Patent Application
20220073616
The field of the invention is molecular biology, immunology and oncology. More particularly, the field is therapeutic antibodies.
Following the approval of Yervoy® (ipilimumab, Bristol-Myers Squibb) for melanoma in 2011, immune checkpoint inhibitors have become a promising class of molecules for therapeutic development (for example, those targeting PD-1, PD-L1, and CTLA-4). Several large companies developing immune checkpoint inhibitor drugs include Bristol-Myers Squibb, Merck & Co., Roche, AstraZeneca and many others. The developmental strategies and investment in immunotherapy, together with compelling clinical efficacy have led to several new approvals of anti-PD(L)-1 drugs: Keytruda® (pembrolizumab, Merck & Co.), Opdivo® (nivolumab, Bristol-Myers Squibb), Tecentriq® (atezolizumab, Roche), Bavencio® (avelumab, EMD Serono), and Imfinzi® (durvalumab, AstraZeneca).
PD-1/PD-L1 checkpoint inhibitors, with their compelling clinical efficacy and safety profiles, have built a solid foundation for combination immunotherapy approaches. These strategies include combining PD-1 pathway inhibitors with inhibitors of other immune checkpoint proteins expressed on T-cells. One such checkpoint protein is T Cell Immunoglobulin and Mucin Domain-3 (TIM-3), also known as Hepatitis A Virus Cellular Receptor 2 (HAVCR2).
Tim-3 was first identified as a molecule selectively expressed on IFN-g-producing CD4+ T helper 1 (Th1) and CD8+ T cytotoxic 1 (Tc1) T cells (Monney et al. (2002) N
Studies suggest that TIM-3 regulates various aspects of the immune response. The interaction of TIM-3 and its ligand galectin-9 (Gal-9) induces cell death. The in vivo blockade of this interaction exacerbated autoimmunity and abrogated tolerance in experimental models, suggesting that TIM-3/Gal-9 interaction negatively regulates immune responses (Zhu et al. (2005), supra; Kanzaki et al. (2012) E
Tim-3 is considered a potential candidate for cancer immunotherapy, in part, because it is upregulated in tumor-infiltrating lymphocytes including Foxp3+CD4+ Treg and exhausted CD8+ T cells, two key immune cell populations that constitute immunosuppression in tumor environment of many human cancers (McMahan et al. (2010) J. C
Further, intratumoral Tim-3+FoxP3+ Treg cells appear to express high amounts of Treg effector molecules (IL-10, perforin, and granzymes). Tim-3+ Tregs are thought to promote the development of a dysfunctional phenotype in CD8+ tumor infiltrating lymphocytes (TILs) in tumor environment (Sakuishi, et al. (2013) O
The synergy of Tim-3/PD-1 co-blockade in inhibiting tumor growth in preclinical mouse tumor models suggests that the co-blockade modulates the functional phenotype of dysfunctional CD8+T cells and/or Tregs (Sakuishi et al. (2010), supra; Ngiow et al. (2011), supra). Indeed, besides in vivo co-blockade with PD(L)-1, co-blockade with many other check-point inhibitors enhances anti-tumor immunity and suppresses tumor growth in many preclinical tumor models (Dardalhon et al. (2010), supra; Nglow et al., C
Despite the success of checkpoint inhibitors such as Yervoy®, Keytruda® and Opdivo® and others, only a fraction of the patients experience durable clinical responses to these therapies. Some tumor types have shown little response to anti-CTLA-4 or anti-PD-1/PD-L1 monotherapies in clinical trials. These include prostate, colorectal, and pancreatic cancers. Accordingly, for these nonresponsive diseases and for the majority who are non-responders within responsive tumor types, there is a need for improved anti-tumor therapies.
The invention relates in part to methods of treating cancer using a family of antibodies that specifically bind human T Cell Immunoglobulin and Mucin Domain-3 (TIM-3). The antibodies contain TIM-3 binding sites based on the complementarity determining regions (CDRs) of the antibodies. The antibodies can be used as therapeutic agents alone or in combination with other therapeutic agents, such as other immune checkpoint inhibitors. When used as therapeutic agents, the antibodies can be optimized, e.g., affinity-matured, to improve biochemical properties (e.g., affinity and/or specificity), to improve biophysical properties (e.g., aggregation, stability, precipitation, and/or non-specific interactions), and/or to reduce or eliminate immunogenicity, when administered to a human patient.
The antibodies described herein inhibit TIM-3 from binding to TIM-3 ligands, e.g., galectin-9, phosphatidylserine (PtdSer), and carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1). The disclosed antibodies can be used to inhibit the proliferation of tumor cells in vitro or in vivo. When administered to a human cancer patient or an animal model, the antibodies inhibit or reduce tumor growth in the human patient or animal model.
Accordingly, in one aspect, the disclosure relates to a method of treating cancer in a mammal, the method comprising administering an effective amount of an anti-TIM-3 antibody and a second therapeutic agent to the mammal in need thereof.
In another aspect, the disclosure relates to an anti-TIM-3 antibody for use in a method of treating cancer in a mammal, the method comprising administering an effective amount of an anti-TIM-3 antibody and a second therapeutic agent to the mammal in need thereof.
In another aspect, the disclosure relates to the use of an anti-TIM-3 antibody in the manufacture of a medicament for use in a method of treating cancer in a mammal, the method comprising administering an effective amount of an anti-TIM-3 antibody and a second therapeutic agent to the mammal in need thereof.
In certain embodiments, the anti-TIM-3 antibody is administered in an amount of from about 0.1 mg/kg to about 100 mg/kg. In certain embodiments, the anti-TIM-3 antibody is administered as a flat (fixed) dose of from about 5 mg to about 3500 mg.
In certain embodiments, the second therapeutic agent is an anti-PD-L1/TGFβ Trap fusion protein. In certain embodiments, the anti-PD-L1/TGFβ Trap fusion protein comprises:
(a) a heavy chain comprising an CDRH1, an CDRH2, and an CDR-13, having at least 80% overall sequence identity to SYIMM (SEQ ID NO: 78), SIYPSGGITFYADTVKG (SEQ ID NO: 79), and IKLGTVTTVDY (SEQ ID NO: 80), respectively, and
(b) a light chain comprising an CDRL1, an CDRL2, and an CDRL3, having at least 80% overall sequence identity to TGTSSDVGGYNYVS (SEQ ID NO: 81), DVSNRPS (SEQ ID NO: 82), and SSYTSSSTRV (SEQ ID NO: 83), respectively.
In certain embodiments, the anti-PD-L1/TGFβ Trap fusion protein is bintrafusp. In certain embodiments, the anti-PD-L1/TGFβ Trap fusion protein is bintrafusp alfa.
In certain embodiments, the anti-PD-L1/TGFβ Trap fusion protein is administered in a flat (fixed) dose of from about 800 mg to about 2600 mg. In certain embodiments, the anti-PD-L1/TGFβ Trap fusion protein is administered in a flat (fixed) dose of about 1200 mg. In certain embodiments, the anti-PD-L1/TGFβ Trap fusion protein is administered in a flat (fixed) dose of about 2400 mg. In certain embodiments, the anti-TIM-3 antibody and/or the anti-PD-L1/TGFβ Trap fusion protein is administered every two weeks. In certain embodiments, the anti-TIM-3 antibody and/or the anti-PD-L1/TGFβ Trap fusion protein is administered every three weeks.
In certain embodiments, the cancer is selected from the group consisting of diffuse large B-cell lymphoma, renal cell carcinoma (RCC), non-small cell lung carcinoma (NSCLC), squamous cell carcinoma of the head and neck (SCCHN), triple negative breast cancer (TNBC) or gastric/stomach adenocarcinoma (STAD).
In certain embodiments, the mammal is a human.
In certain embodiments, the anti-TIM-3 antibody comprises
(i) an immunoglobulin heavy chain variable region comprising a CDRH1 comprising the amino acid sequence of SEQ ID NO: 1, a CDRH2 comprising the amino acid sequence of SEQ ID NO: 2, and a CDRH3 comprising the amino acid sequence of SEQ ID NO: 3; and
(ii) an immunoglobulin light chain variable region comprising a CDRL1 comprising the amino acid sequence of SEQ ID NO: 4, a CDRL2 comprising the amino acid sequence of SEQ ID NO: 5, and a CDRL3 comprising the amino acid sequence of SEQ ID NO: 6.
In certain embodiments, the anti-TIM-3 antibody comprises an immunoglobulin heavy chain variable region selected from the group consisting of SEQ ID NO: 53, SEQ ID NO: 24, SEQ ID NO: 55, SEQ ID NO: 34, and an immunoglobulin light chain variable region selected from the group consisting of SEQ ID NO: 52, SEQ ID NO: 54, SEQ ID NO: 23 and SEQ ID NO: 33.
In certain embodiments, the anti-TIM-3 antibody comprises an immunoglobulin heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 24, and an immunoglobulin light chain variable region comprising the amino acid sequence of SEQ ID NO: 23.
In certain embodiments, the anti-TIM-3 antibody comprises an immunoglobulin heavy chain and an immunoglobulin light chain selected from the group consisting of:
(a) an immunoglobulin heavy chain comprising the amino acid sequence of SEQ ID NO: 22, and an immunoglobulin light chain comprising the amino acid sequence of SEQ ID NO: 21; and
(b) an immunoglobulin heavy chain comprising the amino acid sequence of SEQ ID NO: 32, and an immunoglobulin light chain comprising the amino acid sequence of SEQ ID NO: 31.
In certain embodiments, the anti-TIM-3 antibody has a KD of 9.2 nM or lower, as measured by surface plasmon resonance.
In certain embodiments, the anti-TIM-3 antibody competes for binding to the galectin-9, the PtdSer, and/or the carcinoembryonic antigen cell adhesion-related molecule 1 (CEACAM1) binding site on human TIM-3 with an antibody comprising:
(A) (i) an immunoglobulin heavy chain variable region comprising a CDRH1 comprising the amino acid sequence of SEQ ID NO: 1, a CDRH2 comprising the amino acid sequence of SEQ ID NO: 2, and a CDRH3 comprising the amino acid sequence of SEQ ID NO: 3; and
(ii) an immunoglobulin light chain variable region comprising a CDRL1 comprising the amino acid sequence of SEQ ID NO: 4, a CDRL2 comprising the amino acid sequence of SEQ ID NO: 5, and a CDRL3 comprising the amino acid sequence of SEQ ID NO: 6; and/or
(B) an immunoglobulin heavy chain variable region selected from the group consisting of SEQ ID NO: 53, SEQ ID NO: 24, SEQ ID NO: 55, SEQ ID NO: 34, and an immunoglobulin light chain variable region selected from the group consisting of SEQ ID NO: 52, SEQ ID NO: 54, SEQ ID NO: 23 and SEQ ID NO: 33; and/or
(C) an immunoglobulin heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 24, and an immunoglobulin light chain variable region comprising the amino acid sequence of SEQ ID NO: 23; and/or
(D) an immunoglobulin heavy chain and an immunoglobulin light chain selected from the group consisting of:
(a) an immunoglobulin heavy chain comprising the amino acid sequence of SEQ ID NO: 22, and an immunoglobulin light chain comprising the amino acid sequence of SEQ ID NO: 21; and
(b) an immunoglobulin heavy chain comprising the amino acid sequence of SEQ ID NO: 32, and an immunoglobulin light chain comprising the amino acid sequence of SEQ ID NO: 31.
In certain embodiments, the anti-TIME-3 antibody binds to the same epitope on a human TIM-3 protein as an antibody as described herein, wherein the epitope includes P59, F61, E62, and D120 of the human TIM-3 protein.
These and other aspects and advantages of the invention will become apparent upon consideration of the following figures, detailed description, and claims. As used herein, “including” means without limitation, and examples cited are non-limiting.
The foregoing and other objects, features and advantages of the invention will become apparent from the following description of preferred embodiments, as illustrated in the accompanying drawings. Like referenced elements identify common features in the corresponding drawings. The drawings are not necessarily to scale, with emphasis instead being placed on illustrating the principles of the present invention, in which:
The anti-TIM-3 antibodies disclosed herein are based on the antigen binding sites of certain monoclonal antibodies that have been selected on the basis of binding and neutralizing the activity of human T Cell Immunoglobulin and Mucin Domain-3 (TIM-3). The antibodies contain immunoglobulin variable region CDR sequences that define a binding site for TIM-3.
In view of the neutralizing activity of these antibodies, they are useful for inhibiting the growth and/or proliferation of certain types of cancer cells. When used as a therapeutic agent, the antibodies can be optimized, e.g., affinity-matured, to improve biochemical properties and/or biophysical properties, and/or to reduce or eliminate immunogenicity when administered to a human patient. Various features and aspects of the invention are discussed in more detail below.
As used herein, unless otherwise indicated, the term “antibody” means an intact antibody (e.g., an intact monoclonal antibody) or antigen-binding fragment of an antibody, including an intact antibody or antigen-binding fragment of an antibody (e.g., a phage display antibody including a fully human antibody, a semisynthetic antibody or a fully synthetic antibody) that has been optimized, engineered or chemically conjugated. Examples of antibodies that have been optimized are affinity-matured antibodies. Examples of antibodies that have been engineered are Fc optimized antibodies, antibody fusion proteins and multispecific antibodies (e.g., bispecific antibodies). Examples of antigen-binding fragments include Fab, Fab′, F(ab)2, Fv, single chain antibodies (e.g., scFv), minibodies and diabodies. An antibody conjugated to a toxin moiety is an example of a chemically conjugated antibody. Antibody fusion proteins include, for example, an antibody genetically fused to a soluble ligand such as a cytokine, or to an extracellular domain of a cellular receptor protein.
I. Antibodies that Bind Human TIM-3
The antibodies disclosed herein comprise: (a) an immunoglobulin heavy chain variable region comprising a CDRH1, a CDRH2, and a CDRH3 and (b) an immunoglobulin light chain variable region comprising a CDRL1, a CDRL2, and a CDRL3, wherein the heavy chain variable region and the light chain variable region together define a single binding site for binding TIM-3 protein.
In some embodiments, the antibody comprises: (a) an immunoglobulin heavy chain variable region comprising a CDRH1, a CDRH2, and a CDRH3 and (b) an immunoglobulin light chain variable region, wherein the heavy chain variable region and the light chain variable region together define a single binding site for binding TIM-3. A CDRH1 comprises the amino acid sequence of SEQ ID NO: 1; a CDRH2 comprises the amino acid sequence of SEQ ID NO: 2; and a CDRH3 comprises the amino acid sequence of SEQ ID NO: 3. The CDRH1, CDRH2, and CDRH3 sequences are interposed between immunoglobulin FR sequences (SEQ ID NO: 7, SEQ ID NO:8, SEQ ID NO: 9, and SEQ ID NO:10).
In some embodiments, the antibody comprises (a) an immunoglobulin light chain variable region comprising a CDRL1, a CDRL2, and a CDRL3, and (b) an immunoglobulin heavy chain variable region, wherein the IgG light chain variable region and the IgG heavy chain variable region together define a single binding site for binding TIM-3. A CDRL1 comprises the amino acid sequence of SEQ ID NO: 4; a CDRL2 comprises the amino acid sequence of SEQ ID NO: 5; and a CDRL3 comprises the amino acid sequence of SEQ ID NO: 6. The CDRL1, CDRL2, and CDRL3 sequences are interposed between immunoglobulin FR sequences (SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, and SEQ ID NO: 14).
In some embodiments, the antibody comprises: (a) an immunoglobulin heavy chain variable region comprising a CDRH1, a CDRH2, and a CDRH3 and (b) an immunoglobulin light chain variable region comprising a CDRL1, a CDRL2, and a CDRL3, wherein the heavy chain variable region and the light chain variable region together define a single binding site for binding TIM-3. The CDRH1 is the amino acid sequence of SEQ ID NO: 1; the CDRH2 is the amino acid sequence of SEQ ID NO: 2; and the CDRH3 is the amino acid sequence of SEQ ID NO: 3. The CDRL1 is the amino acid sequence of SEQ ID NO: 4; the CDRL2 is the amino acid sequence of SEQ ID NO: 5; and the CDRL3 is the amino acid sequence of SEQ ID NO: 6.
In other embodiments, the antibodies disclosed herein comprise an immunoglobulin heavy chain variable region and an immunoglobulin light chain variable region. In some embodiments, the antibody comprises an immunoglobulin heavy chain variable region comprising an amino acid sequence selected from the group consisting of SEQ ID NO: 53, SEQ ID NO: 24, SEQ ID NO: 55, and SEQ ID NO: 34; and an immunoglobulin light chain variable region.
In other embodiments, the antibody comprises an immunoglobulin light chain variable region selected from the group consisting of SEQ ID NO: 52, SEQ ID NO: 54, SEQ ID NO: 23 and SEQ ID NO: 33; and an immunoglobulin heavy chain variable region.
In some embodiments, the antibody comprises an immunoglobulin heavy chain variable region comprising an amino acid sequence selected from the group consisting of SEQ ID NO: 53, SEQ ID NO: 24, SEQ ID NO: 55, and SEQ ID NO: 34; and an immunoglobulin light chain variable region selected from the group consisting of SEQ ID NO: 52, SEQ ID NO: 54, SEQ ID NO: 23 and SEQ ID NO: 33.
In some embodiments, the antibody comprises an immunoglobulin heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 24, and an immunoglobulin light chain variable region comprising the amino acid sequence of SEQ ID NO: 23.
In certain embodiments, the antibodies disclosed herein comprise an immunoglobulin heavy chain and an immunoglobulin light chain. In some embodiments, the antibody comprises an immunoglobulin heavy chain selected from the group consisting of SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO: 20, SEQ ID NO: 22, and SEQ ID NO: 32; and an immunoglobulin light chain.
In other embodiments, the antibody comprises an immunoglobulin light chain selected from the group consisting of SEQ ID NO: 15, SEQ ID NO: 17, SEQ ID NO: 19, SEQ ID NO: 21, and SEQ ID NO: 31; and an immunoglobulin heavy chain.
In some embodiments, the antibody comprises (i) an immunoglobulin heavy chain comprising an amino acid sequence selected from the group consisting of SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO: 20, SEQ ID NO: 22, and SEQ ID NO: 32; and (ii) an immunoglobulin light chain selected from the group consisting of SEQ ID NO: 15, SEQ ID NO: 17, SEQ ID NO: 19, SEQ ID NO: 21, and SEQ ID NO: 31.
In some embodiments, the antibody comprises an immunoglobulin heavy chain comprising the amino acid sequence of SEQ ID NO: 22 and an immunoglobulin light chain comprising the amino acid sequence of SEQ ID NO: 21.
In certain embodiments, an isolated antibody that binds TIM-3 comprises an immunoglobulin heavy chain variable region comprising an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99% identical to the entire variable region or the framework region sequence of SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO: 20, SEQ ID NO: 22, or SEQ ID NO: 32. In certain embodiments, an isolated antibody that binds TIM-3 comprises an immunoglobulin heavy chain variable region comprising a CDRH1 comprising the amino acid sequence of SEQ ID NO: 1; a CDRH2 comprising the amino acid sequence of SEQ ID NO: 2; and a CDRH3 comprising the amino acid sequence of SEQ ID NO: 3; and an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99% identical to the entire variable region or the framework region sequence of SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO: 20, SEQ ID NO: 22, or SEQ ID NO: 32.
In certain embodiments, an isolated antibody that binds TIM-3 comprises an immunoglobulin light chain variable region comprising an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99% identical to the entire variable region or the framework region sequence of SEQ ID NO: 15, SEQ ID NO: 17, SEQ ID NO: 19, SEQ ID NO: 21, or SEQ ID NO: 31. In certain embodiments, an isolated antibody that binds TIM-3 comprises an immunoglobulin light chain variable region comprising a CDRL1 comprising the amino acid sequence of SEQ ID NO: 4; a CDRL2 comprising the amino acid sequence of SEQ ID NO: 5; and a CDRL3 comprising the amino acid sequence of SEQ ID NO: 6; and an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99% identical to the entire variable region or the framework region sequence of SEQ ID NO: 15, SEQ ID NO: 17, SEQ ID NO: 19, SEQ ID NO: 21, or SEQ ID NO: 31.
Sequence identity may be determined in various ways that are within the skill in the art, e.g., using publicly available computer software such as BLAST, BLAST-2, ALIGN or Megalign (DNASTAR) software. BLAST (Basic Local Alignment Search Tool) analysis using the algorithm employed by the programs blastp, blastn, blastx, tblastn and tblastx (Karlin et al., (1990) P
In each of the foregoing embodiments, it is contemplated herein that immunoglobulin heavy chain variable region sequences and/or light chain variable region sequences that together bind TIM-3 may contain amino acid alterations (e.g., at least 1, 2, 3, 4, 5, or 10 amino acid substitutions, deletions, or additions) in the framework regions of the heavy and/or light chain variable regions. In certain embodiments, the amino acid alterations are conservative substitutions. As used herein, the term “conservative substitution” refers to a substitution with a structurally similar amino acid. For example, conservative substitutions may include those within the following groups: Ser and Cys; Leu, Ile, and Val; Glu and Asp; Lys and Arg; Phe, Tyr, and Trp; and Gln, Asn, Glu, Asp, and His. Conservative substitutions may also be defined by the BLAST (Basic Local Alignment Search Tool) algorithm, the BLOSUM substitution matrix (e.g., BLOSUM 62 matrix), or the PAM substitution:p matrix (e.g., the PAM 250 matrix).
In certain embodiments, the antibody binds TIM-3 with a KD of 20 nM, 15 nM, 10 nM, 9 nM, 8 nM, 7 nM, 6 nM, 5 nM, 4 nM, 3 nM, 2 nM, 1 nM or lower. Unless otherwise specified, KD values are determined by surface plasmon resonance. For example, surface plasmon resonance can be measured using a GE Healthcare Biacore 4000 instrument as follows. Goat anti-human Fc antibody (Jackson Immunoresearch Laboratories #109-005-098) is immobilized on BIAcore carboxymethylated dextran CM5 chip using direct coupling to free amino groups following the procedure described by the manufacturer. Antibodies are captured on the CMS biosensor chip to achieve approximately 200 response units (RU). Binding measurements are performed using the running HBS-EP+ buffer. A 2-fold dilution series starting at 100 nM of anti-TIM-3 antibodies are injected at a flow rate of 30 μl/min at 25° C. Association rates (kon, M-1s-1) and dissociation rates (koff, s-1) are calculated using a simple 1:1 Langmuir binding model (Biacore 4000 Evaluation Software). The equilibrium dissociation constant (KD, M) is calculated as the ratio of koff/kon.
In some embodiments, monoclonal antibodies bind to the same epitope on TIM-3 as any of the anti-TIM-3 antibodies disclosed herein (e.g., M6903). In some embodiments, monoclonal antibodies compete for binding to TIM-3 with any of the anti-TIM-3 antibodies disclosed herein. For example, monoclonal antibodies may compete for binding to the galectin-9 binding domain of TIM-3 with an anti-TIM-3 antibody described herein. In another example, monoclonal antibodies may compete for binding to the PtdSer binding domain of TIM-3 with an anti-TIM-3 antibody described herein. In another example, monoclonal antibodies may compete for binding to the CEACAM1 binding domain of TIM-3 with an anti-TIM-3 antibody described herein. In a further example, monoclonal antibodies may compete for binding to the galectin-9 binding domain and the PtdSer binding domain of TIM-3 with an anti-TIM-3 antibody described herein. In another example, monoclonal antibodies may compete for binding to the galectin-9 binding domain and the CEACAM1 binding domain of TIM-3 with an anti-TIM-3 antibody described herein. In another example, monoclonal antibodies may compete for binding to the PtdSer binding domain and the CEACAM1 binding domain of TIM-3 with an anti-TIM-3 antibody described herein. In another example, monoclonal antibodies may compete for binding to the galectin-9 binding domain, the PtdSer binding domain, and the CEACAM1 binding domain of TIM-3 with an anti-TIM-3 antibody described herein.
Competition assays for determining whether an antibody binds to the same epitope as an anti-TIM-3 antibody described herein, or competes for binding with galectin-9, PtdSer, and/or CEACAM1 with an anti-TIM-3 antibody described herein are known in the art. Exemplary competition assays include immunoassays (e.g., ELISA assays, RIA assays), BIAcore analysis, biolayer interferometry and flow cytometry.
Typically, a competition assay involves the use of an antigen (e.g., a TIM-3 protein or fragment thereof) bound to a solid surface or expressed on a cell surface, a test TIM-3-binding antibody and a reference antibody (e.g., antibody M6903). The reference antibody is labeled and the test antibody is unlabeled. Competitive inhibition is measured by determining the amount of labeled reference antibody bound to the solid surface or cells in the presence of the test antibody. Usually the test antibody is present in excess (e.g., 1×, 5×, 10×, 20× or 100×). Antibodies identified by competition assay (i.e., competing antibodies) include antibodies binding to the same epitope, or similar (e.g., overlapping) epitopes, as the reference antibody, and antibodies binding to an adjacent epitope sufficiently proximal to the epitope bound by the reference antibody for steric hindrance to occur.
In an exemplary competition assay, a reference TIM-3 antibody (e.g., antibody M6903) is biotinylated using commercially available reagents. The biotinylated reference antibody is mixed with serial dilutions of the test antibody or unlabeled reference antibody (self-competition control) resulting in a mixture of various molar ratios (e.g., 1×, 5×, 10×, 20× or 100×) of test antibody (or unlabeled reference antibody) to labeled reference antibody. The antibody mixture is added to a TIM-3 (e.g., TIM-3 extracellular domain) polypeptide coated-ELISA plate. The plate is then washed and HRP (horseradish peroxidase)-strepavidin is added to the plate as the detection reagent. The amount of labeled reference antibody bound to the target antigen is detected following addition of a chromogenic substrate (e.g., TMB (3,3′,5,5′-tetramethylbenzidine) or ABTS (2,2″-azino-di-(3-ethylbenzthiazoline-6-sulfonate)), which are well-known in the art. Optical density readings (OD units) are measured using a SpectraMax M2 spectrometer (Molecular Devices). OD units corresponding to zero percent inhibition are determined from wells without any competing antibody. OD units corresponding to 100% inhibition, i.e., the assay background are determined from wells without any labeled reference antibody or test antibody. Percent inhibition of labeled reference antibody to TIM-3 by the test antibody (or the unlabeled reference antibody) at each concentration is calculated as follows: % inhibition=(1−(OD units−100% inhibition)/(0% inhibition−100% inhibition))*100. Persons skilled in the art will appreciate that the competition assay can be performed using various detection systems well-known in the art.
A competition assay may be conducted in both directions to ensure that the presence of the label does not interfere or otherwise inhibit binding. For example, in the first direction the reference antibody is labeled and the test antibody is unlabeled, and in the second direction, the test antibody is labeled and the reference antibody is unlabeled.
A test antibody competes with the reference antibody for specific binding to the antigen if an excess of one antibody (e.g., 1×, 5×, 10×, 20× or 100×) inhibits binding of the other antibody, e.g., by at least 50%, 75%, 90%, 95% or 99% as measured in a competitive binding assay.
Two antibodies may be determined to bind to the same epitope if essentially all amino acid mutations in the antigen that reduce or eliminate binding of one antibody reduce or eliminate binding of the other. Two antibodies may be determined to bind to overlapping epitopes if only a subset of the amino acid mutations that reduce or eliminate binding of one antibody reduce or eliminate binding of the other.
The anti-TIM-3 antibodies described herein can be administered in combination with any anti-PD-L1/TGFβ Trap known in the art. “Anti-PD-L1/TGFβ Trap” refers to a fusion molecule comprising 1) an antibody or antigen-binding fragment thereof that is capable of binding PD-L1 and antagonizing the interaction between PD-1 and PD-L1 and 2) a TGFβRII or fragment of TGFβRII that is capable of binding TGFβ and antagonizing the interaction between TGFβ and TGFβRII.
In one embodiment, the anti-PD-L1/TGFβ Trap comprises an anti-PD-L1 antibody known in the art. Anti-PD-L1 antibodies are commercially available, for example, the 29E2A3 antibody (Biolegend, Cat. No. 329701). Antibodies can be monoclonal, chimeric, humanized, or human. Antibody fragments include Fab, F(ab′)2, scFv and Fv fragments, which are described in further detail below.
Exemplary anti-PD-L1 antibodies are described in PCT Publication WO 2013/079174, which describes avelumab. These antibodies can include a heavy chain variable region polypeptide including a CDRH1, CDRH2, and CDRH3 sequence, where:
(a) the CDRH1 sequence is X1YX2MX3 (SEQ ID NO: 58);
(b) the CDRH2 sequence is SIYPSGGX4TFYADX5VKG (SEQ ID NO: 59);
(c) the CDRH3 sequence is IKLGTVTTVX6Y (SEQ ID NO: 60);
further where: X1 is K, R, T, Q, G, A, W, M, I, or S; X2 is V, R, K, L, M, or I; X3 is H, T, N, Q, A, V, Y, W, F, or M; X4 is F or I; X5 is S or T; X6 is E or D.
In a one embodiment, X1 is M, I, or S; X2 is R, K, L, M, or I; X3 is F or M; X4 is F or I; X5 is S or T; X6 is E or D.
In another embodiment X1 is M, I, or S; X2 is L, M, or I; X3 is F or M; X4 is I; X5 is S or T; X6 is D.
In still another embodiment, X1 is S; X2 is I; X3 is M; X4 is I; X5 is T; X6 is D.
In another aspect, the polypeptide further includes variable region heavy chain framework (FR) sequences juxtaposed between the CDRs according to the formula: (HC-FR1)-(CDRH1)-(HC-FR2)-(CDRH2)-(HC-FR3)-(CDRH3)-(HC-FR4).
In yet another aspect, the framework sequences are derived from human consensus framework sequences or human germline framework sequences.
In a still further aspect, at least one of the framework sequences is the following:
In a still further aspect, the heavy chain polypeptide is further combined with a variable region light chain including a CDRL1, CDRL2, and CDRL3, where:
(a) the CDRL1 sequence is TGTX7X8DVGX9YNYVS (SEQ ID NO: 65);
(b) the CDRL2 sequence is X10VX11X12RPS (SEQ ID NO: 66);
(c) the CDRL3 sequence is SSX13TX14X15X16X17RV (SEQ ID NO: 67);
further where: X7 is N or S; X8 is T, R, or S; X9 is A or G; X10 is E or D; X11 is I, N or S; X12 is D, H or N; X13 is F or Y; X14 is N or S; X15 is R, T or S; X16 is G or S; X17 is I or T.
In another embodiment, X7 is N or S; X8 is T, R, or S; X9 is A or G; X10 is E or D; X11 is N or S; X12 is N; X13 is F or Y; X14 is S; X15 is S; X16 is G or S; X17 is T.
In still another embodiment, X7 is S; X8 is S; X9 is G; X10 is D; X11 is S; X12 is N; X13 is Y; X14 is S; X15 is S; X16 is S; X17 is T.
In a still further aspect, the light chain further includes variable region light chain framework sequences juxtaposed between the CDRs according to the formula: (LC-CDRL1)-(LC-FR2)-(CDRL2)-(LC-FR3)-(CDRL3)-(LC-FR4).
In a still further aspect, the light chain framework sequences are derived from human consensus framework sequences or human germline framework sequences.
In a still further aspect, the light chain framework sequences are lambda light chain sequences.
In a still further aspect, at least one of the framework sequence is the following:
In another embodiment, the invention provides an anti-PD-L1 antibody or antigen binding fragment including a heavy chain and a light chain variable region sequence, where:
(a) the heavy chain includes a CDRH1, CDRH2, and CDRH3, wherein further: (i) the CDRH1 sequence is X1YX2MX3 (SEQ ID NO: 72); (ii) the CDRH2 sequence is SIYPSGGX4TFYADX5VKG (SEQ ID NO: 73); (iii) the CDRH3 sequence is IKLGTVTTVX6Y (SEQ ID NO: 74), and;
(b) the light chain includes a CDRL1, CDRL2, and CDRL3, wherein further: (iv) the CDRL1 sequence is TGTX7X8DVGX9YNYVS (SEQ ID NO: 75); (v) the CDRL2 sequence is X10VX11X12RPS (SEQ ID NO: 76); (vi) the CDRL3 sequence is SSX13TX14X15X16X17RV (SEQ ID NO: 77); wherein: X1 is K, R, T, Q, G, A, W, M, I, or S; X2 is V, R, K, L, M, or I; X3 is H, T, N, Q, A, V, Y, W, F, or M; X4 is F or I; X5 is S or T; X6 is E or D; X7 is N or S; X8 is T, R, or S; X9 is A or G; X10 is E or D; X11 is I, N, or S; X12 is D, H, or N; X13 is F or Y; X14 is N or S; X15 is R, T, or S; X16 is G or S; X17 is I or T.
In one embodiment, X1 is M, I, or S; X2 is R, K, L, M, or I; X3 is F or M; X4 is F or I; X5 is S or T; X6 is E or D; X7 is N or S; X8 is T, R, or S; X9 is A or G; X10 is E or D; X11 is N or S; X12 is N; X13 is F or Y; X14 is S; X15 is S; X16 is G or S; X17 is T.
In another embodiment, X1 is M, I, or S; X2 is L, M, or I; X3 is F or M; X4 is I; X5 is S or T; X6 is D; X7 is N or S; X8 is T, R, or S; X9 is A or G; X10 is E or D; X11 is N or S; X12 is N; X13 is F or Y; X14 is S; X15 is S; X16 is G or S; X17 is T.
In still another embodiment, X1 is S; X2 is I; X3 is M; X4 is I; X5 is T; X6 is D; X7 is S; X8 is S; X9 is G; X10 is D; X11 is S; X12 is N; X13 is Y; X14 is S; X15 is S; X16 is S; X17 is T.
In a further aspect, the heavy chain variable region includes one or more framework sequences juxtaposed between the CDRs as: (HC-FR1)-(CDRH1)-(HC-FR2)-(CDRH2)-(HC-FR3)-(CDRH3)-(HC-FR4), and the light chain variable regions include one or more framework sequences juxtaposed between the CDRs as: (LC-FR1 MCDRL1)-(LC-FR2)-(CDRL2)-(LC-FR3)-(CDRL3)-(LC-FR4).
In a still further aspect, the framework sequences are derived from human consensus framework sequences or human germline sequences.
In a still further aspect, one or more of the heavy chain framework sequences is the following:
In a still further aspect, the light chain framework sequences are lambda light chain sequences.
In a still further aspect, one or more of the light chain framework sequences is the following:
In a still further aspect, the heavy chain variable region polypeptide, antibody, or antibody fragment further includes at least a CH1 domain.
In a more specific aspect, the heavy chain variable region polypeptide, antibody, or antibody fragment further includes a CH1, a CH2, and a CH3 domain.
In a still further aspect, the variable region light chain, antibody, or antibody fragment further includes a CL domain.
In a still further aspect, the antibody further includes a CH1, a CH2, a CH3, and a CL domain.
In a still further specific aspect, the antibody further includes a human or murine constant region.
In a still further aspect, the human constant region is selected from the group consisting of IgG1, IgG2, IgG2, IgG3, IgG4.
In a still further specific aspect, the human or murine constant region is IgG1.
In yet another embodiment, the invention features an anti-PD-L1 antibody including a heavy chain and a light chain variable region sequence, where:
(a) the heavy chain includes a CDRH1, a CDRH2, and a CDRH3, having at least 80% overall sequence identity to SYIMM (SEQ ID NO: 78), SIYPSGGITFYADTVKG (SEQ ID NO: 79), and IKLGTVTTVDY (SEQ ID NO: 80), respectively, and
(b) the light chain includes a CDRL1, a CDRL2, and a CDRL3, having at least 80% overall sequence identity to TGTSSDVGGYNYVS (SEQ ID NO: 81), DVSNRPS (SEQ ID NO: 82), and SSYTSSSTRV (SEQ ID NO: 83), respectively.
In a specific aspect, the sequence identity is 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%.
In yet another embodiment, the invention features an anti-PD-L1 antibody including a heavy chain and a light chain variable region sequence, where:
(a) the heavy chain includes a CDRH1, a CDRH2, and a CDRH3, having at least 80% overall sequence identity to MYMMM (SEQ ID NO: 84), SIYPSGGITFYADSVKG (SEQ ID NO: 85), and IKLGTVTTVDY (SEQ ID NO: 80), respectively, and
(b) the light chain includes a CDRL1, a CDRL2, and a CDRL3, having at least 80% overall sequence identity to TGTSSDVGAYNYVS (SEQ ID NO: 86), DVSNRPS (SEQ ID NO: 82), and SSYTSSSTRV (SEQ ID NO: 83), respectively.
In a specific aspect, the sequence identity is 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%.
In a still further aspect, in the antibody or antibody fragment according to the invention, as compared to the sequences of CDRH1, CDRH2, and CDRH3, at least those amino acids remain unchanged that are highlighted by underlining as follows:
and further where, as compared to the sequences of CDRL1, CDRL2, and CDRL3 at least those amino acids remain unchanged that are highlighted by underlining as follows:
In another aspect, the heavy chain variable region includes one or more framework sequences juxtaposed between the CDRs as: (HC-FR1)-(CDRH1)-(HC-FR2)-(CDRH2)-(HC-FR3)-(CDRH3)-(HC-FR4), and the light chain variable regions include one or more framework sequences juxtaposed between the CDRs as: (LC-FR1)-(CDRL1)-(LC-FR2)-(CDRL2)-(LC-FR3)-(CDRL3)-(LC-FR4).
In yet another aspect, the framework sequences are derived from human germline sequences.
In a still further aspect, one or more of the heavy chain framework sequences is the following:
In a still further aspect, the light chain framework sequences are derived from a lambda light chain sequence.
In a still further aspect, one or more of the light chain framework sequences is the following:
In a still further specific aspect, the antibody further includes a human or murine constant region.
In a still further aspect, the human constant region is selected from the group consisting of IgG1, IgG2, IgG2, IgG3, IgG4.
In a still further embodiment, the invention features an anti-PD-L1 antibody including a heavy chain and a light chain variable region sequence, where:
(a) the heavy chain sequence has at least 85% sequence identity to the heavy chain sequence: EVQLLESGGGLVQPGGSLRLSCAASGFTFSSYIMMVWRQAPGKGLEWVSSIYPSGGITF YADWKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARIKLGTVTTVDYWGQGTLVT VSS (SEQ ID NO: 87), and
(b) the light chain sequence has at least 85% sequence identity to the light chain sequence: QSALTQPASVSGSPGQSITISCTGTSSDVGGYNYVSWYQQHPGKAPKLMIYDVSN RPSGVSNRFSGSKSGNTASLTISGLQAEDEADYYCSSYTSSSTRVFGTGTKVTVL (SEQ ID NO: 88).
In a specific aspect, the sequence identity is 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%.
In a still further embodiment, the invention provides for an anti-PD-L1 antibody including a heavy chain and a light chain variable region sequence, where:
(a) the heavy chain sequence has at least 85% sequence identity to the heavy chain sequence: EVQLLESGGGLVQPGGSLRLSCAASGFTFSMYMMMWVRQAPGKGLEVWSSIYPSGGIT FYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAIYYCARIKLGTVTTVDYWG QGTLVTVSS (SEQ ID NO: 89), and
(b) the light chain sequence has at least 85% sequence identity to the light chain sequence: QSALTQPASVSGSPGQSMSCTGTSSDVGAYNYVSWYQQHPGKAPKLMIYDVSNR PSGVSNRFSGSKSGNTASLTISGLQAEDEADYYCSSYTSSSTRVFGTGTKVTVL (SEQ ID NO: 90).
In a specific aspect, the sequence identity is 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%.
In a particular embodiment, anti-PD-L1/TGFβ Trap is one of the fusion molecules disclosed in WO 2015/118175 or WO 2018/205985. For instance, anti-PD-LUTGFβ Trap may comprise the light chains and heavy chains of SEQ ID NO: 1 and SEQ ID NO: 3 of WO 2015/118175, respectively. In another embodiment, anti-PD-L1/TGFβ Trap is one of the constructs listed in Table 2 of WO 2018/205985, such as construct 9 or 15 thereof. In other embodiments, the antibody having the heavy chain sequence of SEQ ID NO: 11 and the light chain sequence of SEQ ID NO: 12 of WO 2018/205985 is fused via a linking sequence (G4S)xG, wherein x is 4-5, to the TGFβRII extracellular domain sequence of SEQ ID NO: 14 or SEQ ID NO: 15 of WO 2018/205985.
In one embodiment, the anti-PD-L1/TGFβ Trap is a protein having the amino acid sequence of bintrafusp alfa, as described in International Patent Publication WO 2015/118175 and as reflected by the amino acid sequence given by CAS Registry Number 1918149-01-5. Bintrafusp alfa comprises a light chain that is identical to the light chain of an anti-PD-L1 antibody (SEQ ID NO: 91). Bintrafusp alfa further comprises a fusion polypeptide having the sequence corresponding SEQ ID NO: 93, composed of the heavy chain of an anti-PD-L1 antibody (SEQ ID NO: 92), wherein the C-terminal lysine residue of heavy chain was mutated to alanine, genetically fused to via a flexible (Gly4Ser)4Gly linker (SEQ ID NO: 97) to the N-terminus of the soluble TGFβ Receptor 11 (SEQ ID NO: 96). Bintrafusp alfa is encoded by SEQ ID NO: 94 (DNA encoding the anti-PD-L1 light chain) and SEQ ID NO: 95 (DNA encoding the anti-PD-L1/TGFβ Receptor II).
In one embodiment, the anti-PD-L1/TGFβ Trap is bintrafusp alfa, a protein having the amino acid sequence of bintrafusp alpha and also a glycosylation form that results from the protein being produced in CHO cells, wherein the heavy chain is glycosylated at Asn-300, Asn-518, Asn-542, and Asn-602 (i.e., of SEQ ID NO: 93). (See, WHO Drug Information, Vol. 32, No. 2, 2018, p. 293.)
DNA sequence from the translation initiation codon to the translation stop codon of the anti-PD-L1 lambda light chain (the leader sequence preceding the VL is the signal peptide from urokinase plasminogen activator)
atgagqgccctgctggctagactgctgctgtgcgtg
ctggtcgtgtccgacagcaagggcCAGTCCGCCCT
DNA sequence from the translation initiation codon to the translation stop codon (mVK SP leader: small underlined; VH: capitals; IgG1m3 with K to A mutation: small letters; (G4S)x4-G linker: bold capital letters; TGFβRII: bold underlined small letters; two stop codons: bold underlined capital letters)
atggaaacagacaccctgctgctgtgggtgctgct
gctgtgggtgcccggctccacaggcGAGGTGCAGC
GCAGCGGTGGCGGTGGCTCCGGCGGAGGTGGCTCC
GGA
atccctccccacgtgcagaagtccgtgaacaa
cgacatgatcgtgaccgacaacaacggcgccgtga
agttccctcagctgtgcaagttctgcgacgtgagg
ttcagcacctgcgacaaccagaagtcctgcatgag
caactgcagcatcacaagcatctgcgagaagcccc
aggaggtgtgtgtggccgtgtggaggaagaacgac
gaaaacatcaccctcgagaccgtgtgccatgaccc
caagctgccctaccacgacttcatcctggaagacg
ccgcctcccccaagtgcatcatgaaggagaagaa
gaagcccggcgagaccttcttcatgtgcagctgca
gcagcgacgagtgcaatgacaacatcatctttag
cgaggagtacaacaccagcaaccccgacTGATAA
Anti-PD-L1/TGFβ Trap molecules useful in the present invention may comprise sequences having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to any one of SEQ ID NOs: 91-96, as described above.
In some embodiments, the anti-PD-L1/TGFβ Trap is an anti-PD-L1/TGFβ Trap molecule disclosed in WO 2018/205985. For example, the anti-PD-L1/TGFβ Trap is one of the constructs listed in Table 2 of WO 2018/205985, such as construct 9 or 15 thereof.
In other embodiments, anti-PD-L1/TGFβ Trap is a heterotetramer, consisting of two polypeptides each having the light chain sequence corresponding to SEQ ID NO: 12 of WO 2018/205985 and two fusion polypeptides each having the heavy chain sequence corresponding to SEQ ID NO: 11 of WO 2018/205985 fused via a linker sequence (G4S)xG (wherein x can be 4 or 5) (SEQ ID NO: 117) to the TGFβRII extracellular domain sequence corresponding to SEQ ID NO: 14 (wherein “x” of the linker sequence is 4) or SEQ ID NO: 15 (wherein “x” of the linker sequence is 5) of WO 2018/205985.
In certain embodiments, an anti-PD-L1/TGFβ Trap molecule includes a first and a second polypeptide. The first polypeptide includes: (a) at least a variable region of a heavy chain of an antibody that binds to human protein Programmed Death Ligand 1 (PD-L1); and (b) human Transforming Growth Factor Receptor II (TGFβRII), or a fragment thereof, capable of binding Transforming Growth Factor β (TGFβ) (e.g., a soluble fragment). The second polypeptide includes at least a variable region of a light chain of an antibody that binds PD-L1, in which the heavy chain of the first polypeptide and the light chain of the second polypeptide, when combined, form an antigen binding site that binds PD-L1 (e.g., any of the antibodies or antibody fragments described herein). In certain embodiments, the anti-PD-L1/TGFβ Trap molecule is a heterotetramer, comprising the two immunoglobulin light chains of anti-PD-L1, and two heavy chains comprising the heavy chain of anti-PD-L1 genetically fused via a flexible glycine-serine linker (e.g., (G4S)xG (wherein x can be 4 or 5) (SEQ ID NO: 117)) to the extracellular domain of the human TGFβRII.
Anti-PD-L1/TGFβ Trap molecules useful in the present invention may comprise sequences having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to any one of SEQ ID NOs: 104-116, as described above.
Methods for producing antibodies, such as those disclosed herein, are known in the art. For example, DNA molecules encoding light chain variable regions and/or heavy chain variable regions can be chemically synthesized using the sequence information provided herein. Synthetic DNA molecules can be ligated to other appropriate nucleotide sequences, including, e.g., constant region coding sequences, and expression control sequences, to produce conventional gene expression constructs encoding the desired antibodies. Production of defined gene constructs is within routine skill in the art.
Nucleic acids encoding desired antibodies can be incorporated (ligated) into expression vectors, which can be introduced into host cells through conventional transfection or transformation techniques. Exemplary host cells are E. coli cells, Chinese hamster ovary (CHO) cells, human embryonic kidney 293 (HEK 293) cells, HeLa cells, baby hamster kidney (BHK) cells, monkey kidney cells (COS), human hepatocellular carcinoma cells (e.g., Hep G2), and myeloma cells that do not otherwise produce IgG protein. Transformed host cells can be grown under conditions that permit the host cells to express the genes that encode the immunoglobulin light and/or heavy chain variable regions.
Specific expression and purification conditions will vary depending upon the expression system employed. For example, if a gene is to be expressed in E. coli, it is first cloned into an expression vector by positioning the engineered gene downstream from a suitable bacterial promoter, e.g., Trp or Tac, and a prokaryotic signal sequence. The expressed secreted protein accumulates in refractile or inclusion bodies, and can be harvested after disruption of the cells by French press or sonication. The refractile bodies then are solubilized, and the proteins refolded and cleaved by methods known in the art.
If the engineered gene is to be expressed in eukaryotic host cells, e.g., CHO cells, it is first inserted into an expression vector containing a suitable eukaryotic promoter, a secretion signal, a poly A sequence, and a stop codon, and, optionally, may contain enhancers, and various introns. This expression vector optionally contains sequences encoding all or part of a constant region, enabling an entire, or a part of, a heavy or light chain to be expressed. The gene construct can be introduced into eukaryotic host cells using conventional techniques. The host cells express VL or VH fragments, VL-VH heterodimers, VH-VL or VL-VH single chain polypeptides, complete heavy or light immunoglobulin chains, or portions thereof, each of which may be attached to a moiety having another function (e.g., cytotoxicity). In some embodiments, a host cell is transfected with a single vector expressing a polypeptide expressing an entire, or part of, a heavy chain (e g., a heavy chain variable region) or a light chain (e g., a light chain variable region). In other embodiments, a host cell is transfected with a single vector encoding (a) a polypeptide comprising a heavy chain variable region and a polypeptide comprising a light chain variable region, or (b) an entire immunoglobulin heavy chain and an entire immunoglobulin light chain. In still other embodiments, a host cell is co-transfected with more than one expression vector (e.g., one expression vector expressing a polypeptide comprising an entire, or part of, a heavy chain or heavy chain variable region, and another expression vector expressing a polypeptide comprising an entire, or part of a light chain or light chain variable region).
A polypeptide comprising an immunoglobulin heavy chain variable region or light chain variable region can be produced by growing (culturing) a host cell transfected with an expression vector encoding such variable region, under conditions that permit expression of the polypeptide. Following expression, the polypeptide can be harvested and purified or isolated using techniques well known in the art, e.g., affinity tags such as glutathione-S-transferase (GST) and histidine tags.
A monoclonal antibody that binds human TIM-3, or an antigen-binding fragment of the antibody, can be produced by growing (culturing) a host cell transfected with: (a) an expression vector that encodes a complete or partial immunoglobulin heavy chain, and a separate expression vector that encodes a complete or partial immunoglobulin light chain; or (b) a single expression vector that encodes both chains (e.g., complete or partial heavy and light chains), under conditions that permit expression of both chains. The intact antibody (or antigen-binding fragment) can be harvested and purified or isolated using techniques well known in the art, e.g., Protein A, Protein G, affinity tags such as glutathione-S-transferase (GST) and histidine tags. It is within ordinary skill in the art to express the heavy chain and the light chain from a single expression vector or from two separate expression vectors.
Human monoclonal antibodies can be isolated or selected from phage display libraries including immune, naive and synthetic libraries. Antibody phage display libraries are known in the art, see, e.g., Hoet et al., N
In some embodiments, isolated human antibodies contain one or more somatic mutations in a framework region. In these cases, framework regions can be modified to a human germline sequence to optimize the antibody (i.e., a process referred to as germlining).
Generally, an optimized antibody has at least the same, or substantially the same, affinity for the antigen as the non-optimized (or parental) antibody from which it was derived. Preferably, an optimized antibody has a higher affinity for the antigen when compared to the parental antibody.
Antibody Fragments
The proteins and polypeptides of the invention can also include antigen-binding fragments of antibodies. Exemplary antibody fragments include scFv, Fv, Fab, F(ab′)2, and single domain VHH fragments such as those of camelid origin.
Single-chain antibody fragments, also known as single-chain antibodies (scFvs), are recombinant polypeptides which typically bind antigens or receptors; these fragments contain at least one fragment of an antibody variable heavy-chain amino acid sequence (VH) tethered to at least one fragment of an antibody variable light-chain sequence (VL) with or without one or more interconnecting linkers. Such a linker may be a short, flexible peptide selected to assure that the proper three-dimensional folding of the VL and VH domains occurs once they are linked so as to maintain the target molecule binding-specificity of the whole antibody from which the single-chain antibody fragment is derived. Generally, the carboxyl terminus of the VL or VH sequence is covalently linked by such a peptide linker to the amino acid terminus of a complementary VL and VH sequence. Single-chain antibody fragments can be generated by molecular cloning, antibody phage display library or similar techniques. These proteins can be produced either in eukaryotic cells or prokaryotic cells, including bacteria.
Single-chain antibody fragments contain amino acid sequences having at least one of the variable regions or CDRs of the whole antibodies described in this specification, but are lacking some or all of the constant domains of those antibodies. These constant domains are not necessary for antigen binding, but constitute a major portion of the structure of whole antibodies. Single-chain antibody fragments may therefore overcome some of the problems associated with the use of antibodies containing part or all of a constant domain. For example, single-chain antibody fragments tend to be free of undesired interactions between biological molecules and the heavy-chain constant region, or other unwanted biological activity. Additionally, single-chain antibody fragments are considerably smaller than whole antibodies and may therefore have greater capillary permeability than whole antibodies, allowing single-chain antibody fragments to localize and bind to target antigen-binding sites more efficiently. Also, antibody fragments can be produced on a relatively large scale in prokaryotic cells, thus facilitating their production. Furthermore, the relatively small size of single-chain antibody fragments makes them less likely than whole antibodies to provoke an immune response in a recipient.
Fragments of antibodies that have the same or comparable binding characteristics to those of the whole antibody may also be present. Such fragments may contain one or both Fab fragments or the F(ab′)2 fragment. The antibody fragments may contain all six CDRs of the whole antibody, although fragments containing fewer than all of such regions, such as three, four or five CDRs, are also functional.
Constant Regions
Unless otherwise specified, constant region antibody amino acid residues are numbered according to the Kabat EU index in Kabat, E.A. et al., (Sequences of proteins of immunological interest. 5th Edition—US Department of Health and Human Services, NIH publication no 91-3242, pp 662,680,689 (1991)). The antibodies and fragments thereof (e.g., parental and optimized variants) as described herein can be engineered to contain certain constant (i.e., Fc) regions with or lacking a specified effector function (e.g., antibody-dependent cellular cytotoxicity (ADCC)). Human constant regions are known in the art.
The proteins and peptides (e.g., antibodies) of the invention can include a constant region of an immunoglobulin or a fragment, analog, variant, mutant, or derivative of the constant region. In preferred embodiments, the constant region is derived from a human immunoglobulin heavy chain, for example, IgG1, IgG2, IgG3, IgG4, or other classes. In one embodiment, the constant region includes a CH2 domain. In another embodiment, the constant region includes CH2 and CH3 domains or includes hinge-CH2-CH3. Alternatively, the constant region can include all or a portion of the hinge region, the CH2 domain and/or the CH3 domain.
In one embodiment, the constant region contains a mutation that reduces affinity for an Fc receptor or reduces Fc effector function. For example, the constant region can contain a mutation that eliminates the glycosylation site within the constant region of an IgG heavy chain. In some embodiments, the constant region contains mutations, deletions, or insertions at an amino acid position corresponding to Leu234, Leu235, Gly236, Gly237, Asn297, or Pro331 of IgG1 (amino acids are numbered according to Kabat EU index). In a particular embodiment, the constant region contains a mutation at an amino acid position corresponding to Asn297 of IgG1. In alternative embodiments, the constant region contains mutations, deletions, or insertions at an amino acid position corresponding to Leu281, Leu282, Gly283, Gly284, Asn344, or Pro378 of IgG1.
In some embodiments, the constant region contains a CH2 domain derived from a human IgG2 or IgG4 heavy chain Preferably, the CH2 domain contains a mutation that eliminates the glycosylation site within the CH2 domain. In one embodiment, the mutation alters the asparagine within the Gln-Phe-Asn-Ser (SEQ ID NO: 98) amino acid sequence within the CH2 domain of the IgG2 or IgG4 heavy chain. Preferably, the mutation changes the asparagine to a glutamine. Alternatively, the mutation alters both the phenylalanine and the asparagine within the Gln-Phe-Asn-Ser (SEQ ID NO: 98) amino acid sequence. In one embodiment, the Gln-Phe-Asn-Ser (SEQ ID NO: 98) amino acid sequence is replaced with a Gln-Ala-Gln-Ser (SEQ ID NO: 99) amino acid sequence. The asparagine within the Gln-Phe-Asn-Ser (SEQ ID NO: 98) amino acid sequence corresponds to Asn297 of IgG1 (Kabat EU index).
In another embodiment, the constant region includes a CH2 domain and at least a portion of a hinge region. The hinge region can be derived from an immunoglobulin heavy chain, e.g., IgG1, IgG2, IgG3, IgG4, or other classes. Preferably, the hinge region is derived from human IgG1, IgG2, IgG3, IgG4, or other suitable classes. More preferably the hinge region is derived from a human IgG1 heavy chain. In one embodiment the cysteine in the Pro-Lys-Ser-Cys-Asp-Lys (SEQ ID NO: 100) amino acid sequence of the IgG1 hinge region is altered. In a preferred embodiment the Pro-Lys-Ser-Cys-Asp-Lys (SEQ ID NO: 100) amino acid sequence is replaced with a Pro-Lys-Ser-Ser-Asp-Lys (SEQ ID NO: 101) amino acid sequence. In one embodiment, the constant region includes a CH2 domain derived from a first antibody isotype and a hinge region derived from a second antibody isotype. In a specific embodiment, the CH2 domain is derived from a human IgG2 or IgG4 heavy chain, while the hinge region is derived from an altered human IgG1 heavy chain.
The alteration of amino acids near the junction of the Fc portion and the non-Fc portion of an antibody or Fc fusion protein can dramatically increase the serum half-life of the Fc fusion protein (PCT publication WO 01/58957, the disclosure of which is hereby incorporated by reference). Accordingly, the junction region of a protein or polypeptide of the present invention can contain alterations that, relative to the naturally-occurring sequences of an immunoglobulin heavy chain, preferably lie within about 10 amino acids of the junction point. These amino acid changes can cause an increase in hydrophobicity. In one embodiment, the constant region is derived from an IgG sequence in which the C-terminal lysine residue is replaced. Preferably, the C-terminal lysine of an IgG sequence is replaced with a non-lysine amino acid, such as alanine or leucine, to further increase serum half-life. In another embodiment, the constant region is derived from an IgG sequence in which the Leu-Ser-Leu-Ser (SEQ ID NO: 102) amino acid sequence near the C-terminus of the constant region is altered to eliminate potential junctional T-cell epitopes. For example, in one embodiment, the Leu-Ser-Leu-Ser (SEQ ID NO: 102) amino acid sequence is replaced with an Ala-Thr-Ala-Thr (SEQ ID NO: 103) amino acid sequence. In other embodiments, the amino acids within the Leu-Ser-Leu-Ser (SEQ ID NO: 102) segment are replaced with other amino acids such as glycine or proline. Detailed methods of generating amino acid substitutions of the Leu-Ser-Leu-Ser (SEQ ID NO: 102) segment near the C-terminus of an IgG1, IgG2, IgG3, IgG4, or other immunoglobulin class molecule have been described in U.S. Patent Publication No. 2003/0166877, the disclosure of which is hereby incorporated by reference.
Suitable hinge regions for the present invention can be derived from IgG1, IgG2, IgG3, IgG4, and other immunoglobulin classes. The IgG1 hinge region has three cysteines, two of which are involved in disulfide bonds between the two heavy chains of the immunoglobulin. These same cysteines permit efficient and consistent disulfide bonding formation between Fc portions. Therefore, a preferred hinge region of the present invention is derived from IgG1, more preferably from human IgG 1. In some embodiments, the first cysteine within the human IgG1 hinge region is mutated to another amino acid, preferably serine. The IgG2 isotype hinge region has four disulfide bonds that tend to promote oligomerization and possibly incorrect disulfide bonding during secretion in recombinant systems. A suitable hinge region can be derived from an IgG2 hinge; the first two cysteines are each preferably mutated to another amino acid. The hinge region of IgG4 is known to form interchain disulfide bonds inefficiently. However, a suitable hinge region for the present invention can be derived from the IgG4 hinge region, preferably containing a mutation that enhances correct formation of disulfide bonds between heavy chain-derived moieties (Angal S, et al. (1993) Mol. Immunol., 30:105-8).
In accordance with the present invention, the constant region can contain CH2 and/or CH3 domains and a hinge region that are derived from different antibody isotypes, i.e., a hybrid constant region. For example, in one embodiment, the constant region contains CH2 and/or CH3 domains derived from IgG2 or IgG4 and a mutant hinge region derived from IgG1. Alternatively, a mutant hinge region from another IgG subclass is used in a hybrid constant region. For example, a mutant form of the IgG4 hinge that allows efficient disulfide bonding between the two heavy chains can be used. A mutant hinge can also be derived from an IgG2 hinge in which the first two cysteines are each mutated to another amino acid. Assembly of such hybrid constant regions has been described in U.S. Patent Publication No. 2003/0044423, the disclosure of which is hereby incorporated by reference.
In accordance with the present invention, the constant region can contain one or more mutations described herein. The combinations of mutations in the Fc portion can have additive or synergistic effects on the prolonged serum half-life and increased in vivo potency of the molecule. Thus, in one exemplary embodiment, the constant region can contain (i) a region derived from an IgG sequence in which the Leu-Ser-Leu-Ser (SEQ ID NO: 102) amino acid sequence is replaced with an Ala-Thr-Ala-Thr (SEQ ID NO: 103) amino acid sequence; (ii) a C-terminal alanine residue instead of lysine; (iii) a CH2 domain and a hinge region that are derived from different antibody isotypes, for example, an IgG2 CH2 domain and an altered IgG1 hinge region; and (iv) a mutation that eliminates the glycosylation site within the IgG2-derived CH2 domain, for example, a Gln-Ala-Gln-Ser (SEQ ID NO: 99) amino acid sequence instead of the Gln-Phe-Asn-Ser (SEQ ID NO: 98) amino acid sequence within the IgG2-derived CH2 domain.
If the antibody is for use as a therapeutic, it can be conjugated to an effector agent such as a small molecule toxin or a radionuclide using standard in vitro conjugation chemistries. If the effector agent is a polypeptide, the antibody can be chemically conjugated to the effector agent or joined to the effector agent as a fusion protein. Construction of fusion proteins is within ordinary skill in the art.
The antibodies described herein can be used in a method of downregulating at least one exhaustion marker in a tumor microenvironment, the method comprising exposing the tumor microenvironment to an effective amount of an anti-TIM-3 antibody to downregulate at least one exhaustion marker, such as CTLA-4, LAG-3, PD-1, or TIM-3. Methods for measuring downregulation of exhaustion markers are known in the art, and include, for example, measuring an exhaustion marker on CD4+ and CD8+ T cells following treatment with an anti-TIM-3 antibody.
In certain embodiments, the method can further include exposing the tumor microenvironment to an effective amount of a second therapeutic agent, such as an immune checkpoint inhibitor. Examples of immune checkpoint inhibitors include inhibitors targeting PD-1, PD-L1, or CTLA-4.
The antibodies described herein also can be used in a method of potentiating T cell activation. The method can include exposing the T cell to an effective amount of an anti-TIM-3 antibody, thereby to potentiate the activation of the T cell. In certain embodiments, the method further includes exposing the T cell to an effective amount of a second therapeutic agent, such as an immune checkpoint inhibitor. Methods for measuring T cell activation are described in Example 2.3, and can include measuring IFN-γ production from human PBMCs that were activated by exposure to CEF antigens. In certain embodiments, the method can further include exposing the tumor microenvironment to an effective amount of a second therapeutic agent, such as an anti-PD-L1 antibody.
The antibodies disclosed herein can be used to treat various forms of cancer. In certain embodiments, the cancer or tumor may be selected from the group consisting of colorectal, breast, ovarian, pancreatic, gastric, prostate, renal, cervical, myeloma, lymphoma, leukemia, thyroid, endometrial, uterine, bladder, neuroendocrine, head and neck, liver, nasopharyngeal, testicular, small cell lung cancer, non-small cell lung cancer, melanoma, basal cell skin cancer, squamous cell skin cancer, dermatofibrosarcoma protuberans, Merkel cell carcinoma, glioblastoma, glioma, sarcoma, mesothelioma, and myelodysplastic syndromes. In certain embodiments, the cancer is diffuse large B-cell lymphoma, renal cell carcinoma (RCC), non-small cell lung carcinoma (NSCLC), squamous cell carcinoma of the head and neck (SCCHN), triple negative breast cancer (TNBC) or gastric/stomach adenocarcinoma (STAD). In certain embodiments, the cancer is metastatic or a locally advanced solid tumor. In certain embodiments, no standard therapy exists to treat the cancer and/or the cancer is relapsed and/or refractory from at least one prior treatment. The cancer cells are exposed to a therapeutically effective amount of the antibody so as to inhibit proliferation of the cancer cell. In some embodiments, the antibodies inhibit cancer cell proliferation by at least 40%, 50%, 60%, 70%, 80%, 90%, 95%, 98%, 99%, or 100%.
In some embodiments, the anti-TIM-3 antibody is used in therapy. For example, the antibody can be used to inhibit tumor growth in a mammal (e.g., a human patient). In some embodiments, use of the antibody to inhibit tumor growth in a mammal comprises administering to the mammal a therapeutically effective amount of the antibody. In other embodiments, the anti-TIM-3 antibody can be used for inhibiting proliferation of a tumor cell.
In some embodiments, the anti-TIM-3 antibody is administered in combination with another therapeutic agent, such as radiation (e.g., stereotactic radiation) or an immune checkpoint inhibitor (e.g., targeting PD-1, PD-L1, or CTLA-4). In some embodiments, the anti-TIM-3 antibody is administered in combination with one or more of the following therapeutic agents: anti-PD1/anti-PD-L1 antibodies including Keytruda® (pembrolizumab, Merck & Co.), Opdivo® (nivolumab, Bristol-Myers Squibb), Tecentriq® (atezolizumab, Roche), Imfinzi® (durvalumab, AstraZeneca), TGF-β pathway targeting agents including galunisertib (LY2157299 monohydrate, a small molecule kinase inhibitor of TGF-βRI), LY3200882 (a small molecule kinase inhibitor TGF-βRI disclosed by Pei et al. (2017) C
Methods of Treatment
As used herein, “treat,” “treating,” and “treatment” mean the treatment of a disease in a mammal, e.g., in a human. This includes: (a) inhibiting the disease, i.e., arresting its development; and (b) relieving the disease, i.e., causing regression of the disease state.
Generally, a therapeutically effective amount of anti-TIM-3 antibody or another therapeutic agent described herein (alone or in combination with another treatment, e.g., a second therapeutic agent) is in the range of about 0.1 mg/kg to about 100 mg/kg, e.g., about 1 mg/kg to about 100 mg/kg, e.g., 1 mg/kg to 10 mg/kg. In certain embodiments, a therapeutically effective amount of an anti-TIM-3 antibody or another therapeutic agent described herein can be administered at a dose from about 0.1 to about 1 mg/kg, from about 0.1 to about 5 mg/kg, from about 0.1 to about 10 mg/kg, from about 0.1 to about 25 mg/kg, from about 0.1 to about 50 mg/kg, from about 0.1 to about 75 mg/kg, from about 0.1 to about 100 mg/kg, from about 0.5 to about 1 mg/kg, from about 0.5 to about 5 mg/kg, from about 0.5 to about 10 mg/kg, from about 0.5 to about 25 mg/kg, from about 0.5 to about 50 mg/kg, from about 0.5 to about 75 mg/kg, from about 0.5 to about 100 mg/kg, from about 1 to about 5 mg/kg, from about 1 to about 10 mg/kg, from about 1 to about 25 mg/kg, from about 1 to about 50 mg/kg, from about 1 to about 75 mg/kg, from about 1 to about 100 mg/kg, from about 5 to about 10 mg/kg, from about 5 to about 25 mg/kg, from about 5 to about 50 mg/kg, from about 5 to about 75 mg/kg, from about 5 to about 100 mg/kg, from about 10 to about 25 mg/kg, from about 10 to about 50 mg/kg, from about 10 to about 75 mg/kg, from about 10 to about 100 mg/kg, from about 25 to about 50 mg/kg, from about 25 to about 75 mg/kg, from about 25 to about 100 mg/kg, from about 50 to about 75 mg/kg, from about 50 to about 100 mg/kg, from about 75 to about 100 mg/kg. The amount administered will depend on variables such as the type and extent of disease or indication to be treated, the overall health of the patient, the in vivo potency of the antibody, the pharmaceutical formulation, and the route of administration. The initial dosage can be increased beyond the upper level in order to rapidly achieve the desired blood-level or tissue level. Alternatively, the initial dosage can be smaller than the optimum, and the dosage may be progressively increased during the course of treatment. Human dosage can be optimized, e.g., in a conventional Phase I dose escalation study designed to run from 0.5 mg/kg to 30 mg/kg.
In certain embodiments, the anti-TIM-3 antibody or another therapeutic agent described herein (alone or in combination with another treatment, e.g., a second therapeutic agent) can be administered as a flat (fixed) dose (rather than in proportion to a mammal's body weight, i.e., a mg/kg dosage). A therapeutically effective amount of an anti-TIM-3 antibody can be a flat (fixed) dose of about 5 mg to about 3500 mg. For example, the dose can be from about 5 to about 250 mg, from about 5 to about 500 mg, from about 5 to about 750 mg, from about 5 to about 1000 mg, from about 5 to about 1250 mg, from about 5 to about 1500 mg, from about 5 to about 1750 mg, from about 5 to about 2000 mg, from about 5 to about 2250 mg, from about 5 to about 2500 mg, from about 5 to about 2750 mg, from about 5 to about 3000 mg, from about 5 to about 3250 mg, from about 5 to about 3500 mg, from about 250 to about 500 mg, from about 250 to about 750 mg, from about 250 to about 1000 mg, from about 250 to about 1250 mg, from about 250 to about 1500 mg, from about 250 to about 1750 mg, from about 250 to about 2000 mg, from about 250 to about 2250 mg, from about 250 to about 2500 mg, from about 250 to about 2750 mg, from about 250 to about 3000 mg, from about 250 to about 3250 mg, from about 250 to about 3500 mg, from about 500 to about 750 mg, from about 500 to about 1000 mg, from about 500 to about 1250 mg, from about 500 to about 1500 mg, from about 500 to about 1750 mg, from about 500 to about 2000 mg, from about 500 to about 2250 mg, from about 500 to about 2500 mg, from about 500 to about 2750 mg, from about 500 to about 3000 mg, from about 500 to about 3250 mg, from about 500 to about 3500 mg, from about 750 to about 1000 mg, from about 750 to about 1250 mg, from about 750 to about 1500 mg, from about 750 to about 1750 mg, from about 750 to about 2000 mg, from about 750 to about 2250 mg, from about 750 to about 2500 mg, from about 750 to about 2750 mg, from about 750 to about 3000 mg, from about 750 to about 3250 mg, from about 750 to about 3500 mg, from about 1000 to about 1250 mg, from about 1000 to about 1500 mg, from about 1000 to about 1750 mg, from about 1000 to about 2000 mg, from about 1000 to about 2250 mg, from about 1000 to about 2500 mg, from about 1000 to about 2750 mg, from about 1000 to about 3000 mg, from about 1000 to about 3250 mg, from about 1000 to about 3500 mg, from about 1250 to about 1500 mg, from about 1250 to about 1750 mg, from about 1250 to about 2000 mg, from about 1250 to about 2250 mg, from about 1250 to about 2500 mg, from about 1250 to about 2750 mg, from about 1250 to about 3000 mg, from about 1250 to about 3250 mg, from about 1250 to about 3500 mg, from about 1500 to about 1750 mg, from about 1500 to about 2000 mg, from about 1500 to about 2250 mg, from about 1500 to about 2500 mg, from about 1500 to about 2750 mg, from about 1500 to about 3000 mg, from about 1500 to about 3250 mg, from about 1500 to about 3500 mg, from about 1750 to about 2000 mg, from about 1750 to about 2250 mg, from about 1750 to about 2500 mg, from about 1750 to about 2750 mg, from about 1750 to about 3000 mg, from about 1750 to about 3250 mg, from about 1750 to about 3500 mg, from about 2000 to about 2250 mg, from about 2000 to about 2500 mg, from about 2000 to about 2750 mg, from about 2000 to about 3000 mg, from about 2000 to about 3250 mg, from about 2000 to about 3500 mg, from about 2250 to about 2500 mg, from about 2250 to about 2750 mg, from about 2250 to about 3000 mg, from about 2250 to about 3250 mg, from about 2250 to about 3500 mg, from about 2500 to about 2750 mg, from about 2500 to about 3000 mg, from about 2500 to about 3250 mg, from about 2500 to about 3500 mg, from about 2750 to about 3000 mg, from about 2750 to about 3250 mg, from about 2750 to about 3500 mg, from about 3000 to about 3250 mg, from about 3000 to about 3500 mg, or from about 3250 to about 3500 mg. Human dosage can be optimized, e.g., in a conventional Phase I dose escalation study designed to run from a flat (fixed) dose of 5 mg to 3200 mg.
In a preferred embodiment, the anti-TIM-3 antibody is administered in a flat (fixed) dose of from about 20 mg to about 1600 mg. For example, the dose can be from about 20 mg to about 80 mg, from about 20 mg to about 240 mg, from about 20 mg to about 800 mg, from about 20 mg to about 1600 mg, from about 80 mg to about 240 mg, from about 80 mg to about 800 mg, from about 80 mg to about 1600 mg, from about 240 mg to about 800 mg, from about 240 mg to about 1600 mg, from about 800 mg to about 1600 mg. In certain embodiments the anti-TIM-3 antibody is administered in a flat (fixed) dose of about 20 mg, about 80 mg, about 240 mg, about 800 mg or about 1600 mg.
In certain embodiments, the anti-TIM-3 antibody is administered in combination with an anti-PD-L1/TGFβ Trap fusion protein (e.g., bintrafusp alfa), wherein the anti-PD-L1/TGFβ Trap fusion protein is administered at a flat (fixed) dose of about 800 mg to about 2600 mg (e.g., about 800 mg to about 1100 mg, about 800 mg to about 1200 mg, about 800 mg to about 1500 mg, about 800 mg to about 2000 mg, about 800 mg to about 2300 mg, about 800 mg to about 2400 mg, about 800 mg to about 2600 mg, about 1100 mg to about 1200 mg, about 1100 mg to about 1500 mg, about 1100 mg to about 2000 mg, about 1100 mg to about 2300 mg, about 1100 mg to about 2400 mg, about 1100 mg to about 2600 mg, about 1200 mg to about 1500 mg, about 1200 mg to about 2000 mg, about 1200 mg to about 2300 mg, about 1200 mg to about 2400 mg, about 1200 mg to about 2600 mg, about 1500 mg to about 2000 mg, about 1500 mg to about 2300 mg, about 1500 mg to about 2400 mg, about 1500 mg to about 2600 mg, about 2000 mg to about 2300 mg, about 2000 mg to about 2400 mg, about 2000 mg to about 2600 mg, about 2300 mg to about 2400 mg, about 2300 mg to about 2600 mg, or about 2400 mg to about 2600 mg. In certain embodiments, the anti-PD-L1/TGFβ Trap fusion protein is administered at a flat (fixed) dose of about 1200 mg. In certain further embodiments, the anti-TIM-3 antibody is administered in combination with an anti-PD-L1/TGFβ Trap fusion protein (e.g., bintrafusp alfa), wherein the anti-PD-L1/TGFβ Trap fusion protein is administered at a flat (fixed) dose of about 2400 mg.
Dosing frequency can vary, depending on factors such as route of administration, dosage amount, serum half-life of the antibody, and the disease being treated. Exemplary dosing frequencies are once per week, once every two weeks, once every three weeks and once every four weeks. In some embodiments, dosing is once every two weeks. In certain embodiments, the anti-TIM-3 antibody is administered in combination with an anti-PD-L1/TGFβ Trap fusion protein (e.g., bintrafusp alfa) every two weeks, wherein anti-PD-L1/TGFβ Trap fusion protein is administered at a flat (fixed) dose of about 1200 mg. In certain embodiments, the anti-TIM-3 antibody is administered in combination with an anti-PD-L1/TGFβ Trap fusion protein (e.g., bintrafusp alfa) every three weeks, wherein anti-PD-LUTGFβ Trap fusion protein is administered at a flat (fixed) dose of about 2400 mg.
A preferred route of administration is parenteral, e.g., intravenous infusion. Formulation of monoclonal antibody-based drugs is within ordinary skill in the art. In some embodiments, the antibody is lyophilized, and then reconstituted in buffered saline, at the time of administration.
For therapeutic use, an antibody preferably is combined with a pharmaceutically acceptable carrier. As used herein, “pharmaceutically acceptable carrier” means buffers, carriers, and excipients suitable for use in contact with the tissues of human beings and animals without excessive toxicity, irritation, allergic response, or other problem or complication, commensurate with a reasonable benefit/risk ratio. The carrier(s) should be “acceptable” in the sense of being compatible with the other ingredients of the formulations and not deleterious to the recipient. Pharmaceutically acceptable carriers include buffers, solvents, dispersion media, coatings, isotonic and absorption delaying agents, and the like, that are compatible with pharmaceutical administration. The use of such media and agents for pharmaceutically active substances is known in the art.
Pharmaceutical compositions containing antibodies, such as those disclosed herein, can be presented in a dosage unit form and can be prepared by any suitable method. A pharmaceutical composition should be formulated to be compatible with its intended route of administration. Examples of routes of administration are intravenous (IV), intradermal, inhalation, transdermal, topical, transmucosal, and rectal administration. A preferred route of administration for monoclonal antibodies is IV infusion. Useful formulations can be prepared by methods well known in the pharmaceutical art. For example, see Remington's Pharmaceutical Sciences, 18th ed. (Mack Publishing Company, 1990). Formulation components suitable for parenteral administration include a sterile diluent such as water for injection, saline solution, fixed oils, polyethylene glycols, glycerine, propylene glycol or other synthetic solvents; antibacterial agents such as benzyl alcohol or methyl paraben; antioxidants such as ascorbic acid or sodium bisulfite; chelating agents such as EDTA; buffers such as acetates, citrates or phosphates; and agents for the adjustment of tonicity such as sodium chloride or dextrose.
For intravenous administration, suitable carriers include physiological saline, bacteriostatic water, Cremophor ELTM (BASF, Parsippany, N.J.) or phosphate buffered saline (PBS). The carrier should be stable under the conditions of manufacture and storage, and should be preserved against microorganisms. The carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid polyethylene glycol), and suitable mixtures thereof.
Pharmaceutical formulations preferably are sterile. Sterilization can be accomplished, for example, by filtration through sterile filtration membranes. Where the composition is lyophilized, filter sterilization can be conducted prior to or following lyophilization and reconstitution.
The intravenous drug delivery formulation of the present disclosure for use in a method of treating cancer or inhibiting tumor growth in a mammal may be contained in a bag, a pen, or a syringe. In certain embodiments, the bag may be connected to a channel comprising a tube and/or a needle. In certain embodiments, the formulation may be a lyophilized formulation or a liquid formulation. In certain embodiments, the formulation may be freeze-dried (lyophilized) and contained. In certain embodiments, the about 40 mg-about 100 mg of freeze-dried formulation may be contained in one vial. In certain embodiments, the formulation may be a liquid formulation of a protein product that includes an anti-TIM-3 antibody as described herein and stored as about 250 mg/vial to about 2000 mg/vial.
Liquid Formulation
This disclosure provides a liquid aqueous pharmaceutical formulation including a therapeutically effective amount of the protein of the present disclosure (e.g., anti-TIM-3 antibody) in a buffered solution forming a formulation for use in a method of treating cancer or inhibiting tumor growth in a mammal.
These compositions for use in a method of treating cancer or inhibiting tumor growth in a mammal may be sterilized by conventional sterilization techniques, or may be sterile filtered. The resulting aqueous solutions may be packaged for use as-is, or lyophilized, the lyophilized preparation being combined with a sterile aqueous carrier prior to administration. The pH of the preparations typically will be between 3 and 11, more preferably between 5 and 9 or between 6 and 8, and most preferably between 7 and 8, such as 7 to 7.5. The resulting compositions in solid form may be packaged in multiple single dose units, each containing a fixed amount of the above-mentioned agent or agents. The composition in solid form can also be packaged in a container for a flexible quantity.
In certain embodiments, the present disclosure provides for use in a method of treating cancer or inhibiting tumor growth in a mammal, a formulation with an extended shelf life including a protein of the present disclosure (e.g., an anti-TIM-3 antibody), in combination with mannitol, citric acid monohydrate, sodium citrate, disodium phosphate dihydrate, sodium dihydrogen phosphate dihydrate, sodium chloride, polysorbate 80, water, and sodium hydroxide.
In certain embodiments, an aqueous formulation for use in a method of treating cancer or inhibiting tumor growth in a mammal is prepared including a protein of the present disclosure (e.g., an anti-TIM-3 antibody) in a pH-buffered solution. The buffer of this invention may have a pH ranging from about 4 to about 8, e.g., from about 4 to about 8, from about 4.5 to about 8, from about 5 to about 8, from about 5.5 to about 8, from about 6 to about 8, from about 6.5 to about 8, from about 7 to about 8, from about 7.5 to about 8, from about 4 to about 7.5, from about 4.5 to about 7.5, from about 5 to about 7.5, from about 5.5 to about 7.5, from about 6 to about 7.5, from about 6.5 to about 7.5, from about 4 to about 7, from about 4.5 to about 7, from about 5 to about 7, from about 5.5 to about 7, from about 6 to about 7, from about 4 to about 6.5, from about 4.5 to about 6.5, from about 5 to about 6.5, from about 5.5 to about 6.5, from about 4 to about 6.0, from about 4.5 to about 6.0, from about 5 to about 6, or from about 4.8 to about 5.5, or may have a pH of about 5.0 to about 5.2. Ranges intermediate to the above recited pH's are also intended to be part of this disclosure. For example, ranges of values using a combination of any of the above recited values as upper and/or lower limits are intended to be included. Examples of buffers that will control the pH within this range include acetate (e.g. sodium acetate), succinate (such as sodium succinate), gluconate, histidine, citrate and other organic acid buffers.
In certain embodiments, the formulation for use in a method of treating cancer or inhibiting tumor growth in a mammal includes a buffer system which contains citrate and phosphate to maintain the pH in a range of about 4 to about 8. In certain embodiments the pH range may be from about 4.5 to about 6.0, or from about pH 4.8 to about 5.5, or in a pH range of about 5.0 to about 5.2. In certain embodiments, the buffer system includes citric acid monohydrate, sodium citrate, disodium phosphate dihydrate, and/or sodium dihydrogen phosphate dihydrate. In certain embodiments, the buffer system includes about 1.3 mg/mL of citric acid (e.g., 1.305 mg/mL), about 0.3 mg/mL of sodium citrate (e.g., 0.305 mg/mL), about 1.5 mg/mL of disodium phosphate dihydrate (e.g., 1.53 mg/mL), about 0.9 mg/mL of sodium dihydrogen phosphate dihydrate (e.g., 0.86 mg/mL), and about 6.2 mg/mL of sodium chloride (e.g., 6.165 mg/mL). In certain embodiments, the buffer system includes about 1-1.5 mg/mL of citric acid, about 0.25 to about 0.5 mg/mL of sodium citrate, about 1.25 to about 1.75 mg/mL of disodium phosphate dihydrate, about 0.7 to about 1.1 mg/mL of sodium dihydrogen phosphate dihydrate, and 6.0 to 6.4 mg/mL of sodium chloride. In certain embodiments, the pH of the formulation is adjusted with sodium hydroxide.
A polyol, which acts as a tonicifier and may stabilize the antibody, may also be included in the formulation. The polyol is added to the formulation in an amount which may vary with respect to the desired isotonicity of the formulation. In certain embodiments, the aqueous formulation may be isotonic. The amount of polyol added may also alter with respect to the molecular weight of the polyol. For example, a lower amount of a monosaccharide (e.g. mannitol) may be added, compared to a disaccharide (such as trehalose). In certain embodiments, the polyol which may be used in the formulation as a tonicity agent is mannitol. In certain embodiments, the mannitol concentration may be about 5 to about 20 mg/mL. In certain embodiments, the concentration of mannitol may be about 7.5 to about 15 mg/mL. In certain embodiments, the concentration of mannitol may be about 10-about 14 mg/mL. In certain embodiments, the concentration of mannitol may be about 12 mg/mL. In certain embodiments, the polyol sorbitol may be included in the formulation.
A detergent or surfactant may also be added to the formulation. Exemplary detergents include nonionic detergents such as polysorbates (e.g. polysorbates 20, 80 etc.) or poloxamers (e.g., poloxamer 188). The amount of detergent added is such that it reduces aggregation of the formulated antibody and/or minimizes the formation of particulates in the formulation and/or reduces adsorption. In certain embodiments, the formulation may include a surfactant which is a polysorbate. In certain embodiments, the formulation may contain the detergent polysorbate 80 or Tween 80. Tween 80 is a term used to describe polyoxyethylene (20) sorbitanmonooleate (see Fiedler, Lexikon der Hilfsstoffe, Editio Cantor Verlag Aulendorf, 4th edi., 1996). In certain embodiments, the formulation may contain between about 0.1 mg/mL and about 10 mg/mL of polysorbate 80, or between about 0.5 mg/mL and about 5 mg/mL. In certain embodiments, about 0.1% polysorbate 80 may be added in the formulation.
In addition to aggregation, deamidation is a common product variant of peptides and proteins that may occur during fermentation, harvest/cell clarification, purification, drug substance/drug product storage and during sample analysis. Deamidation is the loss of NH3 from a protein forming a succinimide intermediate that can undergo hydrolysis. The succinimide intermediate results in a 17 u mass decrease of the parent peptide. The subsequent hydrolysis results in an 18 u mass increase. Isolation of the succinimide intermediate is difficult due to instability under aqueous conditions. As such, deamidation is typically detectable as 1 u mass increase. Deamidation of an asparagine results in either aspartic or isoaspartic acid. The parameters affecting the rate of deamidation include pH, temperature, solvent dielectric constant, ionic strength, primary sequence, local polypeptide conformation and tertiary structure. The amino acid residues adjacent to Asn in the peptide chain affect deamidation rates. Gly and Ser following an Asn in protein sequences results in a higher susceptibility to deamidation.
In certain embodiments, the liquid formulation for use in a method of treating cancer or inhibiting tumor growth in a mammal of the present disclosure may be preserved under conditions of pH and humidity to prevent deamidation of the protein product.
The aqueous carrier of interest herein is one which is pharmaceutically acceptable (safe and non-toxic for administration to a human) and is useful for the preparation of a liquid formulation. Illustrative carriers include sterile water for injection (SWFI), bacteriostatic water for injection (BWFI), a pH buffered solution (e.g. phosphate-buffered saline), sterile saline solution, Ringer's solution or dextrose solution.
A preservative may be optionally added to the formulations herein to reduce bacterial action. The addition of a preservative may, for example, facilitate the production of a multi-use (multiple-dose) formulation.
Intravenous (IV) formulations may be the preferred administration route in particular instances, such as when a patient is in the hospital after transplantation receiving all drugs via the IV route. In certain embodiments, the liquid formulation is diluted with 0.9% Sodium Chloride solution before administration. In certain embodiments, the diluted drug product for injection is isotonic and suitable for administration by intravenous infusion.
In certain embodiments, a salt or buffer components may be added in an amount of 10 mM-200 mM. The salts and/or buffers are pharmaceutically acceptable and are derived from various known acids (inorganic and organic) with “base forming” metals or amines. In certain embodiments, the buffer may be phosphate buffer. In certain embodiments, the buffer may be glycinate, carbonate, citrate buffers, in which case, sodium, potassium or ammonium ions can serve as counterion.
In one embodiment, the liquid formulation contains 10 mg/mL M6903, 8% (w/v) Trehalose, 10 mM L-Histidine and 0.05% Polysorbate 20, pH 5.5. Prior to administration of M6903 by intravenous infusion, the solution is diluted in sterile 0.9% sodium chloride.
Lyophilized Formulation
The lyophilized formulation for use in a method of treating cancer or inhibiting tumor growth in a mammal of the present disclosure includes the anti-TIM-3 antibody molecule and a lyoprotectant. The lyoprotectant may be sugar, e.g., disaccharides. In certain embodiments, the lycoprotectant may be sucrose or maltose. The lyophilized formulation may also include one or more of a buffering agent, a surfactant, a bulking agent, and/or a preservative.
The amount of sucrose or maltose useful for stabilization of the lyophilized drug product may be in a weight ratio of at least 1:2 protein to sucrose or maltose. In certain embodiments, the protein to sucrose or maltose weight ratio may be of from 1:2 to 1:5.
In certain embodiments, the pH of the formulation, prior to lyophilization, may be set by addition of a pharmaceutically acceptable acid and/or base. In certain embodiments the pharmaceutically acceptable acid may be hydrochloric acid. In certain embodiments, the pharmaceutically acceptable base may be sodium hydroxide.
Before lyophilization, the pH of the solution containing the protein of the present disclosure may be adjusted between about 6 to about 8. In certain embodiments, the pH range for the lyophilized drug product may be from about 7 to about 8.
In certain embodiments, a salt or buffer components may be added in an amount of about 10 mM-about 200 mM. The salts and/or buffers are pharmaceutically acceptable and are derived from various known acids (inorganic and organic) with “base forming” metals or amines. In certain embodiments, the buffer may be phosphate buffer. In certain embodiments, the buffer may be glycinate, carbonate, citrate buffers, in which case, sodium, potassium or ammonium ions can serve as counterion.
In certain embodiments, a “bulking agent” may be added. A “bulking agent” is a compound which adds mass to a lyophilized mixture and contributes to the physical structure of the lyophilized cake (e. g. , facilitates the production of an essentially uniform lyophilized cake which maintains an open pore structure). Illustrative bulking agents include mannitol, glycine, polyethylene glycol and sorbitol. The lyophilized formulations of the present invention may contain such bulking agents.
A preservative may be optionally added to the formulations herein to reduce bacterial action. The addition of a preservative may, for example, facilitate the production of a multi-use (multiple-dose) formulation.
In certain embodiments, the lyophilized drug product for use in a method of treating cancer or inhibiting tumor growth in a mammal may be constituted with an aqueous carrier. The aqueous carrier of interest herein is one which is pharmaceutically acceptable (e.g., safe and non-toxic for administration to a human) and is useful for the preparation of a liquid formulation, after lyophilization. Illustrative diluents include sterile water for injection (SWFI), bacteriostatic water for injection (BWFI), a pH buffered solution (e.g. phosphate-buffered saline), sterile saline solution, Ringer's solution or dextrose solution.
In certain embodiments, the lyophilized drug product of the current disclosure is reconstituted with either Sterile Water for Injection, USP (SWFI) or 0.9% Sodium Chloride Injection, USP. During reconstitution, the lyophilized powder dissolves into a solution.
In certain embodiments, the lyophilized protein product of the instant disclosure is constituted to about 4.5 mL water for injection and diluted with 0.9% saline solution (sodium chloride solution).
Practice of the invention will be more fully understood from the foregoing examples, which are presented herein for illustrative purposes only, and should not be construed as limiting the invention in any way.
1.1 Co-Crystallization of TIM-3 with 3903E11 (VL1.3, VH1.2) Fab
A crystal structure of the complex of TIM-3 ECD and the Fab fragment of the 3903E11 (VL1.3,VH1.2) (heavy chain: SEQ ID NO: 47; light chain: SEQ ID NO: 48) was determined. Human TIM-3 (SEQ ID NO: 49 (amino acid); SEQ ID NO: 50 (nucleotide)) was expressed in E. coli inclusion bodies, refolded, and purified by affinity and size exclusion chromatography. The Fab fragment of 3903E11 (VL1.3,VH1.2) was expressed as a His-tagged construct in Expi293F cells and purified by affinity chromatography. The complex of TIM-3 and 3903E11 (VL1.3,VH1.2) Fab fragment was formed and purified by gel filtration chromatography yielding a homogenous protein with a purity greater than 95%.
Crystals of Fab 3903E11 (VL1.3,VH1.2) in complex with human TIM-3 were grown by mixing 0.75 μl protein solution (21.8 mg/mL in 20 mM TrisHCL pH 8.0, 100 mM NaCl) with 0.5 μl reservoirs solution (20% PEG400 (v/v), 0.1 M Tris HCl pH 8.0) at 4° C. using hanging drop vapor diffusion method.
Crystals were flash-frozen and measured at a temperature of 100 K. The X-ray diffraction data was collected at the SWISS LIGHT SOURCE (SLS, Villigen, Switzerland) using cryogenic conditions. The crystals belong to space group C 2 2 21. Data were processed using the programs XDS and XSCALE.
The phase in-formation necessary to determine and analyse the structure was obtained by molecular replacement. The published structures PDB-ID 5F71 and 1NL0 were used as search models for TIM3 and the Fab fragment, respectively. Subsequent model building and refinement was performed according to standard protocols with the software packages CCP4 and COOT. For the calculation of the free R-factor, a measure to cross-validate the correctness of the final model, about 0.9% of measured reflections were excluded from the refinement procedure (see TABLE 1). TLS refinement (using REFMAC5, CCP4) was carried out, which resulted in lower R-factors and higher quality of the electron density map. The ligand parameterisation and generation of the corresponding library files were carried out with CHEMSKETCH and LIBCHECK (CCP4), respectively. The water model was built with the “Find waters”-algorithm of COOT by putting water molecules in peaks of the Fo-Fc map contoured at 3.0 followed by refinement with REFMAC5 and checking all waters with the validation tool of COOT. The criteria for the list of suspicious waters were: B-factor greater 80 Å2, 2Fo-Fc map less than 1.2 Å, distance to closest contact less than 2.3 Å or more than 3.5 Å. The suspicious water molecules and those in the ligand binding site (distance to ligand less than The suspicious water molecules and those in the ligand binding site (distance to ligand less than 10 Å) were checked manually. The Ramachandran Plot of the final model shows 85.4% of all residues in the most favored region, 13.9% in the additionally al-lowed region, and 0.2% in the generously allowed region. The residues Arg81(A), Arg81(B), Va153(L), Asp153(L), Va153(M), Asp153(M), Va153(N), Va153(O), and Asp153(O) are found in the disallowed region of the Ramachandran plot. They are either confirmed by the electron density map or could not be modelled in another sensible conformation.
1SWISS LIGHT SOURCE (SLS, Villigen, Switzerland)
2values in parenthesis refer to the highest resolution
of the ith measurement of h
the ith measurement of h
5calculated with independent reflections
Epitope residues are defined as all residues of TIM-3 with a heavy atom within 5 angstroms of a heavy atom of 3903E11 (VL1.3,VH1.2 Fab. Distances were measured from the final crystallographic coordinates using the BioPython package. Only contacts present in 3 of the 4 complexes of the asymmetric unit are reported (TABLE 2). TABLE 2 tabulates interactions between TIM-3 and 3903E11 (VL1.3,VH1.2). TIM-3 residues are numbered as in Uniprot Code Q8TDQ0-1 (SEQ ID NO: 51). The antibody residues are numbered with reference to SEQ ID NO:47 (heavy chain, “H”) and SEQ ID NO:48 (light chain, “L”). Residues listed here have at least one heavy atom within 5 angstroms of a heavy atom across the interface.
The crystal structure of human TIM-3 in complex with M6903 is shown in
1.2 Mutagenesis
To identify residues of the epitope which contribute energetically to binding selected residues in human TIM-3 were mutated either to alanine (large to small) or to glycine if the selected residue was alanine or to switch the charge of the side-chain In total 11 human TIM-3 point mutants were designed, expressed and purified in HEK cells, and tested for binding to 3903E11 (VL1.3,VH1.2)-IgG2h(FN-AQ,322A)-delK antibody (M6903) using surface plasmon resonance using a GE Healthcare Biacore 4000 instrument as follows. Goat anti-human Fc antibody (Jackson Immunoresearch Laboratories #109-005-098) was first immobilized on BIAcore carboxymethylated dextran CM5 chip using direct coupling to free amino groups following the procedure described by the manufacturer. Antibodies were then captured on the CM5 biosensor chip to achieve approximately 200 response units (RU). Binding measurements were performed using the running HBS-EP+ buffer. A 2-fold dilution series starting at 100 nM of the anti-TIM-3 antibodies were injected at a flow rate of 30 μl/min at 25° C. Association rates (kon, M-1s-1) and dissociation rates (koff, s-1) were calculated using a simple 1:1 Langmuir binding model (Biacore 4000 Evaluation Software). The equilibrium dissociation constant (KD, M) was calculated as the ratio of koff/kon. The affinity of the antibody for wild-type and each mutant was determined. Results are summarized in TABLE 3. Mutants were compared to wild-type TIM-3 (hu TIM-3). The temperature midpoint of fluorescently monitored thermal denaturation is given for the wild-type and mutant proteins. The percent monomer as determine by analytical SEC is given. For KD and T1/2, the mean and standard deviation is given where n>1. It was important to confirm that the lack of binding for a particular point mutant was indeed due to loss of residue interaction and not to global unfolding of the antigen. The structural integrity of the mutated proteins was confirmed using a fluorescence monitored thermal unfolding (FMTU) assay in which the protein is incubated with a dye that is quenched in aqueous solution but fluoresces when bound by exposed hydrophobic residues. As the temperature increases, thermal denaturation of the protein exposes the hydrophobic core residues and this can be monitored by an increase in fluorescence of the dye. A melting curve is fit to the data with the Boltzmann equation outlined in Equation 1, adapted from (Bullock et al. 1997) to determine the temperature at the inflection point of the curve (T1/2). The calculated T1/2 are reported in TABLE 3.
M6903 showed a decrease or loss of binding for the TIM-3 single point mutants P59A, F61A, E62A, I114A, N119A, and K122A (see TABLE 3). Residues P59A, F61A, E62A, I114A, N119A, and K122A reside on the face of one beta sheet of the immunoglobulin fold as shown with the model (see
TIM-3 mutants R111 and F123 showed low stability as assessed by SEC, FMTU, and any reduced binding observed for R111 and F123 mutants likely due to destabilization of the protein and not critical interactions with the antibody. Therefore, TABLE 3 indicates hotspot residues for binding of M6903 to include P59A, F61A, and E62A (see also
The experiment was repeated using known antibodies ABTIM3-h03 ABTIM3-mAB 15, and 27.12E12. Results are shown in TABLE 3 and TABLE 4. For known antibody mAb h03, residues P59A, I114A, M118A, and K122A are identified as residues in the binding interface given the effect on binding. In particular, K122 and F123 are shown as hotspots for mAb h03. These positions are in the reported binding footprint for mAb h03 (US20150218274A1, hum21 is Fab form of h03). Accordingly, while some mutant hu TIM-3 proteins resulted in loss of binding to M6903 and ABTIM3-h03, other huTIM-3 mutants resulted in loss of binding only to M6903, suggesting that the two antibodies have partially overlapping but distinct epitopes.
The other known antibodies, 27.12E12 and mab15, do not have hotspots revealed among this set of TIM-3 variant proteins despite competition observed in epitope binning experiments, suggesting that M6903 and ABTIM-3-mab15 have non-overlapping epitopes.
The following studies refer to the anti-TIM3 antibody M6903. M6903 contains the light and heavy chain variable regions of 3903E11 (VL1.3,VH1.2) in an IgG2h(FN-AQ,322A)-delK background (anti-TIM3-3903E11(VL1.3,VH1.2)-IgG2h(FN-AQ,322A)-delK). The light and heavy chains of M6903 correspond to SEQ ID NO: 21 and SEQ ID NO: 22, respectively.
2.1 Target Occupancy of anti-TIM-3
The ability of M6903 to bind to TIM-3 was demonstrated using anti-TIM-3 (A16-019-1), which is identical to M6903, but produced in Expi293F, not CHOK1SV, cells. The target occupancy of anti-TIM-3 (A16-019-1) on CD14+ monocytes was measured via flow cytometry using human whole blood samples. The samples were incubated with serial dilutions of anti-TIM-3 (A16-019-1) followed by anti-TIM-3(2E2)-APC, which has been shown to compete with anti-TIM-3 (A16-019-1) in binding to TIM-3 on CD14+ monocytes. As expected, target occupancy % increased with increasing concentrations of anti-TIM-3 (A16-019-1), and the average EC50 across all 10 donors was 111.1±85.6 ng/ml (see
2.2 M6903 Efficiently Blocked the Interaction of rhTIM-3 and PtdSer on Apoptotic Jurkat Cells.
The ability of M6903 to block the interaction of TIM-3 with one if its ligands, PtdSer, was determined by a flow cytometry-based binding assay. Apoptotic Jurkat cells were used as the source for PtdSer, as the induction of apoptosis led to PtdSer exposure on the cell membrane of these cells. Specifically, prior to flow cytometry analysis, apoptosis was induced in Jurkat cells via treatment with Staurosporine (2 μg/mL, 18 hrs), leading to surface expression of a TIM-3 ligand, PtdSer. Binding of rhTIM-3-Fc PtdSer on the surface of apoptotic Jurkat cells was evaluated via flow cytometry by measuring the mean fluorescence intensity (MFI) of rhTIM-3-Fc AF647 after pre-incubation with serial dilutions of M6903 or an anti-HEL IgG2h isotype control. Pre-incubation of rhTIM-3 AF647 with M6903 led to reduced binding of TIM-3-Fc to apoptotic Jurkat cells, whereas pre-incubation with an isotype control had no effect on rhTIM-3-Fc binding (see
2.3 Effect of M6903 on T Cell Recall Response and Activation as Monotherapy or in Combination with Bintrafusp Alfa
M6903 treatment increased IFN-γ production from human PBMCs that were activated by exposure to CEF antigens, which specifically elicits CEF antigen-specific T cell recall responses in the PBMCs from the donors who were previously infected with CEF. PBMCs were treated with 40 μg/ml CEF viral peptide pool for (A) 6 days or (B) 4 days in the presence of serial dilutions of M6903. As shown
As shown in
Irradiated Daudi tumor cells were co-cultured with human T cells for 7 days using IL-2 to induce allogenic reactive T cell expansion. The T cells were then harvested and co-cultured with freshly irradiated Daudi cells and treated with M6903 antibody or isotype control for 2 days. T cell activation was measured by an IFN-γ ELISA, and M6903 was shown to dose-dependently enhance IFN-γ production in these cells compared to the isotype control, with an EC50=116±117 ng/mL (sec
M6903 treatment increased IFN-γ production in human PBMCs that were activated by exposure to superantigen SEB, which activates CD4+ T cells non-specifically via cross-linking T cell receptor (TCR) and MHC class II molecules. M6903 (10 μg/mL) was incubated with 100 ng/mL SEB either alone or in combination with bintrafusp alfa (10 μg/mL) for 9 days, and cells were then washed once with medium and re-stimulated with 100 ng/mL SEB and antibody solutions with the same concentrations for an additional 2 days. Human IFN-γ in the supernatant was measured by using a human IFN-γ ELISA kit. M6903 treatment enhanced IFN-γ production (see
2.4 Dual Blocking of Gal-9/PtdSer is Required to Potentiate T-Cell Activity, Correlating with M6903 Activity
PBMCs were stimulated with 40 μg/ml CEF (Cytomegalovirus, Epstein Barr and Influenza) viral peptide pool (AnaSpec, AS-61036-025) for 4 days in AIM-V medium (Invitrogen #12055-091) with 5% human AB serum (Valley Biomedical, HP1022) in the presence of 10 μg/ml M6903, 10 μg/ml anti-Gal-9 (9M1-3; Biolegend, 348902), or 10 μg/ml anti-PtdSer (bavituximab; Creative Biolabs, TAB-175), or with antibody combinations 10 μg/ml M6903 and 10 μg/ml anti-Gal-9, 10 μg/ml M6903 and 10 μg/ml anti-PtdSer, or 10 μg/ml anti-Gal-9 and 10 μg/ml anti-PtdSer. Proliferation was measured by thymidine incorporation. IFN-γ in culture supernatant was measured by ELISA (R&D Systems, DY285B) and the results are shown in
2.5 Profiling TIM-3 Receptor and Ligand Expression in Normal Human Tissue and Tumors
Expression of TIM-3 and its ligands were then explored using chromogenic IHC and mIF validated assays. TIM-3 expression in normal human tissues was then evaluated using FDA normal tissue microarrays (TMA) representing 35 distinct tissues in the human body. Expression of TIM-3 was observed across most tissues and was specific to immune cells, except in the kidney cortex, where specific TIM-3 expression was also observed on epithelial cells. Highest immune reactivity was observed in immune tissues: spleen, tonsil, and lymph node, as well as in immune-rich organs: lung, placenta, and liver tissues. In immune organs, TIM-3 expression was primarily observed on macrophages (and possibly DCs) but not on lymphocytes (data not shown). TIM-3 expression on lymphocytes was observed only in inflamed tissue (data not shown).
A review of the staining patterns across 15 tumor TMAs, representing 12 different tumor types, showed that TIM-3 expression was observed primarily on infiltrating immune cells across all indications except renal cell carcinoma (RCC). Phenotypically, both T cells and myeloid cells stained positive for TIM-3 (data not shown). Tumor cell expression of TIM-3 was seen only in RCC (data not shown). When the frequency of TIM-3+ cells was quantified using digital image analysis staining from these tumor TMAs, RCC showed the highest frequency of TIM-3 positivity (see
Tumor TMAs were then stained to identify immune cells expressing TIM-3 in the TME using mIF analysis. TIM-3 was found to be expressed on a subset of CD3+ lymphocytes and CD68+ macrophages. Digital quantitation showed that, while macrophages formed a significant fraction of TIM-3+ cells across all indications analyzed, a high frequency of TIM-3+ T cells were observed only in NSCLC and STAD tumors (see
Finally, correlation of TIM-3 expression with ligands, Gal-9, CEACAM-1, and HMGB1, was evaluated both in the TCGA RNASeq data and mIF analyses (sec TABLE 5). Pearson correlation of TIM-3 expression with expression of ligands (mRNA and protein), showed that Gal-9 expression was positively correlated across multiple indications. This was not true for CEACAM-1 and HMGB1 expression. Values approaching 1 are the most positively correlated and those approaching −1 are the most negatively correlated, with values near 0 showing little to no correlation.
2.6 Explant Platform
Due to the lack of cross-reactivity of human TIM-3 protein with mouse TIM-3 protein, in vivo models are not readily available to interrogate the antitumor activity of M6903. Therefore, to determine whether M6903 had any anti-tumor efficacy, the CANscript™ human tumor microenvironment (TME) platform (developed at MITRA Biotech) was used. The CANscript™ platform is a functional assay that replicates a patient's personal tumor microenvironment, including the immune compartment. Responses to drug treatment applied to pieces of the tumor tissue in vitro are read out using multiple biochemical and phenotypic assays. These tumor responses are integrated by CANscript™ technology's algorithm into a single ‘M’-score that can predict efficacy of the drug.
Using this platform, M6903 was tested in samples from 20 patients with squamous cell carcinoma of the head and neck (SCCHN) either as monotherapy or in combination with bintrafusp alfa. The M-Score predicts treatment outcome based on multiple input parameters for the given tumor specimen. A positive prediction of response correlates to an M-Score greater than 25 (bold numbers in TABLE 6). A negative prediction of response correlates to an M-Score of 25 or lower. There are no M-Scores for the Control treatment as M-Score values are derived from parameters relative to the control untreated samples.
Using M-score as a readout of efficacy, positive predicted response was observed in 3/20 (15%) of tumor samples treated with M6903, 7/20 (35%) of tumor samples treated with bintrafusp alfa, and 9/20 (45%) of tumor samples treated with a combination of M6903 and bintrafusp alfa (see TABLE 6), suggesting that M6903 has anti-tumor activity which is increased in combination with bintrafusp.
3.1 Animals
A human TIM-3 knock-in mouse model was obtained from Beijing Biocytogen Co., Ltd, in which the murine extracellular domain of TIM-3 receptor was replaced with the human extracellular domain of TIM-3 receptor in a mouse C57BL/6 genetic background (“B-hu-TIM-3 KI” mice). B-hu-TIM-3 KI mice were generated using CRISPR/Cas9 recombination technology by replacing only the IgV extracellular domain (exon 2) of mouse with the corresponding human domain, which kept the remaining intracellular and cytoplasmic domains of the mouse TIM-3 receptor intact.
3.2 Anti-Tumor Efficacy of M6903/Bintrafusp Alfa in MC38 Tumor-Bearing B-huTIM-3 KI Mice
The antitumor efficacy effects of M6903 and bintrafusp alfa combination therapy were tested in a B-huTIM-3 KI mouse model subcutaneously implanted with MC38 tumors. 6-8 week old female mice (N=10/group) were treated with either isotype control (20 mg/kg; i.v; on days 0, 3, 6), bintrafusp alfa (24 mg/kg; i.v.; on days 0, 3, 6), M6903 (10 mg/kg; i.p.; q3dx12), or the combination of bintrafusp alfa and M6903. Significant anti-tumor activity was found with bintrafusp alfa monotherapy (TGI=25.7%, P=0.0054)) or with M6903 monotherapy (TGI=18.2%, P=0.0281) relative to isotype control, 28 days after the start of treatment (see
4.1 Study Design
This is an exemplary single center, open-label, Phase I dose-escalation study investigating the safety, tolerability, pharmacokinetics, biological and clinical activity of the combination of M6903 and bintrafusp alfa in subjects with metastatic or advanced solid tumors that are relapsed/refractory or for which no standard therapy is available. Approximately 21-24 subjects (range 15-45) may be enrolled in this study. However, the total sample size will depend on the number of cohorts to be evaluated and the number of participants per cohort. The study will involve a total of five dose levels, with three dose levels with three subjects each and two dose levels with six subjects each, totaling 21 subjects. A Bayesian two-parameter logistic regression model will be applied to assist the safety monitoring committee (SMC) in dosing recommendations.
The study includes a screening period, a lead-in M6903 monotherapy and subsequent M6903 and bintrafusp alfa combination therapy treatment period and a follow-up period. M6903 and bintrafusp alfa are administered at a fixed rather than weight-based dose by intravenous infusion (IV) every two weeks. For M6903, the escalation doses are 20 mg (DL1), 80 mg (DL2), 240 mg (DL3), 800 mg (DL4) and 1600 mg (DL5). For bintrafusp alfa, the dose is 1200 mg. Each subject's DLT (dose limiting toxicity) period is six weeks (two weeks M6903 monotherapy lead-in followed by four weeks of combination therapy of M6903 and bintrafusp alfa). The subjects are treated until disease progression, unacceptable toxicity or removal of consent. Subjects will be followed for longer-term efficacy parameters such as PFS and OS if on active treatment or follow-up.
The dose escalation schema is presented in
To characterize pharmacokinetic (PK) properties and pharmacodynamic responses to treatment, blood samples are taken at various time points during the M6903 monotherapy lead-in and the combination treatment of M6903 and bintrafusp alfa. M6903 PK parameters measured on Day 1, Day 15 and Day 43 are: AUClast, AUC0-∞, AUCτ, Cmax, Cpre, Tmax, t1/2 and terminal rate constant. Further assessments are presented in TABLE 7 (Schedule of Assessments).
4.2 Study Objectives
The primary objectives of this study are to evaluate the safety and tolerability of M6903 and to determine the recommended expansion dose of M6903 for expansion studies.
The secondary objectives are as follows:
The exploratory objectives are as follows:
and
4.3 Study Population
Subjects must meet the following key inclusion criteria for study entry:
In addition, subjects who meet any of the following exclusion criteria are excluded from study entry:
The entire disclosure of each of the patent and scientific documents referred to herein is incorporated by reference for all purposes.
The invention may be embodied in other specific forms without departing from the spirit or essential characteristics thereof. The foregoing embodiments are therefore to be considered in all respects illustrative rather than limiting on the invention described herein. Scope of the invention is thus indicated by the appended claims rather than by the foregoing description, and all changes that come within the meaning and range of equivalency of the claims are intended to be embraced therein.
QSA
LTQPRSVSGSPGQSVTISCTGTSSDVGG
QSA
LTQPRSVSGSPGQSVTISCTGTSSDVGG
QSA
LTQPRSVSGSPGQSVTISCTGTSSDVGG
QSA
LTQPRSVSGSPGQSVTISCTGTSSDVGG
YAMSWVRQAPGKGLEWVSAISVSGGSTYYAD
AMSWVRQAPGKGLEWVSAISVSGGSTYYADSV
AKANWGFFDYWGQGTLVTVSSASTKGPSVFPL
This application claims the benefit of and priority to U.S. Provisional Patent Application No. 62/754,378, filed Nov. 1, 2018, the entire disclosures of which are incorporated by reference herein.
| Number | Date | Country | |
|---|---|---|---|
| 62754378 | Nov 2018 | US |
| Number | Date | Country | |
|---|---|---|---|
| Parent | PCT/US2019/059556 | Nov 2019 | US |
| Child | 17245476 | US |
