anti-PD-1 Antibodies

Five-week old female NOD mice are administered masked anti-CTLA-4 antibodies, parent anti-CTLA-4 antibody, anti-PD-1 antibody, and/or isotype controls in combination at 10 mg/kg intraperitoneally each article on days 0, 4 and 7. The following six combinations are used: 1) isotype controls, 2) parent anti-CTLA-4 antibody plus isotype control, 3) masked anti-CTLA-4 antibody plus isotype control, 4) anti-PD-1 antibody plus isotype control, 5) anti-PD-1 antibody plus parent anti-CTLA-4, or 6) anti-PD-1 antibody plus masked anti-CTLA-4 antibody. Mice are monitored daily for the induction of diabetes by glucosuria plus confirmation of two consecutive blood glucose levels ≥250 mg/dL. Monitoring is continued for a minimum of 7 days until 48 hours have passed with no new incidents of glucosuria.

Example 20

In Vivo Peripheral T-Cell Activation Using Masked anti-CTLA-4 Antibodies Alone or in Combination with anti-PD-1 Antibody

Four to six week old C57Bl/6 mice are administered masked anti-CTLA-4 antibody, parent anti-CTLA-4 antibody, isotype control, anti-PD-1 antibody plus isotype control, anti-PD-1 antibody plus parent anti-CTLA-4 antibody, or anti-PD-1 antibody plus masked anti-CTLA-4 antibody at 10 mg/kg intraperitoneally each article on days 0, 4 and 7. On day 14 animals are euthanized. Blood and spleen are harvested from animals. Blood is stored in EDTA blood collection tubes. Spleens are digested using the mouse spleen dissociation kit from Miltenyi Biotec. Lymphocytes from blood and spleen derived cells are enriched using a Ficoll gradient. Enriched lymphocytes are stained for FoxP3 followed by either Ki67 or ICOS and measured via flow cytometry. Percent Ki67 or ICOS positive cells are calculated from total number of FoxP3 positive cells.
While preferred embodiments of the present invention have been shown and described herein, it will be obvious to those skilled in the art that such embodiments are provided by way of example only. Numerous variations, changes, and substitutions will now occur to those skilled in the art without departing from the invention. It should be understood that various alternatives to the embodiments of the invention described herein may be employed in practicing the invention. It is intended that the following claims define the scope of the invention and that methods and structures within the scope of these claims and their equivalents be covered thereby.

Claims

1. A modified antibody comprising a formula:

A-L-P

wherein

A is an antibody or antibody fragment that binds to a target antigen,

P is a peptide that reduces binding of A to the target antigen at physiological pH and that does not reduce binding of A to the target antigen at acidic pH, and

L is a linking moiety that connects A to P at physiological pH and in a tumor microenvironment and L is bound to A outside an antigen binding site.

2. (canceled)

3. The modified antibody of claim 1, wherein at physiological pH P is reversibly bound to A at or near the antigen binding site.

4. The modified antibody of claim 1, wherein P inhibits the binding of A to the target antigen at physiological pH and P does not inhibit the binding of A to the target antigen at acidic pH.

5. The modified antibody of claim 1, wherein in tissue other than the tumor microenvironment, P sterically blocks A from binding to the target antigen.

6. (canceled)

7. The modified antibody of claim 1, wherein the modified antibody has an increased binding affinity for the target antigen in the tumor microenvironment compared to the binding affinity of the modified antibody for the target antigen in a non-tumor microenvironment.

8. The modified antibody of claim 1, wherein P comprises a peptide sequence with at least one histidine.

9. The modified antibody of claim 8, wherein the histidine forms a binding interaction at or near the antigen binding site of A at physiological pH.

10.-19. (canceled)

20. The modified antibody of claim 8, wherein at acidic pH P is reversibly bound to L.

21. The modified antibody of claim 20, wherein L comprises a peptide sequence with at least one aspartic acid or glutamic acid, or a combination thereof.

22. The modified antibody of claim 21, wherein the histidine of P forms an interaction with the aspartic acid or glutamic acid of L.

23.-39. (canceled)

40. The modified antibody of claim 1, wherein A is a full length antibody, a single-chain antibody, an Fab fragment, an Fab′ fragment, an (Fab′)2 fragment, an Fv fragment, a divalent single chain antibody, bispecific antibody, a trispecific antibody, a tetraspecific antibody, or an antibody drug conjugate.

41.-49. (canceled)

50. The modified antibody of claim 1, wherein the target antigen is CTLA4 and P comprises an amino acid sequence selected from the group consisting of Peptide 1, Peptide 2, Peptide 5, Peptide 6, Peptide 10, Peptide 13, Peptide 26, Peptide 14, and Peptide 15.

51.-60. (canceled)

61. The modified antibody of claim 1, wherein the target antigen is PD-L1 and P comprises an amino acid sequence selected from the group consisting of Peptide 20, Peptide 27, Peptide 21, Peptide 22, Peptide 23, Peptide 28, Peptide 29, Peptide 30, Peptide 31, and Peptide 24.

62.-76. (canceled)

77. The modified antibody of claim 1, wherein P comprises a peptide sequence with at least two histidines.

78. (canceled)

79. The modified antibody of claim 77, wherein P comprises a peptide sequence with at least two histidines and at least two cysteines.

80. The modified antibody of claim 1, wherein P comprises a peptide sequence with at least two charged amino acid residues wherein the charged amino acid residues are selected from the group consisting of aspartate, glutamate, and histidine.

81. (canceled)

82. The modified antibody of claim 1, wherein P comprises a peptide sequence with at least three charged amino acid residues wherein the charged amino acid residues are selected from the group consisting of aspartate, glutamate, and histidine.

83. (canceled)

84. The modified antibody of claim 82, wherein P comprises a peptide sequence with at least one histidine and at least two aspartates.

85. The modified antibody of claim 1, wherein P comprises a peptide sequence with at least one cysteine.

86. (canceled)

87. The modified antibody of claim 1, wherein P comprises a peptide sequence with at least two cysteine amino acid residues.

88. (canceled)

89. The modified antibody of claim 87, wherein P comprises a peptide sequence with at least two cysteines and at least three charged amino acid residues wherein the charged amino acid residues are selected from the group consisting of aspartate, glutamate, and histidine.

90.-93. (canceled)

94. The modified antibody of claim 1, wherein P does not comprise a lysine or arginine.

95. The modified antibody of claim 1, wherein P comprises at least one histidine and at least one aspartate.

96. The modified antibody of claim 1, wherein P comprises at least one histidine and at least one glutamate.

97. The modified antibody of claim 1, wherein P comprises at least one histidine and at least two glutamates.

98. The modified antibody of claim 1, wherein P comprises at least two histidines and at least one aspartate or at least one glutamate.

99. The modified antibody of claim 1, wherein P comprises at least one histidine, wherein at least one hydrogen bonding amino acid residue is within two amino acid positions to the histidine, wherein the hydrogen bonding amino acid residue is selected from the group consisting of serine, threonine, tyrosine, asparagine, and glutamine.

100.-105. (canceled)

106. The modified antibody of claim 1, wherein A-L-P does not comprise a protease cleavage site that releases A from P in a tumor microenvironment.

107. The modified antibody of claim 1, wherein L comprises a peptide sequence with at least one histidine.

108. The modified antibody of claim 107, wherein at acidic pH L is reversibly bound to P.

109. The modified antibody of claim 108, wherein P comprises a peptide sequence with at least one aspartic acid or glutamic acid, or a combination thereof.

110. The modified antibody of claim 109, wherein the histidine of L forms an interaction with the aspartic acid or glutamic acid of P.

111. A pharmaceutical composition, comprising:

(a) a modified antibody according to claim 1; and

(b) a pharmaceutically acceptable excipient.