Patent Application
20220411504
The instant application contains a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on May 11, 2021, is named JBI6316USNP1_SL.txt and is 1,061 bytes in size.
The disclosure provides antigen binding domains that bind cluster of differentiation 3 (CD3) protein comprising the antigen binding domains that bind CD3, polynucleotides encoding them, vectors, host cells, methods of making and using them.
Bispecific antibodies and antibody fragments have been explored as a means to recruit cytolytic T cells to kill tumor cells. However, the clinical use of many T cell-recruiting bispecific antibodies has been limited by challenges including unfavorable toxicity, potential immunogenicity, and manufacturing issues. There thus exists a considerable need for improved bispecific antibodies that recruit cytolytic T cells to kill tumor cells that include, for example, reduced toxicity and favorable manufacturing profiles.
The human CD3 T cell antigen receptor protein complex is composed of six distinct chains: a CD3γ chain (SwissProt P09693), a CD3δ chain (SwissProt P04234), two CD3ε chains (SwissProt P07766), and one CD3ζ chain homodimer (SwissProt P20963) (ε γ: ε δ:ζ), which is associated with the T cell receptor α and β chain. This complex plays an important role in coupling antigen recognition to several intracellular signal-transduction pathways. The CD3 complex mediates signal transduction, resulting in T cell activation and proliferation. CD3 is required for immune response.
Redirection of cytotoxic T cells to kill tumor cells has become an important therapeutic mechanism for numerous oncologic indications (Labrijn, A. F., Janmaat, M. L., Reichert, J. M. & Parren, P. Bispecific antibodies: a mechanistic review of the pipeline. Nat Rev Drug Discov 18, 585-608, doi:10.1038/s41573-019-0028-1 (2019)). T cell activation follows a two-signal hypothesis, in which the first signal is supplied by engagement of the T cell receptor (TCR) complex with its cognate peptide MHC complex on an antigen presenting cell (APC), and the second signal may be either co-stimulatory or co-inhibitory (Chen, L. & Flies, D. B. Molecular mechanisms of T cell co-stimulation and co-inhibition. Nat Rev Immunol 13, 227-242, doi: 10.1038/nri3405 (2013)). Tumors often fail to present sufficient non-self antigens to induce a T cell-based immune response, and T cell-engaging BsAbs (bsTCE) can overcome this challenge by inducing T cell activation in the absence of TCR-pMHC interaction. T cell receptor signaling occurs through the ITAM motifs in the cytoplasmic region of the CD3 subunits of the TCR (Chen, D. S. & Mellman, I. Oncology meets immunology: the cancer-immunity cycle. Immunity 39, 1-10, doi:10.1016/j.immuni.2013.07.012 (2013)). In particular, the CD3ε subunit is present in two copies per TCR complex and represents an attractive antigen for T cell engagement. Indeed, numerous bsTCE that target CD3ε have shown clinical anti-tumor efficacy where mAbs have failed, and significant pharmaceutical development efforts are ongoing for several tumor targets (Labrijn, A. F. et al., 2019). Three major challenges for clinical development of bsTCE are 1) the potential for rapid and severe toxicity associated with cytokine release via systemic or off-tumor T cell activation, 2) practical challenges of formulation and dosing for bsTCE with high potency and sharp therapeutic indices, and 3) the potential for reactivation-induced T cell death, wherein tumor-infiltrating T cells (TILS) undergo apoptosis in response to over-activation by bsTCE (Wu, Z. & Cheung, N. V. T cell engaging bispecific antibody (T-BsAb): From technology to therapeutics. Pharmacol Ther 182, 161-175, doi:10.1016/j.pharmthera.2017.08.005 (2018)).
Together, these observations suggest that there is a need in the art for novel CD3 specific binding proteins that are more advantageous and can be used to treat cancers.
The disclosure satisfies this need, for example, by providing novel CD3ε specific binding proteins that possess high affinity for the tumor antigen and weak affinity for the T cell. The proteins comprising an antigen binding domain that binds CD3ε of the disclosure demonstrated high thermostability, reduced deamidation risk, and decreased immunogenicity.
In certain embodiments, the disclosure provides an isolated protein comprising an antigen binding domain that binds to cluster of differentiation 3ε (CD3ε), wherein the antigen binding domain that binds CD3ε comprises:
a. a heavy chain complementarity determining region (HCDR) 1, a HCDR2 and a HCDR3 of a heavy chain variable region (VH) of SEQ ID NO: 23 and a light chain complementarity determining region (LCDR) 1, a LCDR2 and a LCDR3 of a light chain variable region (VL) of SEQ ID NO: 24;
b. the HCDR1, the HCDR2 and the HCDR3 of the VH of SEQ ID NO: 23 and the LCDR1, the LCDR2 and the LCDR3 of the VL of SEQ ID NO: 27;
c. the HCDR1, the HCDR2 and the HCDR3 of the VH of SEQ ID NO: 23 and the LCDR1, the LCDR2 and the LCDR3 of the VL of SEQ ID NO: 28;
d. the HCDR1, the HCDR2 and the HCDR3 of the VH of SEQ ID NO: 23 and the LCDR1, the LCDR2 and the LCDR3 of the VL of SEQ ID NO: 29; or
e. the HCDR1, the HCDR2 and the HCDR3 of the VH of SEQ ID NO: 23 and the LCDR1, the LCDR2 and the LCDR3 of the VL of SEQ ID NO: 30.
In other embodiments, the isolated protein comprises the HCDR1, the HCDR2, the HCDR3, the LCDR1, the LCDR2 and the LCDR3 of
a. SEQ ID NOs: 6, 7, 8, 9, 10, and 11, respectively;
b. SEQ ID NOs:12, 13, 14, 15, 16, and 17, respectively; or
c. SEQ ID NOs: 18, 19, 20, 21, 16, and 22, respectively.
In other embodiments, the antigen binding domain that binds CD3ε is a scFv, a (scFv)2, a Fv, a Fab, a F(ab′)2, a Fd, a dAb or a VHH.
In other embodiments, the antigen binding domain that binds CD3ε is the Fab.
In other embodiments, the antigen binding domain that binds CD3ε is the VHH.
In other embodiments, the antigen binding domain that binds CD3ε is the scFv.
In other embodiments, the scFv comprises, from the N- to C-terminus, a VH, a first linker (L1) and a VL (VH-L1-VL) or the VL, the L1 and the VH (VL-L1-VH).
In certain embodiments, the L1 comprises
a. about 5-50 amino acids;
b. about 5-40 amino acids;
c. about 10-30 amino acids; or
d. about 10-20 amino acids.
In certain embodiments, the L1 comprises an amino acid sequence of SEQ ID NOs: 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, or 64.
In certain embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 31, 37, or 64.
In other embodiments, the antigen binding domain that binds CD3ε comprises the VH of SEQ ID NOs: 23 and the VL of SEQ ID NOs: 24, 27, 28, 29 or 30.
In other embodiments, the antigen binding domain that binds CD3ε comprises:
a. the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 24;
b. the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 27;
c. the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 28;
d. the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 29; or
e. the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 30.
In other embodiments, the antigen binding domain that binds CD3ε comprises the amino acid sequence of SEQ ID NOs: 65, 66, 67, 68, 69, 70, 71, 72, 73, or 74.
The disclosure provides an isolated protein comprising an antigen binding domain that binds CD3ε, wherein the antigen binding domain that binds CD3ε comprises a heavy chain variable region (VH) of SEQ ID NO: 23 and a light chain variable region (VL) of SEQ ID NO: 103. In other embodiments, the antigen binding domain that binds CD3ε is a scFv, a (scFv)2, a Fv, a Fab, a F(ab′)2, a Fd, a dAb or a VHH. In other embodiments, the scFv comprises, from the N- to C-terminus, a VH, a first linker (L1) and a VL (VH-L1-VL) or the VL, the L1 and the VH (VL-L1-VH). In other embodiments, the L1 comprises a. about 5-50 amino acids; b. about 5-40 amino acids; c. about 10-30 amino acids; or d. about 10-20 amino acids. In other embodiments, the L1 comprises an amino acid sequence of SEQ ID NOs: 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, or 64. In other embodiments, the antigen binding domain that binds CD3ε comprises the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 24, 27, 28, 29, or 30. In various embodiments, the antigen binding domain that binds CD3ε comprises: the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 24; the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 27; the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 28; the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 29; or the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 30.
In other embodiments, the isolated protein is a monospecific protein. In other embodiments, the isolated protein is a multispecific protein. In other embodiments, the multispecific protein is a bispecific protein. In other embodiments, the multispecific protein is a trispecific protein.
In other embodiments, the protein is conjugated to a half-life extending moiety.
In other embodiments, the half-life extending moiety is an immunoglobulin (Ig), a fragment of the Ig, an Ig constant region, a fragment of the Ig constant region, a Fc region, transferrin, albumin, an albumin binding domain or polyethylene glycol.
In other embodiments, the isolated protein further comprises an immunoglobulin (Ig) constant region or a fragment of the Ig constant region thereof.
In other embodiments, the fragment of the Ig constant region comprises a Fc region.
In other embodiments, the fragment of the Ig constant region comprises a CH2 domain.
In other embodiments, the fragment of the Ig constant region comprises a CH3 domain.
In other embodiments, the fragment of the Ig constant region comprises the CH2 domain and the CH3 domain.
In other embodiments, the fragment of the Ig constant region comprises at least portion of a hinge, the CH2 domain and the CH3 domain.
In other embodiments, the fragment of the Ig constant region comprises a hinge, the CH2 domain and the CH3 domain.
In other embodiments, the antigen binding domain that binds CD3ε is conjugated to the N-terminus of the Ig constant region or the fragment of the Ig constant region.
In other embodiments, the antigen binding domain that binds CD3ε is conjugated to the C-terminus of the Ig constant region or the fragment of the Ig constant region.
In other embodiments, the antigen binding domain that binds CD3ε is conjugated to the Ig constant region or the fragment of the Ig constant region via a second linker (L2).
In other embodiments, the L2 comprises the amino acid sequence of SEQ ID NOs: 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, or 64.
In other embodiments, the multispecific protein comprises an antigen binding domain that binds an antigen other than CD3ε.
In other embodiments, the cell antigen is a tumor associated antigen. In other embodiments, the tumor associated antigen is kallikrein related peptidase 2 (hK2) protein. In other embodiments, the tumor associated antigen is human leukocyte antigen G (HLA-G). In other embodiments, the tumor associated antigen is prostate-specific membrane antigen (PSMA). In other embodiments, the tumor associated antigen is delta-like protein 3 (DLL3). In other embodiments, the Ig constant region or the fragment of the Ig constant region is an IgG1, an IgG2, an IgG3 or an IgG4 isotype.
In other embodiments, the Ig constant region or the fragment of the Ig constant region comprises at least one mutation that results in reduced binding of the protein to a Fcγ receptor (FcγR). In other embodiments, the at least one mutation that results in reduced binding of the protein to the FcγR is selected from the group consisting of F234A/L235A, L234A/L235A, L234A/L235A/D265S, V234A/G237A/P238S/H268A/V309L/A330S/P331S, F234A/L235A, S228P/F234A/L235A, N297A, V234A/G237A, K214T/E233P/L234V/L235A/G236-deleted/A327G/P331A/D365E/L358M, H268Q/V309L/A330S/P331S, S267E/L328F, L234F/L235E/D265A, L234A/L235A/G237A/P238S/H268A/A330S/P331S, S228P/F234A/L235A/G237A/P238S and S228P/F234A/L235A/G236-deleted/G237A/P238S, wherein residue numbering is according to the EU index.
In other embodiments, the Ig constant region or the fragment of the Ig constant region comprises at least one mutation that results in enhanced binding of the protein to the FcγR.
In other embodiments, the at least one mutation that results in enhanced binding of the protein to the FcγR is selected from the group consisting of S239D/I332E, S298A/E333A/K334A, F243L/R292P/Y300L, F243L/R292P/Y300L/P396L, F243L/R292P/Y300L/V305I/P396L and G236A/S239D/I332E, wherein residue numbering is according to the EU index.
In other embodiments, the FcγR is FcγRI, FcγRIIA, FcγRIIB or FcγRIII, or any combination thereof.
In other embodiments, the Ig constant region or the fragment of the Ig constant region comprises at least one mutation that modulates a half-life of the protein.
In other embodiments, the at least one mutation that modulates the half-life of the protein is selected from the group consisting of H435A, P257I/N434H, D376V/N434H, M252Y/S254T/T256E/H433K/N434F, T308P/N434A and H435R, wherein residue numbering is according to the EU index.
In other embodiments, the protein comprises at least one mutation in a CH3 domain of the Ig constant region.
In other embodiments, the at least one mutation in the CH3 domain of the Ig constant region is selected from the group consisting of T350V, L351Y, F405A, Y407V, T366Y, T366W, T366L, F405W, K392L, T394W, T394S, Y407T, Y407A, T366S/L368A/Y407V, L351Y/F405A/Y407V, T366I/K392M/T394W, T366L/K392L/T394W, F405A/Y407V, T366L/K392M/T394W, L351Y/Y407A, T366A/K409F, L351Y/Y407A, L351Y/Y407V, T366V/K409F, T366A/K409F, T350V/L351Y/F405A/Y407V and T350V/T366L/K392L/T394W, wherein residue numbering is according to the EU index.
The disclosure also provides a pharmaceutical composition comprising the isolated protein comprising the antigen binding domain that binds to CD3ε of the disclosure and a pharmaceutically acceptable carrier.
The disclosure also provides a polynucleotide encoding the protein comprising the antigen binding domain that binds to CD3ε of the disclosure.
The disclosure also provides a vector comprising the polynucleotide encoding the protein comprising the antigen binding domain that binds to CD3ε of the disclosure.
The disclosure also provides a host cell comprising the vector comprising the polynucleotide encoding the protein comprising the antigen binding domain that binds to CD3ε of the disclosure.
The disclosure also provides a method of producing the isolated protein of the disclosure, comprising culturing the host cell of the disclosure in conditions that the protein is expressed, and recovering the protein produced by the host cell.
The disclosure also provides a method of treating a cancer in a subject, comprising administering a therapeutically effective amount of the compositions comprising the isolated antibody comprising the antigen binding domain that binds to CD3ε to the subject in need thereof to treat the cancer. In other embodiments, the cancer is a solid tumor or a hematological malignancy. In other embodiments, the solid tumor is a prostate cancer, a colorectal cancer, a gastric cancer, a clear cell renal carcinoma, a bladder cancer, a lung cancer, a squamous cell carcinoma, a glioma, a breast cancer, a kidney cancer, a neovascular disorder, a clear cell renal carcinoma (CCRCC), a pancreatic cancer, a renal cancer, a urothelial cancer or an adenocarcinoma to the liver. In other embodiments, the hematological malignancy is acute myeloid leukemia (AML), myelodysplastic syndrome (MDS), acute lymphocytic leukemia (ALL), diffuse large B-cell lymphoma (DLBCL), chronic myeloid leukemia (CML) or blastic plasmacytoid dendritic cell neoplasm (DPDCN). In other embodiments, the antibody is administered in combination with a second therapeutic agent.
The disclosure also provides an anti-idiotypic antibody binding to the isolated protein comprising the antigen binding domain that binds to CD3ε of the disclosure.
The disclosure also provides an isolated protein comprising an antigen binding domain that binds to an epitope on CD3ε (SEQ ID NO: 1), wherein the epitope is a discontinuous epitope comprising the amino acid sequences of SEQ ID NO: 100, 101, and 102.
The disclosure also provides an isolated protein comprising an amino acid sequence selected from the group consisting of SEQ ID NOs: 747, 748, 77, 78, 749, 750, 751, 752, 753, and 754.
In one embodiment, the disclosure provides an isolated protein comprising amino acid sequences of SEQ ID NO: 747. In one embodiment, the disclosure provides an isolated protein comprising amino acid sequences of SEQ ID NO: 748. In one embodiment, the disclosure provides an isolated protein comprising amino acid sequences of SEQ ID NO: 77. In one embodiment, the disclosure provides an isolated protein comprising amino acid sequences of SEQ ID NO: 78. In one embodiment, the disclosure provides an isolated protein comprising amino acid sequences of SEQ ID NO: 749. In one embodiment, the disclosure provides an isolated protein comprising amino acid sequences of SEQ ID NO: 750. In one embodiment, the disclosure provides an isolated protein comprising amino acid sequences of SEQ ID NO: 751. In one embodiment, the disclosure provides an isolated protein comprising amino acid sequences of SEQ ID NO: 752. In one embodiment, the disclosure provides an isolated protein comprising amino acid sequences of SEQ ID NO: 753. In one embodiment, the disclosure provides an isolated protein comprising amino acid sequences of SEQ ID NO: 754.
The disclosure also provides an isolated protein comprising amino acid sequences of SEQ ID NOs: 85 and 86.
The disclosure also provides an isolated protein comprising amino acid sequences of SEQ ID NOs: 85 and 88.
The disclosure also provides an isolated protein comprising amino acid sequences of SEQ ID NOs: 85 and 90.
The disclosure also provides an isolated protein comprising amino acid sequences of SEQ ID NOs: 85 and 92.
The disclosure also provides an isolated protein comprising amino acid sequences of SEQ ID NOs: 85 and 94.
The summary, as well as the following detailed description, is further understood when read in conjunction with the appended drawings. For the purpose of illustrating the disclosed antibodies and methods, there are shown in the drawings exemplary embodiments of the antibodies and methods; however, antibodies and methods are not limited to the specific embodiments disclosed. In the drawings:
All publications, including but not limited to patents and patent applications, cited in this specification are herein incorporated by reference as though fully set forth.
It is to be understood that the terminology used herein is for the purpose of describing particular embodiments only and is not intended to be limiting. Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which the invention pertains.
Although any methods and materials similar or equivalent to those described herein may be used in the practice for testing of the present invention, exemplary materials and methods are described herein. In describing and claiming the present invention, the following terminology will be used.
When a list is presented, unless stated otherwise, it is to be understood that each individual element of that list, and every combination of that list, is a separate embodiment. For example, a list of embodiments presented as “A, B, or C” is to be interpreted as including the embodiments, “A,” “B,” “C,” “A or B,” “A or C,” “B or C,” or “A, B, or C.”
As used in this specification and the appended claims, the singular forms “a,” “an,” and “the” include plural referents unless the content clearly dictates otherwise. Thus, for example, reference to “a cell” includes a combination of two or more cells, and the like.
The transitional terms “comprising,” “consisting essentially of,” and “consisting of” are intended to connote their generally accepted meanings in the patent vernacular; that is, (i) “comprising,” which is synonymous with “including,” “containing,” or “characterized by,” is inclusive or open-ended and does not exclude additional, unrecited elements or method steps; (ii) “consisting of” excludes any element, step, or ingredient not specified in the claim; and (iii) “consisting essentially of” limits the scope of a claim to the specified materials or steps “and those that do not materially affect the basic and novel characteristic(s)” of the claimed invention. Embodiments described in terms of the phrase “comprising” (or its equivalents) also provide as embodiments those independently described in terms of “consisting of” and “consisting essentially of”
“About” means within an acceptable error range for the particular value as determined by one of ordinary skill in the art, which will depend in part on how the value is measured or determined, i.e., the limitations of the measurement system. Unless explicitly stated otherwise within the Examples or elsewhere in the Specification in the context of a particular assay, result or embodiment, “about” means within one standard deviation per the practice in the art, or a range of up to 5%, whichever is larger.
“Activation” or “stimulation” or “activated” or “stimulated” refers to induction of a change in the biologic state of a cell resulting in expression of activation markers, cytokine production, proliferation or mediating cytotoxicity of target cells. Cells may be activated by primary stimulatory signals. Co-stimulatory signals can amplify the magnitude of the primary signals and suppress cell death following initial stimulation resulting in a more durable activation state and thus a higher cytotoxic capacity. A “co-stimulatory signal” refers to a signal, which in combination with a primary signal, such as TCR/CD3 ligation, leads to T cell and/or NK cell proliferation and/or upregulation or downregulation of key molecules.
“Alternative scaffold” refers to a single chain protein framework that contains a structured core associated with variable domains of high conformational tolerance. The variable domains tolerate variation to be introduced without compromising scaffold integrity, and hence the variable domains can be engineered and selected for binding to a specific antigen.
“Antibody-dependent cellular cytotoxicity”, “antibody-dependent cell-mediated cytotoxicity” or “ADCC” refers to the mechanism of inducing cell death that depends upon the interaction of antibody-coated target cells with effector cells possessing lytic activity, such as natural killer cells (NK), monocytes, macrophages and neutrophils via Fc gamma receptors (FcγR) expressed on effector cells.
“Antibody-dependent cellular phagocytosis” or “ADCP” refers to the mechanism of elimination of antibody-coated target cells by internalization by phagocytic cells, such as macrophages or dendritic cells.
“Antigen” refers to any molecule (e.g., protein, peptide, polysaccharide, glycoprotein, glycolipid, nucleic acid, portions thereof, or combinations thereof) capable of being bound by an antigen binding domain or a T-cell receptor that is capable of mediating an immune response. Exemplary immune responses include antibody production and activation of immune cells, such as T cells, B cells or NK cells. Antigens may be expressed by genes, synthetized, or purified from biological samples such as a tissue sample, a tumor sample, a cell or a fluid with other biological components, organisms, subunits of proteins/antigens, killed or inactivated whole cells or lysates.
“Antigen binding fragment” or “antigen binding domain” refers to a portion of the protein that binds an antigen. Antigen binding fragments may be synthetic, enzymatically obtainable or genetically engineered polypeptides and include portions of an immunoglobulin that bind an antigen, such as the VH, the VL, the VH and the VL, Fab, Fab′, F(ab′)2, Fd and Fv fragments, domain antibodies (dAb) consisting of one VH domain or one VL domain, shark variable IgNAR domains, camelized VH domains, VHH domains, minimal recognition units consisting of the amino acid residues that mimic the CDRs of an antibody, such as FR3-CDR3-FR4 portions, the HCDR1, the HCDR2 and/or the HCDR3 and the LCDR1, the LCDR2 and/or the LCDR3, alternative scaffolds that bind an antigen, and multispecific proteins comprising the antigen binding fragments. Antigen binding fragments (such as VH and VL) may be linked together via a synthetic linker to form various types of single antibody designs where the VH/VL domains may pair intramolecularly, or intermolecularly in those cases when the VH and VL domains are expressed by separate single chains, to form a monovalent antigen binding domain, such as single chain Fv (scFv) or diabody. Antigen binding fragments may also be conjugated to other antibodies, proteins, antigen binding fragments or alternative scaffolds which may be monospecific or multispecific to engineer bispecific and multispecific proteins.
“Antibodies” is meant in a broad sense and includes immunoglobulin molecules including monoclonal antibodies including murine, human, humanized and chimeric monoclonal antibodies, antigen binding fragments, multispecific antibodies, such as bispecific, trispecific, tetraspecific etc., dimeric, tetrameric or multimeric antibodies, single chain antibodies, domain antibodies and any other modified configuration of the immunoglobulin molecule that comprises an antigen binding site of the required specificity. “Full length antibodies” are comprised of two heavy chains (HC) and two light chains (LC) inter-connected by disulfide bonds as well as multimers thereof (e.g. IgM). Each heavy chain is comprised of a heavy chain variable region (VH) and a heavy chain constant region (comprised of domains CH1, hinge, CH2 and CH3). Each light chain is comprised of a light chain variable region (VL) and a light chain constant region (CL). The VH and the VL regions may be further subdivided into regions of hypervariability, termed complementarity determining regions (CDR), interspersed with framework regions (FR). Each VH and VL is composed of three CDRs and four FR segments, arranged from amino-to-carboxy-terminus in the following order: FR1, CDR1, FR2, CDR2, FR3, CDR3 and FR4. Immunoglobulins may be assigned to five major classes, IgA, IgD, IgE, IgG and IgM, depending on the heavy chain constant domain amino acid sequence. IgA and IgG are further sub-classified as the isotypes IgA1, IgA2, IgG1, IgG2, IgG3 and IgG4. Antibody light chains of any vertebrate species may be assigned to one of two clearly distinct types, namely kappa (κ) and lambda (λ), based on the amino acid sequences of their constant domains.
“Bispecific” refers to a molecule (such as a protein or an antibody) that specifically binds two distinct antigens or two distinct epitopes within the same antigen. The bispecific molecule may have cross-reactivity to other related antigens, for example to the same antigen from other species (homologs), such as human or monkey, for example Macaca cynomolgus (cynomolgus, cyno) or Pan troglodytes, or may bind an epitope that is shared between two or more distinct antigens.
“Bispecific anti-hK2/anti-CD3 antibody”, “hk2/CD3 antibody”, “hk2×CD3 antibody,” “anti-hK2/anti-CD3 protein,” and the like refer to an antibody that binds hk2 and CD3 and that comprises at least one binding domain specifically binding hK2 and at least one binding domain specifically binding CD3. The domains specifically binding hK2 and CD3 are typically VH/VL pairs. The bispecific anti-hk2×CD3 antibody may be monovalent in terms of its binding to either hk2 or CD3.
“Bispecific anti-HLA-G/anti-CD3 antibody”, “HLA-G/CD3 antibody”, “HLA-GxCD3 antibody,” “anti-HLA-G/anti-CD3 protein,” and the like refer to an antibody that binds HLA-G and CD3 and that comprises at least one binding domain specifically binding HLA-G and at least one binding domain specifically binding CD3. The domains specifically binding HLA-G and CD3 are typically VH/VL pairs. The bispecific anti-HLA-GxCD3 antibody may be monovalent in terms of its binding to either HLA-G or CD3.
“Bispecific anti-DLL3/anti-CD3 antibody”, “anti-DLL3×CD3”, “DLL3/CD3 antibody”, “DLL3×CD3 antibody,” “anti-DLL3/anti-CD3 protein,” and the like refer to an antibody that binds DLL3 and CD3 and that comprises at least one binding domain specifically binding DLL3 and at least one binding domain specifically binding CD3. The domains specifically binding DLL3 and CD3 are typically VH/VL pairs. The bispecific anti-DLL3×CD3 antibody may be monovalent in terms of its binding to either DLL3 or CD3.
“Cancer” refers to a broad group of various diseases characterized by the uncontrolled growth of abnormal cells in the body. Unregulated cell division and growth results in the formation of malignant tumors that invade neighboring tissues and may also metastasize to distant parts of the body through the lymphatic system or bloodstream. A “cancer” or “cancer tissue” can include a tumor.
“Cluster of Differentiation 3 ε” or “CD3ε” refers to a known protein which is also called “T-cell surface glycoprotein CD3 epsilon chain”, or “T3E”. CD3ε, together with CD3-gamma, -delta and -zeta, and the T-cell receptor alpha/beta and gamma/delta heterodimers, forms the T-cell receptor-CD3 complex. This complex plays an important role in coupling antigen recognition to several intracellular signal-transduction pathways. The CD3 complex mediates signal transduction, resulting in T cell activation and proliferation. CD3 is required for the immune response. The amino acid sequence of a full length CD3ε is shown in SEQ ID NO: 1. The amino acid sequence of the extracellular domain (ECD) of CD3ε is shown in SEQ ID NO: 2. Throughout the specification, “CD3ε-specific” or “specifically binds CD3ε” or “anti-CD3ε antibody” refers to antibodies that bind specifically to the CD3ε polypeptide (SEQ ID NO: 1), including antibodies that bind specifically to the CD3ε extracellular domain (ECD) (SEQ ID NO: 2).
“Complement-dependent cytotoxicity” or “CDC”, refers to the mechanism of inducing cell death in which the Fc effector domain of a target-bound protein binds and activates complement component C1q which in turn activates the complement cascade leading to target cell death. Activation of complement may also result in deposition of complement components on the target cell surface that facilitate CDC by binding complement receptors (e.g., CR3) on leukocytes.
“Complementarity determining regions” (CDR) are antibody regions that bind an antigen. There are three CDRs in the VH (HCDR1, HCDR2, HCDR3) and three CDRs in the VL (LCDR1, LCDR2, LCDR3). CDRs may be defined using various delineations such as Kabat (Wu et al. (1970) J Exp Med 132: 211-50; Kabat et al., Sequences of Proteins of Immunological Interest, 5th Ed. Public Health Service, National Institutes of Health, Bethesda, Md., 1991), Chothia (Chothia et al. (1987) J Mol Biol 196: 901-17), IMGT (Lefranc et al. (2003) Dev Comp Immunol 27: 55-77) and AbM (Martin and Thornton J Bmol Biol 263: 800-15, 1996). The correspondence between the various delineations and variable region numbering is described (see e.g. Lefranc et al. (2003) Dev Comp Immunol 27: 55-77; Honegger and Pluckthun, J Mol Biol (2001) 309:657-70; International ImMunoGeneTics (IMGT) database; Web resources (for example, can be retrieved from the Internet <URL: http://www.imgt.org>)). Available programs such as abYsis by UCL Business PLC may be used to delineate CDRs. The term “CDR”, “HCDR1”, “HCDR2”, “HCDR3”, “LCDR1”, “LCDR2” and “LCDR3” as used herein includes CDRs defined by any of the methods described supra, Kabat, Chothia, IMGT or AbM, unless otherwise explicitly stated in the specification.
“Decrease,” “lower,” “lessen,” “reduce,” or “abate” refers generally to the ability of a test molecule to mediate a reduced response (i.e., downstream effect) when compared to the response mediated by a control or a vehicle. Exemplary responses are T cell expansion, T cell activation or T-cell mediated tumor cell killing or binding of a protein to its antigen or receptor, enhanced binding to a Fcγ or enhanced Fc effector functions such as enhanced ADCC, CDC and/or ADCP. Decrease may be a statistically significant difference in the measured response between the test molecule and the control (or the vehicle), or a decrease in the measured response, such as a decrease of about 1.1, 1.2, 1.5, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or 30 fold or more, such as 500, 600, 700, 800, 900 or 1000 fold or more (including all integers and decimal points in between and above 1, e.g., 1.5, 1.6, 1.7, 1.8, etc.).
“Differentiation” refers to a method of decreasing the potency or proliferation of a cell or moving the cell to a more developmentally restricted state.
“Delta-like protein 3” or “DLL3” refers to a known protein which is also called delta-like 3, delta 3, or drosophila Delta homolog 3. Unless specified, as used herein, DLL3 refers to human DLL3. All DLL3 isoforms and variants are encompassed in “DLL3”. The amino acid sequences of the various isoforms are retrievable from NCBI accession numbers NP_058637.1 (isoform 1 precursor, 618 amino acids) and NP_982353.1 (isoform 2 precursor, 587 amino acids). The amino acid sequence of a full length DLL3 is shown in SEQ ID NO: 255. The sequence of DLL3 includes the DSL domain (residues 176-215), EGF-1 domain (residues 216-249), EGF-2 domain (residues 274-310), EGF-3 domain (residues 312-351), EGF-4 domain (residues 353-389), EGF-5 domain (residues 391-427), and EGF-6 domain (residues 429-465).
“Encode” or “encoding” refers to the inherent property of specific sequences of nucleotides in a polynucleotide, such as a gene, a cDNA, or an mRNA, to serve as templates for synthesis of other polymers and macromolecules in biological processes having either a defined sequence of nucleotides (e.g., rRNA, tRNA and mRNA) or a defined sequence of amino acids and the biological properties resulting therefrom. Thus, a gene, cDNA, or RNA, encodes a protein if transcription and translation of mRNA corresponding to that gene produces the protein in a cell or other biological system. Both the coding strand, the nucleotide sequence of which is identical to the mRNA sequence, and the non-coding strand, used as the template for transcription of a gene or cDNA, can be referred to as encoding the protein or other product of that gene or cDNA.
“Enhance,” “promote,” “increase,” “expand” or “improve” refers generally to the ability of a test molecule to mediate a greater response (i.e., downstream effect) when compared to the response mediated by a control or a vehicle. Exemplary responses are T cell expansion, T cell activation or T-cell mediated tumor cell killing or binding of a protein to its antigen or receptor, enhanced binding to a Fcγ or enhanced Fc effector functions such as enhanced ADCC, CDC and/or ADCP. Enhance may be a statistically significant difference in the measured response between the test molecule and control (or vehicle), or an increase in the measured response, such as an increase of about 1.1, 1.2, 1.5, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or 30 fold or more, such as 500, 600, 700, 800, 900 or 1000 fold or more (including all integers and decimal points in between and above 1, e.g., 1.5, 1.6, 1.7, 1.8, etc.).
“Epitope” refers to a portion of an antigen to which an antibody, or the antigen binding portion thereof, specifically binds. Epitopes typically consist of chemically active (such as polar, non-polar or hydrophobic) surface groupings of moieties such as amino acids or polysaccharide side chains and may have specific three-dimensional structural characteristics, as well as specific charge characteristics. An epitope may be composed of contiguous and/or discontiguous amino acids that form a conformational spatial unit. For a discontiguous epitope, amino acids from differing portions of the linear sequence of the antigen come in close proximity in 3-dimensional space through the folding of the protein molecule. Antibody “epitope” depends on the methodology used to identify the epitope.
“Expansion” refers to the outcome of cell division and cell death.
“Express” and “expression” refers the to the well-known transcription and translation occurring in cells or in vitro. The expression product, e.g., the protein, is thus expressed by the cell or in vitro and may be an intracellular, extracellular or a transmembrane protein.
“Expression vector” refers to a vector that can be utilized in a biological system or in a reconstituted biological system to direct the translation of a polypeptide encoded by a polynucleotide sequence present in the expression vector.
“dAb” or “dAb fragment” refers to an antibody fragment composed of a VH domain (Ward et al., Nature 341:544 546 (1989)).
“Fab” or “Fab fragment” refers to an antibody fragment composed of VH, CH1, VL and CL domains.
“F(ab′)2” or “F(ab′)2 fragment” refers to an antibody fragment containing two Fab fragments connected by a disulfide bridge in the hinge region.
“Fd” or “Fd fragment” refers to an antibody fragment composed of VH and CH1 domains.
“Fv” or “Fv fragment” refers to an antibody fragment composed of the VH and the VL domains from a single arm of the antibody.
“Full length antibody” is comprised of two heavy chains (HC) and two light chains (LC) inter-connected by disulfide bonds as well as multimers thereof (e.g. IgM). Each heavy chain is comprised of a heavy chain variable domain (VH) and a heavy chain constant domain, the heavy chain constant domain comprised of subdomains CH1, hinge, CH2 and CH3. Each light chain is comprised of a light chain variable domain (VL) and a light chain constant domain (CL). The VH and the VL may be further subdivided into regions of hypervariability, termed complementarity determining regions (CDR), interspersed with framework regions (FR). Each VH and VL is composed of three CDRs and four FR segments, arranged from amino-to-carboxy-terminus in the following order: FR1, CDR1, FR2, CDR2, FR3, CDR3 and FR4.
“Genetic modification” refers to the introduction of a “foreign” (i.e., extrinsic or extracellular) gene, DNA or RNA sequence to a host cell, so that the host cell will express the introduced gene or sequence to produce a desired substance, typically a protein or enzyme coded by the introduced gene or sequence. The introduced gene or sequence may also be called a “cloned” or “foreign” gene or sequence, may include regulatory or control sequences operably linked to polynucleotide encoding the chimeric antigen receptor, such as start, stop, promoter, signal, secretion, or other sequences used by a cell's genetic machinery. The gene or sequence may include nonfunctional sequences or sequences with no known function. A host cell that receives and expresses introduced DNA or RNA has been “genetically engineered.” The DNA or RNA introduced to a host cell can come from any source, including cells of the same genus or species as the host cell, or from a different genus or species.
“Heterologous” refers to two or more polynucleotides or two or more polypeptides that are not found in the same relationship to each other in nature.
“Heterologous polynucleotide” refers to a non-naturally occurring polynucleotide that encodes two or more neoantigens as described herein.
“Heterologous polypeptide” refers to a non-naturally occurring polypeptide comprising two or more neoantigen polypeptides as described herein.
“Host cell” refers to any cell that contains a heterologous nucleic acid. An exemplary heterologous nucleic acid is a vector (e.g., an expression vector).
“Human antibody” refers to an antibody that is optimized to have minimal immune response when administered to a human subject. Variable regions of human antibody are derived from human immunoglobulin sequences. If human antibody contains a constant region or a portion of the constant region, the constant region is also derived from human immunoglobulin sequences. Human antibody comprises heavy and light chain variable regions that are “derived from” sequences of human origin if the variable regions of the human antibody are obtained from a system that uses human germline immunoglobulin or rearranged immunoglobulin genes. Such exemplary systems are human immunoglobulin gene libraries displayed on phage, and transgenic non-human animals such as mice or rats carrying human immunoglobulin loci. “Human antibody” typically contains amino acid differences when compared to the immunoglobulins expressed in humans due to differences between the systems used to obtain the human antibody and human immunoglobulin loci, introduction of somatic mutations or intentional introduction of substitutions into the frameworks or CDRs, or both. Typically, “human antibody” is at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical in amino acid sequence to an amino acid sequence encoded by human germline immunoglobulin or rearranged immunoglobulin genes. In some cases, “human antibody” may contain consensus framework sequences derived from human framework sequence analyses, for example as described in Knappik et al., (2000) J Mol Biol 296:57-86, or a synthetic HCDR3 incorporated into human immunoglobulin gene libraries displayed on phage, for example as described in Shi et al., (2010) J Mol Biol 397:385-96, and in Int. Patent Publ. No. WO2009/085462. Antibodies in which at least one CDR is derived from a non-human species are not included in the definition of “human antibody”.
“Humanized antibody” refers to an antibody in which at least one CDR is derived from non-human species and at least one framework is derived from human immunoglobulin sequences. Humanized antibody may include substitutions in the frameworks so that the frameworks may not be exact copies of expressed human immunoglobulin or human immunoglobulin germline gene sequences.
“In combination with” means that two or more therapeutic agents are be administered to a subject together in a mixture, concurrently as single agents or sequentially as single agents in any order.
“Intracellular signaling domain” or “cytoplasmic signaling domain” refers to an intracellular portion of a molecule. It is the functional portion of the protein which acts by transmitting information within the cell to regulate cellular activity via defined signaling pathways by generating second messengers or functioning as effectors by responding to such messengers. The intracellular signaling domain generates a signal that promotes an immune effector function of the CAR containing cell, e.g., a CAR-T cell.
“Isolated” refers to a homogenous population of molecules (such as synthetic polynucleotides or polypeptides) which have been substantially separated and/or purified away from other components of the system the molecules are produced in, such as a recombinant cell, as well as a protein that has been subjected to at least one purification or isolation step. “Isolated” refers to a molecule that is substantially free of other cellular material and/or chemicals and encompasses molecules that are isolated to a higher purity, such as to 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% purity.
“Kallikrein related peptidase 2” or “hK2” refers to a known protein which is also called kallikrein-2, grandular kallikrein 2, or HK2. hK2 is produced as a preproprotein and cleaved during proteolysis to generate active protease. All hK2 isoforms and variants are encompassed in “hK2”. The amino acid sequences of the various isoforms are retrievable from GenBank accession numbers NP_005542.1, NP_001002231.1 and NP_001243009. The amino acid sequence of a full length hK2 is shown in SEQ ID NO: 98. The sequence includes the signal peptide (residues 1-18) and the pro-peptide region (residues 19-24).
“Human leukocyte antigen G” or “HLA-G” refers to a known protein which is also called “HLA class I histocompatibility antigen, alpha chain G” or “MHC class I antigen G”. All HLA-G isoforms and variants are encompassed in “HLA-G”. The amino acid sequences of the various isoforms are retrievable from Uniprot ID numbers P17693-1 through P17693-7. SEQ ID No: 691 represents an examplery HLA-G isoform termed HLA-G1.
MVVMAPRTLFLLLSGALTLTETWAGSHSMRYFSAAVSRPGRGEPRFIAMG
“Modulate” refers to either enhanced or decreased ability of a test molecule to mediate an enhanced or a reduced response_(i.e., downstream effect) when compared to the response mediated by a control or a vehicle.
“Monoclonal antibody” refers to an antibody obtained from a substantially homogenous population of antibody molecules, i.e., the individual antibodies comprising the population are identical except for possible well-known alterations such as removal of C-terminal lysine from the antibody heavy chain or post-translational modifications such as amino acid isomerization or deamidation, methionine oxidation or asparagine or glutamine deamidation. Monoclonal antibodies typically bind one antigenic epitope. A bispecific monoclonal antibody binds two distinct antigenic epitopes. Monoclonal antibodies may have heterogeneous glycosylation within the antibody population. Monoclonal antibody may be monospecific or multispecific such as bispecific, monovalent, bivalent or multivalent.
“Multispecific” refers to a molecule, such as an antibody that specifically binds two or more distinct antigens or two or more distinct epitopes within the same antigen. Multispecific molecule may have cross-reactivity to other related antigens, for example to the same antigen from other species (homologs), such as human or monkey, for example Macaca fascicularis (cynomolgus, cyno) or Pan troglodytes, or may bind an epitope that is shared between two or more distinct antigens.
“Natural killer cell” and “NK cell” are used interchangeably and synonymously herein. NK cell refers to a differentiated lymphocyte with a CD16+CD56+ and/or CD57+ TCR− phenotype. NK cells are characterized by their ability to bind to and kill cells that fail to express “self” MHC/HLA antigens by the activation of specific cytolytic enzymes, the ability to kill tumor cells or other diseased cells that express a ligand for NK activating receptors, and the ability to release protein molecules called cytokines that stimulate or inhibit the immune response.
“Operatively linked” and similar phrases, when used in reference to nucleic acids or amino acids, refers to the operational linkage of nucleic acid sequences or amino acid sequence, respectively, placed in functional relationships with each other. For example, an operatively linked promoter, enhancer elements, open reading frame, 5′ and 3′ UTR, and terminator sequences result in the accurate production of a nucleic acid molecule (e.g., RNA) and in some instances to the production of a polypeptide (i.e., expression of the open reading frame). Operatively linked peptide refers to a peptide in which the functional domains of the peptide are placed with appropriate distance from each other to impart the intended function of each domain.
The term “paratope” refers to the area or region of an antibody molecule which is involved in binding of an antigen and comprise residues that interact with an antigen. A paratope may composed of continuous and/or discontinuous amino acids that form a conformational spatial unit. The paratope for a given antibody can be defined and characterized at different levels of details using a variety of experimental and computational methods. The experimental methods include hydrogen/deuterium exchange mass spectrometry (HX-MS). The paratope will be defined differently depending on the mapping method employed.
“Pharmaceutical combination” refers to a combination of two or more active ingredients administered either together or separately.
“Pharmaceutical composition” refers to a composition that results from combining an active ingredient and a pharmaceutically acceptable carrier.
“Pharmaceutically acceptable carrier” or “excipient” refers to an ingredient in a pharmaceutical composition, other than the active ingredient, which is nontoxic to a subject. Exemplary pharmaceutically acceptable carriers are a buffer, stabilizer or preservative.
“Polynucleotide” or “nucleic acid” refers to a synthetic molecule comprising a chain of nucleotides covalently linked by a sugar-phosphate backbone or other equivalent covalent chemistry. cDNA is a typical example of a polynucleotide. Polynucleotide may be a DNA or a RNA molecule.
“Prevent,” “preventing,” “prevention,” or “prophylaxis” of a disease or disorder means preventing that a disorder occurs in a subject.
“Proliferation” refers to an increase in cell division, either symmetric or asymmetric division of cells.
“Promoter” refers to the minimal sequences required to initiate transcription. Promoter may also include enhancers or repressor elements which enhance or suppress transcription, respectively.
“Protein” or “polypeptide” are used interchangeably herein and refer to a molecule that comprises one or more polypeptides each comprised of at least two amino acid residues linked by a peptide bond. Protein may be a monomer, or may be protein complex of two or more subunits, the subunits being identical or distinct. Small polypeptides of less than 50 amino acids may be referred to as “peptides”. Protein may be a heterologous fusion protein, a glycoprotein, or a protein modified by post-translational modifications such as phosphorylation, acetylation, myristoylation, palmitoylation, glycosylation, oxidation, formylation, amidation, citrullination, polyglutamylation, ADP-ribosylation, pegylation or biotinylation. Protein may be an antibody or may comprise an antigen binding fragment of an antibody. Protein may be recombinantly expressed.
“Recombinant” refers to polynucleotides, polypeptides, vectors, viruses and other macromolecules that are prepared, expressed, created or isolated by recombinant means.
“Regulatory element” refers to any cis- or trans acting genetic element that controls some aspect of the expression of nucleic acid sequences.
“Relapsed” refers to the return of a disease or the signs and symptoms of a disease after a period of improvement after prior treatment with a therapeutic.
“Refractory” refers to a disease that does not respond to a treatment. A refractory disease can be resistant to a treatment before or at the beginning of the treatment, or a refractory disease can become resistant during a treatment.
“Single chain Fv” or “scFv” refers to a fusion protein comprising at least one antibody fragment comprising a light chain variable region (VL) and at least one antibody fragment comprising a heavy chain variable region (VH), wherein the VL and the VH are contiguously linked via a polypeptide linker, and capable of being expressed as a single chain polypeptide. Unless specified, as used herein, a scFv may have the VL and VH variable regions in either order, e.g., with respect to the N-terminal and C-terminal ends of the polypeptide, the scFv may comprise VL-linker-VH or may comprise VH-linker-VL.
“(scFv)2” or “tandem scFv” or “bis-scFv” fragments refers to a fusion protein comprising two light chain variable region (VL) and two heavy chain variable region (VH), wherein the two VL and the two VH are contiguously linked via polypeptide linkers, and capable of being expressed as a single chain polypeptide. The two VL and two VH are fused by peptide linkers to form a bivalent molecule VLA-linker-VHA-linker-VLB-linker-VHB to form two binding sites, capable of binding two different antigens or epitopes concurrently.
“Specifically binds,” “specific binding,” “specifically binding” or “binds” refer to a proteinaceous molecule binding to an antigen or an epitope within the antigen with greater affinity than for other antigens. Typically, the proteinaceous molecule binds to the antigen or the epitope within the antigen with an equilibrium dissociation constant (KD) of about 1×10−7 M or less, for example about 5×10−8 M or less, about 1×10−8 M or less, about 1×10−9 M or less, about 1×10−0 M or less, about 1×10−1 M or less, or about 1×10−2 M or less, typically with the KD that is at least one hundred fold less than its KD for binding to a non-specific antigen (e.g., BSA, casein). In the context of the prostate neoantigens described here, “specific binding” refers to binding of the proteinaceous molecule to the prostate neoantigen without detectable binding to a wild-type protein the neoantigen is a variant of.
“Subject” includes any human or nonhuman animal. “Nonhuman animal” includes all vertebrates, e.g., mammals and non-mammals, such as nonhuman primates, sheep, dogs, cats, horses, cows, chickens, amphibians, reptiles, etc. The terms “subject” and “patient” can be used interchangeably herein.
“T cell” and “T lymphocyte” are interchangeable and used synonymously herein. T cell includes thymocytes, naïve T lymphocytes, memory T cells, immature T lymphocytes, mature T lymphocytes, resting T lymphocytes, or activated T lymphocytes. A T cell can be a T helper (Th) cell, for example a T helper 1 (Th1) or a T helper 2 (Th2) cell. The T cell can be a helper T cell (HTL; CD4+ T cell) CD4+ T cell, a cytotoxic T cell (CTL; CD8+ T cell), a tumor infiltrating cytotoxic T cell (TIL; CD8+ T cell), CD4+CD8+ T cell, or any other subset of T cells. Also included are “NKT cells”, which refer to a specialized population of T cells that express a semi-invariant αβ T-cell receptor, but also express a variety of molecular markers that are typically associated with NK cells, such as NK1.1. NKT cells include NK1.1+ and NK1.1−, as well as CD4+, CD4−, CD8+ and CD8− cells. The TCR on NKT cells is unique in that it recognizes glycolipid antigens presented by the MHC I-like molecule CD Id. NKT cells can have either protective or deleterious effects due to their abilities to produce cytokines that promote either inflammation or immune tolerance. Also included are “gamma-delta T cells (γδ T cells),” which refer to a specialized population that to a small subset of T cells possessing a distinct TCR on their surface, and unlike the majority of T cells in which the TCR is composed of two glycoprotein chains designated α- and β-TCR chains, the TCR in γδ T cells is made up of a γ-chain and a δ-chain. γδ T cells can play a role in immunosurveillance and immunoregulation, and were found to be an important source of IL-17 and to induce robust CD8+ cytotoxic T cell response. Also included are “regulatory T cells” or “Tregs” which refer to T cells that suppress an abnormal or excessive immune response and play a role in immune tolerance. Tregs are typically transcription factor Foxp3-positive CD4+ T cells and can also include transcription factor Foxp3-negative regulatory T cells that are IL-10-producing CD4+ T cells.
“Therapeutically effective amount” or “effective amount” used interchangeably herein, refers to an amount effective, at dosages and for periods of time necessary, to achieve a desired therapeutic result. A therapeutically effective amount may vary according to factors such as the disease state, age, sex, and weight of the individual, and the ability of a therapeutic or a combination of therapeutics to elicit a desired response in the individual. Example indicators of an effective therapeutic or combination of therapeutics that include, for example, improved wellbeing of the patient, reduction of a tumor burden, arrested or slowed growth of a tumor, and/or absence of metastasis of cancer cells to other locations in the body.
“Transduction” refers to the introduction of a foreign nucleic acid into a cell using a viral vector.
“Treat,” “treating” or “treatment” of a disease or disorder such as cancer refers to accomplishing one or more of the following: reducing the severity and/or duration of the disorder, inhibiting worsening of symptoms characteristic of the disorder being treated, limiting or preventing recurrence of the disorder in subjects that have previously had the disorder, or limiting or preventing recurrence of symptoms in subjects that were previously symptomatic for the disorder.
“Tumor cell” or a “cancer cell” refers to a cancerous, pre-cancerous or transformed cell, either in vivo, ex vivo, or in tissue culture, that has spontaneous or induced phenotypic changes. These changes do not necessarily involve the uptake of new genetic material. Although transformation may arise from infection with a transforming virus and incorporation of new genomic nucleic acid, uptake of exogenous nucleic acid or it can also arise spontaneously or following exposure to a carcinogen, thereby mutating an endogenous gene. Transformation/cancer is exemplified by morphological changes, immortalization of cells, aberrant growth control, foci formation, proliferation, malignancy, modulation of tumor specific marker levels, invasiveness, tumor growth in suitable animal hosts such as nude mice, and the like, in vitro, in vivo, and ex vivo.
“Variant,” “mutant” or “altered” refers to a polypeptide or a polynucleotide that differs from a reference polypeptide or a reference polynucleotide by one or more modifications, for example one or more substitutions, insertions or deletions.
The numbering of amino acid residues in the antibody constant region throughout the specification is according to the EU index as described in Kabat et al., Sequences of Proteins of Immunological Interest, 5th Ed. Public Health Service, National Institutes of Health, Bethesda, Md. (1991), unless otherwise explicitly stated.
Mutations in the Ig constant regions are referred to as follows: L351Y_F405A_Y407V refers to L351Y, F405A and Y407V mutations in one immunoglobulin constant region. L351Y_F405A_Y407V/T394W refers to L351Y, F405A and Y407V mutations in the first Ig constant region and T394W mutation in the second Ig constant region, which are present in one multimeric protein.
“VHH” refers to a single-domain antibody or nanobody, exclusively composed by heavy chain homodimers A VHH single domain antibody lack the light chain and the CH1 domain of the heavy chain of conventional Fab region.
Unless otherwise stated, any numerical values, such as a concentration or a concentration range described herein, are to be understood as being modified in all instances by the term “about.” Thus, a numerical value typically includes ±10% of the recited value. For example, a concentration of 1 mg/mL includes 0.9 mg/mL to 1.1 mg/mL. Likewise, a concentration range of 1% to 10% (w/v) includes 0.9% (w/v) to 11% (w/v). As used herein, the use of a numerical range expressly includes all possible subranges, all individual numerical values within that range, including integers within such ranges and fractions of the values unless the context clearly indicates otherwise.
The numbering of amino acid residues in the antibody constant region throughout the specification is according to the EU index as described in Kabat et al., Sequences of Proteins of Immunological Interest, 5th Ed. Public Health Service, National Institutes of Health, Bethesda, Md. (1991), unless otherwise explicitly stated.
Antigen Binding Domains that Bind CD3ε.
The disclosure provides antigen binding domains that bind CD3ε, monospecific and multispecific proteins comprising the antigen binding domains that bind CD3ε, polynucleotides encoding the foregoing, vectors, host cells and methods of making and using the foregoing. The antigen binding domains that bind CD3ε identified herein demonstrated advantageous properties in terms of high thermostability, reduced deamidation risk, and decreased immunogenicity.
The disclosure also provides an isolated protein comprising an antigen binding domain that binds CD3ε, wherein the antigen binding domain that binds CD3ε comprises a heavy chain variable region (VH) of SEQ ID NO: 23 and a light chain variable region (VL) of SEQ ID NO: 103. SEQ ID NO: 103 represent genus VL amino acid sequences encompassing variants demonstrating improved properties, including high thermostability, reduced deamidation risk, and decreased immunogenicity. For example, the position engineered to confer reduced deamidation risk was residue N92 in the VL (residue numbering using the CD3B815 VL sequence of SEQ ID NO: 24, according to Kabat numbering (Kabat et al., Sequences of Proteins of Immunological Interest, 5th Ed. Public Health Service, National Institutes of Health, Bethesda, Md., 1991)) and the positions engineered to confer decreased immunogenicity were human to mouse back mutations at residues Y49 and/or L78 (residue numbering according to Kabat, using the CD3B815 VL of SEQ ID NO: 24). The engineered position at residue N92 was within LCDR3. Even with mutations at this position, antibodies retained the ability to bind antigen.
The disclosure provides an isolated protein comprising an antigen binding domain that binds CD3ε, wherein the antigen binding domain that binds CD3ε comprises a heavy chain complementarity determining region (HCDR) 1, a HCDR2 and a HCDR3 of a heavy chain variable region (VH) of SEQ ID NO: 23 and a light chain complementarity determining region (LCDR) 1, a LCDR2 and a LCDR3 of a light chain variable region (VL) of SEQ ID NO: 24.
The disclosure provides an isolated protein comprising an antigen binding domain that binds CD3ε, wherein the antigen binding domain that binds CD3ε comprises the HCDR1, the HCDR1, the HCDR3, the LCDR1, the LCDR2 and the LCDR3 of
SEQ ID NOs: 6, 7, 8, 9, 10, and 11, respectively;
SEQ ID NOs: 12, 13, 14, 15, 16, and 17, respectively; or
SEQ ID NOs: 18, 19, 20, 21, 16, and 22, respectively.
The disclosure provides an isolated protein comprising an antigen binding domain that binds CD3ε, wherein the antigen binding domain that binds CD3ε comprises the VH of SEQ ID NOs: 23 and the VL of SEQ ID NOs: 24, 27, 28, 29 or 30.
The disclosure provides an isolated protein comprising an antigen binding domain that binds CD3ε, wherein the antigen binding domain that binds CD3ε comprises
the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 24;
the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 27;
the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 28;
the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 29; or
the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 30.
The disclosure provides an isolated protein comprising an antigen binding domain that binds CD3ε, wherein the antigen binding domain that binds CD3ε comprises the amino acid sequence of SEQ ID NOs: 25 or 26. In other embodiments, the antigen binding domain that binds CD3ε comprises the amino acid sequence of SEQ ID NOs: 85 or 86. In other embodiments, the antigen binding domain that binds CD3ε comprises the amino acid sequence of SEQ ID NOs: 85 or 88. In other embodiments, the antigen binding domain that binds CD3ε comprises the amino acid sequence of SEQ ID NOs: 85 or 90. In other embodiments, the antigen binding domain that binds CD3ε comprises the amino acid sequence of SEQ ID NOs: 85 or 92. In other embodiments, the antigen binding domain that binds CD3ε comprises the amino acid sequence of SEQ ID NOs: 85 or 94.
In other embodiments, the antigen binding domain that binds CD3ε is a scFv.
In other embodiments, the antigen binding domain that binds CD3ε is a (scFv)2.
In other embodiments, the antigen binding domain that binds CD3ε is a Fv.
In other embodiments, the antigen binding domain that binds CD3ε is a Fab.
In other embodiments, the antigen binding domain that binds CD3ε is a F(ab′)2.
In other embodiments, the antigen binding domain that binds CD3ε is a Fd.
In other embodiments, the CD3ε antigen binding domain is a dAb.
In other embodiments, the CD3ε antigen binding domain is a VHH.
CD3ε Binding scFvs
Any of the VH and the VL domains identified herein that bind CD3ε may be engineered into scFv format in either VH-linker-VL or VL-linker-VH orientation. Any of the VH and the VL domains identified herein may also be used to generate sc(Fv)2 structures, such as VH-linker-VL-linker-VL-linker-VH, VH-linker-VL-linker-VH-linker-VL. VH-linker-VH-linker-VL-linker-VL. VL-linker-VH-linker-VH-linker-VL. VL-linker-VH-linker-VL-linker-VH or VL-linker-VL-linker-VH-linker-VH.
The VH and the VL domains identified herein may be incorporated into a scFv format and the binding and thermostability of the resulting scFv to CD3ε may be assessed using known methods.
Binding may be assessed using ProteOn XPR36, Biacore 3000 or KinExA instrumentation, ELISA or competitive binding assays known to those skilled in the art. Binding may be evaluated using purified scFvs or E. coli supernatants or lysed cells containing the expressed scFv. The measured affinity of a test scFv to CD3ε may vary if measured under different conditions (e.g., osmolarity, pH). Thus, measurements of affinity and other binding parameters (e.g., KD, Kon, Koff) are typically made with standardized conditions and standardized buffers. Thermostability may be evaluated by heating the test scFv at elevated temperatures, such as at 50° C., 55° C. or 60° C. for a period of time, such as 5 minutes (min), 10 min, 15 min, 20 min, 25 min or 30 min and measuring binding of the test scFv to CD3ε. The scFvs retaining comparable binding to CD3ε when compared to a non-heated scFv sample are referred to as being thermostable.
In recombinant expression systems, the linker is a peptide linker and may include any naturally occurring amino acid. Exemplary amino acids that may be included into the linker are Gly, Ser Pro, Thr, Glu, Lys, Arg, Ile, Leu, His and The. The linker should have a length that is adequate to link the VH and the VL in such a way that they form the correct conformation relative to one another so that they retain the desired activity, such as binding to CD3ε.
The linker may be about 5-50 amino acids long. In other embodiments, the linker is about 10-40 amino acids long. In other embodiments, the linker is about 10-35 amino acids long. In other embodiments, the linker is about 10-30 amino acids long. In other embodiments, the linker is about 10-25 amino acids long. In other embodiments, the linker is about 10-20 amino acids long. In other embodiments, the linker is about 15-20 amino acids long. In other embodiments, the linker is about 16-19 amino acids long. In other embodiments, the linker is 6 amino acids long. In other embodiments, the linker is 7 amino acids long. In other embodiments, the linker is 8 amino acids long. In other embodiments, the linker is 9 amino acids long. In other embodiments, the linker is 10 amino acids long. In other embodiments, the linker is 11 amino acids long. In other embodiments, the linker is 12 amino acids long. In other embodiments, the linker is 13 amino acids long. In other embodiments, the linker is 14 amino acids long. In other embodiments, the linker is 15 amino acids long. In other embodiments, the linker is 16 amino acids long. In other embodiments, the linker is 17 amino acids long. In other embodiments, the linker is 18 amino acids long. In other embodiments, the linker is 19 amino acids long. In other embodiments, the linker is 20 amino acids long. In other embodiments, the linker is 21 amino acids long. In other embodiments, the linker is 22 amino acids long. In other embodiments, the linker is 23 amino acids long. In other embodiments, the linker is 24 amino acids long. In other embodiments, the linker is 25 amino acids long. In other embodiments, the linker is 26 amino acids long. In other embodiments, the linker is 27 amino acids long. In other embodiments, the linker is 28 amino acids long. In other embodiments, the linker is 29 amino acids long. In other embodiments, the linker is 30 amino acids long. In other embodiments, the linker is 31 amino acids long. In other embodiments, the linker is 32 amino acids long. In other embodiments, the linker is 33 amino acids long. In other embodiments, the linker is 34 amino acids long. In other embodiments, the linker is 35 amino acids long. In other embodiments, the linker is 36 amino acids long. In other embodiments, the linker is 37 amino acids long. In other embodiments, the linker is 38 amino acids long. In other embodiments, the linker is 39 amino acids long. In other embodiments, the linker is 40 amino acids long. Exemplary linkers that may be used are Gly rich linkers, Gly and Ser containing linkers, Gly and Ala containing linkers, Ala and Ser containing linkers, and other flexible linkers.
Other linker sequences may include portions of immunoglobulin hinge area, CL or CH1 derived from any immunoglobulin heavy or light chain isotype. Alternatively, a variety of non-proteinaceous polymers, including polyethylene glycol (PEG), polypropylene glycol, polyoxyalkylenes, or copolymers of polyethylene glycol and polypropylene glycol, may find use as linkers. Exemplary linkers that may be used are shown in Table 2. Additional linkers are described for example in Int. Pat. Publ. No. WO2019/060695.
In other embodiments, the scFv comprises, from the N- to C-terminus, a VH, a first linker (L1) and a VL (VH-L1-VL).
In other embodiments, the scFv comprises, from the N-to C-terminus, the VL, the L1 and the VH (VL-L1-VH).
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 31.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 32.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 33.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 34.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 35.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 36.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 37.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 38.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 39.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 40.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 41.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 42.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 43.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 44.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 45.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 46.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 47.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 48.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 49.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 50.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 51.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 52.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 53.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 54.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 55.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 56.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 57.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 58.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 59.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 60.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 61.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 62.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 63.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 64.
In other embodiments, the scFv comprises
a heavy chain complementarity determining region (HCDR) 1, a HCDR2 and a HCDR3 of a heavy chain variable region (VH) of SEQ ID NO: 23 and a light chain complementarity determining region (LCDR) 1, a LCDR2 and a LCDR3 of a light chain variable region (VL) of SEQ ID NO: 24.
In other embodiments, the scFv comprises the HCDR1, the HCDR1, the HCDR3, the LCDR1, the LCDR2 and the LCDR3 of
SEQ ID NOs: 6, 7, 8, 9, 10, and 11, respectively; or
SEQ ID NOs: 12, 13, 14, 15, 16, and 17, respectively; or
SEQ ID NOs: 18, 19, 20, 21, 16, and 22, respectively.
In other embodiments, the scFv comprises the HCDR1, the HCDR1, the HCDR3, the LCDR1, the LCDR2 and the LCDR3 of SEQ ID NOs: 6, 7, 8, 9, 10, and 11, respectively.
In other embodiments, the scFv comprises the HCDR1, the HCDR1, the HCDR3, the LCDR1, the LCDR2 and the LCDR3 of SEQ ID NOs: 12, 13, 14, 15, 16, and 17, respectively.
In other embodiments, the scFv comprises the HCDR1, the HCDR1, the HCDR3, the LCDR1, the LCDR2 and the LCDR3 of SEQ ID NOs: 18, 19, 20, 21, 16, and 22, respectively.
In other embodiments, the scFv comprises the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 24.
In other embodiments, the scFv comprises the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 27.
In other embodiments, the scFv comprises the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 28.
In other embodiments, the scFv comprises the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 29.
In other embodiments, the scFv comprises the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 30.
In other embodiments, the scFv comprises the amino acid sequence of SEQ ID NOs: 65, 66, 67, 68, 69, 70, 71, 72, 73, or 74.
In other embodiments, the scFv comprises the amino acid sequence of SEQ ID NO: 65.
In other embodiments, the scFv comprises the amino acid sequence of SEQ ID NO: 66.
In other embodiments, the scFv comprises the amino acid sequence of SEQ ID NO: 67.
In other embodiments, the scFv comprises the amino acid sequence of SEQ ID NO: 68.
In other embodiments, the scFv comprises the amino acid sequence of SEQ ID NO: 69.
In other embodiments, the scFv comprises the amino acid sequence of SEQ ID NO: 70.
In other embodiments, the scFv comprises the amino acid sequence of SEQ ID NO: 71.
In other embodiments, the scFv comprises the amino acid sequence of SEQ ID NO: 72.
In other embodiments, the scFv comprises the amino acid sequence of SEQ ID NO: 73.
In other embodiments, the scFv comprises the amino acid sequence of SEQ ID NO: 74.
Other Antigen Binding Domains that Bind CD3ε
Any of the VH and the VL domains identified herein that bind CD3ε may also be engineered into Fab, F(ab′)2, Fd or Fv format and their binding to CD3ε and thermostability may be assessed using the assays described herein.
In other embodiments, the Fab comprises
a heavy chain complementarity determining region (HCDR) 1, a HCDR2 and a HCDR3 of a heavy chain variable region (VH) of SEQ ID NO: 23 and a light chain complementarity determining region (LCDR) 1, a LCDR2 and a LCDR3 of a light chain variable region (VL) of SEQ ID NO: 24.
In other embodiments, the Fab comprises the HCDR1, the HCDR1, the HCDR3, the LCDR1, the LCDR2 and the LCDR3 of
SEQ ID NOs: 6, 7, 8, 9, 10, and 11, respectively;
SEQ ID NOs: 12, 13, 14, 15, 16, and 17, respectively; or
SEQ ID NOs: 18, 19, 20, 21, 16 and 22, respectively.
In other embodiments, the Fab comprises the HCDR1, the HCDR1, the HCDR3, the LCDR1, the LCDR2 and the LCDR3 of SEQ ID NOs: 6, 7, 8, 9, 10, and 11, respectively.
In other embodiments, the Fab comprises the HCDR1, the HCDR1, the HCDR3, the LCDR1, the LCDR2 and the LCDR3 of SEQ ID NOs: 12, 13, 14, 15, 16, and 17, respectively.
In other embodiments, the Fab comprises the HCDR1, the HCDR1, the HCDR3, the LCDR1, the LCDR2 and the LCDR3 of SEQ ID NOs: 18, 19, 20, 21, 16 and 22, respectively.
In other embodiments, the Fab comprises the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 24.
In other embodiments, the Fab comprises the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 27.
In other embodiments, the Fab comprises the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 28.
In other embodiments, the Fab comprises the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 29.
In other embodiments, the Fab comprises the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 30.
In other embodiments, the Fab comprises the VH of SEQ ID NO: 23 and the VL of SEQ ID NOs: 24, 27, 28, 29 or 30.
In other embodiments, the F(ab′)2 comprises
a heavy chain complementarity determining region (HCDR) 1, a HCDR2 and a HCDR3 of a heavy chain variable region (VH) of SEQ ID NO: 23 and a light chain complementarity determining region (LCDR) 1, a LCDR2 and a LCDR3 of a light chain variable region (VL) of SEQ ID NO: 24.
In other embodiments, the F(ab′)2 comprises the HCDR1, the HCDR1, the HCDR3, the LCDR1, the LCDR2 and the LCDR3 of
SEQ ID NOs: 6, 7, 8, 9, 10, and 11, respectively;
SEQ ID NOs: 12, 13, 14, 15, 16, and 17, respectively; or
SEQ ID NOs: 18, 19, 20, 21, 16 and 22, respectively.
In other embodiments, the F(ab′)2 comprises the HCDR1, the HCDR1, the HCDR3, the LCDR1, the LCDR2 and the LCDR3 of SEQ ID NOs: 6, 7, 8, 9, 10, and 11, respectively.
In other embodiments, the F(ab′)2 comprises the HCDR1, the HCDR1, the HCDR3, the LCDR1, the LCDR2 and the LCDR3 of SEQ ID NOs: 12, 13, 14, 15, 16, and 17, respectively.
In other embodiments, the F(ab′)2 comprises the HCDR1, the HCDR1, the HCDR3, the LCDR1, the LCDR2 and the LCDR3 of SEQ ID NOs: 18, 19, 20, 21, 16 and 22, respectively.
In other embodiments, the F(ab′)2 comprises the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 24.
In other embodiments, the F(ab′)2 comprises the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 27.
In other embodiments, the F(ab′)2 comprises the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 28.
In other embodiments, the F(ab′)2 comprises the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 29.
In other embodiments, the F(ab′)2 comprises the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 30.
In other embodiments, the F(ab′)2 comprises the VH of SEQ ID NO: 23 and the VL of SEQ ID NOs: 24, 27, 28, 29 or 30.
In Other Embodiments, the Fv Comprises
a heavy chain complementarity determining region (HCDR) 1, a HCDR2 and a HCDR3 of a heavy chain variable region (VH) of SEQ ID NO: 23 and a light chain complementarity determining region (LCDR) 1, a LCDR2 and a LCDR3 of a light chain variable region (VL) of SEQ ID NO: 24.
In other embodiments, the Fv comprises the HCDR1, the HCDR1, the HCDR3, the LCDR1, the LCDR2 and the LCDR3 of
SEQ ID NOs: 6, 7, 8, 9, 10, and 11, respectively;
SEQ ID NOs: 12, 13, 14, 15, 16, and 17, respectively; or
SEQ ID NOs: 18, 19, 20, 21, 16 and 22, respectively.
In other embodiments, the Fv comprises the HCDR1, the HCDR1, the HCDR3, the LCDR1, the LCDR2 and the LCDR3 of SEQ ID NOs: 6, 7, 8, 9, 10, and 11, respectively.
In other embodiments, the Fv comprises the HCDR1, the HCDR1, the HCDR3, the LCDR1, the LCDR2 and the LCDR3 of SEQ ID NOs: 12, 13, 14, 15, 16, and 17, respectively.
In other embodiments, the Fv comprises the HCDR1, the HCDR1, the HCDR3, the LCDR1, the LCDR2 and the LCDR3 of SEQ ID NOs: 18, 19, 20, 21, 16 and 22, respectively.
In other embodiments, the Fv comprises the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 24.
In other embodiments, the Fv comprises the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 27.
In other embodiments, the Fv comprises the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 28.
In other embodiments, the Fv comprises the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 29.
In other embodiments, the Fv comprises the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 30.
In other embodiments, the Fv comprises the VH of SEQ ID NO: 23 and the VL of SEQ ID NOs: 24, 27, 28, 29 or 30.
In other embodiments, the Fd comprises
a heavy chain complementarity determining region (HCDR) 1, a HCDR2 and a HCDR3 of a heavy chain variable region (VH) of SEQ ID NO: 23.
In other embodiments, the Fd comprises the HCDR1, the HCDR1, and the HCDR3 of SEQ ID NOs: 6, 7, and 8, respectively.
In other embodiments, the Fd comprises the HCDR1, the HCDR1, and the HCDR3 of SEQ ID NOs: 12, 13, and 14, respectively.
In other embodiments, the Fd comprises the HCDR1, the HCDR1, and the HCDR3 of SEQ ID NOs: 18, 19, and 20, respectively.
In other embodiments, the Fd comprises the VH of SEQ ID NO: 23.
Homologous Antigen Binding Domains and Antigen Binding Domains with Conservative Substitutions
Variants of the antigen binding domains that bind CD3ε are within the scope of the disclosure. For example, variants may comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28 or 29 amino acid substitutions in the antigen binding domain that bind CD3ε as long as they retain or have improved functional properties when compared to the parent antigen binding domains. In other embodiments, the sequence identity may be about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% to the antigen binding domains that bind CD3ε of the disclosure. In other embodiments, the variation is in the framework regions. In other embodiments, variants are generated by conservative substitutions.
For example, the antigen binding domains that bind CD3ε may comprise substitutions at residue positions Y49, L78, or N92 in the VL (residue numbering according Kabat). Conservative substitutions may be made at any indicated positions and the resulting variant antigen binding domains that bind CD3ε are tested for their desired characteristics in the assays described herein.
Also provided are antigen binding domains that bind CD3ε comprising the VH and the VL which are at least 80% identical to
the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 24;
the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 27;
the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 28;
the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 29; or
the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 30.
In other embodiments, the identity is 85%. In other embodiments, the identity is 90%. In other embodiments, the identity is 91%. In other embodiments, the identity is 91%. In other embodiments, the identity is 92%. In other embodiments, the identity is 93%. In other embodiments, the identity is 94%. In other embodiments, the identity is 94%. In other embodiments, the identity is 95%. In other embodiments, the identity is 96%. In other embodiments, the identity is 97%. In other embodiments, the identity is 98%. In other embodiments, the identity is 99%.
The percent identity between the two sequences is a function of the number of identical positions shared by the sequences (i.e., % identity=number of identical positions/total number of positions×100), taking into account the number of gaps, and the length of each gap, which need to be introduced for optimal alignment of the two sequences.
The percent identity between two amino acid sequences may be determined using the algorithm of E. Meyers and W. Miller (Comput Appl Biosci 4:11-17 (1988)) which has been incorporated into the ALIGN program (version 2.0), using a PAM120 weight residue table, a gap length penalty of 12 and a gap penalty of 4. In addition, the percent identity between two amino acid sequences may be determined using the Needleman and Wunsch (J Mol Biol 48:444-453 (1970)) algorithm which has been incorporated into the GAP program in the GCG software package (can be retrieved from the Internet <URL: http://www.gcg.com>), using either a Blossum 62 matrix or a PAM250 matrix, and a gap weight of 16, 14, 12, 10, 8, 6, or 4 and a length weight of 1, 2, 3, 4, 5, or 6.
In other embodiments, variant antigen binding domains that bind CD3ε comprise one or two conservative substitutions in any of the CDR regions, while retaining desired functional properties of the parent antigen binding fragments that bind CD3ε.
“Conservative modifications” refer to amino acid modifications that do not significantly affect or alter the binding characteristics of the antibody containing the amino acid modifications. Conservative modifications include amino acid substitutions, additions and deletions. Conservative amino acid substitutions are those in which the amino acid is replaced with an amino acid residue having a similar side chain. The families of amino acid residues having similar side chains are well defined and include amino acids with acidic side chains (e.g., aspartic acid, glutamic acid), basic side chains (e.g., lysine, arginine, histidine), nonpolar side chains (e.g., alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine), uncharged polar side chains (e.g., glycine, asparagine, glutamine, cysteine, serine, threonine, tyrosine, tryptophan), aromatic side chains (e.g., phenylalanine, tryptophan, histidine, tyrosine), aliphatic side chains (e.g., glycine, alanine, valine, leucine, isoleucine, serine, threonine), amide (e.g., asparagine, glutamine), beta-branched side chains (e.g., threonine, valine, isoleucine) and sulfur-containing side chains (cysteine, methionine). Furthermore, any native residue in the polypeptide may also be substituted with alanine, as has been previously described for alanine scanning mutagenesis (MacLennan et al., (1988) Acta Physiol Scand Suppl 643:55-67; Sasaki et al., (1988) Adv Biophys 35:1-24). Amino acid substitutions to the antibodies of the invention may be made by known methods for example by PCR mutagenesis (U.S. Pat. No. 4,683,195). Alternatively, libraries of variants may be generated for example using random (NNK) or non-random codons, for example DVK codons, which encode 11 amino acids (Ala, Cys, Asp, Glu, Gly, Lys, Asn, Arg, Ser, Tyr, Trp). The resulting variants may be tested for their characteristics using assays described herein.
Methods of Generating Antigen Binding Fragment that Bind CD3ε
Antigen binding domains that bind CD3ε provided in the disclosure may be generated using various technologies. For example, the hybridoma method of Kohler and Milstein may be used to identify VH/VL pairs that bind CD3ε. In the hybridoma method, a mouse or other host animal, such as a hamster, rat or chicken is immunized with human and/or cyno CD3ε, followed by fusion of spleen cells from immunized animals with myeloma cells using standard methods to form hybridoma cells. Colonies arising from single immortalized hybridoma cells may be screened for production of the antibodies containing the antigen binding domains that bind CD3ε with desired properties, such as specificity of binding, cross-reactivity or lack thereof, affinity for the antigen, and any desired functionality.
Antigen binding domains that bind CD3ε generated by immunizing non-human animals may be humanized. Exemplary humanization techniques including selection of human acceptor frameworks include CDR grafting (U.S. Pat. No. 5,225,539), SDR grafting (U.S. Pat. No. 6,818,749), Resurfacing (Padlan, (1991) Mol Immunol 28:489-499), Specificity Determining Residues Resurfacing (U.S. Patent Publ. No. 2010/0261620), human framework adaptation (U.S. Pat. No. 8,748,356) or superhumanization (U.S. Pat. No. 7,709,226). In these methods, CDRs or a subset of CDR residues of parental antibodies are transferred onto human frameworks that may be selected based on their overall homology to the parental frameworks, based on similarity in CDR length, or canonical structure identity, or a combination thereof.
Humanized antigen biding domains may be further optimized to improve their selectivity or affinity to a desired antigen by incorporating altered framework support residues to preserve binding affinity (backmutations) by techniques such as those described in Int. Patent Publ. Nos. WO1090/007861 and WO1992/22653, or by introducing variation at any of the CDRs for example to improve affinity of the antigen binding domain.
Transgenic animals, such as mice, rat or chicken carrying human immunoglobulin (Ig) loci in their genome may be used to generate antigen binding fragments that bind CD3ε, and are described in for example U.S. Pat. No. 6,150,584, Int. Patent Publ. No. WO1999/45962, Int. Patent Publ. Nos. WO2002/066630, WO2002/43478, WO2002/043478 and WO1990/04036. The endogenous immunoglobulin loci in such animal may be disrupted or deleted, and at least one complete or partial human immunoglobulin locus may be inserted into the genome of the animal using homologous or non-homologous recombination, using transchromosomes, or using minigenes. Companies such as Regeneron (<URL: http://www.regeneron.com>), Harbour Antibodies (http://www.harbourantibodies.com), Open Monoclonal Technology, Inc. (OMT) (<URL: http://www.omtinc.net>), KyMab (<URL: http://www.kymab.com>), Trianni (<URL: http://www.trianni.com>) and Ablexis (<URL: http://www.ablexis.com>) may be engaged to provide human antibodies directed against a selected antigen using technologies as described above.
Antigen binding domains that bind CD3ε may be selected from a phage display library, where the phage is engineered to express human immunoglobulins or portions thereof such as Fabs, single chain antibodies (scFv), or unpaired or paired antibody variable regions. The antigen binding domains that bind CD3ε may be isolated for example from phage display library expressing antibody heavy and light chain variable regions as fusion proteins with bacteriophage pIX coat protein as described in Shi et al., (2010) J Mol Biol 397:385-96, and Int. Patent Publ. No. WO09/085462). The libraries may be screened for phage binding to human and/or cyno CD3ε and the obtained positive clones may be further characterized, the Fabs isolated from the clone lysates, and converted to scFvs or other configurations of antigen binding fragments.
Preparation of immunogenic antigens and expression and production of antigen binding domains of the disclosure may be performed using any suitable technique, such as recombinant protein production. The immunogenic antigens may be administered to an animal in the form of purified protein, or protein mixtures including whole cells or cell or tissue extracts, or the antigen may be formed de novo in the animal's body from nucleic acids encoding said antigen or a portion thereof.
The antigen binding domains that bind CD3ε of the disclosure may be conjugated to a half-life extending moiety. Exemplary half-life extending moieties are albumin, albumin variants, albumin-binding proteins and/or domains, transferrin and fragments and analogues thereof, immunoglobulins (Ig) or fragments thereof, such as Fc regions. Amino acid sequences of the aforementioned half-life extending moieties are known. Ig or fragments thereof include all isotypes (i.e., IgG1, IgG2, IgG3, IgG4, IgM, IgA and IgE).
Additional half-life extending moieties that may be conjugated to the antigen binding domains that bind CD3ε of the disclosure include polyethylene glycol (PEG) molecules, such as PEG5000 or PEG20,000, fatty acids and fatty acid esters of different chain lengths, for example laurate, myristate, stearate, arachidate, behenate, oleate, arachidonate, octanedioic acid, tetradecanedioic acid, octadecanedioic acid, docosanedioic acid, and the like, polylysine, octane, carbohydrates (dextran, cellulose, oligo- or polysaccharides) for desired properties. These moieties may be direct fusions with the antigen binding domains that bind CD3ε of the disclosure and may be generated by standard cloning and expression techniques. Alternatively, well known chemical coupling methods may be used to attach the moieties to recombinantly produced antigen binding domains that bind CD3ε of the disclosure.
A pegyl moiety may for example be conjugated to the antigen binding domain that bind CD3ε of the disclosure by incorporating a cysteine residue to the C-terminus of the antigen binding domain that bind CD3ε of the disclosure, or engineering cysteines into residue positions that face away from the CD3ε binding site and attaching a pegyl group to the cysteine using well known methods.
In other embodiments, the antigen binding fragment that binds CD3ε is conjugated to a half-life extending moiety.
In other embodiments, the half-life extending moiety is an immunoglobulin (Ig), a fragment of the Ig, an Ig constant region, a fragment of the Ig constant region, a Fc region, transferrin, albumin, an albumin binding domain or polyethylene glycol. In other embodiments, the half-life extending moiety is an Ig constant region.
In other embodiments, the half-life extending moiety is the Ig.
In other embodiments, the half-life extending moiety is the fragment of the Ig.
In other embodiments, the half-life extending moiety is the Ig constant region.
In other embodiments, the half-life extending moiety is the fragment of the Ig constant region.
In other embodiments, the half-life extending moiety is the Fc region.
In other embodiments, the half-life extending moiety is albumin.
In other embodiments, the half-life extending moiety is the albumin binding domain.
In other embodiments, the half-life extending moiety is transferrin.
In other embodiments, the half-life extending moiety is polyethylene glycol.
The antigen binding domains that bind CD3ε conjugated to a half-life extending moiety may be evaluated for their pharmacokinetic properties utilizing known in vivo models.
The antigen binding domains that bind CD3ε of the disclosure may be conjugated to an Ig constant region or a fragment of the Ig constant region to impart antibody-like properties, including Fc effector functions C1q binding, complement dependent cytotoxicity (CDC), Fc receptor binding, antibody-dependent cell-mediated cytotoxicity (ADCC), phagocytosis or down regulation of cell surface receptors (e.g., B cell receptor; BCR). The Ig constant region or the fragment of the Ig constant region functions also as a half-life extending moiety as discussed herein. The antigen binding domains that bind CD3ε of the disclosure may be engineered into conventional full-length antibodies using standard methods. The full-length antibodies comprising the antigen binding domain that binds CD3ε may further be engineered as described herein.
Immunoglobulin heavy chain constant region comprised of subdomains CH1, hinge, CH2 and CH3. The CH1 domain spans residues A118-V215, the CH2 domain residues A231-K340 and the CH3 domain residues G341-K447 on the heavy chain, residue numbering according to the EU Index. In some instances, G341 is referred as a CH2 domain residue. Hinge is generally defined as including E216 and terminating at P230 of human IgG1. Ig Fc region comprises at least the CH2 and the CH3 domains of the Ig constant region, and therefore comprises at least a region from about A231 to K447 of Ig heavy chain constant region.
The invention also provides an antigen binding domain that binds CD3ε conjugated to an immunoglobulin (Ig) constant region or a fragment of the Ig constant region.
In other embodiments, the Ig constant region is a heavy chain constant region
In other embodiments, the Ig constant region is a light chain constant region.
In other embodiments, the fragment of the Ig constant region comprises a Fc region.
In other embodiments, the fragment of the Ig constant region comprises a CH2 domain.
In other embodiments, the fragment of the Ig constant region comprises a CH3 domain.
In other embodiments, the fragment of the Ig constant region comprises the CH2 domain and the CH3 domain.
In other embodiments, the fragment of the Ig constant region comprises at least portion of a hinge, the CH2 domain and the CH3 domain. Portion of the hinge refers to one or more amino acid residues of the Ig hinge.
In other embodiments, the fragment of the Ig constant region comprises the hinge, the CH2 domain and the CH3 domain.
In other embodiments, the antigen binding domain that binds CD3ε is conjugated to the N-terminus of the Ig constant region or the fragment of the Ig constant region.
In other embodiments, the antigen binding domain that binds CD3ε is conjugated to the C-terminus of the Ig constant region or the fragment of the Ig constant region.
In other embodiments, the antigen binding domain that binds CD3ε is conjugated to the Ig constant region or the fragment of the Ig constant region via a second linker (L2).
In other embodiments, the L2 comprises the amino acid sequence of SEQ ID NOs: 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, or 64.
In other embodiments, the L2 comprises the amino acid sequence of SEQ ID NO: 31.
In other embodiments, the L2 comprises the amino acid sequence of SEQ ID NO: 32.
In other embodiments, the L2 comprises the amino acid sequence of SEQ ID NO: 33.
In other embodiments, the L2 comprises the amino acid sequence of SEQ ID NO: 34.
In other embodiments, the L2 comprises the amino acid sequence of SEQ ID NO: 35.
In other embodiments, the L2 comprises the amino acid sequence of SEQ ID NO: 36.
In other embodiments, the L2 comprises the amino acid sequence of SEQ ID NO: 37.
In other embodiments, the L2 comprises the amino acid sequence of SEQ ID NO: 38.
In other embodiments, the L2 comprises the amino acid sequence of SEQ ID NO: 39.
In other embodiments, the L2 comprises the amino acid sequence of SEQ ID NO: 40.
In other embodiments, the L2 comprises the amino acid sequence of SEQ ID NO: 41.
In other embodiments, the L2 comprises the amino acid sequence of SEQ ID NO: 42.
In other embodiments, the L2 comprises the amino acid sequence of SEQ ID NO: 43.
In other embodiments, the L2 comprises the amino acid sequence of SEQ ID NO: 44.
In other embodiments, the L2 comprises the amino acid sequence of SEQ ID NO: 45.
In other embodiments, the L2 comprises the amino acid sequence of SEQ ID NO: 46.
In other embodiments, the L2 comprises the amino acid sequence of SEQ ID NO: 47.
In other embodiments, the L2 comprises the amino acid sequence of SEQ ID NO: 48.
In other embodiments, the L2 comprises the amino acid sequence of SEQ ID NO: 49.
In other embodiments, the L2 comprises the amino acid sequence of SEQ ID NO: 50.
In other embodiments, the L2 comprises the amino acid sequence of SEQ ID NO: 51.
In other embodiments, the L2 comprises the amino acid sequence of SEQ ID NO: 52.
In other embodiments, the L2 comprises the amino acid sequence of SEQ ID NO: 53.
In other embodiments, the L2 comprises the amino acid sequence of SEQ ID NO: 54.
In other embodiments, the L2 comprises the amino acid sequence of SEQ ID NO: 55.
In other embodiments, the L2 comprises the amino acid sequence of SEQ ID NO: 56.
In other embodiments, the L2 comprises the amino acid sequence of SEQ ID NO: 57.
In other embodiments, the L2 comprises the amino acid sequence of SEQ ID NO: 58.
In other embodiments, the L2 comprises the amino acid sequence of SEQ ID NO: 59.
In other embodiments, the L2 comprises the amino acid sequence of SEQ ID NO: 60.
In other embodiments, the L2 comprises the amino acid sequence of SEQ ID NO: 61.
In other embodiments, the L2 comprises the amino acid sequence of SEQ ID NO: 62.
In other embodiments, the L2 comprises the amino acid sequence of SEQ ID NO: 63.
In other embodiments, the L2 comprises the amino acid sequence of SEQ ID NO: 64.
The antigen binding domains that bind CD3ε of the disclosure conjugated to Ig constant region or the fragment of the Ig constant region may be assessed for their functionality using several known assays. Binding to CD3ε may be assessed using methods described herein. Altered properties imparted by the Ig constant domain or the fragment of the Ig constant region such as Fc region may be assayed in Fc receptor binding assays using soluble forms of the receptors, such as the FcγRI, FcγRII, FcγRIII or FcRn receptors, or using cell-based assays measuring for example ADCC, CDC or ADCP.
ADCC may be assessed using an in vitro assay using CD3ε expressing cells as target cells and NK cells as effector cells. Cytolysis may be detected by the release of label (e.g. radioactive substrates, fluorescent dyes or natural intracellular proteins) from the lysed cells. In an exemplary assay, target cells are used with a ratio of 1 target cell to 4 effector cells. Target cells are pre-labeled with BATDA and combined with effector cells and the test antibody. The samples are incubated for 2 hours and cell lysis measured by measuring released BATDA into the supernatant. Data is normalized to maximal cytotoxicity with 0.67% Triton X-100 (Sigma Aldrich) and minimal control determined by spontaneous release of BATDA from target cells in the absence of any antibody.
ADCP may be evaluated by using monocyte-derived macrophages as effector cells and any CD3ε expressing cells as target cells which are engineered to express GFP or other labeled molecule. In an exemplary assay, effector:target cell ratio may be for example 4:1. Effector cells may be incubated with target cells for 4 hours with or without the antibody of the invention. After incubation, cells may be detached using accutase. Macrophages may be identified with anti-CD11b and anti-CD14 antibodies coupled to a fluorescent label, and percent phagocytosis may be determined based on % GFP fluorescence in the CD11+CD14+macrophages using standard methods.
CDC of cells may be measured for example by plating Daudi cells at 1×105 cells/well (50 μL/well) in RPMI-B (RPMI supplemented with 1% BSA), adding 50 μL of test protein to the wells at final concentration between 0-100 μg/mL, incubating the reaction for 15 min at room temperature, adding 11 μL of pooled human serum to the wells, and incubation the reaction for 45 min at 37° C. Percentage (%) lysed cells may be detected as % propidium iodide stained cells in FACS assay using standard methods.
Proteins Comprising the Antigen Binding Domains that Bind CD3ε of the Disclosure
The antigen binding domains that bind CD3ε of the disclosure may be engineered into monospecific or multispecific proteins of various designs using standard methods.
The disclosure also provides a monospecific protein comprising the antigen binding domain that binds CD3ε of the disclosure.
In other embodiments, the monospecific protein is an antibody.
The disclosure also provides a multispecific protein comprising the antigen binding domain that binds CD3ε of the disclosure.
In other embodiments, the multispecific protein is bispecific.
In other embodiments, the multispecific protein is trispecific.
In other embodiments, the multispecific protein is tetraspecific.
In other embodiments, the multispecific protein is monovalent for binding to CD3ε.
In other embodiments, the multispecific protein is bivalent for binding to CD3ε.
The disclosure also provides an isolated multispecific protein comprising a first antigen binding domain that binds CD3ε and a second antigen binding domain that binds a tumor antigen.
In other embodiments, the tumor antigen is a hK2 antigen. In other embodiments, the tumor antigen is a HLA-G antigen. In other embodiments, the tumor antigen is a DLL3 antigen.
In other embodiments, the first antigen binding domain that binds CD3ε and/or the second antigen binding domain that binds the tumor antigen comprise a scFv, a (scFv)2, a Fv, a Fab, a F(ab′)2, a Fd, a dAb or a VHH.
In other embodiments, the first antigen binding domain that binds CD3ε and/or the second antigen binding domain that binds the tumor antigen comprise the Fab.
In other embodiments, the first antigen binding domain that binds CD3ε and/or the second antigen binding domain that binds the tumor antigen comprise the F(ab′)2.
In other embodiments, the first antigen binding domain that binds CD3ε and/or the second antigen binding domain that binds the tumor antigen comprise the VHH.
In other embodiments, the first antigen binding domain that binds CD3ε and/or the second antigen binding domain that binds the tumor antigen comprise the Fv.
In other embodiments, the first antigen binding domain that binds CD3ε and/or the second antigen binding domain that binds the tumor antigen comprise the Fd.
In other embodiments, the first antigen binding domain that binds CD3ε and/or the second antigen binding domain that binds the tumor antigen comprise the scFv.
In other embodiments, the scFv comprises, from the N- to C-terminus, a VH, a first linker (L1) and a VL (VH-L1-VL) or the VL, the L1 and the VH (VL-L1-VH).
In other embodiments, the L1 comprises about 5-50 amino acids.
In other embodiments, the L1 comprises about 5-40 amino acids.
In other embodiments, the L1 comprises about 10-30 amino acids.
In other embodiments, the L1 comprises about 10-20 amino acids.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NOs: 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, or 64.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 31.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 32.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 33.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 34.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 35.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 36.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 37.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 38.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 39.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 40.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 41.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 42.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 43.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 44.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 45.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 46.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 47.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 48.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 49.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 50.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 51.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 52.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 53.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 54.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 55.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 56.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 57.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 58.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 59.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 60.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 61.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 62.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 63.
In other embodiments, the L1 comprises the amino acid sequence of SEQ ID NO: 64.
In other embodiments, the first antigen binding domain that binds CD3ε comprises the HCDR1 of SEQ ID NOs: 6, 12, or 18, the HCDR2 of SEQ ID NOs: 7, 13, or 19, the HCDR3 of SEQ ID NOs: 8, 14, or 20, the LCDR1 of SEQ ID NOs: 9, 15, or 21, the LCDR2 of SEQ ID NOs: 10 or 16, and the LCDR3 of SEQ ID NOs: 11, 17, or 22.
In other embodiments, the first antigen binding domain that binds CD3ε comprises the HCDR1, the HCDR2, the HCDR3, the LCDR1, the LCDR2 and the LCDR3 of
SEQ ID NOs: 6, 7, 8, 9, 10, and 11, respectively;
SEQ ID NOs: 12, 13, 14, 15, 16, and 17, respectively; or
SEQ ID NOs: 18, 19, 20, 21, 16, and 22, respectively.
In other embodiments, the first antigen binding domain that binds CD3ε comprises the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 24.
In other embodiments, the first antigen binding domain that binds CD3ε comprises the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 27.
In other embodiments, the first antigen binding domain that binds CD3ε comprises the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 28.
In other embodiments, the first antigen binding domain that binds CD3ε comprises the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 29.
In other embodiments, the first antigen binding domain that binds CD3ε comprises the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 30.
In other embodiments, the first antigen binding domain that binds CD3ε comprises the VH of SEQ ID NOs: 23 and the VL of SEQ ID NOs: 24, 27, 28, 29 or 30.
In other embodiments, the first antigen binding domain that binds CD3ε comprises the amino acid sequence of SEQ ID Nos: 65, 66, 67, 68, 69, 60, 71, 72, 73, or 74.
In other embodiments, the first antigen binding domain that binds CD3ε comprises the amino acid sequence of SEQ ID NO: 65.
In other embodiments, the first antigen binding domain that binds CD3ε comprises the amino acid sequence of SEQ ID NO: 66.
In other embodiments, the first antigen binding domain that binds CD3ε comprises the amino acid sequence of SEQ ID NO: 67.
In other embodiments, the first antigen binding domain that binds CD3ε comprises the amino acid sequence of SEQ ID NO: 68.
In other embodiments, the first antigen binding domain that binds CD3ε comprises the amino acid sequence of SEQ ID NO: 69.
In other embodiments, the first antigen binding domain that binds CD3ε comprises the amino acid sequence of SEQ ID NO: 70.
In other embodiments, the first antigen binding domain that binds CD3ε comprises the amino acid sequence of SEQ ID NO: 71.
In other embodiments, the first antigen binding domain that binds CD3ε comprises the amino acid sequence of SEQ ID NO: 72.
In other embodiments, the first antigen binding domain that binds CD3ε comprises the amino acid sequence of SEQ ID NO: 73.
In other embodiments, the first antigen binding domain that binds CD3ε comprises the amino acid sequence of SEQ ID NO: 74.
In other embodiments, the second antigen binding domain that binds a tumor antigen comprises the HCDR1 of SEQ ID NO: 149, the HCDR2 of SEQ ID NO: 150, the HCDR3 of SEQ ID NO: 151, the LCDR1 of SEQ ID NO: 171, the LCDR2 of SEQ ID NO: 172 and the LCDR3 of SEQ ID NO: 173; or
the VH of SEQ ID NO: 126 and the VL of SEQ ID NO: 127.
In other embodiments, the second antigen binding domain that binds a tumor antigen comprises
the HCDR1 of SEQ ID NO: 149, the HCDR2 of SEQ ID NO: 152, the HCDR3 of SEQ ID NO: 151, the LCDR1 of SEQ ID NO: 174, the LCDR2 of SEQ ID NO: 175 and the LCDR3 of SEQ ID NO: 173; or
the VH of SEQ ID NO: 124 and the VL of SEQ ID NO: 125.
In other embodiments, the second antigen binding domain that binds a tumor antigen comprises
the HCDR1 of SEQ ID NO: 149, the HCDR2 of SEQ ID NO: 152, the HCDR3 of SEQ ID NO: 151, the LCDR1 of SEQ ID NO: 174, the LCDR2 of SEQ ID NO: 175 and the LCDR3 of SEQ ID NO: 173; or
the VH of SEQ ID NO: 128 and the VL of SEQ ID NO: 129.
In other embodiments, the second antigen binding domain that binds a tumor antigen comprises
the HCDR1 of SEQ ID NO: 149, the HCDR2 of SEQ ID NO: 152, the HCDR3 of SEQ ID NO: 151, the LCDR1 of SEQ ID NO: 174, the LCDR2 of SEQ ID NO: 175 and the LCDR3 of SEQ ID NO: 173; or
the VH of SEQ ID NO: 130 and the VL of SEQ ID NO: 131.
In other embodiments, the second antigen binding domain that binds a tumor antigen comprises
the HCDR1 of SEQ ID NO: 149, the HCDR2 of SEQ ID NO: 152, the HCDR3 of SEQ ID NO: 151, the LCDR1 of SEQ ID NO: 171, the LCDR2 of SEQ ID NO: 172 and the LCDR3 of SEQ ID NO: 173; or
the VH of SEQ ID NO: 132 and the VL of SEQ ID NO: 133.
In other embodiments, the second antigen binding domain that binds a tumor antigen comprises
the HCDR1 of SEQ ID NO: 149, the HCDR2 of SEQ ID NO: 152, the HCDR3 of SEQ ID NO: 151, the LCDR1 of SEQ ID NO: 171, the LCDR2 of SEQ ID NO: 172 and the LCDR3 of SEQ ID NO: 173; or
the VH of SEQ ID NO: 134 and the VL of SEQ ID NO: 135.
In other embodiments, the second antigen binding domain that binds a tumor antigen comprises
the HCDR1 of SEQ ID NO: 149, the HCDR2 of SEQ ID NO: 152, the HCDR3 of SEQ ID NO: 151, the LCDR1 of SEQ ID NO: 171, the LCDR2 of SEQ ID NO: 172 and the LCDR3 of SEQ ID NO: 173; or
the VH of SEQ ID NO: 136 and the VL of SEQ ID NO: 135.
In other embodiments, the second antigen binding domain that binds a tumor antigen comprises
the HCDR1 of SEQ ID NO: 149, the HCDR2 of SEQ ID NO: 152, the HCDR3 of SEQ ID NO: 151, the LCDR1 of SEQ ID NO: 171, the LCDR2 of SEQ ID NO: 172 and the LCDR3 of SEQ ID NO: 173; or
the VH of SEQ ID NO: 132 and the VL of SEQ ID NO: 135.
In other embodiments, the second antigen binding domain that binds a tumor antigen comprises
the HCDR1 of SEQ ID NO: 153, the HCDR2 of SEQ ID NO: 154, the HCDR3 of SEQ ID NO: 155, the LCDR1 of SEQ ID NO: 176, the LCDR2 of SEQ ID NO: 177 and the LCDR3 of SEQ ID NO: 178; or
the VH of SEQ ID NO: 137 and the VL of SEQ ID NO: 138.
In other embodiments, the second antigen binding domain that binds a tumor antigen comprises
the HCDR1 of SEQ ID NO: 156, the HCDR2 of SEQ ID NO: 157, the HCDR3 of SEQ ID NO: 158, the LCDR1 of SEQ ID NO: 182, the LCDR2 of SEQ ID NO: 183 and the LCDR3 of SEQ ID NO: 184; or
the VH of SEQ ID NO: 139 and the VL of SEQ ID NO: 140.
In other embodiments, the second antigen binding domain that binds a tumor antigen comprises
the HCDR1 of SEQ ID NO: 159, the HCDR2 of SEQ ID NO: 160, the HCDR3 of SEQ ID NO: 161, the LCDR1 of SEQ ID NO: 179, the LCDR2 of SEQ ID NO: 180 and the LCDR3 of SEQ ID NO: 181; or
the VH of SEQ ID NO: 141 and the VL of SEQ ID NO: 142.
In other embodiments, the second antigen binding domain that binds a tumor antigen comprises
the HCDR1 of SEQ ID NO: 162, the HCDR2 of SEQ ID NO: 163, the HCDR3 of SEQ ID NO: 164, the LCDR1 of SEQ ID NO: 185, the LCDR2 of SEQ ID NO: 186 and the LCDR3 of SEQ ID NO: 187; or
the VH of SEQ ID NO: 143 and the VL of SEQ ID NO: 144.
In other embodiments, the second antigen binding domain that binds a tumor antigen comprises
the HCDR1 of SEQ ID NO: 165, the HCDR2 of SEQ ID NO: 166, the HCDR3 of SEQ ID NO: 167, the LCDR1 of SEQ ID NO: 191, the LCDR2 of SEQ ID NO: 192 and the LCDR3 of SEQ ID NO: 193; or
the VH of SEQ ID NO: 145 and the VL of SEQ ID NO: 146.
In other embodiments, the second antigen binding domain that binds a tumor antigen comprises
the HCDR1 of SEQ ID NO: 168, the HCDR2 of SEQ ID NO: 169, the HCDR3 of SEQ ID NO: 170, the LCDR1 of SEQ ID NO: 191, the LCDR2 of SEQ ID NO: 192 and the LCDR3 of SEQ ID NO: 188; or
the VH of SEQ ID NO: 147 and the VL of SEQ ID NO: 148.
In other embodiments, the second antigen binding domain that binds a tumor antigen comprises the VH of SEQ ID NO: 143 and the VL of SEQ ID NO: 358.
In other embodiments, the first antigen binding domain that binds CD3ε is conjugated to a first immunoglobulin (Ig) constant region or a fragment of the first Ig constant region and/or the second antigen binding domain that binds the tumor antigen is conjugated to a second immunoglobulin (Ig) constant region or a fragment of the second Ig constant region.
In other embodiments, the fragment of the first Ig constant region and/or the fragment of the second Ig constant region comprises a Fc region.
In other embodiments, the fragment of the first Ig constant region and/or the fragment of the second Ig constant region comprises a CH2 domain.
In other embodiments, the fragment of the first Ig constant region and/or the fragment of the second Ig constant region comprises a CH3 domain.
In other embodiments, the fragment of the first Ig constant region and/or the fragment of the second Ig constant region comprises the CH2 domain and the CH3 domain.
In other embodiments, the fragment of the first Ig constant region and/or the fragment of the second Ig constant region comprises at least portion of a hinge, the CH2 domain and the CH3 domain.
In other embodiments, the fragment of the Ig constant region comprises the hinge, the CH2 domain and the CH3 domain.
In other embodiments, the multispecific protein further comprises a second linker (L2) between the first antigen binding domain that binds CD3ε and the first Ig constant region or the fragment of the first Ig constant region and the second antigen binding domain that binds the tumor antigen and the second Ig constant region or the fragment of the second Ig constant region.
In other embodiments, the L2 comprises the amino acid sequence of SEQ ID NOs: 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, or 64.
In other embodiments, the first Ig constant region or the fragment of the first Ig constant region and the second Ig constant region or the fragment of the second Ig constant region is an IgG1, an IgG2, and IgG3 or an IgG4 isotype.
In other embodiments, the first Ig constant region or the fragment of the first Ig constant region and the second Ig constant region or the fragment of the second Ig constant region is an IgG1 isotype.
In other embodiments, the first Ig constant region or the fragment of the first Ig constant region and the second Ig constant region or the fragment of the second Ig constant region is an IgG2 isotype.
In other embodiments, the first Ig constant region or the fragment of the first Ig constant region and the second Ig constant region or the fragment of the second Ig constant region is an IgG3 isotype.
In other embodiments, the first Ig constant region or the fragment of the first Ig constant region and the second Ig constant region or the fragment of the second Ig constant region is an IgG4 isotype.
The first Ig constant region or the fragment of the first Ig constant region and the second Ig constant region or the fragment of the second Ig constant region can further be engineered as described herein.
In other embodiments, the first Ig constant region or the fragment of the first Ig constant region and the second Ig constant region or the fragment of the second Ig constant region comprises at least one mutation that results in reduced binding of the multispecific protein to a FcγR.
In other embodiments, the at least one mutation that results in reduced binding of the multispecific protein to the FcγR is selected from the group consisting of F234A/L235A, L234A/L235A, L234A/L235A/D265S, V234A/G237A/P238S/H268A/V309L/A330S/P331S, F234A/L235A, S228P/F234A/L235A, N297A, V234A/G237A, K214T/E233P/L234V/L235A/G236-deleted/A327G/P331A/D365E/L358M, H268Q/V309L/A330S/P331S, S267E/L328F, L234F/L235E/D265A, L234A/L235A/G237A/P238S/H268A/A330S/P331S, S228P/F234A/L235A/G237A/P238S and S228P/F234A/L235A/G236-deleted/G237A/P238S, wherein residue numbering is according to the EU index.
In other embodiments, the first Ig constant region or the fragment of the first Ig constant region and the second Ig constant region or the fragment of the second Ig constant region comprises at least one mutation that results in enhanced binding of the multispecific protein to a Fcγ receptor (FcγR).
In other embodiments, the at least one mutation that results in enhanced binding of the multispecific protein to the FcγR is selected from the group consisting of S239D/I332E, S298A/E333A/K334A, F243L/R292P/Y300L, F243L/R292P/Y300L/P396L, F243L/R292P/Y300L/V305I/P396L and G236A/S239D/I332E, wherein residue numbering is according to the EU index.
In other embodiments, the FcγR is FcγRI, FcγRIIA, FcγRIIB or FcγRIII, or any combination thereof.
In other embodiments, the first Ig constant region or the fragment of the first Ig constant region and the second Ig constant region or the fragment of the second Ig constant region comprises at least one mutation that modulates a half-life of the multispecific protein.
In other embodiments, the at least one mutation that modulates the half-life of the multispecific protein is selected from the group consisting of H435A, P257I/N434H, D376V/N434H, M252Y/S254T/T256E/H433K/N434F, T308P/N434A and H435R, wherein residue numbering is according to the EU index.
In other embodiments, the multispecific protein comprises at least one mutation in a CH3 domain of the first Ig constant region or in a CH3 domain of the fragment of the first Ig constant region and/or at least one mutation in a CH3 domain of the second Ig constant region or in a CH3 domain of the fragment of the second Ig constant region.
In other embodiments, the at least one mutation in a CH3 domain of the first Ig constant region or in a CH3 domain of the fragment of the first Ig constant region and/or at least one mutation in a CH3 domain of the second Ig constant region or in a CH3 domain of the fragment of the second Ig constant region is selected from the group consisting of T350V, L351Y, F405A, Y407V, T366Y, T366W, T366L, F405W, K392L, T394W, T394S, Y407T, Y407A, T366S/L368A/Y407V, L351Y/F405A/Y407V, T366I/K392M/T394W, T366L/K392L/T394W, F405A/Y407V, T366L/K392M/T394W, L351Y/Y407A, L351Y/Y407V, T366A/K409F, L351Y/Y407A, T366V/K409F, T366A/K409F, T350V/L351Y/F405A/Y407V and T350V/T366L/K392L/T394W, wherein residue numbering is according to the EU index.
In other embodiments, the first Ig constant region or the fragment of the first Ig constant region and the second Ig constant region or the fragment of the second Ig constant region comprise the following mutations
L235A_L235A_D265S_T350V_L351Y_F405A_Y407V in the first Ig constant region and L235A_L235A_D265S_T350V_T366L_K392L_T394W in the second Ig constant region; or
L235A_L235A_D265S_T350V_T366L_K392L_T394W in the first Ig constant region and L235A_L235A_D265S_T350V_L351Y_F405A_Y407V in the second Ig constant region.
Generation of Multispecific Proteins that Comprise Antigen Binding Fragments that Bind CD3ε.
The antigen binding fragments that bind CD3ε of the disclosure may be engineered into multispecific antibodies which are also encompassed within the scope of the invention.
The antigen binding fragments that bind CD3ε may be engineered into full length multispecific antibodies which are generated using Fab arm exchange, in which substitutions are introduced into two monospecific bivalent antibodies within the Ig constant region CH3 domain which promote Fab arm exchange in vitro. In the methods, two monospecific bivalent antibodies are engineered to have certain substitutions at the CH3 domain that promote heterodimer stability; the antibodies are incubated together under reducing conditions sufficient to allow the cysteines in the hinge region to undergo disulfide bond isomerization; thereby generating the bispecific antibody by Fab arm exchange. The incubation conditions may optimally be restored to non-reducing. Exemplary reducing agents that may be used are 2-mercaptoethylamine (2-MEA), dithiothreitol (DTT), dithioerythritol (DTE), glutathione, tris(2-carboxyethyl)phosphine (TCEP), L-cysteine and beta-mercaptoethanol, preferably a reducing agent selected from the group consisting of: 2-mercaptoethylamine, dithiothreitol and tris(2-carboxyethyl)phosphine. For example, incubation for at least 90 min at a temperature of at least 20° C. in the presence of at least 25 mM 2-MEA or in the presence of at least 0.5 mM dithiothreitol at a pH of from 5-8, for example at pH of 7.0 or at pH of 7.4 may be used.
CH3 mutations that may be used include technologies such as Knob-in-Hole mutations (Genentech), electrostatically-matched mutations (Chugai, Amgen, NovoNordisk, Oncomed), the Strand Exchange Engineered Domain body (SEEDbody) (EMD Serono), Duobody® mutations (Genmab), and other asymmetric mutations (e.g. Zymeworks).
Knob-in-hole mutations are disclosed for example in WO1996/027011 and include mutations on the interface of CH3 region in which an amino acid with a small side chain (hole) is introduced into the first CH3 region and an amino acid with a large side chain (knob) is introduced into the second CH3 region, resulting in preferential interaction between the first CH3 region and the second CH3 region. Exemplary CH3 region mutations forming a knob and a hole are T366Y/F405A, T366W/F405W, F405W/Y407A, T394W/Y407T, T394S/Y407A, T366W/T394S, F405W/T394S and T366W/T366S_L368A_Y407V.
Heavy chain heterodimer formation may be promoted by using electrostatic interactions by substituting positively charged residues on the first CH3 region and negatively charged residues on the second CH3 region as described in US2010/0015133, US2009/0182127, US2010/028637 or US2011/0123532.
Other asymmetric mutations that can be used to promote heavy chain heterodimerization are L351Y_F405A_Y407V/T394W, T366I_K392M_T394W/F405A_Y407V, T366L_K392M_T394W/F405A_Y407V, L351Y_Y407A/T366A_K409F, L351Y_Y407A/T366V_K409F, Y407A/T366A_K409F, or T350V_L351Y_F405A_Y407V/T350V_T366L_K392L_T394W as described in US2012/0149876 or US2013/0195849 (Zymeworks).
SEEDbody mutations involve substituting select IgG residues with IgA residues to promote heavy chain heterodimerization as described in US20070287170.
Other exemplary mutations that may be used are R409D_K370E/D399K_E357K, S354C_T366W/Y349C_T366S_L368A_Y407V, Y349C_T366W/S354C_T366S_L368A_Y407V, T366K/L351D, L351K/Y349E, L351K/Y349D, L351K/L368E, L351Y_Y407A/T366A_K409F, L351Y_Y407A/T366V_K409F, K392D/D399K, K392D/E356K, K253E_D282K_K322D/D239K_E240K_K292D, K392D_K409D/D356K D399K as described in WO2007/147901, WO 2011/143545, WO2013157954, WO2013096291 and US2018/0118849.
Duobody® mutations (Genmab) are disclosed for example in U.S. Pat. No. 9,150,663 and US2014/0303356 and include mutations F405L/K409R, wild-type/F405L_R409K, T350I_K370T_F405L/K409R, K370W/K409R, D399AFGHILMNRSTVWY/K409R, T366ADEFGHILMQVY/K409R, L368ADEGHNRSTVQ/K409AGRH, D399FHKRQ/K409AGRH, F405IKLSTVW/K409AGRH and Y407LWQ/K409AGRH.
Additional bispecific or multispecific structures into which the antigen binding domains that bind CD3ε can be incorporated include Dual Variable Domain Immunoglobulins (DVD) (Int. Pat. Publ. No. WO2009/134776; DVDs are full length antibodies comprising the heavy chain having a structure VH1-linker-VH2-CH and the light chain having the structure VL1-linker-VL2-CL; linker being optional), structures that include various dimerization domains to connect the two antibody arms with different specificity, such as leucine zipper or collagen dimerization domains (Int. Pat. Publ. No. WO2012/022811, U.S. Pat. Nos. 5,932,448; 6,833,441), two or more domain antibodies (dAbs) conjugated together, diabodies, heavy chain only antibodies such as camelid antibodies and engineered camelid antibodies, Dual Targeting (DT)-Ig (GSK/Domantis), Two-in-one Antibody (Genentech), Cross-linked Mabs (Karmanos Cancer Center), mAb2 (F-Star) and CovX-body (CovX/Pfizer), IgG-like Bispecific (InnClone/Eli Lilly), Ts2Ab (MedImmune/AZ) and BsAb (Zymogenetics), HERCULES (Biogen Idec) and TvAb (Roche), ScFv/Fc Fusions (Academic Institution), SCORPION (Emergent BioSolutions/Trubion, Zymogenetics/BMS), Dual Affinity Retargeting Technology (Fc-DART) (MacroGenics) and Dual(ScFv)2-Fab (National Research Center for Antibody Medicine—China), Dual-Action or Bis-Fab (Genentech), Dock-and-Lock (DNL) (ImmunoMedics), Bivalent Bispecific (Biotecnol) and Fab-Fv (UCB-Celltech). ScFv-, diabody-based, and domain antibodies, include but are not limited to, Bispecific T Cell Engager (BiTE) (Micromet), Tandem Diabody (Tandab) (Affimed), Dual Affinity Retargeting Technology (DART) (MacroGenics), Single-chain Diabody (Academic), TCR-like Antibodies (AIT, ReceptorLogics), Human Serum Albumin ScFv Fusion (Merrimack) and COMBODY (Epigen Biotech), dual targeting nanobodies (Ablynx), dual targeting heavy chain only domain antibodies.
The antigen binding domains that bind CD3ε of the disclosure may also be engineered into multispecific proteins which comprise three polypeptide chains. In such designs, at least one antigen binding domain is in the form of a scFv. Exemplary designs include (in which “1” indicates the first antigen binding domain, “2” indicates the second antigen binding domain and “3” indicates the third antigen binding domain:
Design 1: Chain A) scFv1-CH2-CH3; Chain B) VL2-CL; Chain C) VH2-CH1-hinge-CH2-CH3
Design 2: Chain A) scFv1-hinge- CH2-CH3; Chain B) VL2-CL; Chain C) VH2-CH1-hinge-CH2-CH3
Design 3: Chain A) scFv1-CH1-hinge-CH2-CH3; Chain B) VL2-CL; Chain C) VH2-CH1-hinge-CH2-CH3
Design 4: Chain A) CH2-CH3-scFv1; Chain B) VL2-CL; Chain C) VH2-CH1-hinge-CH2-CH3
CH3 engineering may be incorporated to the Designs 1-4, such as mutations L351Y_F405A_Y407V/T394W, T366I_K392M_T394W/F405A_Y407V, T366L_K392M_T394W/F405A_Y407V, L351Y_Y407A/T366A_K409F, L351Y_Y407A/T366V_K409F, Y407A/T366A_K409F, or T350V_L351Y_F405A_Y407V/T350V_T366L_K392L_T394W as described in US2012/0149876 or US2013/0195849 (Zymeworks).
The Ig constant region or the fragment of the Ig constant region, such as the Fc region present in the proteins of the disclosure may be of any allotype or isotype.
In other embodiments, the Ig constant region or the fragment of the Ig constant region is an IgG1 isotype.
In other embodiments, the Ig constant region or the fragment of the Ig constant region is an IgG2 isotype.
In other embodiments, the Ig constant region or the fragment of the Ig constant region is an IgG3 isotype.
In other embodiments, the Ig constant region or the fragment of the Ig constant region is an IgG4 isotype.
The Ig constant region or the fragment of the Ig constant region may be of any allotype. It is expected that allotype has no influence on properties of the Ig constant region, such as binding or Fc-mediated effector functions. Immunogenicity of therapeutic proteins comprising Ig constant regions of fragments thereof is associated with increased risk of infusion reactions and decreased duration of therapeutic response (Baert et al., (2003) N Engl J Med 348:602-08). The extent to which therapeutic proteins comprising Ig constant regions of fragments thereof induce an immune response in the host may be determined in part by the allotype of the Ig constant region (Stickler et al., (2011) Genes and Immunity 12:213-21). Ig constant region allotype is related to amino acid sequence variations at specific locations in the constant region sequences of the antibody. Table 3 shows select IgG1, IgG2 and IgG4 allotypes.
C-terminal lysine (CTL) may be removed from the Ig constant region by endogenous circulating carboxypeptidases in the blood stream (Cai et al., (2011) Biotechnol Bioeng 108:404-412). During manufacturing, CTL removal may be controlled to less than the maximum level by control of concentration of extracellular Zn2+, EDTA or EDTA—Fe3+ as described in U.S. Patent Publ. No. US20140273092. CTL content of proteins may be measured using known methods.
In other embodiments, the antigen binding fragment that binds CD3ε conjugated to the Ig constant region has a C-terminal lysine content from about 10% to about 90%. In other embodiments, the C-terminal lysine content is from about 20% to about 80%. In other embodiments, the C-terminal lysine content is from about 40% to about 70%. In other embodiments, the C-terminal lysine content is from about 55% to about 70%. In other embodiments, the C-terminal lysine content is about 60%.
Fc region mutations may be made to the antigen binding domains that bind CD3ε conjugated to the Ig constant region or to the fragment of the Ig constant region to modulate their effector functions such as ADCC, ADCP and/or ADCP and/or pharmacokinetic properties. This may be achieved by introducing mutation(s) into the Fc that modulate binding of the mutated Fc to activating FcγRs (FcγRI, FcγRIIa, FcγRIII), inhibitory FcγRIIb and/or to FcRn.
In other embodiments, the antigen binding domain that binds CD3ε conjugated to the Ig constant region or the fragment of the Ig constant region comprises at least one mutation in the Ig constant region or in the fragment of the Ig constant region.
In other embodiments, the at least one mutation is in the Fc region.
In other embodiments, the antigen binding domain that binds CD3ε conjugated to the Ig constant region or to the fragment of the Ig constant region comprises at least one, two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen or fifteen mutations in the Fc region.
In other embodiments, the antigen binding domain that binds CD3ε conjugated to the Ig constant region or to the fragment of the Ig constant region comprises at least one mutation in the Fc region that modulates binding of the antibody to FcRn.
Fc positions that may be mutated to modulate half-life (e.g. binding to FcRn) include positions 250, 252, 253, 254, 256, 257, 307, 376, 380, 428, 434 and 435. Exemplary mutations that may be made singularly or in combination are mutations T250Q, M252Y, I253A, S254T, T256E, P257I, T307A, D376V, E380A, M428L, H433K, N434S, N434A, N434H, N434F, H435A and H435R. Exemplary singular or combination mutations that may be made to increase the half-life are mutations M428L/N434S, M252Y/S254T/T256E, T250Q/M428L, N434A and T307A/E380A/N434A. Exemplary singular or combination mutations that may be made to reduce the half-life are mutations H435A, P257I/N434H, D376V/N434H, M252Y/S254T/T256E/H433K/N434F, T308P/N434A and H435R.
In other embodiments, the antigen binding domain that binds CD3ε conjugated to the Ig constant region or to the fragment of the Ig constant region comprises M252Y/S254T/T256E mutation.
In other embodiments, the antigen binding domain that binds CD3ε conjugated to the Ig constant region or to the fragment of the Ig constant region comprises at least one mutation in the Fc region that reduces binding of the protein to an activating Fcγ receptor (FcγR) and/or reduces Fc effector functions such as C1q binding, complement dependent cytotoxicity (CDC), antibody-dependent cell-mediated cytotoxicity (ADCC) or phagocytosis (ADCP).
Fc positions that may be mutated to reduce binding of the protein to the activating FcγR and subsequently to reduce effector function include positions 214, 233, 234, 235, 236, 237, 238, 265, 267, 268, 270, 295, 297, 309, 327, 328, 329, 330, 331 and 365. Exemplary mutations that may be made singularly or in combination are mutations K214T, E233P, L234V, L234A, deletion of G236, V234A, F234A, L235A, G237A, P238A, P238S, D265A, S267E, H268A, H268Q, Q268A, N297A, A327Q, P329A, D270A, Q295A, V309L, A327S, L328F, A330S and P331S in IgG1, IgG2, IgG3 or IgG4. Exemplary combination mutations that result in proteins with reduced ADCC are mutations L234A/L235A on IgG1, L234A/L235A/D265S on IgG1, V234A/G237A/P238S/H268A/V309L/A330S/P331S on IgG2, F234A/L235A on IgG4, S228P/F234A/L235A on IgG4, N297A on all Ig isotypes, V234A/G237A on IgG2, K214T/E233P/L234V/L235A/G236-deleted/A327G/P331A/D365E/L358M on IgG1, H268Q/V309L/A330S/P331S on IgG2, S267E/L328F on IgG1, L234F/L235E/D265A on IgG1, L234A/L235A/G237A/P238S/H268A/A330S/P331S on IgG1, S228P/F234A/L235A/G237A/P238S on IgG4, and S228P/F234A/L235A/G236-deleted/G237A/P238S on IgG4. Hybrid IgG2/4 Fc domains may also be used, such as Fc with residues 117-260 from IgG2 and residues 261-447 from IgG4.
Exemplary mutation that result in proteins with reduced CDC is a K322A mutation.
Well-known S228P mutation may be made in IgG4 to enhance IgG4 stability.
In other embodiments, the antigen binding domain that binds CD3ε conjugated to the Ig constant region or to the fragment of the Ig constant region comprises at least one mutation selected from the group consisting of K214T, E233P, L234V, L234A, deletion of G236, V234A, F234A, L235A, G237A, P238A, P238S, D265A, S267E, H268A, H268Q, Q268A, N297A, A327Q, P329A, D270A, Q295A, V309L, A327S, L328F, K322, A330S and P331S.
In other embodiments, the antigen binding domain that binds CD3ε conjugated to the Ig constant region or to the fragment of the Ig constant region comprises L234A/L235A/D265S mutation.
In other embodiments, the antigen binding domain that binds CD3ε conjugated to the Ig constant region or to the fragment of the Ig constant region comprises L234A/L235A mutation.
In other embodiments, the antigen binding domain that binds CD3ε conjugated to the Ig constant region or to the fragment of the Ig constant region comprises at least one mutation in the Fc region that enhances binding of the protein to an Fcγ receptor (FcγR) and/or enhances Fc effector functions such as C1q binding, complement dependent cytotoxicity (CDC), antibody-dependent cell-mediated cytotoxicity (ADCC) and/or phagocytosis (ADCP).
Fc positions that may be mutated to increase binding of the protein to the activating FcγR and/or enhance Fc effector functions include positions 236, 239, 243, 256, 290, 292, 298, 300, 305, 312, 326, 330, 332, 333, 334, 345, 360, 339, 378, 396 or 430 (residue numbering according to the EU index). Exemplary mutations that may be made singularly or in combination are G236A, S239D, F243L, T256A, K290A, R292P, S298A, Y300L, V305L, K326A, A330K, 1332E, E333A, K334A, A339T and P396L. Exemplary combination mutations that result in proteins with increased ADCC or ADCP are a S239D/1332E, S298A/E333A/K334A, F243L/R292P/Y300L, F243L/R292P/Y300L/P396L, F243L/R292P/Y300L/V305I/P396L and G236A/S239D/I332E.
Fc positions that may be mutated to enhance CDC include positions 267, 268, 324, 326, 333, 345 and 430. Exemplary mutations that may be made singularly or in combination are S267E, F1268F, S324T, K326A, K326W, E333A, E345K, E345Q, E345R, E345Y, E430S, E430F and E430T. Exemplary combination mutations that result in proteins with increased CDC are K326A/E333A, K326W/E333A, H268F/S324T, S267E/H268F, S267E/S324T and S267E/H268F/S324T.
The specific mutations described herein are mutations when compared to the IgG1, IgG2 and IgG4 wild-type amino acid sequences of SEQ ID NOs: 95, 96, and 97, respectively.
Binding of the antibody to FcγR or FcRn may be assessed on cells engineered to express each receptor using flow cytometry. In an exemplary binding assay, 2×105 cells per well are seeded in 96-well plate and blocked in BSA Stain Buffer (BD Biosciences, San Jose, USA) for 30 min at 4° C. Cells are incubated with a test antibody on ice for 1.5 hour at 4° C. After being washed twice with BSA stain buffer, the cells are incubated with R-PE labeled anti-human IgG secondary antibody (Jackson Immunoresearch Laboratories) for 45 min at 4° C. The cells are washed twice in stain buffer and then resuspended in 150 μL of Stain Buffer containing 1:200 diluted DRAQ7 live/dead stain (Cell Signaling Technology, Danvers, USA). PE and DRAQ7 signals of the stained cells are detected by Miltenyi MACSQuant flow cytometer (Miltenyi Biotec, Auburn, USA) using B2 and B4 channel respectively. Live cells are gated on DRAQ7 exclusion and the geometric mean fluorescence signals are determined for at least 10,000 live events collected. FlowJo software (Tree Star) is used for analysis. Data is plotted as the logarithm of antibody concentration versus mean fluorescence signals. Nonlinear regression analysis is performed.
The ability of the antigen binding domain that binds CD3ε conjugated to the Ig constant region or to the fragment of the Ig constant region to mediate ADCC can be enhanced by engineering the Ig constant region or the fragment of the Ig constant region oligosaccharide component. Human IgG1 or IgG3 are N-glycosylated at Asn297 with the majority of the glycans in the well-known biantennary GO, G0F, G1, G1F, G2 or G2F forms. Ig constant region containing proteins may be produced by non-engineered CHO cells typically have a glycan fucose content of about at least 85%. The removal of the core fucose from the biantennary complex-type oligosaccharides attached to the antigen binding domain that binds CD3ε conjugated to the Ig constant region or to the fragment of the Ig constant region enhances the ADCC of the protein via improved FcγRIIIa binding without altering antigen binding or CDC activity. Such proteins can be achieved using different methods reported to lead to the successful expression of relatively high defucosylated immunoglobulins bearing the biantennary complex-type of Fc oligosaccharides such as control of culture osmolality (Konno et al., Cytotechnology 64(:249-65, 2012), application of a variant CHO line Lec13 as the host cell line (Shields et al., J Biol Chem 277:26733-26740, 2002), application of a variant CHO line EB66 as the host cell line (Olivier et al., MAbs; 2(4): 405-415, 2010; PMID:20562582), application of a rat hybridoma cell line YB2/0 as the host cell line (Shinkawa et al., J Biol Chem 278:3466-3473, 2003), introduction of small interfering RNA specifically against the a 1,6-fucosyltrasferase (FUT8) gene (Mori et al., Biotechnol Bioeng 88:901-908, 2004), or coexpression of β-1,4-N-acetylglucosaminyltransferase III and Golgi α-mannosidase II or a potent alpha-mannosidase I inhibitor, kifunensine (Ferrara et al., J Biol Chem 281:5032-5036, 2006, Ferrara et al., Biotechnol Bioeng 93:851-861, 2006; Xhou et al., Biotechnol Bioeng 99:652-65, 2008).
In other embodiments, the antigen binding domain that binds CD3ε conjugated to the Ig constant region or to the fragment of the Ig constant region of the disclosure has a biantennary glycan structure with fucose content of about between 1% to about 15%, for example about 15%, 14%, 13%, 12%, 11% 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2% or 1%. In other embodiments, the antigen binding domain that binds CD3ε conjugated to the Ig constant region or to the fragment of the Ig constant region has a glycan structure with fucose content of about 50%, 40%, 45%, 40%, 35%, 30%, 25%, or 20%. “Fucose content” means the amount of the fucose monosaccharide within the sugar chain at Asn297. The relative amount of fucose is the percentage of fucose-containing structures related to all glycostructures. These may be characterized and quantified by multiple methods, for example: 1) using MALDI-TOF of N-glycosidase F treated sample (e.g. complex, hybrid and oligo- and high-mannose structures) as described in Int Pat. Publ. No. WO2008/077546 2); 2) by enzymatic release of the Asn297 glycans with subsequent derivatization and detection/quantitation by HPLC (UPLC) with fluorescence detection and/or HPLC-MS (UPLC-MS); 3) intact protein analysis of the native or reduced mAb, with or without treatment of the Asn297 glycans with Endo S or other enzyme that cleaves between the first and the second GlcNAc monosaccharides, leaving the fucose attached to the first GlcNAc; 4) digestion of the mAb to constituent peptides by enzymatic digestion (e.g., trypsin or endopeptidase Lys-C), and subsequent separation, detection and quantitation by HPLC-MS (UPLC-MS); 5) Separation of the mAb oligosaccharides from the mAb protein by specific enzymatic deglycosylation with PNGase F at Asn 297. The oligosaccharides thus released can be labeled with a fluorophore, separated and identified by various complementary techniques which allow: fine characterization of the glycan structures by matrix-assisted laser desorption ionization (MALDI) mass spectrometry by comparison of the experimental masses with the theoretical masses, determination of the degree of sialylation by ion exchange HPLC (GlycoSep C), separation and quantification of the oligosaccharide forms according to hydrophilicity criteria by normal-phase HPLC (GlycoSep N), and separation and quantification of the oligosaccharides by high performance capillary electrophoresis-laser induced fluorescence (HPCE-LIF).
“Low fucose” or “low fucose content” as used herein refers to the antigen binding domain that bind CD3ε conjugated to the Ig constant region or to the fragment of the Ig constant region with fucose content of about between 1%-15%.
“Normal fucose” or “normal fucose content” as used herein refers to the antigen binding domain that bind CD3ε conjugated to the Ig constant region or to the fragment of the Ig constant region with fucose content of about over 50%, typically about over 80% or over 85%.
Anti-idiotypic antibodies are antibodies that specifically bind to the antigen binding domain that binds CD3ε of the disclosure.
The invention also provides an anti-idiotypic antibody that specifically binds to the antigen binding domain that binds CD3ε of the disclosure.
The invention also provides an anti-idiotypic antibody that specifically binds to the antigen binding domain that binds CD3ε comprising
the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 24;
the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 27;
the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 28;
the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 29; or
the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 30.
An anti-idiotypic (Id) antibody is an antibody which recognizes the antigenic determinants (e.g. the paratope or CDRs) of the antibody. The Id antibody may be antigen-blocking or non-blocking. The antigen-blocking Id may be used to detect the free antigen binding domain in a sample (e.g. the antigen binding domain that binds CD3ε of the disclosure). The non-blocking Id may be used to detect the total antibody (free, partially bond to antigen, or fully bound to antigen) in a sample. An Id antibody may be prepared by immunizing an animal with the antibody to which an anti-Id is being prepared.
An anti-Id antibody may also be used as an immunogen to induce an immune response in yet another animal, producing a so-called anti-anti-Id antibody. An anti-anti-Id may be epitopically identical to the original antigen binding domain which induced the anti-Id. Thus, by using antibodies to the idiotypic determinants of the antigen binding domain, it is possible to identify other clones expressing antigen binding domains of identical specificity. Anti-Id antibodies may be varied (thereby producing anti-Id antibody variants) and/or derivatized by any suitable technique, such as those described elsewhere herein.
The antigen binding domains that bind CD3ε of the disclosure, the proteins comprising the antigen binding domains that bind CD3ε or the multispecific proteins that comprise the antigen binding domains that bind CD3ε (collectively referred herein as to CD3ε binding proteins) may be conjugated to a heterologous molecule.
In other embodiments, the heterologous molecule is a detectable label or a cytotoxic agent.
The invention also provides an antigen binding domain that binds CD3ε conjugated to a detectable label.
The invention also provides a protein comprising an antigen binding domain that binds CD3ε conjugated to a detectable label.
The invention also provides a multispecific protein comprising an antigen binding domain that binds CD3ε conjugated to a detectable label.
The invention also provides an antigen binding domain that binds CD3ε conjugated to a cytotoxic agent.
The invention also provides a protein comprising an antigen binding domain that binds CD3ε conjugated to a cytotoxic agent.
The invention also provides a multispecific protein comprising an antigen binding domain that binds CD3ε conjugated to a cytotoxic agent.
CD3ε binding proteins of the disclosure may be used to direct therapeutics to tumor antigen expressing cells. Alternatively, CD3ε expressing cells may be targeted with a CD3ε binding protein of the disclosure coupled to a therapeutic intended to modify cell function once internalized.
In other embodiments, the detectable label is also a cytotoxic agent.
The CD3ε binding proteins of the disclosure conjugated to a detectable label may be used to evaluate expression of CD3ε on a variety of samples.
Detectable label includes compositions that when conjugated to the CD3ε binding proteins of the disclosure renders the latter detectable, via spectroscopic, photochemical, biochemical, immunochemical, or chemical means.
Exemplary detectable labels include radioactive isotopes, magnetic beads, metallic beads, colloidal particles, fluorescent dyes, electron-dense reagents, enzymes (for example, as commonly used in an ELISA), biotin, digoxigenin, haptens, luminescent molecules, chemiluminescent molecules, fluorochromes, fluorophores, fluorescent quenching agents, colored molecules, radioactive isotopes, scintillates, avidin, streptavidin, protein A, protein G, antibodies or fragments thereof, polyhistidine, Ni2+, Flag tags, myc tags, heavy metals, enzymes, alkaline phosphatase, peroxidase, luciferase, electron donors/acceptors, acridinium esters, and colorimetric substrates.
A detectable label may emit a signal spontaneously, such as when the detectable label is a radioactive isotope. In other cases, the detectable label emits a signal as a result of being stimulated by an external field.
Exemplary radioactive isotopes may be γ-emitting, Auger-emitting, β-emitting, an alpha-emitting or positron-emitting radioactive isotope. Exemplary radioactive isotopes include 3H, 11C, 13C, 15N, 18F, 19F, 55Co, 57Co, 60Co, 61Cu, 62Cu, 64Cu, 67Cu, 68Ga, 72As, 75Br, 86Y, 89Zr, 90Sr, 94mTc, 99mTc, 115In, 123I, 124I, 125I, 131I, 211At, 212Bi, 213Bi, 223Ra, 226Ra, 225Ac and 227Ac.
Exemplary metal atoms are metals with an atomic number greater than 20, such as calcium atoms, scandium atoms, titanium atoms, vanadium atoms, chromium atoms, manganese atoms, iron atoms, cobalt atoms, nickel atoms, copper atoms, zinc atoms, gallium atoms, germanium atoms, arsenic atoms, selenium atoms, bromine atoms, krypton atoms, rubidium atoms, strontium atoms, yttrium atoms, zirconium atoms, niobium atoms, molybdenum atoms, technetium atoms, ruthenium atoms, rhodium atoms, palladium atoms, silver atoms, cadmium atoms, indium atoms, tin atoms, antimony atoms, tellurium atoms, iodine atoms, xenon atoms, cesium atoms, barium atoms, lanthanum atoms, hafnium atoms, tantalum atoms, tungsten atoms, rhenium atoms, osmium atoms, iridium atoms, platinum atoms, gold atoms, mercury atoms, thallium atoms, lead atoms, bismuth atoms, francium atoms, radium atoms, actinium atoms, cerium atoms, praseodymium atoms, neodymium atoms, promethium atoms, samarium atoms, europium atoms, gadolinium atoms, terbium atoms, dysprosium atoms, holmium atoms, erbium atoms, thulium atoms, ytterbium atoms, lutetium atoms, thorium atoms, protactinium atoms, uranium atoms, neptunium atoms, plutonium atoms, americium atoms, curium atoms, berkelium atoms, californium atoms, einsteinium atoms, fermium atoms, mendelevium atoms, nobelium atoms, or lawrencium atoms.
In other embodiments, the metal atoms may be alkaline earth metals with an atomic number greater than twenty.
In other embodiments, the metal atoms may be lanthanides.
In other embodiments, the metal atoms may be actinides.
In other embodiments, the metal atoms may be transition metals.
In other embodiments, the metal atoms may be poor metals.
In other embodiments, the metal atoms may be gold atoms, bismuth atoms, tantalum atoms, and gadolinium atoms.
In other embodiments, the metal atoms may be metals with an atomic number of 53 (i.e. iodine) to 83 (i.e. bismuth).
In other embodiments, the metal atoms may be atoms suitable for magnetic resonance imaging.
The metal atoms may be metal ions in the form of +1, +2, or +3 oxidation states, such as Ba2+, Bi3+, Cs+, Ca2+, Cr2+, Cr3+, Cr6+, Co2+, Co3+, Cu+, Cu2+, Cu3+, Ga3+, Gd3+, Au+, Au3+, Fe2+, Fe3+, F3+, Pb2+, Mn2+, Mn+3, Mn4+, Mn7+, Hg2+, Ni2+, Ni3+, Ag+, Sr2+, Sn2+, Sn4+, and Zn2+. The metal atoms may comprise a metal oxide, such as iron oxide, manganese oxide, or gadolinium oxide.
Suitable dyes include any commercially available dyes such as, for example, 5(6)-carboxyfluorescein, IRDye 680RD maleimide or IRDye 800CW, ruthenium polypyridyl dyes, and the like.
Suitable fluorophores are fluorescein isothiocyanate (FITC), fluorescein thiosemicarbazide, rhodamine, Texas Red, CyDyes (e.g., Cy3, Cy5, Cy5.5), Alexa Fluors (e.g., Alexa488, Alexa555, Alexa594; Alexa647), near infrared (NIR) (700-900 nm) fluorescent dyes, and carbocyanine and aminostyryl dyes.
The antigen binding domain that binds CD3ε conjugated to a detectable label may be used as an imaging agent.
The protein comprising an antigen binding domain that binds CD3ε conjugated to a detectable label may be used as an imaging agent.
The multispecific protein comprising an antigen binding domain that binds CD3ε conjugated to a detectable label may be used as an imaging agent.
In other embodiments, the cytotoxic agent is a chemotherapeutic agent, a drug, a growth inhibitory agent, a toxin (e.g., an enzymatically active toxin of bacterial, fungal, plant, or animal origin, or fragments thereof), or a radioactive isotope (i.e., a radioconjugate).
In other embodiments, the cytotoxic agent is daunomycin, doxorubicin, methotrexate, vindesine, bacterial toxins such as diphtheria toxin, ricin, geldanamycin, maytansinoids or calicheamicin. The cytotoxic agent may elicit their cytotoxic and cytostatic effects by mechanisms including tubulin binding, DNA binding, or topoisomerase inhibition.
In other embodiments, the cytotoxic agent is an enzymatically active toxin such as diphtheria A chain, nonbinding active fragments of diphtheria toxin, exotoxin A chain (from Pseudomonas aeruginosa), ricin A chain, abrin A chain, modeccin A chain, alpha-sarcin, Aleurites fordii proteins, dianthin proteins, Phytolaca americana proteins (PAPI, PAPII, and PAP-S), Momordica charantia inhibitor, curcin, crotin, Sapaonaria officinalis inhibitor, gelonin, mitogellin, restrictocin, phenomycin, enomycin, and the tricothecenes.
In other embodiments, the cytotoxic agent is a radionuclide, such as 212Bi, 131I, 131In, 90Y, and 186Re.
In other embodiments, the cytotoxic agent is dolastatins or dolostatin peptidic analogs and derivatives, auristatin or monomethyl auristatin phenylalanine. Exemplary molecules are disclosed in U.S. Pat. Nos. 5,635,483 and 5,780,588. Dolastatins and auristatins have been shown to interfere with microtubule dynamics, GTP hydrolysis, and nuclear and cellular division (Woyke et al (2001) Antimicrob Agents and Chemother. 45(12):3580-3584) and have anticancer and antifungal activity. The dolastatin or auristatin drug moiety may be attached to the antibody of the invention through the N (amino) terminus or the C (carboxyl) terminus of the peptidic drug moiety (WO02/088172), or via any cysteine engineered into the antibody.
The CD3ε binding proteins of the disclosure may be conjugated to a detectable label using known methods.
In other embodiments, the detectable label is complexed with a chelating agent.
In other embodiments, the detectable label is conjugated to the CD3ε binding proteins of the disclosure via a linker.
The detectable label or the cytotoxic moiety may be linked directly, or indirectly, to the CD3ε binding proteins of the disclosure using known methods. Suitable linkers are known in the art and include, for example, prosthetic groups, non-phenolic linkers (derivatives of N-succimidyl-benzoates; dodecaborate), chelating moieties of both macrocyclics and acyclic chelators, such as derivatives of 1,4,7,10-tetraazacyclododecane-1,4,7,10,tetraacetic acid (DOTA), derivatives of diethylenetriaminepentaacetic avid (DTPA), derivatives of S-2-(4-Isothiocyanatobenzyl)-1,4,7-triazacyclononane-1,4,7-triacetic acid (NOTA) and derivatives of 1,4,8,11-tetraazacyclodocedan-1,4,8,11-tetraacetic acid (TETA), N-succinimidyl-3-(2-pyridyldithiol) propionate (SPDP), iminothiolane (IT), bifunctional derivatives of imidoesters (such as dimethyl adipimidate HCl), active esters (such as disuccinimidyl suberate), aldehydes (such as glutaraldehyde), bis-azido compounds (such as bis(p-azidobenzoyl)hexanediamine), bis-diazonium derivatives (such as bis-(p-diazoniumbenzoyl)-ethylenediamine), diisocyanates (such as toluene 2,6-diisocyanate), and bis-active fluorine compounds (such as 1,5-difluoro-2,4-dinitrobenzene) and other chelating moieties. Suitable peptide linkers are well known.
In other embodiments, the CD3ε binding proteins of the disclosure is removed from the blood via renal clearance.
The invention also provides a kit comprising the antigen binding domain that binds CD3ε.
The invention also provides a kit comprising the protein comprising an antigen binding domain that binds CD3ε.
The invention also provides a kit comprising the multispecific protein comprising an antigen binding domain that binds CD3ε.
The kit may be used for therapeutic uses and as diagnostic kits.
The kit may be used to detect the presence of CD3ε in a sample.
In other embodiments, the kit comprises the CD3ε binding protein of the disclosure and reagents for detecting the CD3ε binding protein. The kit can include one or more other elements including: instructions for use; other reagents, e.g., a label, a therapeutic agent, or an agent useful for chelating, or otherwise coupling, an antibody to a label or therapeutic agent, or a radioprotective composition; devices or other materials for preparing the antibody for administration; pharmaceutically acceptable carriers; and devices or other materials for administration to a subject.
In other embodiments, the kit comprises the antigen binding domain that binds CD3ε in a container and instructions for use of the kit.
In other embodiments, the kit comprises the protein comprising an antigen binding domain that binds CD3ε in a container and instructions for use of the kit.
In other embodiments, the kit comprises the multispecific protein comprising an antigen binding domain that binds CD3ε in a container and instructions for use of the kit.
In other embodiments, the antigen binding domain that binds CD3ε in the kit is labeled.
In other embodiments, the protein comprising an antigen binding domain that binds CD3ε in the kit is labeled.
In other embodiments, the multispecific protein comprising an antigen binding domain that binds CD3ε in the kit is labeled.
In other embodiments, the kit comprises the antigen binding domain that binds CD3ε comprising
the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 24;
the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 27;
the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 28;
the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 29; or
the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 30;
In other embodiments, the kit comprises the antigen binding domain that binds CD3ε comprising SEQ ID NOs: 65, 66, 67, 68, 69, 70, 71, 72, 73, or 74.
The invention also provides a method of detecting CD3ε in a sample, comprising obtaining the sample, contacting the sample with the antigen binding domain that binds CD3ε of the disclosure and detecting the bound CD3ε in the sample.
In other embodiments, the sample may be derived from urine, blood, serum, plasma, saliva, ascites, circulating cells, synovial fluid, circulating cells, cells that are not tissue associated (i.e., free cells), tissues (e.g., surgically resected tissue, biopsies, including fine needle aspiration), histological preparations, and the like.
The antigen binding domain that binds CD3ε of the disclosure may be detected using known methods. Exemplary methods include direct labeling of the antibodies using fluorescent or chemiluminescent labels, or radiolabels, or attaching to the antibodies of the invention a moiety which is readily detectable, such as biotin, enzymes or epitope tags. Exemplary labels and moieties are ruthenium, 111In-DOTA, 111In-diethylenetriaminepentaacetic acid (DTPA), horseradish peroxidase, alkaline phosphatase and beta-galactosidase, poly-histidine (HIS tag), acridine dyes, cyanine dyes, fluorone dyes, oxazin dyes, phenanthridine dyes, rhodamine dyes and Alexafluor® dyes.
The antigen binding domain that binds CD3ε of the disclosure may be used in a variety of assays to detect CD3ε in the sample. Exemplary assays are western blot analysis, radioimmunoassay, surface plasmon resonance, immunoprecipitation, equilibrium dialysis, immunodiffusion, electrochemiluminescence (ECL) immunoassay, immunohistochemistry, fluorescence-activated cell sorting (FACS) or ELISA assay.
The disclosure also provides an isolated polynucleotide encoding any of the CD3ε binding proteins of the disclosure. The CD3ε binding protein includes the antigen binding domains that bind CD3ε, the proteins comprising the antigen binding domains that bind CD3ε, the multispecific proteins that comprise the antigen binding domains that bind CD3ε of the disclosure.
The invention also provides an isolated polynucleotide encoding any of CD3ε biding proteins or fragments thereof.
The invention also provides an isolated polynucleotide encoding the VH of SEQ ID NO: 23.
The invention also provides an isolated polynucleotide encoding the VL of SEQ ID NOs: 24, 27, 28, 29 or 30.
The invention also provides an isolated polynucleotide encoding the VL of SEQ ID NO: 24.
The invention also provides an isolated polynucleotide encoding the VL of SEQ ID NO: 27.
The invention also provides an isolated polynucleotide encoding the VL of SEQ ID NO: 28.
The invention also provides an isolated polynucleotide encoding the VL of SEQ ID NO: 29.
The invention also provides an isolated polynucleotide encoding the VL of SEQ ID NO: 30.
The invention also provides an isolated polynucleotide encoding the VH of SEQ ID NO: 23 and the VL of SEQ ID NOs: 24, 27, 28, 29 or 30.
The invention also provides for an isolated polynucleotide encoding
the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 24;
the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 27;
the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 28;
the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 29; or
the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 30.
The invention also provides an isolated polynucleotide encoding the polypeptide of SEQ ID NOs: SEQ ID NOs: 65, 66, 67, 68, 69, 70, 71, 72, 73 or 74.
The invention also provides an isolated polynucleotide encoding the polypeptide of SEQ ID NO: 65.
The invention also provides an isolated polynucleotide encoding the polypeptide of SEQ ID NO: 66.
The invention also provides an isolated polynucleotide encoding the polypeptide of SEQ ID NO: 67.
The invention also provides an isolated polynucleotide encoding the polypeptide of SEQ ID NO: 68.
The invention also provides an isolated polynucleotide encoding the polypeptide of SEQ ID NO: 69.
The invention also provides an isolated polynucleotide encoding the polypeptide of SEQ ID NO: 70.
The invention also provides an isolated polynucleotide encoding the polypeptide of SEQ ID NO: 71.
The invention also provides an isolated polynucleotide encoding the polypeptide of SEQ ID NO: 72.
The invention also provides an isolated polynucleotide encoding the polypeptide of SEQ ID NO: 73.
The invention also provides an isolated polynucleotide encoding the polypeptide of SEQ ID NO: 74.
Some embodiments of the disclosure also provide an isolated or purified nucleic acid comprising a polynucleotide which is complementary to the polynucleotides encoding the CD3ε binding proteins of the disclosure or polynucleotides which hybridize under stringent conditions to the polynucleotides encoding the CD3ε binding proteins of the disclosure.
The polynucleotides which hybridize under stringent conditions may hybridize under high stringency conditions. By “high stringency conditions” is meant that the polynucleotide specifically hybridizes to a target sequence (the nucleotide sequence of any of the nucleic acids described herein) in an amount that is detectably stronger than non-specific hybridization. High stringency conditions include conditions which would distinguish a polynucleotide with an exact complementary sequence, or one containing only a few scattered mismatches from a random sequence that happened to have a few small regions (e.g., 3-12 bases) that matched the nucleotide sequence. Such small regions of complementarity are more easily melted than a full-length complement of 14-17 or more bases, and high stringency hybridization makes them easily distinguishable. Relatively high stringency conditions would include, for example, low salt and/or high temperature conditions, such as provided by about 0.02-0.1 M NaCl or the equivalent, at temperatures of about 50-70° C. Such high stringency conditions tolerate little, if any, mismatch between the nucleotide sequence and the template or target strand. It is generally appreciated that conditions can be rendered more stringent by the addition of increasing amounts of formamide.
The polynucleotide sequences of the disclosure may be operably linked to one or more regulatory elements, such as a promoter or enhancer, that allow expression of the nucleotide sequence in the intended host cell. The polynucleotide may be a cDNA. The promoter bay be a strong, weak, tissue-specific, inducible or developmental-specific promoter. Exemplary promoters that may be used are hypoxanthine phosphoribosyl transferase (HPRT), adenosine deaminase, pyruvate kinase, beta-actin, human myosin, human hemoglobin, human muscle creatine, and others. In addition, many viral promoters function constitutively in eukaryotic cells and are suitable for use with the described embodiments. Such viral promoters include Cytomegalovirus (CMV) immediate early promoter, the early and late promoters of SV40, the Mouse Mammary Tumor Virus (MMTV) promoter, the long terminal repeats (LTRs) of Maloney leukemia virus, Human Immunodeficiency Virus (HIV), Epstein Barr Virus (EBV), Rous Sarcoma Virus (RSV), and other retroviruses, and the thymidine kinase promoter of Herpes Simplex Virus. Inducible promoters such as the metallothionein promoter, tetracycline-inducible promoter, doxycycline-inducible promoter, promoters that contain one or more interferon-stimulated response elements (ISRE) such as protein kinase R 2′,5′-oligoadenylate synthetases, Mx genes, ADAR1, and the like may also be sued.
The invention also provides a vector comprising the polynucleotide of the invention. The disclosure also provide an expression vector comprising the polynucleotide of the invention. Such vectors may be plasmid vectors, viral vectors, vectors for baculovirus expression, transposon based vectors or any other vector suitable for introduction of the synthetic polynucleotide of the invention into a given organism or genetic background by any means. Polynucleotides encoding the CD3ε binding proteins of the disclosure may be operably linked to control sequences in the expression vector(s) that ensure the expression of the CD3ε binding proteins. Such regulatory elements may include a transcriptional promoter, sequences encoding suitable mRNA ribosomal binding sites, and sequences that control the termination of transcription and translation. Expression vectors may also include one or more nontranscribed elements such as an origin of replication, a suitable promoter and enhancer linked to the gene to be expressed, other 5′ or 3′ flanking nontranscribed sequences, 5′ or 3′ nontranslated sequences (such as necessary ribosome binding sites), a polyadenylation site, splice donor and acceptor sites, or transcriptional termination sequences. An origin of replication that confers the ability to replicate in a host may also be incorporated.
The expression vectors can comprise naturally-occurring or non-naturally-occurring internucleotide linkages, or both types of linkages. The non-naturally occurring or altered nucleotides or internucleotide linkages do not hinder the transcription or replication of the vector.
Once the vector has been incorporated into the appropriate host, the host is maintained under conditions suitable for high level expression of the CD3ε binding proteins of the disclosure encoded by the incorporated polynucleotides. The transcriptional and translational control sequences in expression vectors to be used in transforming vertebrate cells may be provided by viral sources. Exemplary vectors may be constructed as described by Okayama and Berg, 3 Mol. Cell. Biol. 280 (1983).
Vectors of the disclosure may also contain one or more Internal Ribosome Entry Site(s) (IRES). Inclusion of an IRES sequence into fusion vectors may be beneficial for enhancing expression of some proteins. In other embodiments, the vector system will include one or more polyadenylation sites (e.g., SV40), which may be upstream or downstream of any of the aforementioned nucleic acid sequences. Vector components may be contiguously linked or arranged in a manner that provides optimal spacing for expressing the gene products (i.e., by the introduction of “spacer” nucleotides between the ORFs) or positioned in another way. Regulatory elements, such as the IRES motif, may also be arranged to provide optimal spacing for expression.
Vectors of the disclosure may be circular or linear. They may be prepared to contain a replication system functional in a prokaryotic or eukaryotic host cell. Replication systems can be derived, e.g., from ColE1, SV40, 2 plasmid, bovine papilloma virus, and the like.
The recombinant expression vectors can be designed for either transient expression, for stable expression, or for both. Also, the recombinant expression vectors can be made for constitutive expression or for inducible expression.
Further, the recombinant expression vectors can be made to include a suicide gene. As used herein, the term “suicide gene” refers to a gene that causes the cell expressing the suicide gene to die. The suicide gene can be a gene that confers sensitivity to an agent, e.g., a drug, upon the cell in which the gene is expressed, and causes the cell to die when the cell is contacted with or exposed to the agent. Suicide genes are known in the art and include, for example, the Herpes Simplex Virus (HSV) thymidine kinase (TK) gene, cytosine deaminase, purine nucleoside phosphoryl The vectors may also comprise selection markers, which are well known in the art. Selection markers include positive and negative selection marker. Marker genes include biocide resistance, e.g., resistance to antibiotics, heavy metals, etc., complementation in an auxotrophic host to provide prototrophy, and the like. Exemplary marker genes include antibiotic resistance genes (e.g., neomycin resistance gene, a hygromycin resistance gene, a kanamycin resistance gene, a tetracycline resistance gene, a penicillin resistance gene, histidinol resistance gene, histidinol×resistance gene), glutamine synthase genes, HSV-TK, HSV-TK derivatives for ganciclovir selection, or bacterial purine nucleoside phosphorylase gene for 6-methylpurine selection (Gadi et al., 7 Gene Ther. 1738-1743 (2000)). A nucleic acid sequence encoding a selection marker or the cloning site may be upstream or downstream of a nucleic acid sequence encoding a polypeptide of interest or cloning site.
Exemplary vectors that may be used are Bacterial: pBs, phagescript, PsiX174, pBluescript SK, pBs KS, pNH8a, pNH16a, pNH18a, pNH46a (Stratagene, La Jolla, Calif., USA); pTrc99A, pKK223-3, pKK233-3, pDR540, and pRIT5 (Pharmacia, Uppsala, Sweden). Eukaryotic: pWLneo, pSV2cat, pOG44, PXR1, pSG (Stratagene) pSVK3, pBPV, pMSG and pSVL (Pharmacia), pEE6.4 (Lonza) and pEE12.4 (Lonza). Additional vectors include the pUC series (Fermentas Life Sciences, Glen Burnie, Md.), the pBluescript series (Stratagene, LaJolla, Calif.), the pET series (Novagen, Madison, Wis.), the pGEX series (Pharmacia Biotech, Uppsala, Sweden), and the pEX series (Clontech, Palo Alto, Calif.). Bacteriophage vectors, such as λGT10, λGT11, λEMBL4, and λNM1149, λZapII (Stratagene) can be used. Exemplary plant expression vectors include pBI01, pBI01.2, pBIl21, pBI101.3, and pBIN19 (Clontech). Exemplary animal expression vectors include pEUK-Cl, pMAM, and pMAMneo (Clontech). The expression vector may be a viral vector, e.g., a retroviral vector, e.g., a gamma retroviral vector.ase, and nitroreductase.
In other embodiments, the vector comprises the polynucleotide encoding the VH of SEQ ID NO: 23.
In other embodiments, the vector comprises the polynucleotide encoding the VL of SEQ ID NOs: 24, 27, 28, 29 or 30.
In other embodiments, the vector comprises the polynucleotide encoding the VL of SEQ ID NO: 24.
In other embodiments, the vector comprises the polynucleotide encoding the VL of SEQ ID NO: 27.
In other embodiments, the vector comprises the polynucleotide encoding the VL of SEQ ID NO: 28.
In other embodiments, the vector comprises the polynucleotide encoding the VL of SEQ ID NO: 29.
In other embodiments, the vector comprises the polynucleotide encoding the VL of SEQ ID NO: 30.
In other embodiments, the vector comprises the polynucleotide encoding the VH of SEQ ID NO: 23 and the VL of SEQ ID NOs: 24, 27, 28, 29 or 30.
In other embodiments, the vector comprises the polynucleotide encoding
the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 24;
the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 27;
the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 28;
the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 29; or
the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 30.
In other embodiments, the vector comprises the polynucleotide encoding the polypeptide of SEQ ID NOs: SEQ ID NOs: 65, 66, 67, 68, 69, 70, 71, 72, 73 or 74.
In other embodiments, the vector comprises the polynucleotide encoding the polypeptide of SEQ ID NO: 65.
In other embodiments, the vector comprises the polynucleotide encoding the polypeptide of SEQ ID NO: 66.
In other embodiments, the vector comprises the polynucleotide encoding the polypeptide of SEQ ID NO: 67.
In other embodiments, the vector comprises the polynucleotide encoding the polypeptide of SEQ ID NO: 68.
In other embodiments, the vector comprises the polynucleotide encoding the polypeptide of SEQ ID NO: 69.
In other embodiments, the vector comprises the polynucleotide encoding the polypeptide of SEQ ID NO: 70.
In other embodiments, the vector comprises the polynucleotide encoding the polypeptide of SEQ ID NO: 71.
In other embodiments, the vector comprises the polynucleotide encoding the polypeptide of SEQ ID NO: 72.
In other embodiments, the vector comprises the polynucleotide encoding the polypeptide of SEQ ID NO: 73.
In other embodiments, the vector comprises the polynucleotide encoding the polypeptide of SEQ ID NO: 74.
The invention also provides for a host cell comprising one or more vectors of the invention. “Host cell” refers to a cell into which a vector has been introduced. It is understood that the term host cell is intended to refer not only to the particular subject cell but to the progeny of such a cell, and also to a stable cell line generated from the particular subject cell. Because certain modifications may occur in succeeding generations due to either mutation or environmental influences, such progeny may not be identical to the parent cell, but are still included within the scope of the term “host cell” as used herein. Such host cells may be eukaryotic cells, prokaryotic cells, plant cells or archeal cells. Escherichia coli, bacilli, such as Bacillus subtilis, and other enterobacteriaceae, such as Salmonella, Serratia, and various Pseudomonas species are examples of prokaryotic host cells. Other microbes, such as yeast, are also useful for expression. Saccharomyces (e.g., S. cerevisiae) and Pichia are examples of suitable yeast host cells. Exemplary eukaryotic cells may be of mammalian, insect, avian or other animal origins. Mammalian eukaryotic cells include immortalized cell lines such as hybridomas or myeloma cell lines such as SP2/0 (American Type Culture Collection (ATCC), Manassas, Va., CRL-1581), NS0 (European Collection of Cell Cultures (ECACC), Salisbury, Wiltshire, UK, ECACC No. 85110503), FO (ATCC CRL-1646) and Ag653 (ATCC CRL-1580) murine cell lines. An exemplary human myeloma cell line is U266 (ATTC CRL-TIB-196). Other useful cell lines include those derived from Chinese Hamster Ovary (CHO) cells such as CHO-K1SV (Lonza Biologics, Walkersville, Md.), CHO-K1 (ATCC CRL-61) or DG44.
The disclosure also provides a method of producing the CD3ε binding protein of the disclosure comprising culturing the host cell of the disclosure in conditions that the CD3ε binding protein is expressed, and recovering the CD3ε binding protein produced by the host cell. Methods of making proteins and purifying them are known. Once synthesized (either chemically or recombinantly), the CD3ε binding proteins may be purified according to standard procedures, including ammonium sulfate precipitation, affinity columns, column chromatography, high performance liquid chromatography (HPLC) purification, gel electrophoresis, and the like (see generally Scopes, Protein Purification (Springer-Verlag, N.Y., (1982)). A subject protein may be substantially pure, e.g., at least about 80% to 85% pure, at least about 85% to 90% pure, at least about 90% to 95% pure, or at least about 98% to 99%, or more, pure, e.g., free from contaminants such as cell debris, macromolecules, etc. other than the subject protein
The polynucleotides encoding the CD3ε binding proteins of the disclosure may be incorporated into vectors using standard molecular biology methods. Host cell transformation, culture, antibody expression and purification are done using well known methods.
Modified nucleotides may be used to generate the polynucleotides of the disclosure. Exemplary modified nucleotides are 5-fluorouracil, 5-bromouracil, 5-chlorouracil, 5-iodouracil, hypoxanthine, xanthine, 4-acetylcytosine, 5-(carboxyhydroxymethyl) uracil, carboxymethylaminomethyl-2-thiouridine, 5-carboxymethylaminomethyluracil, dihydrouracil, N6-substituted adenine, 7-methylguanine, 5-methylaminomethyluracil, 5-methoxyaminomethyl-2-thiouracil, beta-D-mannosylqueosine, 5″-methoxycarboxymethyluracil, 5-methoxyuracil, 2-methylthio-N6-isopentenyladenine, uracil-5-oxyacetic acid (v), wybutoxosine, pseudouracil, queuosine, beta-D-galactosylqueosine, inosine, N6-isopentenyladenine, 1-methylguanine, 1-methylinosine, 2,2-dimethylguanine, 2-methyladenine, 2-methylguanine, 3-methylcytosine, 5-methylcytosine, 2-thiocytosine, 5-methyl-2-thiouracil, 2-thiouracil, 4-thiouracil, 5-methyluracil, uracil-5-oxyacetic acid methylester, 3-(3-amino-3-N-2-carboxypropyl) uracil, and 2,6-diaminopurine.
The disclosure also provides a pharmaceutical composition comprising the CD3ε binding protein of the disclosure and a pharmaceutically acceptable carrier.
The disclosure also provides a pharmaceutical composition comprising the antigen binding domain that binds CD3ε of the disclosure and a pharmaceutically acceptable carrier.
The disclosure also provides a pharmaceutical composition comprising the protein comprising the antigen binding domain that binds CD3ε of the disclosure and a pharmaceutically acceptable carrier.
The disclosure also provides a pharmaceutical composition comprising the multispecific protein comprising the antigen binding domain that binds CD3ε of the disclosure and a pharmaceutically acceptable carrier.
The disclosure also provides a pharmaceutical composition comprising the multispecific protein comprising the antigen binding domain that binds CD3ε and antigen binding domain that binds a tumor antigen of the disclosure and a pharmaceutically acceptable carrier.
For therapeutic use, the CD3ε binding protein of the disclosure may be prepared as pharmaceutical compositions containing an effective amount of the antibody as an active ingredient in a pharmaceutically acceptable carrier. These solutions are sterile and generally free of particulate matter. They may be sterilized by conventional, well-known sterilization techniques (e.g., filtration). The compositions may contain pharmaceutically acceptable auxiliary substances as required to approximate physiological conditions such as pH adjusting and buffering agents, stabilizing, thickening, lubricating and coloring agents, etc.
The term “pharmaceutically acceptable,” as used herein with regard to pharmaceutical compositions, means approved by a regulatory agency of the Federal or a state government or listed in the U.S. Pharmacopeia or other generally recognized pharmacopeia for use in animals and/or in humans.
The disclosure also provides the bispecific or multispecific protein comprising a first antigen biding domain that specifically binds CD3ε and a second antigen biding domain that specifically binds a second antigen of the disclosure for use in therapy.
The disclosure also provides the bispecific or multispecific protein comprising a first antigen biding domain that specifically binds CD3ε and a second antigen biding domain that specifically binds a second antigen of the disclosure for use in treating a cell proliferative disorder.
The disclosure also provides the bispecific or multispecific protein comprising a first antigen biding domain that specifically binds CD3ε and a second antigen biding domain that specifically binds a second antigen of the disclosure for use in treating cancer.
The disclosure also provides the bispecific or multispecific protein comprising a first antigen biding domain that specifically binds CD3ε and a second antigen biding domain that specifically binds a second antigen of the disclosure for use in the manufacture of a medicament for treating cancer.
In one aspect, the disclosure relates generally to the treatment of a subject at risk of developing cancer. The invention also includes treating a malignancy in which chemotherapy and/or immunotherapy results in significant immunosuppression in a subject, thereby increasing the risk of the subject developing cancer.
The disclosure also provides a method of treating a noncancerous condition in a subject at risk of developing a cancerous condition, comprising administering the antigen binding domain that bind CD3ε of the disclosure to the subject to treat the noncancerous condition.
The disclosure also provides a method of treating a noncancerous condition in a subject at risk of developing a cancerous condition, comprising administering the protein comprising the antigen binding domain that bind CD3ε of the disclosure to the subject to treat the noncancerous condition.
The disclosure also provides a method of treating a noncancerous condition in a subject at risk of developing a cancerous condition, comprising administering the multispecific protein comprising the antigen binding domain that bind CD3ε of the disclosure to the subject to treat the noncancerous condition.
The disclosure also provides a method of treating a noncancerous condition in a subject at risk of developing a cancerous condition, comprising administering the immunoconjugate of the disclosure to the subject to treat the noncancerous condition.
The disclosure also provides a method of treating a noncancerous condition in a subject at risk of developing a cancerous condition, comprising administering the pharmaceutical composition of the disclosure to the subject to treat the noncancerous condition.
The disclosure also provides a method of treating cancer in a subject, comprising administering a therapeutically effective amount of the multispecific protein comprising the antigen binding domain that binds CD3ε to the subject to treat the cancer, wherein the antigen binding domain that bind CD3ε comprises
the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 24;
the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 27;
the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 28;
the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 29; or
the VH of SEQ ID NO: 23 and the VL of SEQ ID NO: 30.
The disclosure also provides a method of treating cancer in a subject, comprising administering a therapeutically effective amount of the multispecific protein comprising the antigen binding domain that binds CD3ε to the subject to treat the cancer, wherein the antigen binding domain that binds CD3ε comprises the amino acid sequence of SEQ ID NOs: 65, 66, 67, 68, 69, 70, 71, 72, 73, or 74.
A further aspect of the disclosure is a method of treating a cell proliferative disorder in a subject in need thereof, the method comprising administering to the subject a therapeutically effective amount of the bispecific or multispecific protein comprising a first antigen biding domain that specifically binds CD3ε and a second antigen biding domain that specifically binds a second antigen of the disclosure. In other embodiments, the bispecific or multispecific protein comprising a first antigen biding domain that specifically binds CD3ε and a second antigen biding domain that specifically binds a second antigen of the disclosure, is administered to the subject.
In any of the preceding uses or methods, the cell proliferative disorder is cancer. In other embodiments, the cancer is selected from the group consisting of esophageal cancer, stomach cancer, small intestine cancer, large intestine cancer, colorectal cancer, breast cancer, non-small cell lung cancer, non-Hodgkin's lymphoma (NHL), B cell lymphoma, B cell leukemia, multiple myeloma, renal cancer, prostate cancer, liver cancer, head and neck cancer, melanoma, ovarian cancer, mesothelioma, glioblastoma, germinal-center B-cell-like (GCB) DLBCL, activated B-cell-like (ABC) DLBCL, follicular lymphoma (FL), mantle cell lymphoma (MCL), acute myeloid leukemia (AML), chronic lymphoid leukemia (CLL), marginal zone lymphoma (MZL), small lymphocytic leukemia (SLL), lymphoplasmacytic lymphoma (LL), Waldenstrom macroglobulinemia (WM), central nervous system lymphoma (CNSL), Burkitt's lymphoma (BL), B-cell prolymphocytic leukemia, Splenic marginal zone lymphoma, Hairy cell leukemia, Splenic lymphoma/leukemia, unclassifiable, Splenic diffuse red pulp small B-cell lymphoma, Hairy cell leukemia variant, Waldenstrom macroglobulinemia, Heavy chain diseases, Plasma cell myeloma, Solitary plasmacytoma of bone, Extraosseous plasmacytoma, Extranodal marginal zone lymphoma of mucosa-associated lymphoid tissue (MALT lymphoma), Nodal marginal zone lymphoma, Pediatric nodal marginal zone lymphoma, Pediatric follicular lymphoma, Primary cutaneous follicle centre lymphoma, T-cell/histiocyte rich large B-cell lymphoma, Primary DLBCL of the CNS, Primary cutaneous DLBCL, leg type, EBV-positive DLBCL of the elderly, DLBCL associated with chronic inflammation, Lymphomatoid granulomatosis, Primary mediastinal (thymic) large B-cell lymphoma. Intravascular large B-cell lymphoma, ALK-positive large B-cell lymphoma, Plasmablastic lymphoma, Large B-cell lymphoma arising in HHV8-associated multicentric Castleman disease, Primary effusion lymphoma: B-cell lymphoma, unclassifiable, with features intermediate between diffuse large B-cell lymphoma and Burkitt lymphoma, and B-cell lymphoma, unclassifiable, with features intermediate between diffuse large B-cell lymphoma, classical Hodgkin lymphoma and light chain amyloidosis.
In other embodiments, the cancer is esophageal cancer. In other embodiments, the cancer is an adenocarcinoma, for example, a metastatic adenocarcinoma (e.g., a colorectal adenocarcinoma, a gastric adenocarcinoma, or a pancreatic adenocarcinoma).
In another aspect, the disclosure features a kit comprising: (a) a composition comprising any one of the preceding the bispecific or multispecific protein comprising a first antigen biding domain that specifically binds CD3ε and a second antigen biding domain that specifically binds a second antigen of the disclosure and (b) a package insert comprising instructions for administering the composition to a subject to treat or delay progression of a cell proliferative disorder.
In any of the preceding uses or methods, the subject can be a human.
The CD3ε binding proteins of the disclosure may be administered in combination with at least one additional therapeutics.
In other embodiments, the delivery of one treatment is still occurring when the delivery of the second begins, so that there is overlap in terms of administration. This is sometimes referred to herein as “simultaneous” or “concurrent delivery”. In other embodiments, the delivery of one treatment ends before the delivery of the other treatment begins. In some embodiments of either case, the treatment is more effective because of combined administration. For example, the second treatment is more effective, e.g., an equivalent effect is seen with less of the second treatment, or the second treatment reduces symptoms to a greater extent, than would be seen if the second treatment were administered in the absence of the first treatment, or the analogous situation is seen with the first treatment. In other embodiments, delivery is such that the reduction in a symptom, or other parameter related to the disorder is greater than what would be observed with one treatment delivered in the absence of the other. The delivery can be such that an effect of the first treatment delivered is still detectable when the second is delivered.
The CD3ε binding proteins described herein and the at least one additional therapeutic agent can be administered simultaneously, in the same or in separate compositions, or sequentially. For sequential administration, the CD3ε binding proteins described herein can be administered first, and the additional agent can be administered second, or the order of administration can be reversed.
This invention provides the following non-limiting embodiments.
The following examples are provided to further describe some of the embodiments disclosed herein. The examples are intended to illustrate, not to limit, the disclosed embodiments.
Anti-CD3 antibodies were generated using Ablexis® transgenic mouse platform. Ablexis® mice generate antibodies having human variable domains linked to human CH1 and CL domains, chimeric human/mouse hinge region, and mouse Fc regions. The two specific strains termed Ablexis® Kappa Mouse and Lambda Mouse strains lack specific mouse sequences and are described in WO11/123708 and WO2003000737.
Ablexis mice were immunized with TRCW5 (SEQ ID NO: 3), including 13 Kappa mice and 12 Lambda mice. TRCW5 is comprised of the extracellular region of CD3δ fused by a 26 amino acid linker to the extracellular region of CD3ε as reported in Kim et al, JMB (2000) 302(4): 899-916. This polypeptide had at its C-terminus a human IgG1 Fc domain with a C-terminal Avi-tag used for site-specific biotinylation (Fairhead & Howarth, Methods Mol Biol (2015); 1266: 171-184).
Mice were immunized twice weekly for the duration of 7 weeks. On day 42, mice were boosted for hybridoma fusion by administration of 50 μg TRCW5 and 50 μg CD40 mAb spread over 8 sites, including 6 subcoutaneous and 2 intradermal injections. For a final boost, mice received 20 μL injections of Jurkat cells, a T cell line which endogenously expresses the T cell receptor complex, including CD3ε (Schneider et al (1977) Int. J. Cancer, 19 (5): 621-6), at 4.74×107 cells/mL.
Lymph nodes and spleens were extracted from mice and fusions performed by cohorts. Lymph node cells were counted and combined in a 1:1 ratio with FO myeloma cells (ATCC (CRL-1646)) and incubated for 10 d at 37° C. prior to antibody screening. Supernatants from hybridoma fusion cells were then assayed for binding to TRCW5 using TRCW5 either non-specifically immobilized on the plate (ELISA, Thermo cat. #34022) or by streptavidin conjugation to biotinylated-TRCW5 (SPARCL ELISA, Lumigen), according to manufacturers' instructions. ELISA assays were performed by coating plates with 0.5 ug/mL TRCW5 and 0.5 ug/mL HVEM-Fc (R&D cat. #365-HV) overnight @4° C. Plates were blocked by addition of 0.4% (w/v) bovine serum albumin (BSA) in phosphate-buffered saline (PBS) overnight @ 4° C. Plates were washed with 1×PBS supplemented with 0.02% (v/v) Tween 20. To each well, 50 uL of hybridoma supernatant was applied and incubated for 1 hr at room temperature. Bound antibody was detected by addition of goat anti-mouse IgG Fc conjugated to horseradish peroxidase (Jackson cat. #115-036-071) diluted 1:10,000 in blocking buffer followed by incubation for 30 min at room temperature. 3, 3′, 5, 5′-tetramethylbenzidine (TMB) substrate buffer (Thermo cat. #34022) was added at 25 uL/well and incubated for 10 min in the dark. Reactions were stopped by addition of 25 uL/well of 4 M H2SO4. Luminescence was read at 450 nm using BioTek® Epoch2 Microplate Reader. Hits were selected having signal at least 3-fold higher than background.
The two assay formats resulted in 426 hits (264 hits from ELISA, 194 from SPARCL ELISA, 70 hits were identified in both assays). Of these 426 initial hits, 49 ELISA and 32 SPARCL ELISA hits were confirmed. The hybridoma fusions corresponding to the positive binders were refed and tested for their abilities to bind Jurkat cells, using flow cytometry. The results suggested that three antibodies, including clone 003_F12, clone 036_E10 and clone 065_D03, showed significant binding to Jurkat cells, endogenously expressing CD3, based on mean fluorescence index (MFI, see Table 4). While clones 003_F12 and 036_E10 (from human kappa mice) were confirmed positive for human kappa light chain by ELISA, clone 065_D03 (from human lambda mouse) was negative for human lambda. The variable genes of these three clones were then sequenced.
Next, these three clones were screened for their abilities to bind primary human and cyno T cells. Briefly, primary human and cyno pan T cells were resuspended at 1×106 cells/mL in flow staining buffer and cells were plated at 50,000 cells/well. To each well, 50 uL of hybridoma supernatant were added and the mixture was incubated on ice for 30 min. After incubation, 200 uL of staining buffer was added and cells were pelleted by centrifugation at 300×G for 5 min. Anti-mouse IgG conjugated to Alexa-647 was added at 2 ug/mL in staining buffer in 50 uL total volume and incubated for 30 min on ice. 150 uL of staining buffer was added and cells were pelleted by centrifugation at 300×G for 5 min. Cells were resuspended in 30 uL of running buffer containing 1:1,000-diluated Sytox green dead cell stain and run on iQue Screener. Cells were gated on FCS vs SCS to eliminate debris. Singlets were gated on SCS-A vs SCS-H, and from singlet population, live cells were chosen using BL1 channel for low-negative with Sytox green. CD3 binding was assessed by comparing test articles to negative control by RL1 (Alexa-647) geomeans. In this assay, clone 065_D03 showed the highest cell binding signal (
Thus, the variable region of the Clone 065_D03 was cloned into an IgG1 backbone, resulting in the antibody termed CD3B815 (sequences are shown in Table 5). CD3B815 was screened again for binding to Jurkat cells and showed positive binding to Jurkat cells.
Humanization and scFv Formatting of CD3 Binding Domains
The light chain (LC) of the v-region of CD3B815 was humanized in scFv format. Briefly, the LC from CD3B815 was grafted onto the human IGHV3B21*54 germline and two positions (Y49K and L78V, according to Kabat numbering system) were identified for human to mouse back mutations. This resulted in variants, having either Y49K, L78V, or both Y49K and L78V. The LC from CD3B815 also contained an NS motif which presents a risk for deamidation at positions 92-93. Therefore several variants generated also contained N92G. These variants and associated mutations are described in Table 6, and the VH and the VL amino acid and nucleic acid sequences are shown in Tables 7 and 8. CDR sequences are shown in Tables 9-11.
wherein, X1 is L or M; X2 is G or S; X3 is I or S; X4 is V or A; X5 is P or V; X6 is E or D; X7 is S or T; X8 is F on; X9 is S or T; X10 is T or P, X11 is N or G, X12 is G or K, X13 is S or A; X14 is R or K, X15 is K or Y; X16 is I or V; X17 is N or S; X18 is V or L; X19 is S or P, X20 is I or F; X21 is D or T, X22 is N or G; or X23 is G or Q.
Binding of Humanized Anti-CD3 scFv Variants to CD3 after Heat Shock.
The variable region from CD3B3815 was next formatted as scFv in VH-VL orientation using linker GTEGKSSGSGSESKST (SEQ ID No: 64) (Table 12) for expression in E. coli, and then screened for binding to recombinant CD3 (CD3W147, SEQ ID NO: 4), binding to T cells, and thermostability.
The binding of anti-CD3 scFv variants (Table 7), expressed in E. coli, to CD3 was determined. Briefly, scFv-coding sequences were cloned into a pADL™-22c vector having a PelB leader sequence for secretion (Antibody Design Labs, San Diego, Calif.). E. coli cells were transformed with plasmid and grown overnight at 37° C. in 2×YT microbial growth medium supplemented with 100 μg/mL Carbenicillin. Overnight cultures were used to inoculate 5 mL expression cultures and grown at 37° C. until OD600˜ 2.0. Protein expression was induced by addition of 1 mM IPTG and cultures were grown overnight. After expression, cells were pelleted by centrifugation at 2,200×g for 5 min and supernatants were collected and tested directly in ELISA analysis.
For ELISA analysis, botinylated CD3W147 (homodimeric CD3εγ-Fc, SEQ ID NO: 4) was immobilized on the plate in concentrations ranging from 0.039 ug/mL to 2.5 ug/mL in 2-fold dilutions followed by incubation at room temperature for 45 min. Plates were blocked with 1×PBS-Tween supplemented with 3% milk. Plates were washed with 1×PBS-Tween. E. coli supernatants were heated to 60° C. then cooled to room temperature to assess their thermal stability. Supernatant was added to each plate and incubated for 45 min at room temperature. Bound scFv was detected using chicken anti-HA-horseradish peroxidase diluted 1:1,000 at 50 uL per well and then detected with chemiluminescence substrate (Sigma cat. #11582950001). All tested scFv molecules derived from CD3B815 bound CD3ε (
The scFv molecules were then tested for their abilities to bind T cells, using flow cytometry. Briefly, human T cells were thawed and resuspended into flow staining buffer at 1×10{circumflex over ( )}6 cells/mL and plated at 50,000 cells/well. A positive control, CD3W36 was comprised of an anti-CD3 antibody SP34 formatted as LH-scFv, and a negative control, B23, an scFv targeted against the F-glycoprotein from respiratory syncytial virus, were used for comparison of binding. E. coli supernatants were added at 150 uL/well and incubated at 4° C. for 1 hr. After incubation, plates were washed with staining buffer and detected with anti-His antibody conjugated to Alexa-647 diluted 1:100 in staining buffer with incubation for 30 min at 4° C. After incubation, 200 uL of IntelliCyt running buffer was added to the mixture, and cells were resuspended in 30 uL running buffer containing 1:1,000 Sytox Green dead cell stain and analyzed on iQue Screener. Gating and analysis was performed as above. All scFv molecules derived from CD3B815 displayed mean fluorescence indices consistent with T cell binding (Table 13).
The epitope on CD3 was determined by hydrogen-deuterium exchange mass spectrometry (HDX-MS). The antibody clone OKT3 was used as a control for the HDX experiment, since its epitope on CD3ε was known from crystal structure (PDB ID 1SY6) (Kjer-Nielsen, L. et al.; Proc Natl Acad Sci US A 101, 7675-7680).
On-Exchange Experiment for HDX-MS. On-exchange reaction was initiated by mixing 10 μL of 10 μM CD3W220 (SEQ ID NO: 5), which was comprised of CD3εγ fused with a 26-aa linker region fused onto a serum albumin domain, with or without 1.2 molar-excess of ligand and 30 μL of H2O or a deuterated buffer (20 mM MES, pH 6.4, 150 mM NaCl in 95% D20 or 20 mM Tris, pH 8.4, 150 mM NaCl in 95% D20). The reaction mixture was incubated for 15, 50, 150, 500, or 1,500 s at 1.2° C. The on-exchanged solution was quenched by the addition of chilled 40 μL of 8 M urea, 1 M TCEP, pH 3.0 and immediately analyzed.
General Procedure for HDX-MS Data Acquisition. HDX-MS sample preparation was performed with automated HDx system (LEAP Technologies, Morrisville, N.C.). The columns and pump were; protease, protease type XIII (protease from Aspergillus saitoi, type XIII)/pepsin column (w/w, 1:1; 2.1×30 mm) (NovaBioAssays Inc., Woburn, Mass.); trap, ACQUITY UPLC BEH C18 VanGuard Pre-column (2.1×5 mm) (Waters, Milford, Mass.), analytical, Accucore C18 (2.1×100 mm) (Thermo Fisher Scientific, Waltham, Mass.); and LC pump, VH-P10-A (Thermo Fisher Scientific). The loading pump (from the protease column to the trap column) was set at 600 μL/min with 99% water, 1% acetonitrile, 0.10% formic acid. The gradient pump (from the trap column to the analytical column) was set from 8% to 28% acetonitrile in 0.1% aqueous formic acid in 20 min at 100 μL/min.
MS Data Acquisition. Mass spectrometric analyses were carried out using an LTQ™ Orbitrap Fusion Lumos mass spectrometer (Thermo Fisher Scientific) with the capillary temperature at 275° C., resolution 150,000, and mass range (m/z) 300-1,800.
HDX-MS Data Extraction. BioPharma Finder 3.0 (Thermo Fisher Scientific) was used for the peptide identification of non-deuterated samples prior to the HDX experiments. HDExaminer version 2.5 (Sierra Analytics, Modesto, Calif.) was used to extract centroid values from the MS raw data files for the HDX experiments.
HDX-MS Data Analysis. The extracted HDX-MS data were further analyzed in Excel. All exchange time points (at pH 6.4 or pH 8.4 at 1.2° C.) were converted to the equivalent time points at pH 7.4 and 23° C. (e.g., 15 s at pH 6.4 at 1.2° C. is equivalent of 0.15 s at pH 7.4 at 23° C.; Table 14).
Results. Incubation of the KLCB91, the bispecific antibodies comprising CD3W245 as an anti-CD3 arm (described in the Example 3), with recombinant CD3ε (SEQ ID NO: 5) resulted in different patterns of overall protection and degrees of protection at specific segments of the antigen. KLCB91 and OKT3 both protected non-continuous segments (
Consistent with the crystal structure of OKT3 bound to CD3ε (Uniprot ID P07766), the epitope of OKT3 was found to consist of peptides covering spanning residues 29-37, 79-84, and 87-89 of CD3F (SEQ ID NO: 5 and
Antibody Generation from Humanization of Parental m11B6 Antibody.
A parental mouse anti-kallikrein related peptidase 2 (hK2) antibody, m11B6, has been described in Vaisanen et al (Clinical Chemistry 50:9, 1607-1617 (2004)). Humanized 11B6 (referred herein to as hu11B6) has been generated and described in U.S. Pat. Nos. 9,345,782 and 10,100,125.
Engineering of hu11B6 were initiated to generate additional anti-HK2 antibodies with improved properties, such as improved thermostability. Residue positions were identified in hu11B6 frameworks which could potentially be altered to improve thermostability of hu11B6 using modeling. The positions identified were residues P41, 149, M70, and A88 in the VH and S80, L82, A88 and Y91 in the VL (residue numbering according to the amino acid sequences of hu11B6_VH of SEQ ID NO: 124 and hu11B6_VL of SEQ ID NO: 125).
Binary combinatorial scFv libraries were generated in the orientation VH-linker-VL in which one of the variable regions represented the combinatorial library and the second one being the parental hu11B6 VH or VL. Linker sequence of GGSEGKSSGSGSESKSTGGS (SEQ ID NO: 31) was used to conjugate the VH/VL regions. The engineered scFvs were expressed in E. coli and the produced scFvs in the supernatants were tested for binding to human hK2 by ELISA and compared to the binding of hu11B6. Any new variants exhibiting binding comparable to hu11B6 were consolidated and further tested for binding to human hK2 after incubation of the supernatants at 55° C., 60° C., and 65° C. for 10 minutes. The molecules which retained comparable binding to hu11B6 after incubation at 55° C., 60° C., and 65° C. and improved thermostability were matrixed in both orientations (VH-linker-VL; VL-linker-VH) and converted to mammalian scFvs for further characterization.
In addition, another humanization of parental mouse 11B6 was performed following the approach outlined by Singh et al (MAbs. 2015; 7(4):778-91). with extensive germ line variation and careful screening of the variants for enhanced thermal stability. Based on sequence conservation, the human heavy chain germline IGHV4-30 and the light chain germline IGKV3D-11, were chosen for framework adaption. A binary scFv library was constructed with residues comprising a select set of somatic hypermutation sites and mouse/human germline variations. The variants were cloned and expressed in E. coli as described above. The supernatants were screened at different temperatures in single point ELISA for enhanced thermal stability. A mouse/human chimeric 11B6 scFv was used as parental control. Clone KL2B359 which maintained binding activity similar to murine 11B6 and a Tm value of 67° C. was converted to scFv-Fc for additional profiling. Measured affinity (KD) of KL2B359 to hK2 by SPR was ˜0.7-1 nM. HCF3-LCD6, HCG5-LCB7, KL2B357, KL2B358 and KL2B360 also resulted from this campaign and were further characterized for functionality.
Antibody Generation Using Transgenic Mice (Ablexis®) and Transgenic Rats (OmniRat®) Expressing Human Immunoglobulin Loci.
The OmniRat® contains a chimeric human/rat IgH locus (comprising 22 human VHs, all human D and JH segments in natural configuration linked to the rat CH locus) together with fully human IgL loci (12 Vκs linked to Jκ-Cκ and 16 VWs linked to JR-C). (see e.g., Osborn, et al. (2013) J Immunol 190(4): 1481-1490). Accordingly, the rats exhibit reduced expression of rat immunoglobulin, and in response to immunization, the introduced human heavy and light chain transgenes undergo class switching and somatic mutation to generate high affinity chimeric human/rat IgG monoclonal antibodies with fully human variable regions. The preparation and use of OmniRat®, and the genomic modifications carried by such rats, is described in WO14/093908.
Ablexis® mice (described in Example 1) and OmniRat® rats were immunized with soluble full length KLK2 protein (human Kallikrein-2 6-His protein).
Lymphocytes from Ablexis mice and OniRats rats were extracted from lymph nodes and fusions performed by cohorts. Cells were combined and sorted for CD138 expression. Hybridoma screening was performed in high throughput miniaturized MSD format using soluble hK2 antigen. Approximately >300 samples were identified to be hK2 binders. The binding of >300 anti-hKLK2 supernatant samples to human KLK2 protein was measured by single cycle kinetics method by Biacore 8K SPR. Additionally the supernatant samples were tested for binding to human KLK3 protein as well. In parallel, supernatants were also tested for binding to KLK2 expressing cell lines VCap and negative cell line DU145 by Flow Cytometry. Selected cell binders were moved forward to scFv conversion in both VH-VL and VL/VH orientation and thermal stability tests as described above. KL2B413, KL2B30, KL2B53 and KL2B242 resulted from the Ablexis mice immunization campaign. KL2B467 and KL2B494 resulted from the OmniRat immunization campaign.
Antibodies generated through the various immunization and humanization campaigns described above were expressed in a Fab format, a mAb format, a scFv format in the VH-linker-VL orientation or a scFv format in VL-linker-VH orientation and were further analyzed as described below. The linker sequence of SEQ ID NO: 31 described above was used to conjugate the VH/VL regions.
Structural Characterization of Anti KLK2 Antibodies
Sequences of antibody variable domains and scFv antibody fragments which showed highest performance in intracellular assay are provided herein. Variable domains were expressed in a Fab format, a scFv format in the VH-linker-VL orientation or a scFv format in VL-linker-VH orientation.
Variable Domains VH, VL and CDRs
Table 15 shows the VH and VL amino acid sequences of selected anti-hK2 antibodies. Table 16 shows the Kabat HCDR1, HCDR2 and HCDR3 of selected anti-hK2 selected antibodies. Table 17 shows the Kabat LCDR1, LCDR2 and LCDR3 of the selected anti-hK2 antibodies. Table 18 shows the AbM HCDR1, HCDR2 and HCDR3 of selected anti-hK2 antibodies. Table 19 shows the AbM LCDR1, LCDR2 and LCDR3 of the anti-hK2. Table 20 summarizes the variable domain sequence and SEQ ID NOs of selected hK2 antibodies. Table 21 shows the protein and DNA SEQ ID NOs for the VH and VL regions.
Consensus VH and VL Sequences
wherein, X1 is D or Q; X2 is A or T; X3 is P or F; X4 is G or R; X5 is I or M; X6 is I or M; X7 is A or P; or X8 is V or A.
wherein, X1 is D or E; X2 is D or A; X3 is S or T; X4 is A or S; X5 is V or L; X6 is L or P; X7 is I or L; X8 is N or S; X9 is R or K; X10 is K or R; X11 is V or R; X12 is V or I; X13 is A or D; X14 is Q or S; X15 is L or V; X16 is Q or E; X17 is P or A; X18 is F or V; X19 is A or S, X20 is Y or F; X21 is Q or G; and X22 is L or V.
Fab-Fc and scFvs
The hK2 specific VH/VL regions were engineered as VH-CH1-linker CH2-CH3 and VL-CL and expressed as IgG2 or IgG4 or were engineered as scFvs in either the VH-Linker-VL or VL-linker-VH orientations. The linker that is used in the scFv was the linker of SEQ ID NO: 31 described above. The scFv were used to generate bispecific antibodies as described in Example 3.
Table 22 shows the HC amino acid sequences of selected anti-hK2 antibodies in the mAb format. Table 23 shows the LC amino acid sequences of selected anti-hK2 antibodies in a mAb. Table 24 summaries the HC and LC DNA SEQ ID NOs of selected anti-hK2 antibodies in the mAb format. Table 25 shows the amino acid sequences of selected scFvs in VH-linker-VL or VL-linker-VH orientation.
Affinity of selected hK2 antibodies for soluble hK2 was measured by surface plasmon resonance (SPR). SPR is a label-free technique to study the strength of an interaction between two binding partners by measuring the change in mass upon complex formation and dissociation. Antibodies were captured on a sensor chip coated with an anti-Fc antibody followed by injection of soluble hK2 at various concentrations and specified association and dissociation times. Post dissociation, the surface was regenerated with an appropriate solution to prepare for the next interaction. Kinetic information (on-rate and off-rate constants) were extracted by fitting sensorgrams to the 1:1 Langmuir model. Binding affinity (KD) are reported as the ratio of rate constants (koff/kon). KD values of selected hK2 antibodies are listed in Table 26.
Thermal stability was determined by Differential Scanning Fluorimetry (NanoDSF) using an automated Prometheus instrument. NanoDSF was used to measure Tm of molecules at a concentration of 0.5 mg/mL in Phosphate Buffered Saline, pH 7.4. Measurements were made by loading samples into 24 well capillary from a 384 well sample plate. Duplicate runs were performed for each sample. The thermal scans span from 20° C. to 95° C. at a rate of 1.0° C./minute. Intrinsic tryptophan and tyrosine fluorescence were monitored at the emission wavelengths of 330 nm and 350 nm, and the F350/F330 nm ratio were plotted against temperature to generate unfolding curves. Measured Tm values are listed in Table 26.
KL2B413 scFv generated from the Ablexis immunization campaign had a thermal stability (Tm) of 67° C. as measured by Nano DSF and a binding affinity (KD) to human hK2 of about 34 nM. Clone KL2B359 obtained for the re-humanization campaign and which had maintained a binding affinity similar to murine 11B6 was converted to scFv-Fc and CAR-T for additional profiling. KL2B359 scFv shows a Tm of 67° C. and a binding affinity (KD) to hK2 of ˜0.7-1 nM. KL2B30, KL2B242, KL2B53, KL2B467 and KL2B494 Fab showed binding affinities below 0.5 nM and Tm values above 70° C.
The epitope and paratope of selected anti-hK2 antibodies was determined by hydrogen-deuterium exchange mass spectrometry (HDX-MS). Human KLK2 antigen was used for epitope and paratope mapping experiment.
Briefly, purified the KLK2 antigen was incubated with and without anti-hK2 antibodies in deuterium oxide labeling buffer. The hydrogen-deuterium exchange (HDX) mixture was quenched at different time point by the addition of 8 M urea, 1M TCEP, pH 3.0. The quenched sample was passed over an immobilized pepsin/FPXIII column at 600 μL/min equilibrated with buffer A (1% acetonitrile, 0.1% FA in H2O) at room temperature. Peptic fragments were loaded onto a reverse phase trap column at 600 μL/min with buffer A and desalted for 1 min (600 μL buffer A). The desalted fragments were separated by a C18 column with a linear gradient of 8% to 35% buffer B (95% acetonitrile, 5% H2O, 0.0025% TFA) at 100 μL/min over 20 min and analyzed by mass spectrometry. Mass spectrometric analyses were carried out using an LTQ™ Orbitrap Fusion Lumos mass spectrometer (Thermo Fisher Scientific) with the capillary temperature at 275° C., resolution 150,000, and mass range (m/z) 300-1,800. BioPharma Finder 3.0 (Thermo Fisher Scientific) was used for the peptide identification of non-deuterated samples prior to the HDX experiments. HDExaminer version 2.5 (Sierra Analytics, Modesto, Calif.) was used to extract centroid values from the MS raw data files for the HDX experiments.
Incubation of hK2 antibodies, hu11B6, KL2B494, KL2B467, KL2B30, KL2B413 and KL2B53 with soluble hK2 protein resulted in different patterns of hydrogen exchange and overall protection. The protected segments were mapped onto the sequence of hK2 antigen to visualize the binding epitopes (FIG. 7). KL2B494, KL2B467 and KL2B30 bound to common sequences of (i) residues 173-178 (SEQ ID NO: 209, KVTEF) (e.g., KL2B494, KL2B467 and KL2B30 bound at least three of the residues of SEQ ID NO: 209, namely, the KVT residues at 173-175) and (ii) residue 230-234 (SEQ ID NO: 216, HYRKW) (e.g., KL2B494, KL2B467 and KL2B30 bound at least three of the residues of SEQ ID NO: 216, namely, the HYR residues at 230-232). KL2B413 also bound all residues of SEQ ID NO: 209 and the KW residues of SEQ ID NO: 216, as shown in
KL2B53 showed a different pattern of protection and bound to a sequence consisting of residues 27-32 (Seq ID NO: 217, SHGWAH), 60-75 (SEQ ID NO: 218, RHNLFEPEDTGQRVP) and 138-147 (SEQ ID NO: 292, GWGSIEPEE).
According to an embodiment, an isolated anti-hK2/anti-CD3 protein (e.g., hu11B6, KL2B494, KL2B467, KL2B30, KL2B413, or KL2B53) comprises an hk2-specific antigen binding domain that specifically binds to a discontinuous epitope (i.e., epitopes whose residues are distantly placed in the sequence) of hK2 comprising one or more amino acid sequences selected from the group consisting of SEQ ID NO: 209, 216, 217, 218, and 292.
The paratope of anti-hK2 antibodies hu11B6, KL2B494, KL2B467, KL2B413 and anti-hK2/CD3 bispecific antibodies KLCB113 and KLCB80 were identified based on significant differences in deuterium uptake from the HDExaminer residue plots. KL2BB494 comprises three paratope regions two of which are located in the KL2B494 heavy chain variable domain (GFTFSH (SEQ ID NO: 729) and TAVYYCAKPHIVMVTAL (SEQ ID NO: 730)) and a single paratope region located within the light chain variable domain (YDDSDRPSGIPER (SEQ ID NO: 731)). KL2B467 comprises three paratope regions, two of which are located in the KL2B467 heavy chain variable domain (FTFSY (SEQ ID NO: 732) and GSYWAFDY (SEQ ID NO: 733)) and a single paratope region within the light chain variable domain (DNSD (SEQ ID NO: 734)). Hu11B6 comprises a single epitope region located in the heavy chain (GNSITSDYA (SEQ ID NO: 735)). KL2B413 comprises two paratope regions located in the heavy chain variable domain (GFTF (SEQ ID NO: 736) and ARDQNYDIL (SEQ ID NO: 737)). KL2B30 of bispecific KLCB80 comprise a paratope region locate in the heavy chain (comprising amino acid residues TIF and VTPNF (SEQ ID NO: 738)) and a paratope region located in the light chain (YAASTLQSG (SEQ ID NO: 739)). KL2B53 of bispecific KLCB113 comprise a single paratope region locate in the heavy chain (comprising amino acid residues ESGWSHY (SEQ ID NO: 740)).
The VH/VL regions of the anti-hK2 antibodies generated in Example 2 and the VH/VL regions of the anti-CD3 antibodies generated in Example 1 were engineered into bispecific format and expressed as IgG1.
Engineering of CD3 scFvs for hK2/CD3 Bispecific Generation
CD3 VH/VL regions were engineered as scFvs in either VH-Linker-VL or VL-linker-VH orientations using the linker of SEQ ID NO: 31 (Table 27). The VH-Linker-VL or VL-linker-VH scFv molecules binding CD3 were further engineered into a scFv-hinge-CH2-CH3 (also called scFv-Fc) format comprising Fc silencing mutation (L234A/L235A/D265S) and the T350V/L351Y/F405A/Y407V mutations designed to promote selective heterodimerization (Table 28). The polypeptide of SEQ ID NO: 293 was used as the constant domain hinge-CH2-CH3. The scFv-hinge-CH2-CH3 proteins binding CD3 were engineered either having or lacking the C-terminal Lysin in the CH3 domain (Table 28). DNA sequences of anti-CD3 molecules in scFv format and scFv-hinge-CH2-CH3 format are shown in Table 29.
Engineering of CD3 Fabs for hK2/CD3 Bispecific Generation
The CD3 specific VH and VL regions were engineered in VH-CH1-linker-CH2-CH3 and VL-CL formats respectively and expressed as IgG1. The polypeptide of SEQ ID NO: 314 comprising the Fc silencing mutation L234A/L235A/D265S and the CH3 mutation T350V/L351Y/F405A/Y407V designed to promote selective heterodimerization was used to generate the CD3 specific VH-CH1-linker-CH2-CH3 (Table 30). The VH-CH1-linker-CH2-CH3 heavy chains were engineered either having or lacking the C-terminal Lysin in the CH3 domain. The VH-CH1-linker-CH2-CH3 heavy chain lacking the C-terminal Lysin is shown in SEQ ID NO: 85.
The polypeptides of SEQ ID NO: 363 or 364 were used to generate the CD3 specific VL-CL (Table 31)
DNA sequences of anti-CD3 molecules as HC in VH-CH1-liker-CH2-CH3 format and LC in VL-CL format are shown in Table 32.
Engineering of hK2 scFvs-Fc for hK2/CD3 Bispecific Generation hK2 VH/VL regions engineered as scFvs in either VH-Linker-VL or VL-linker-VH orientations using the linker of SEQ ID NO: 31 (Table 2), as described in Example 2, were further engineered into a scFv-hinge-CH2-CH3 format comprising the Fc silencing mutation (L234A/L235A/D265S) and the T350V/T366L/K392L/T394W mutations designed to promote selective heterodimerization and expressed as IgG1 (Table 33). The polypeptide of SEQ ID NO: 321 was used as the constant domain hinge-CH2-CH3 (Fc).
Engineering of hK2 Fab-Fc for hK2/CD3 Bispecific Generation
The hK2 specific VH and VL regions were engineered in VH-CH1-linker-CH2-CH3 and VL-CL formats respectively. The polypeptide of SEQ ID NO: 326 comprising the Fc silencing mutation L234A/L235A/D265S and the CH3 mutation T350V/T366L/K392L/T394W designed to promote selective heterodimerization was used to generate the CD3 specific VH-CH1-linker-CH2-CH3).
The polypeptides of SEQ ID NO: 363 or 364 were used to generate the hK2 specific VL-CL.
The amino acid sequences of hK2 Fab-Fc HCare shown in Table 34.
hK2/CD3 Bispecifics
CD3W245 and CD3B376 anti-CD3 specific arms, engineered as Fabs, and the hK2 VH/VL regions of KL2B359, KL2B413, KL2B467 and KL2B494 engineered as scFvs in both HL and LH orientations as described above, were expressed to generate bispecific antibodies, yielding hK2/CD3 bispecific antibodies with a hK2 binding arm in a format scFv-hinge-CH2-CH3 and a CD3 binding arm in a format of: heavy chain: VH-CH1-linker-CH2-CH3 and light chain: VL-CL. Alternatively, the VH/VL regions of the anti-CD3 antibodies CD3W245 engineered as scFvs in the LH-linker-VH orientation and the VH/VL regions of the anti-hK2 antibodies KL2B30, KL2B242 and KL2B53 engineered as Fabs as described above, were expressed to generate bispecific antibodies, yielding hK2/CD3 bispecific antibodies with a hK2 binding arm in the format of a heavy chain VH-CH1-linker-CH2-CH3 and light chain VL-CL and a CD3 binding arm in a format scFv-hinge-CH2-CH3. The linker used to generate the anti-scFv is the linker of SEQ ID NO: 31.
T350V_L351Y_F405A_Y407V CH3 mutations were engineered into one heavy chain and T350V_T366L_K392L_T394W CH3 mutations were engineered into the other heavy chain as described above. In addition, both HK2 and CD3 binding arms were engineered to contain Fc effector silencing mutations L234A_L235A_D265S as described above.
The engineered chains were expressed, and the resulting bispecific antibodies purified using standard methods. The bispecific antibodies were characterized for their binding to hK2 and CD3, and their cytotoxicity as described in Example 5. Table 35 shows the CDR SEQ ID NOs: of selected anti hKL2/CD3 bispecific antibodies. Table 36 shows the VH, VL and scFv SEQ ID NOs: of selected anti hKL2/CD3 bispecific antibodies. Table 37 shows the HC1, HC2, LC1 and LC2 SEQ ID NOs of selected anti hKL2/CD3 bispecific antibodies. HC1 and LC1 refer to the heavy and light chain of the hKL2 binding arm. Alternatively, HC1 can also refer to the scFv-hinge-CH2-CH3 of the hK12 binding arm. HC2 and LC2 refer to the heavy and light chain of the CD3 binding arm. Alternatively, HC2 can also refer to the scFv-hinge-CH2-CH3 of the CD3 binding arm. Table 38 shows the amino acid sequences of HC1, LC1, HC2 and LC2. Table 39 shows the cDNA sequences of HC1, LC1, HC2 and LC2.
Affinity of Selected hK2×CD3 Bispecific Antibodies
Affinity of selected hK2×CD3 bispecific antibodies to hK2 or human CD3 was measured by surface plasmon resonance (SPR). SPR is a label-free technique to study the strength of an interaction between two binding partners by measuring the change in mass upon complex formation and dissociation. Antibodies were captured on a sensor chip coated with an anti-Fc antibody followed by injection of soluble hK2 (or soluble recombinant CD3) at various concentrations and specified association and dissociation times. Post dissociation, the surface was regenerated with an appropriate solution to prepare for the next interaction. Kinetic information (on-rate and off-rate constants) were extracted by fitting sensorgrams to the 1:1 Langmuir model. Binding affinity (KD) are reported as the ratio of rate constants (koff/kon). KD values of selected hK2/CD3 bispecific antibodies are listed in Table 40.
Thermal Stability of Selected hK2×CD3 Bispecific Antibodies
Thermal stability of the bispecific antibody samples was determined by NanoDSF method using an automated Prometheus instrument. Measurements were made by loading sample into 24 well capillary from a 384 well sample plate. Duplicate runs were performed for each sample. Prometheus NanoDSF user interface (Melting Scan tab) was used to set up the experimental parameters for the run. The thermal scans for the samples span from 20° C. to 95° C. at a rate of 1.0° C./minute. Dual-UV technology monitors intrinsic tryptophan and tyrosine fluorescence at the emission wavelengths of 330 nm and 350 nm, and this ratio (F350 nm/F330 nm) is plotted against temperature to generate an unfolding curve. Nano DSF is used for measuring Tm of all molecules at 0.5 mg/mL concentration in Phosphate Buffered Saline, pH 7.4. Measured Tm values are listed in Table 41.
A high throughput screening assay was used to measure the propensity of an Ab candidate to self-interact. Propensity for self-interaction usually translates into poor Ab solubility and challenges in downstream Ab manufacturing. In this assay, gold nanoparticles (AuNPs) were coated with goat anti-human IgG (H+L) capture antibody and later incubated with candidate Abs in the presence of polyclonal goat IgG. Any candidate Ab that self-associates brings the AuNPs into proximity, resulting in a shift of the nanoparticles' plasmon wavelength (λp), also referred to as the wavelength at maximum absorbance (λmax). The magnitude of the shift (Δλmax) for each candidate Ab is indicative of the strength of its self-association. Proper control antibodies which showed none to high self-association potential were used in this assay. All molecules tested in this assay showed none to low risks for self-association.
In Vitro Cytotoxicity of hK2×CD3 Bi-Specific Antibodies
The cytotoxicity potential of the generated bispecific antibodies was measured in vitro with a T-cell-mediated cytotoxicity assay using live-time lapse imaging on the Incucyte platform. The bispecific antibodies were tested in hK2 positive cell line VCaP cells, in the presence of isolated pan human CD3+ T cells from healthy donors at a Effector:Target ratio (E:T ratio) of 3:1. Cell death by apoptosis was monitored by measuring the fluorescence signal from a dye which is stably expressed by target VCaP cells.
Normal donor pan T cells were co-incubated with KLK2+VCaP cells. KLK2×CD3 bispecific antibodies were dosed from 0 to 100 nM for 96 hours. 3:1 Effector-to-Target (ET) ratio was used. (A) Target cells were stably expressing a red nuclear dye which was measured by IncuCyte imaging system in real-time for quantifying target cell death. Overall tumor cell lysis was graphed based on AUC of real-time kinetic killing curve of VCaP cells (
In Vitro T Cell Activation and Proliferation by hK2×CD3 Bi-Specific Molecules
hK2×CD3 bispecific antibodies were tested for their ability to promote T cell activation and proliferation. Normal donor pan T cells were labelled with CFSE (5 uM) and co-cultured with KLK2 (+) VCap cells. KLK2×CD3 bispecific antibodies were dosed from 0 to 100 nM for 96 hours. 3:1 Effector-to-Target (ET) ratio was used. After 96 hours co-incubation, cells were harvested and stained with CD25, live/dead Dye. Flow cytometric analysis was performed on a Fortessa flow cytometer with Flowjo software. The frequencies of CTV dye dilution and activation marker CD25 were determined. The frequency of CD25 positive cells at different doses were used to graph in vitro T activation (
In Vitro T Cell Cytokine Release by hK2×CD3 Bi-Specific Molecules.
The effect of anti-hK2×CD3 antibodies on T-cell cytokines release was measured in vitro. Supernatant samples were collected from the in vitro cytotoxicity experiment described above. A 13-plex cytokine Luminex assay was carried out to quantify IFN-γ and TNF-α concentrations at different doses of hK2×CD3 bispecific antibodies.
Efficacy of Bispecific hK2×CD3 Antibodies in Established Subcutaneous (SC) Human Prostate Xenograph Model in T Cell Humanized Mice.
In vivo efficacy of KLK2×CD3 bispecifics was evaluated in human prostate tumor VCaP s.c. mouse xenograft model. The antitumor efficacy of KLK2×CD3 molecules was evaluated in established SC human prostate VCaP xenografts. Intact male NSG mice were used to provide a suitable host for engrafting human tumors and human T cells. The human prostate cell line VCaP was obtained from American Type Culture Collection (ATCC). VCaP cells were harvested during exponential growth and mice were injected with 1×107 cells SC in a volume of 0.2 mL in the right flank. 20e6 human T cells were injected i.p for each animal. Three dose levels were evaluated with 5-fold escalation: 0.2 mg/kg, 1 mg/kg and 5 mg/kg. Bispecific antibodies were dosed twice a week via i.p. Eye blood was sampled at 6 hours post first i.p dosing and functional cytokine levels were measured using Luminex based assays. Tumor volume and body weight measurements were collected twice weekly throughout all studies. The percent delta tumor growth inhibition (ATGI) was defined as the difference between mean tumor burden of the treated and control groups, calculated as % ΔTGI=([(TVc-TVc0)-(TVt-TVt0)]/(TVc-TVc0))×100; where ‘TVc’ is the mean tumor burden of a given control group, ‘TVc0’ is the mean initial tumor burden of a given control group, ‘TVt’ is the mean tumor burden of the treated group, and ‘TVt0’ is the mean initial tumor burden of the treated group. % TGI was defined as ([TVc-TVt]/TVc)×100.
A KLK2×CD3 compound of the present invention showed dose-dependent anti-tumor effect, i.e., at 1 mg/kg, showed marginal tumor growth inhibition and at 5 mg/kg showed anti-tumor effect. Cytokine assessment at 6 hours post first dosing showed above-background functional cytokine release of the active KLK2×CD3 compound, which is consistent with in vivo efficacy.
K562 chronic myelogenous leukemia cell line (ATCC, CCL-243) lacking expression of all HLAs, including the MHC class I proteins: HLA-A (Uniprot P01892), HLA-B (Uniprot P18464), HLA-C (Uniprot P30508), and HLA-E (Uniprot P13747) (therefore suitable for NK cell based killing), was transduced using a pCDH lentiviral vector to express HLA-G1-IRES (internal ribosome entry site)—β-2-microglobulin (β2M, LPP—CS-Z7412-I0035-02-200, Genecopoeia) or the human HLA-G (C42S)—IRES—β2M (LPP—CS-Z7412-I0035-01-200, Genecopoeia) in lentiviral particles (Genecopoeia) and cultured in IMDM, 10% FBS. At passage one, selection with 10 μg/ml puromycin (Gibco, A1113803) to ensure stable HLA-G expression. Cells were split 1:10 when density reached ˜ 3×106 cells/ml, approximately every 3-4 days.
Anti-HLA-G antibodies were generated using OmniRat® transgenic humanized rats. The OmniRat® contains a chimeric human/rat IgH locus (comprising 22 human VHS, all human D and JH segments in natural configuration linked to the rat CH locus) together with fully human IgL loci (12 Vκs linked to Jκ-Cκ and 16 VWs linked to Jλ-Cλ). (see e.g., Osborn, et al. (2013) J Immunol 190(4): 1481-1490). Accordingly, the rats exhibit reduced expression of rat immunoglobulin, and in response to immunization, the introduced human heavy and light chain transgenes undergo class switching and somatic mutation to generate high affinity chimeric human/rat IgG monoclonal antibodies with fully human variable regions. The preparation and use of OmniRat®, and the genomic modifications carried by such rats, is described in WO14/093908.
OmniRat® rats were immunized using a construct comprising a subunit of either recombinant human HLA-G1 or recombinant human HLA-G5, a soluble isoform of HLA-G containing the α1, α2, and α3 domains but lacking the transmembrane region, fused to the β2m subunit and histone H2A, K562 cells expressing HLA-G1, or DNA encoding HLA-G1 extracellular domain with C42S mutation (Table 42). In some cases the histone H2A peptide was fused to the antigen for enhanced stability. Table 42 shows the sequences of the antigens.
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPS
DIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYY
TEFTPTEKDEYACRVNHVTLSQPKIVKWDRDMG
KIEWHE
RIIPRHLQLGGGGSGGGGSIQRTPKIQVYSRHPAEN
GKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEH
SDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHV
TLSQPKIVKWDRDMGGGGSGGGGSGGGGSGSHS
EAQKIEWHE
FLHLA-G1
QARIIPRHLQLGGGGSGGGGSGGGGSIQRTPKIQVY
SRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGE
RIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEY
ACRVNHVTLSQPKIVKWDRDMGGGGSGGGGSGG
RIIPRHLQLGGGGSGGGGSGGGGSIQRTPKIQVYSR
HPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERI
EKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYAC
RVNHVTLSQPKIVKWDRDMGGGGSGGGGSGGGG
For HYB:420, OmniRats were immunized twice weekly for a total of 12 immunization boosts by following a Repetitive Immunizations Multiple Sites (RIMMS) protocol with recombinant human HLA-G1, human HLA-G5 and cynomolgus monkey Mafa-AG (homolog of HLA-G1) proteins. A final cell boost was performed using a hHLA-G1 K562 expressing cell line derived from K562 cells (ATCC© CCL-243™). Sera titers were determined via a solid phase ELISA with immunogen being coated on the plate. Draining lymph nodes were harvested for lymphocytes fusion with FO myeloma cells (ATCC® CRL-1646™) for hybridoma generation.
For HYB:423, OmniRats were immunized with human HLA-G pDNA (pDR000057441 (Table 3); C>S variant) via the tibialis muscle immediately followed by in vivo electroporation multiple times. Rats received a final boost of a combination of both human and cyno HLA-G over expressing cells. Draining lymph nodes were collected and fused with FO myeloma cells for hybridoma generation.
For HYB:421, OmniRats were immunized with human HLA-G pDNA into each tibialis muscle followed by in-vivo electroporation. Titers were assessed and ranged from 0-800 at Day 25. Rats were rested for several months and then further immunized with pDNA followed by a final boost with K562 cells exogenously overexpressing human HLA-G. Lower draining lymph nodes were used in downstream hybridoma generation.
To select antibody clones for downstream screening, hybridoma supernatants were screened for their abilities to bind cells expressing human HLA-G only and not to cells exogenously expressing HLA-A, HLA-B, and HLA-C, or wild type K562 cells, which do not express cell surface MHC class I antigens. Supernatants which displayed >20-fold higher binding to K562-HLA-G and 10-fold lower binding to K562-HLA-A/B/C (compared to isotype control) were selected for v-region sequencing and cloning. Monoclonal antibodies were generated in both silent format—lacking effector function (IgG4 PAA or IgG1 AAS, where “PAA” indicates P228S, L234A, L235A and “AAS” indicates mutation of L234A, L235A, D265S in EU numbering) and in active format—having normal effector function (IgG1). Antibodies were expressed in the supernatant from CHO cells and isolated by protein A affinity chromatography. Recombinant antibodies were then re-screened (as described above) for selectivity to HLA-G expressing cells as well as for their abilities to bind recombinant HLA-G (MHGW2). From these analyses, a panel of 48 unique v-regions was identified and 8 unique v-regions were selected for further analysis. Two of these 8 v-regions, derived from MHGB688 and MHGB694 were germline-optimized to result in MHGB738 and MHGB737, respectively.
Variable domains of the select anti-HLA-G antibodies were expressed in a Fab format, a scFv format in the VH-linker-VL orientation or a scFv format in VL-linker-VH orientation.
Table 43 shows the VH and VL amino acid sequences of selected anti-HLA-G antibodies. Table 44 shows the Kabat HCDR1, HCDR2 and HCDR3 of selected anti-HLA-G antibodies. Table 45 shows the Kabat LCDR1, LCDR2 and LCDR3 of the selected anti-HLA-G antibodies. Table 46 shows the Chothia HCDR1, HCDR2 and HCDR3 of selected anti-HLA-G antibodies. Table 47 shows the Chothia LCDR1, LCDR2 and LCDR3 of the anti-HLA-G. Table 48 shows the IMGT HCDR1, HCDR2 and HCDR3 of selected anti-HLA-G antibodies. Table 49 shows the IMGT LCDR1, LCDR2 and LCDR3 of the anti-HLA-G. Table 50 shows the AbM HCDR1, HCDR2 and HCDR3 of selected anti-HLA-G antibodies. Table 51 shows the AbM LCDR1, LCDR2 and LCDR3 of the anti-HLA-G.
The v-region sequences of the antibodies were analyzed for risks of potential post-translational modifications, for germline fitness, and for their abilities to format as scFv. Two antibodies, MHGB694 and MHGB688 were germline-optimized. The v-region of MHGB694 contained two germline mutations (E46D and N77H), and this v-region was thus was optimized by back-mutation of these residues to the germline sequence at those sites to generate MHGB737 variable region by mutation of D46E and H77N in the VH domain. The v-region of MHGB688 was similarly optimized by mutation of E1Q, L5Q, E6Q, and S71P in the VH domain and by mutation of K30E, G66V in the VL. We found that MHGB688 also contained an “NS” motif at position 92-93 (Kabat) which presents a risk for deamidation. Since the VL of MHGB672 had identical LC-CDRs except that it contained “HS” at positions 92-93, we mutated N92H. This combination of changes resulted in MHGB738.
Fab-Fc and scFvs
The HLA-G specific VH/VL domains were engineered to be expressed either in an antibody format, or as an scFv, or as an arm of a bi-specific (as either Fab-Fc or scFv-Fc). The antibody format and the Fab-Fc bi-specific arm format included a heavy chain as VH-CH1-hinge-CH2-CH3 and the light chain as VL-CL and expressed as IgG2 or IgG4. The scFv-Fc format included either the VH-Linker-VL-Fc or VL-linker-VH-Fc orientations. The linker that is used in the scFv was the linker of SEQ ID NO: 31 described above. The scFv-Fc and Fab-Fc were used to generate bispecific antibodies as described in Example 14.
Table 52 shows the HC amino acid sequences of selected anti-HLA-G antibodies. Table 53 shows the LC amino acid sequences of selected anti-HLA-G antibodies. Table 54 summarizes the HC and LC DNA SEQ ID NOs of selected anti-HLA-G antibodies. Table 55 shows the amino acid sequences of selected scFvs in VH-linker-VL or VL-linker-VH orientation. Table 56 shows the amino acid sequences of selected scFv-Fc. Table 57 shows the scFv and scFv-Fc DNA SEQ ID NOs of selected anti-HLA-G antibodies in the scFv-Fc format.
The original and germline-optimized v-regions were screened for thermal stability in scFv format. Briefly, v-regions were cloned into scFv format and were expressed in E. coli. The culture supernatants were assessed by ELISA for their abilities to bind recombinant HLA-G. Supernatant samples were also heat shocked at either 55, 60, or 65° C., and the binding of the heat-shocked samples was compared to the unheated samples. This analysis provided an estimate of the thermal stability of the v-regions when formatted as scFv. Based on this analysis, MHGB737 and MHGB738, the germline-optimized versions of MHGB694 and MHGB688, respectively, were preferred.
The v-regions in IgG1 mAb format were tested for their abilities to specifically bind cells expressing HLA-G but not other MHC class I molecules (Table 59). Briefly, 1.5×107 cells were washed 2 times with 1×PBS and resuspended in 7 mL of 1×PBS and incubated for 10 min. After incubation, 8 mL of fetal bovine serum (FBS) were added, cells were washed by centrifugation at 300×g for 5 min and resuspended at 1×106 cells/mL in DMEM supplemented with 10% FBS. Cells were then washed by centrifugation at 300×g for 5 min and resuspended in staining buffer supplemented with goat anti-human Fc A647 (Jackson cat. #109-606-098) and incubated for 30 min at 4° C. After incubation, 150 μL of staining buffer were added and cells were washed by centrifugation at 300×g for 5 min. Cells were resuspended in 200 μL of running buffer (staining buffer supplemented with 1 mM EDTA, 0.1% (v/v) pluronic acid) and washed by centrifugation at 300×g for 5 min. Cells were resuspended in 30 mL of running buffer and analyzed for antibody binding by flow cytometry.
Next, the v-regions were tested for their abilities to bind recombinant HLA-G as mAbs using surface plasmon resonance (SPR). SPR is a label-free technique to study the strength of an interaction between two binding partners by measuring the change in mass upon complex formation and dissociation. Briefly, antibodies were immobilized on a sensor chip, which was coupled with goat anti-human Fc. Soluble HLA-G1 extracellular domain (MHGW8) was flowed over the immobilized antibody and association/dissociation responses were monitored. Kinetic information (on-rate and off-rate constants) were extracted by fitting sensorgrams to the 1:1 Langmuir model. Binding affinity (KD) were reported as the ratio of rate constants (koff/kon). Antibody affinities (Kd) ranged from ˜77 pM—2.6 nM and are shown in Table 60.
HLA-G is over-expressed on certain tumor types and can thus serve as a marker for tumor cells. Additionally, HLA-G binds to the ligands ILT2 and ILT4, which are expressed on immune effector cells such as NK cells4,5. The interaction between HLA-G and ILT2/ILT4 leads to inhibition of NK cell activity. Thus, we hypothesized that antibodies which bind to HLA-G competitively with ILT2/4 would prevent inhibitory interaction between tumor cells and NK cells and lead to increased NK mediated tumor cell killing. To address this hypothesis, we first assayed whether the antibodies could block interaction between HLA-G and ILT2/4 using a competition assay. Binding between the HLA-G-dextramer complex and HEK293T cells exogenously expressing ILT2 or ILT4 receptors results in a fluorescence signal. Addition of a mAb which competes with the interaction between HLA-G-dextramer and ILT-2/4 cells results in a decrease in fluorescence signal. The inverse of the fluorescence signal inhibition was related to the ligand blocking inhibition of the mAbs (Table 60). Briefly, recombinant biotinylated HLA-G1 (MHGW8) was bound up to a streptavidin APC-dextramer (Immudex cat. #DX01-APC) to a final ratio of approximately 4 HLA-G1 proteins per dextramer molecule. Dextramer-HLA-G complex was mixed with HEK293T cells exogenously expressing ILT-2 or cells exogenously expressing ILT-4 and incubated for 30 min. at 4° C. Anti-HLA-G antibody was added at each concentration and incubated with dextramer-HLA-G complex for 30 min at ° C. Cells were added (25,000 cells) and incubated for 30 min at 4° C. After incubation, the mixture of cells and dextramer HLA-G complex were washed by centrifugation resuspended in 30 μL of running buffer (Thermo BD cat. #554657). The resuspended mixture was analyzed for fluorescence signal by flow cytometry using an Intellicyt® iQue Screener Plus. Gating was done first on singlet cells, then live cells using Sytox™ Blue Dead Cell stain (ThermoFisher), then on GFP for cells expressing ILT-2/4, then on APC for bound dextramer-HLA-G complex. All antibodies except MHGB737 could inhibit HLA-G interaction with ILT4, and all antibodies except MHGB737 and MHGB687 could inhibit interaction with ILT2 (Table 61). This suggested that antibodies discovered in this campaign could both target tumors and relieve immune inhibition by the tumor cells.
We then asked whether this inhibition of ligand binding was due to direct competition with ILT2/4 for the same binding site on HLA-G. To address this hypothesis, we used hydrogen-deuterium exchange-based LC-MS (described in Example 9) to identify the epitopes on HLA-G for either ILT-2, ILT-4, MHGB732, or MHGB738 (
We then asked whether inhibition of the interaction with HLA-G with ILT-2/4 could mediate anti-tumor activity via NK cell-based cytotoxicity. To address this, we cloned each variable region onto either an IgG1 or a silent IgG4-PAA constant region which lacks effector function. We then tested the ability of each antibody to mediate cytotoxicity of K562-HLA-G cells mediated by NK cells which either express Fc receptors (NK-92) or which lack Fc receptors (NKL). Briefly, K562 cells overexpressing HLA-G cells were labeled with Carboxyfluorescein succinimidyl ester (CFSE) which served as a cell proliferation dye. Antibodies were diluted into a 96-well plate according to the dilutions in
We tested the ability of antibodies to further mediate tumor cell killing via antibody-dependent cellular cytotoxicity (ADCC) against the choriocarcinoma cell line JEG-3 (ATCC HTB-36) which endogenously expresses HLA-G (
Since the anti-HLA-G Abs could display ADCC in vitro, we asked whether this activity could be enhanced. Several studies showed that antibodies having less than 10% terminal fucosylated Fc display enhanced effector function due to higher affinity binding to Fc receptors 7. Thus, we generated MHGB732 and MHGB738 in a low fucose CHO host to produce an antibody with <10% terminal fucose (MHGB738.CLF) (Table 62,
The normal fucose and low fucose antibodies were tested for their abilities to induce NK cell-based ADCC against either JEG-3 cells (
We next tested the abilities of the antibodies to mediate complement-dependent cytotoxicity (CDC) (
The VH/VL regions of the anti-HLA-G antibodies generated in Examples 7-13 and the VH/VL regions of the anti-CD3 antibody of Example 1 were engineered into bispecific format and expressed as IgG1.
Engineering of CD3 scFv-Fcs and CD3 Fabs for HLA-G×CD3 Bispecific Generation.
The CD3-specific scFvs, scFv-Fcs, and Fab-Fcs were generated as described in Example 3. Additionally, the CD3-specific scFvs, scFv-Fcs, and Fab-Fcs were generated using VH/VL regions from CD3B450, that has been describe in US20200048349, and CD3B219, derived from SP34-2 antibody (BD Biosciences 551916). Null-scFv-Fc and B23B62-Fab-Fc were used as negative controls.
The HLA-G specific VH and VL regions were engineered in VH-CH1-hinge-CH2-CH3 and VL-CL formats respectively. The polypeptide of SEQ ID NO: 326 comprising the Fc silencing mutations L234A/L235A/D265S and the CH3 mutations T350V/T366L/K392L/T394W designed to promote selective heterodimerization was used to generate the HLA-G specific VH-CH1-hinge-CH2-CH3. The polypeptides of SEQ ID NO: 363 or 364 were used to generate the HLA-G specific VL-CL.
The amino acid sequences of HLA-G Fab-Fc HC and LC are shown in Tables 63 and 64, respectively. The cDNA SEQ ID Nos of HLA-G Fab-Fc HC and LC are listed in Table 65.
Table 63 shows the amino acid sequences of anti-HLA-G Fab-Fc heavy chains (HCs).
Table 64 shows the amino acid sequences of anti-HLA-G Fab-Fc light chains (LCs).
Table 65 shows the cDNA sequences of anti-HLA-G Fab-Fc light chains (LCs) and heavy chains (HCs).
Engineering of HLA-G scFv-Fc for HLA-G/CD3 Bispecific Generation
HLA-G VH/VL regions engineered as scFvs in either VH-Linker-VL or VL-linker-VH orientations using the linker of SEQ ID NO: 31 (Table 2) as described in Example 2 were further engineered into a scFv-hinge-CH2-CH3 format comprising the Fc silencing mutation (L234A/L235A/D265S) and the T350V/T366L/K392L/T394W mutations designed to promote selective heterodimerization and expressed as IgG1. The polypeptide of SEQ ID NO: 321 was used as the constant domain hinge-CH2-CH3.
Amino acid sequences of anti-HLA-G molecules in scFv-hinge-CH2-CH3 format (scFv-Fc) are shown in Table 66. cDNA sequences of anti-HLA-G molecules in scFv-hinge-CH2-CH3 format (scFv-Fc) are listed in Table 67.
The VH/VL regions of the anti-CD3 antibodies CD3B376, CD3B450, CD3B219, and CD3W246, engineered as Fab-Fcs and the VH/VL regions of the anti-HLA-G antibodies MHGB738, MHGB732 and MHGB737 engineered as scFv-Fcs in both HL and LH orientations as described above, were expressed to generate bispecific antibodies, yielding HLA-G/CD3 bispecific antibodies with a HLA-G binding arm in a format scFv-hinge-CH2-CH3 and a CD3 binding arm in a format of: heavy chain: VH-CH1-linker-CH2-CH3 and light chain: VL-CL (Table 68). B23B62-Fab-Fc arm was used as an isotype control for the CD3-specific arm.
Alternatively, the VH/VL regions of the anti-CD3 antibodies CD3W246, CD3B450, and CD3B219 engineered as scFv-Fcs in HL and/or LH orientations (see Table 68) and the VH/VL regions of the anti-HLA-G antibodies MHGB738, MHGB732 and MHGB737 engineered as Fabs as described above, were expressed to generate bispecific antibodies, yielding HLA-G/CD3 bispecific antibodies with a HLA-G binding arm in the format of a heavy chain VH-CH1-linker-CH2-CH3 and light chain VL-CL and a CD3 binding arm in a format scFv-hinge-CH2-CH3. The linker used to generate the anti-scFv is the linker of SEQ ID NO: 31 (Table 68).
T350V_L351Y_F405A_Y407V CH3 mutations were engineered into one heavy chain and T350V_T366L_K392L_T394W CH3 mutations were engineered into the other heavy chain as described above. In addition, both HK2 and CD3 binding arms were engineered to contain Fc effector silencing mutations L234A_L235A_D265S as described above.
The engineered chains were expressed, and the resulting bispecific constructs purified using standard methods. The bispecifics were characterized for their binding to HLA-G and CD3, their in vitro cytotoxicity, immune checkpoint response, and in vivo efficacy as described in Examples 15-17.
T cell redirection against tumor cells has shown significant promise in the clinic, and we asked whether a bispecific antibody (BsAb) which targets HLA-G and the CD3 subunit of the T cell receptor complex would show cytotoxicity against HLA-G expressing tumor cells. Lead v-regions were formatted as BsAbs with a series of CD3-binding redirection arms (Table 69). Briefly, target cells (NCI-H2009-b2m) at 50,000 cells per well were incubated with antibody at concentrations starting from 10 nM and serially by half-log per well. Purified primary T cells were added at a ratio of 3:1 and the mixture was incubated for 72 hr at 37° C. Staining solution was prepared adding LIVE/DEAD Near-IR stain (Dead Cell Stain, L34976, Invitrogen) at 1 uL per 10{circumflex over ( )}6 cells and Brilliant violet anti CD25 (Biolegend cat. #302630) at 5 uL per 10{circumflex over ( )}6 cells in BD FACS staining buffer. Cell mixtures were dissociated with Accutase prior to addition analysis by flow cytometry. Cells were gated on FSC-A vs SSC-A and CFSE (BL-1) vs SSC-A and non-viable tumor cells were identified by total tumor target cell population for CFSE (BL-1) vs Near IR Live/Dead (RL2-H) gating. Data was analyzed using ForeCyt (Sartorius) advanced metrics to calculate tumor cytoxity. All BsAbs displayed the ability to enhance T cell-mediated cytotoxicity when the HLA-G binding v-region was paired with a CD3 binding arm with EC50 values that were correlated to the binding affinities of both the HLA-G targeting arm and the CD3 targeting arm (Table 69).
The BsAbs were further tested for their abilities to mediate T-cell activation and T cell-based cytotoxicity against additional cell lines: Hup-T3 and RERF-LC-Ad-1 (
Two BsAbs, HC3B125 and HC3B258, differed only in the presence (HC3B258) or absence (HC3B125) of a codon to express the C-terminal lysine, K447 in the heavy chain. Since the C-terminal lysine of the heavy chain of antibodies is normally proteolytically processed, the two Abs displayed identical mass spectra (Table 70). Additionally, they displayed identical biophysical properties, such as thermal stability and binding affinity for both T cells and for K562-HLA-G cells. Additionally, HC3B258 displayed similar cytotoxicity properties as HC3B125 (
We observed that anti-HLA-G mAbs whose mechanism of cytotoxicity features effector function (e.g. ADCC) and CD3×HLA-G BsAbs could induce killing of all cell types which expressing HLA-G. Tumors often escape immune surveillance via up-regulation of certain immune checkpoint modulators which can inhibit immune cells, such as PD-L1 or CTLA-49. We thus asked whether targeting cancer cells for T cell mediated cytotoxicity via CD3×HLA-G BsAbs could overcome expression of immune checkpoint modulators on tumor cells. We measured whether HLA-G-expressing tumor cells expressed immune checkpoint ligands (Table 71). Briefly, cells were cultured as in Example 11, and were then stained with commercial antibodies targeting the receptors indicated in Table 71. Fluorescence was measured using flow cytometry to determine relative expression levels of each receptor. Interestingly, we observed that RERF-LC-Ad1 cells expressed PD-L1 at levels significantly higher than other target cells and that CD3×HLA-G BsAbs could still mediate T cell based cytotoxicity against RERF-LC-Ad1 cells (
While the correlation between HLA-G expression in patients and a poor prognosis has been established in most types of cancer, the direct role of HLA-G in tumor escape in vivo has thus far not been demonstrated. There are no murine homologues of HLA-G, but also ILT-2, therefore studying of the role of HLA-G requires xenograft models and humanized mice.
Abs and BsAbs were tested for their abilities to mediate anti-tumor efficacy in vivo in a series of mouse studies. The study shown in (
Tumor growth was not inhibited by HC3B128 at either dose level tested. While a small reduction in group mean tumor volume was observed at the higher doses of HC3B128 compared to the control group, the differences were not statistically significant (Table 71).
2 Delta TGI values in each group were calculated on the first measurement day after the final 2QW treatment was administered (day 25) according to the formula given in the section Error! Reference source not found.; for additional TGI, T/C and tumor regression values, see Appendix 1.
3 Partial (PR) and complete regressions (CR) were determined according to the section Error! Reference source not found.
Treatment with HC3B125 could also result in tumor growth inhibition in a HuP-T3 cell line derived xenograft (CDX) model (
The VH/VL regions of the anti-Delta-like ligand 3 (DLL3) antibodies generated using transgenic mice (Ablexis®) and the VH/VL regions of the anti-CD3 antibodies of Example 1 were engineered into bispecific format and expressed as IgG1. Additionally, the VH/VL regions of CD3-specific antibodies CD3B376 and CD3B450, described in US20200048349, were used.
The designed heavy chain molecules were synthesized into gblocks (IDT; Coralville, Iowa) containing 15 bp overlaps at the 5′ and 3′ ends for ligation independent cloning using InFusion method (ClonTech). All light chain constructs were inserted into pLonza vector containing the BswiI and HindIII restriction sites for in-frame ligation to the human kappa constant domain. Murine IgH signal peptides were encoded to allow for efficient secretion of mAbs into culture supernatant. All gblocks were reconstituted in sterile water and incubated at 50° C. for 10 minutes as per manufacturer protocol. pLonza vector (Lonza; Basel, Switzerland) was linearized using EcoRI and HindIII followed by gel extraction and cleanup. A 2:1 mass ratio of linearized vector to insert was used followed by heat pulse at 50° C. for 15 minutes. The infusion reactions were transformed into Stellar competent cells (ClonTech) and resultant colonies were scaled for miniprep. All constructs were sequence verified and scaled up using Endotoxin free maxi preparation kits (Qiagen; Hilden, Germany).
Engineering of CD3 and DLL3 scFvs for Bispecific DLL3×CD3 Generation
CD3 VH/VL regions were engineered as scFvs in either VH-Linker-VL or VL-linker-VH orientations using the linker of SEQ ID NO:31 (Table 2). The VH-Linker-VL or VL-linker-VH scFv molecules binding CD3 were further engineered into a scFv-hinge-CH2-CH3 format comprising Fc silencing mutation (L234A/L235A/D265S) and dimerization mutations to allow for heterodimerization of the DLL3 and CD3 heavy chains.
DLL3 VH/VL regions were engineered as scFvs in a VL-linker-VH orientation using the same linker as for CD3 scFv generation described above of SEQ ID NO:31 (Table 2). The VL-linker-VH scFv molecules binding DLL3 were further engineered into a scFv-hinge-CH2-CH3 format comprising the Fc silencing mutation (L234A/L235A/D265S). Mutations designed to promote selective heterodimerization of the Fc domain were also engineered in the Fc domain.
Engineering of CD3 and DLL3 Fabs for DLL3/CD3 Bispecific Generation
The CD3 and DLL3 specific VH and VL regions were also engineered in VH-CH1-hinge-CH2-CH3 and VL-CL formats respectively and expressed as IgG1. The Fc silencing mutation L234A/L235A/D265S were introduced in the Fc region. Mutations designed to promote selective heterodimerization of the Fc domain were also engineered in the Fc domain.
Expression of Bispecific DLL3×CD3 Antibodies
The bispecific antibodies were expressed in ExpiCHO-S™ cells by transient transfection with purified plasmid DNA following the manufacturer's recommendations. Briefly, ExpiCHO-S™ cells were maintained in suspension in ExpiCHO™ expression medium (ThermoFisher Scientific, Cat #A29100) in an orbital shaking incubator set at 37° C., 8% CO2 and 125 RPM. The cells were passaged and diluted prior to transfection to 6.0×106 cells per ml, maintaining cell viability at 99.0% or better. Transient transfections were done using the ExpiFectamine™ CHO transfection kit (ThermoFisher Scientific, Cat #A29131). For each ml of diluted cells to be transfected, 0.5 microgram of each bispecific antibody encoding DNA in ratios of HC1:LC1:HC2=1:2:2 and 0.5 microgram of pAdVAntage DNA (Promega, Cat #E1711) was used and diluted into OptiPRO™ SFM complexation medium. For each liter of cells, 2.56 mL of ExpiFectamine™ CHO reagent was diluted into 8 mL of OptiPRO™. The diluted DNA and transfection reagent were combined for one minute, allowing DNA/lipid complex formation, and then added to the cells. After overnight incubation, ExpiCHO™ feed and ExpiFectamine™ CHO enhancers were added to the cells as per the manufacturer's Standard protocol. Cells were incubated with orbital shaking (125 rpm) at 37° C. for seven days prior to harvesting the culture broth. The culture supernatant from the transiently transfected ExpiCHO-S™ cells was clarified by centrifugation (30 min 3000rcf) followed by filtration (0.2 μm PES membrane, Corning; Corning, N.Y.).
Purification of Bispecific DLL3×CD3
The filtered cell culture supernatant was loaded onto a pre-equilibrated (1×DPBS, pH 7.2) HiTrap MabSelect SuRe Protein A column (GE Healthcare) using an AKTA Avant 150 chromatography system. After loading, the column was washed with 5 column volumes of 1×DPBS, pH7.2. The protein was eluted with 8 column volumes of 0.1 M sodium (Na)-Acetate, pH 3.5. Protein fractions were completely neutralized by the addition of 2.5 M Tris HCl, pH 7.2 to 15% (v/v) of the final volume and syringe filtered (0.2 m). The neutralized protein solution was loaded onto 2×5 mL prepacked CaptureSelect™ IgG-CH1 Affinity Matrix (Thermo Fisher Scientific). The column was washed with 10 column volumes of 1×DPBS, pH7.2. The protein was eluted with 10 column volumes of 0.1 M sodium (Na)-Acetate, pH 3.5. Protein fractions were completely neutralized by the addition of 2.5 M Tris HCl, pH 7.2 to 15% (v/v) of the final volume. The major peak fractions were pooled, dialyzed into 1×DPBS, pH 7.2 with a total of 3 dialysis changes and filtered (0.2 in).
Tables 74-77 show sequence information for the select DLL3/CD3 bispecific antibodies.
Effect of DLL3 Epitope on the Bispecific DLL3×CD3 Mediated Cytotoxicity
To determine the effect of DLL3 epitope on bispecific DLL3×CD3 mediated killing on DLL3+ target cells, a T cell redirection was performed using human pan T cells as effectors and SHP-77 cells as targets at a 3:1 ratio for 72 hours. An equal volume (100 ul) of 2× test sample, in 1/2 log dilutions from 20 nM (final starting at 10 nM) was added to 50,000 CSFE-labelled SHP-77 cells mixed with 150,000 pan T cells in a final volume of 200 ul RPMI, 10% FBS for 72 hr at 37° C. After 72 hours, plates were washed 1× with PBS, incubated for 20 minutes with Near IR L/D stain and BV421-labeled anti-CD25 antibody in stain buffer. The cells were washed twice with stain buffer, resuspended in 25 ul Accutase for 10 minutes, and then 25 ul of QSol buffer was added. The plates were read on an IQue plus and cells were gated on CSFE positive populations (Tumor cells) and CSFE-negative cells (T cells) and both populations were subsequently gated on live/dead staining. Live T cells were further gated on CD25 staining. Outputs calculated were % Tumor killing, % CD25 T cell activation, and T cell viability. A ruby red stained control (mock 100% dead) and T cell only/SHP-77 only were used to gate nuclei containing cells from debris and then the individual cell populations. Data was analyzed in GeneData Screenr using 4 parameter curve fits. The tables below show the maximal percent lysis of SHP-77 cells observed at the end of 72 hours for each DLL3 binder paired with the various CD3 arms. The results indicate that the % tumor killing is dependent on the binding epitope on DLL3, the further it is from the membrane the lesser the cell lysis (Table 78-80). The % tumor killing was improved as the DLL3 binding epitopes became more membrane proximal. This trend is relatively consistent when the DLL3 binders were paired with 3 different CD3.
Inventors have unexpectedly discovered that an interesting trend appears where maximum killing in each domain increases as the binding domain within the DLL3 moves towards the C-terminus in the primary sequence or proximal to the tumor membrane. In particular, maximum killing efficiency improves from EGF2 to EGF6 and reaches the highest percentage, when the tested antibody binds at the EGF-6 domain or closer to the c-terminus.
The binding affinity of anti-DLL3×CD3 antibodies to the recombinant human DLL3 was determined by surface plasmon resonance (SPR) using a Biacore T200 instrument. The antibodies were captured on a goat anti-Fc antibody-modified C1 chip and titrated with 3-fold serial dilutions of DLL3 antigen spanning concentrations of 90 nM to 1.1 nM. The association was monitored for 2 minutes and the and dissociation for 5 or 60 minutes, using a flow rate of 100 μL/min. Raw binding data was referenced by subtracting the analyte binding signals from blanks and analyzed using a 1:1 Langmuir binding model using the Biacore Insight evaluation software to obtain the kinetics which were used to calculate the binding affinity. Binding affinities of anti-DLL3×CD3 antibodies to the recombinant human DLL3 are summarized in Table 81.
Thermal Stability of Bispecific Anti-DLL3×CD3 Antibodies
The thermal stability (conformational stability) bispecific anti-DLL3×CD3 antibodies was determined by NanoDSF method using an automated Prometheus instrument. Measurements were made by loading sample into 24 well capillary from a 384 well sample plate. Duplicate runs were performed. The thermal scans span from 20° C. to 95° C. at a rate of 1.0° C./minute. The data was proceed to obtain integrated data and first derivation analysis for 330 nm, 350 nm, Ratio 330/350, and scatter data from which thermal transitions, onset of unfolding, Tm and Tagg were obtained.
The results show that these bispecific anti-DLL3×CD3 antibodies have a first transition (Tm1) higher than 59° C. The results also show that most proteins, except DL3B585 have low aggregation potential with Tagg above 70° C. and 5 degrees or more higher than Tm1 (Table 82).
Binding of Bispecific Anti-DLL3×CD3 Antibodies on DLL3+ Tumor Cells
We determined the cell binding profiles of the bispecific anti-DLL3×CD3 antibodies to DLL3+ human tumor cell lines (HCC1833 and SHP-77). The adherent SCLC HCC1833 cells were washed with DPBS and 0.25% trypsin was added to allow cells to detach. The media was added to neutralize trypsin and the cells were transferred to a 15 mL conical tube. The suspension SCLC SHP77 cells were transferred to a 15 mL conical tube and were centrifuged 1200 rpm for 3 minutes. The media was aspirated and the cells were washed once more with DPBS. The cells were counted using the Vi-cell XR cell viability analyzer and were plated at 100K/well in 100 uL DPBS. The plate was centrifuged 1200 rpm for 3 minutes and washed 2× with DPBS. The cells were stained with Violet Live/Dead stain (Thermo-Fisher) and incubated at RT in the dark for 25 min. The cells were centrifuged and washed 2× with FACS staining buffer (BD Pharmingen).
The test antibodies were diluted to a final starting concentration of 100 nM in FACS staining buffer and 3-fold serial dilutions were prepared from the starting concentration for a total of 10 dilution points. The serially diluted test antibodies (100 uL/well) were added to the cells and incubated for 30 min at 37°. The cells were washed 2× with FACS staining buffer and AlexaFluor 647-conjugated Donkey anti-human secondary antibody (Jackson Immunoresearch) was added and allowed to incubate with the cells for 30 min at 4°. Then the cells were washed 2× with FACS staining buffer and re-suspended in 100 uL FACS Buffer. The cells were run on BD Celesta using FACS Diva software and analyzed using FlowJo software. As shown in
Binding of Bispecific Anti-DLL3×CD3 Antibodies on Pan T-Cells
The cell binding profiles of the bispecific anti-DLL3×CD3 antibodies to normal human T cells were also evaluated. Human Pan T Cells (Biological Specialty Corporation, Colmar, Pa.) were thawed and transferred to a 15 mL conical with DPBS (Dulbecco's Phosphate Saline Buffer). The cells were centrifuged 1300 rpm for 5 minutes. DPBS was aspirated and the cells were re-suspended in DPBS. The cells were counted using the Vi-cell XR cell viability analyzer and were plated at 100K/well in 100 uL DPBS. The plate was centrifuged 1200 rpm for 3 minutes and washed 2× with DPBS. The cells were stained with Violet Live/Dead stain (Thermo-Fisher) and incubated at RT in the dark for 25 min. The cells were centrifuged and washed 2× with FACS staining buffer (BD Pharmingen). Test antibodies were diluted to a final starting concentration of 100 nM in FACS staining buffer and 3-fold serial dilutions were prepared from the starting concentration for a total of 10 dilution points. The serially diluted test antibodies (100 uL/well) were added to the cells and incubated for 30 min at 37°. Cells were washed 2× with FACS staining buffer and AlexaFluor 647-conjugated Donkey anti-human secondary antibody (Jackson Immunoresearch) was added and allowed to incubate with the cells for 30 min at 4°. Cells were washed 2× with FACS staining buffer and re-suspended in 100 uL FACS Buffer. Cells were run on BD Celesta using FACS Diva software and analyzed using FlowJo software. As shown in
Bispecific DLL3×CD3 Mediated Cytotoxicity Against DLL3+ Target Cell Lines in Pan T-Cells
We evaluated the T-cell mediated killing potential of the bispecific anti-DLL3×CD3 antibodies in DLL3+ and DLL3− cell lines. DLL3+ SHP77 and DLL3-HEK293 stably expressing red nuclear dye were generated to be used in the IncuCyte-based cytotoxicity assay. Frozen vials of healthy donor T-cells (Biological Specialty Corporation, Colmar, Pa.) were thawed in a 37° C. water bath, transferred to a 15 mL conical tube, and washed once with 5 mL phenol-red-free RPMI/10% HI FBS medium. The cells were counted using the Viacell XR cell viability analyzer and the T-cells were combined with target cells for a final effector T-cell to target cell (E: T) ratio of 5:1. The cell mixture (100 uL/well) was combined in a 50 mL conical tube and added to a clear 96-well flat-bottom plate. The test antibodies were then diluted to a final starting concentration of 60 nM in phenol-red-free RPMI/10% HI FBS medium and 3-fold serial dilutions were prepared from the starting concentration for a total of 11 dilution points. The serially diluted test antibodies (100 uL/well) were added to the combined cells. The plates were placed in either an IncuCyte® Zoom or an IncuCyte S3® (Essen) at 37° C. with 5% CO2 for 120 hours. The target cell lines stably express red nuclear dye which was used to track the kinetics of target cell lysis. Percent cell growth inhibition (%)=(Initial viable target cell number—Current viable target cell number)/Initial viable cell number*100%. As shown in
We evaluated the cytokine release profiles of the bispecific anti-DLL3×CD3 antibodies in a DLL3+ human tumor cell line. The supernatants were analyzed using the Human Proinflammatory Panel I tissue culture kit (Meso Scale Discovery) and were thawed on wet ice, spun at 1,500 rpm for 5 minutes at 4° C., then placed on ice. The MULT-SPOT assay plates were pre-washed per the manufacturer's protocol. A standard curve was prepared by serial dilution of the provided calibrators in MSD Diluent 1. The standards and test antibody samples (25 uL/well) were added to the pre-washed plates. Assay plates were read on the SECTOR Imager 6000. As shown in
Bispecific DLL3×CD3 Mediated Cytotoxicity Against DLL3+ Target Cell Lines in PBMCs
In order to test the efficacy of the bispecifics against DLL3+ target cells with varying levels of antigen expression, DLL3 high expression (SHP-77 and HCC1833) and DLL3 low expression cell line (G361) were tested in the cytotoxicity assay. SHP-77 and HCC1833 are lung epithelial and lung adenocarcinoma cell lines, respectively. G361 cells are derived from malignant skin melanoma. DLL3+ SHP-77 cell line stably expressing the nuclear restricted NucLight Red (NLR) protein was used in the cytotoxicity assay. On the day of the assay, SHP-77-NLR cells were collected into a 50 ml falcon tube and spun down at 1300 rpm for 5 min. The cell pellet was then resuspended in modified RPMI 1640 media+10% FBS (complete media) and cell count was estimated using trypan blue live dead marker using a hemocytometer. SHP-77-NLR cells were then plated onto a collagen coated 96 well plate at 10,000 cells/well/90β1 of complete media. The cells were evenly distributed by gentle agitation and allowed to settle for 1 hour in a 5% CO2 incubator. In the case of HCC1833 and G361 target cell lines, 3000 cells/well/90β1 complete media were plated in a 96 well flat bottom tissue culture plates one day prior to the PBMC addition.
The vials of PBMCs frozen from healthy donors (Clinigene) were rapidly thawed in a 37° C. water bath, transferred to a 15 mL conical tube, and washed once with 10 mL complete medium. The cells were stained with anti-human CD3 antibody and analyzed by flow cytometer to determine the CD3% within PBMCs. PBMCs from each donor were counted using trypan blue live dead marker using a hemocytometer and the number of PBMCs required to get required effector to target (ET) ratios (CD3: target cell) were added to the plated target cells in 90β1 complete media. The test antibodies were then prepared as 10× stocks in complete media and 3-fold serial dilutions were prepared. The serially diluted test antibodies were added to the PBMC-tumor coculture at 20 μl/well so that the final concentration of antibody became 1×. Wells with no antibody (NBS) were used as control for the basal cytotoxicity. The plates were placed in an IncuCyte S3® (Essen BioScience) at 37° C. with 5% CO2 for 5 days. Increase in red signal corresponds to target cell proliferation and a decrease in signal corresponds to target cell death. Results are summarized in Table 83. % lysis was calculated as ={100−(red signal intensity at a specific time point with Antibody/red signal intensity at that time point in NBS wells)*100}.
Potent tumor cell lysis was observed with bispecifics DLL3×CD3 antibodies across cell lines of different origin and antigen densities. To compare the efficacy of the high affinity CD3 bispecific (DL3B583) with the low affinity CD3 bispecific (DL3B585), the cytotoxicity against DLL3 high expression SHP-77 cells was tested at various ET ratios. The whole PBMCs from 3 donors were cultured with DLL3+ SHP-77-NLR cells at the indicated ET ratios (CD3: SHP-77) in the presence of the bispecific DLL3×CD3 antibodies. Wells with PBMCs and target cells but no antibody were used as control for basal cytotoxicity. Plates were scanned for up to 120 hours in an IncuCyte S3® (Essen BioScience) in a 37° C. with 5% CO2 incubator. % lysis was calculated as ={100−(red signal intensity at a specific time point with Antibody/red signal intensity at that time point in NBS wells)*100}. Each point on the graph represents an average of 3 donors. As shown in
In order to test if the binding of bispecific DLL3×CD3 antibodies to CD8+ T cells can induce proliferation and expansion of CD8+ T cells, the time course analysis of CD8+ T cell proliferation was performed. DLL3+ SHP-77 cells were used for the assay. On the day of the assay, SHP-77 cells were collected into a 50 ml falcon tube and spun down at 1300 rpm for 5 min. The cell pellet was then resuspended in 1 ml modified RPMI 1640 media+10% FBS (complete media) and cell count was estimated using trypan blue live dead marker using a hemocytometer. SHP77 cells were then plated in a U-bottom 96 well plate at 10,000 cells/well/90β1 of complete media.
The vials of PBMCs frozen from healthy donors (Clinigene) were rapidly thawed in a 37° C. water bath, transferred to a 15 mL conical tube, and washed once with 10 mL complete medium. The cells were stained with anti-human CD3 antibody and analyzed by flow cytometer to determine the CD3% within PBMCs. PBMCs were stained Cell Trace Violet dye (C34571, Thermo Fisher Scientific). PBMCs from each donor were counted using trypan blue live dead marker using a hemocytometer and the number of PBMCs required to get effector to target (ET) ratio of 10:1 (CD3: target cell) were added to the plated target cells in 90β1 complete media.
The test antibodies were then prepared as 10× stocks in complete media and 3-fold serial dilutions were prepared from the starting concentration for a total of 3 dilution points. The serially diluted test antibodies were added to the PBMC-tumor coculture at 20 μl/well so that the final concentration of antibody became 1×. Wells with no antibody (NBS) were used as control for the basal cytotoxicity. The plates were incubated in a 5% CO2 incubator for the indicated time periods. At the end of the incubation period, the cells suspension was transferred to a v-bottom plate and was spun down at 1500 rpm for 5 min. The pellet was resuspended in 100p of DPBS. 10p of the cell suspension was taken for determining the total cell count at each antibody concentration using Trypan blue with a hemocytometer. The rest of the cell suspension was subjected to LIVE/DEAD™ Fixable Near-IR Dead Cell Stain Kit (L10119) and incubated for 20 min on ice. The viability stain was inactivated using FACS buffer and was spun down at 1500 rpm for 5 min. Cells were stained with BD Fc block (564220, BD Pharmingen) for 10 min followed by staining with CD3 and CD8 antibodies and acquired on a flow cytometer. Gating on CD8 T cells was performed to estimate the expansion of the cytotoxic CD8 T cell population within the CD3 T cells. As shown in
In order to look at the activation status of the cytotoxic CD8 T cell population in response to the binding of the DLL3×CD3 bispecifics, kinetic analysis of CD25, CD69 and CD71 markers was performed. DLL3+ SHP-77 cells were used for the assay. SHP-77 cells were collected into a 50 ml falcon tube and spun down at 1300 rpm for 5 min. The cell pellet was then resuspended in 1 ml modified RPMI 1640 media+10% FBS (complete media) and cell count was estimated using trypan blue live dead marker using a hemocytometer. SHP-77 cells were then plated in a U-bottom 96 well plate at 10,000 cells/well/90β1 of complete media.
Vials of PBMCs frozen from healthy donors (Clinigene) were rapidly thawed in a 37° C. water bath, transferred to a 15 mL conical tube, and washed once with 10 mL complete medium. The cells were stained with anti-human CD3 antibody and analyzed by flow cytometer to determine the CD3% within PBMCs. PBMCs from each donor were counted using trypan blue live dead marker using a hemocytometer and the number of PBMCs required to get effector to target (ET) ratio of 10:1 (CD3: target cell) were added to the plated target cells in 90β1 complete media.
The test antibodies were prepared as 10× stocks in complete media and 3-fold serial dilutions were prepared from the starting concentration for a total of 3 dilution points. The serially diluted test antibodies were added to the PBMC-tumor coculture at 20 μl/well so that the final concentration of antibody became 1×. Wells with no antibody (NBS) were used as control for the basal cytotoxicity. The plates were incubated in a 5% CO2 incubator for the indicated time periods. At the end of the incubation period the cells suspension was transferred to a v-bottom plate and was spun down at 1500 rpm for 5 min. The pellet was resuspended in 100 μl of DPBS. 10 μl of the cell suspension was taken for determining the total cell count at each antibody concentration using Trypan blue with a hemocytometer.
The rest of the cell suspension was subjected to LIVE/DEAD™ Fixable Near-IR Dead Cell Stain Kit (L10119) and incubated for 20 min on ice. The viability stain was inactivated using FACS buffer and was spun down at 1500 rpm for 5 min. The cells were stained with BD Fc block (564220, BD Pharmingen) for 10 min followed by staining with CD3, CD8, CD25, CD69 and CD71 antibodies and acquired on a flow cytometer. As shown in
T cell redirecting bispecific antibodies can cause toxicity because of the induction of cytokine release syndrome. These cytokines can be produced by T cell themselves or myeloid cells and results in a feedback loop of more cytokine production. In order to understand the release of cytokines such as IL-6, TNF-α, IL-10, GMCSF and other T cell cytokines by the addition of DLL3×CD3 bispecifics, culture supernatants from cytotoxicity assays were tested for the levels of these cytokines. DLL3+ SHP-77 cells were used for the assay. SHP-77 cells were collected into a 50 ml falcon tube and spun down at 1300 rpm for 5 min. The cell pellet was then resuspended in 1 ml modified RPMI 1640 media+10% FBS (complete media) and the cell count was estimated using trypan blue live dead marker using a hemocytometer. SHP-77 cells were then plated in a U-bottom 96 well plate at 10,000 cells/well/90 μl of complete media.
The vials of PBMCs frozen from healthy donors (Clinigene) were rapidly thawed in a 37° C. water bath, transferred to a 15 mL conical tube, and washed once with 10 mL complete medium. The cells were stained with anti-human CD3 antibody and analyzed by flow cytometer to determine the CD3% within PBMCs. PBMCs from each donor were counted using trypan blue live dead marker using a hemocytometer and the number of PBMCs required to get effector to target (ET) ratio of 10:1 (CD3: target cell) were added to the plated target cells in 90β1 complete media.
The test antibodies were prepared as 10× stocks in complete media and added to the PBMC-tumor coculture at 20 μl/well so that the final concentration of antibody became 1×. Wells with no antibody (NBS) were used as control for the basal cytotoxicity. The plates were incubated in a 5% CO2 incubator for the indicated time periods. At the end of the incubation period the cells suspension was transferred to a v-bottom plate and was spun down at 1500 rpm for 5 min. The supernatant was collected and stored at −20° C. to perform Luminex using the MILLIPLEX MAP Human CD8+ T Cell Magnetic Bead Panel (HCD8MAG-15K, Millipore). Plate was analyzed using MAGPIX with eXPONENT software. Results are summarized in Table 84.
Low levels of cytokine release was observed with the bispecific DLL3×CD3 antibody with lower affinity CD3 (DL3B585) as compared to the ones with higher affinity CD3 arms (DL3B582 and DL3B583), in particular, IL-10, IL-6, IL-2 and IL-4, while the cytotoxic potency of these bispecific DLL3×CD3 was comparable.
Binding Affinity of Bispecific Anti-DLL3 Variant×CD3 Antibody to DLL3
In order to ensure the N to Q mutation in the HCDR1 region (or near the HCDR1 region depending on the delineation used) of the DL3B279 variant, as described in Example 1, did not result in change in binding to DLL3, the binding affinity of the DL3B279 variant to the recombinant human DLL3 was determined by surface plasmon resonance (SPR) using a Biacore T200 instrument and compared to the parental DL3B279. The antibody was captured on a goat anti-Fc antibody-modified C1 chip and titrated with 3-fold serial dilutions of human and cyno DLL3 antigen spanning concentrations of 90 nM to 1.1 nM. The association was monitored for 3 minutes and the dissociation for 60 minutes, using a flow rate of 50 μL/min. Raw binding data was referenced by subtracting the analyte binding signals from blanks and analyzed using a 1:1 Langmuir binding model using the Biacore Insight evaluation software to obtain the kinetics which were used to calculate the binding affinity. The results (Table 85) showed that the binding affinity of the DLL3×CD3 bispecific (C3C3B80) containing the DL3B279 variant (DL3B279-VL-A99G-VH-N27Q_M105T-LH-scFV) is comparable to that of the original DLL3×CD3 bispecific (DL3B585) containing the original DL3B279-LH-scFV molecule (DL3B585: 24 pM).
The thermal stability (conformational stability) of bispecific anti-DLL3 CD3 antibody containing the new DL3B279 sequence of the DL3B279 variant (D3C3B80) was determined by NanoDSF method using an automated Prometheus instrument. Measurements were made by loading sample into 24 well capillary from a 384 well sample plate. Duplicate runs were performed. The thermal scans span from 20° C. to 95° C. at a rate of 1.0° C./minute. The data was processed to obtain integrated data and first derivation analysis for 330 nm, 350 nm, Ratio 330/350, and scatter data from which thermal transitions, onset of unfolding, Tm1 and Tagg were obtained. The results (Table 86) showed that the thermostability of the bispecific DLL3×CD3 antibody with DL3B279-VL-A99G-VH-N27Q_M105T-LH-scFV variant (D3C3B80) is comparable to that in the original bispecific molecule with the original DL3B279-LH-scFv sequence (DL3B585: Tagg=62.7, Tm1=60.8 shown in Table 86).
Binding of Bispecific Anti-DLL3 Variant×CD3 Antibody on T-Cells
Human Pan T Cells (Biological Specialty Corporation, Colmar, Pa.) were thawed and transferred to a 15 mL conical with DPBS. The cells were centrifuged 1300 rpm for 5 minutes. DPBS was aspirated and cells were re-suspended in DPBS. The cells were counted using the Vi-cell XR cell viability analyzer and were plated at 100K/well in 100 uL DPBS. The plate was centrifuged 1200 rpm for 3 minutes and washed 2× with DPBS. Cells were stained with Violet Live/Dead stain (Thermo-Fisher) and incubated at RT in the dark for 25 min. The cells were centrifuged and washed 2× with FACS staining buffer (BD Pharmingen). Test antibodies were diluted to a final starting concentration of 100 nM in FACS staining buffer and 3-fold serial dilutions were prepared from the starting concentration for a total of 10 dilution points. The serially diluted test antibodies (100 uL/well) were added to the cells and incubated for 30 min at 37°. Cells were washed 2× with FACS staining buffer and AlexaFluor 647-conjugated Donkey anti-human secondary antibody (Jackson Immunoresearch) was added and allowed to incubate with the cells for 30 min at 4° C. Cells were washed 2× with FACS staining buffer and re-suspended in 100 uL FACS Buffer. Cells were run on BD Celesta using FACS Diva software and analyzed using FlowJo software. As shown in
Bispecific Anti-DLL3 Variant×CD3 Mediated Cytotoxicity Against DLL3+ Target Cell Lines in Pan T-Cells by IncuCyte
DLL3+ SHP77 stably expressing red nuclear dye were generated to be used in the IncuCyte-based cytotoxicity assay. Frozen vials of healthy donor T-cells (Biological Specialty Corporation, Colmar, Pa.) were thawed in a 37° C. water bath, transferred to a 15 mL conical tube, and washed once with 5 mL phenol-red-free RPMI/10% HI FBS medium. The cells were counted using the Viacell XR cell viability analyzer and the T-cells were combined with target cells for a final effector T-cell to target cell (E: T) ratio of 5:1. The cell mixture was combined in a 50 mL conical tube. The cell mixture (100 uL/well) was added to a clear 96-well flat-bottom plate. Next, the test antibodies were diluted to a final starting concentration of 60 nM in phenol-red-free RPMI/10% HI FBS medium and 3-fold serial dilutions were prepared from the starting concentration for a total of 11 dilution points. The serially diluted test antibodies (100 uL/well) were added to the combined cells. The plates were placed in either an IncuCyte® Zoom or an IncuCyte S3® (Essen) at 37° C. with 5% CO2 for 120 hours. The target cell lines stably express red nuclear dye which is used to track the kinetics of target cell lysis. Percent cell growth inhibition is equal to the difference between the initial variable target cell number and the current viable target cell number divided by the initial viable cell number. As shown in
The present examples demonstrate that the isolated multispecific proteins disclosed herein are particularly effective at mediating T cell mediated cytotoxicity, promoting T cell activation and proliferation, increasing T cell cytokine release and/or displaying increased anti-tumor efficacy. These activities are a reflection of the combination of antigen binding domains targeting DLL3 on the target cell and CD3 on the T cell. The skilled person would understand that such activity would be expected from assembling the binding domains into a bispecific antibody, irrespective of the mechanism by which the bispecific antibody is assembled.
This application claims priority to U.S. Provisional Application Ser. No. 63/030,448, filed May 27, 2020, Ser. No. 63/057,958, filed Jul. 29, 2020, and Ser. No. 63/094,931, filed Oct. 22, 2020. The disclosure of each of the aforementioned applications is incorporated herein by reference in its entirety.
| Number | Date | Country | |
|---|---|---|---|
| 63030448 | May 2020 | US | |
| 63057958 | Jul 2020 | US | |
| 63094931 | Oct 2020 | US |
