ANTIBODY FC REGION HAVING ENHANCED BINDING AFFINITY TO FCYRIIB
20230220042 · 2023-07-13
Assignee
Inventors
- Fubin LI (Shanghai, CN)
- Yan ZHANG (Shanghai, CN)
- Mi ZHANG (Shanghai, CN)
- Yanxia BI (Shanghai, CN)
- Shihao TIAN (Shangha, CN)
- Huihui Zhang (Shanghai, CN)
- Shujun LIU (Shanghai, CN)
Cpc classification
C07K14/70535
CHEMISTRY; METALLURGY
C07K2317/72
CHEMISTRY; METALLURGY
C12N15/63
CHEMISTRY; METALLURGY
C07K16/00
CHEMISTRY; METALLURGY
C07K16/2878
CHEMISTRY; METALLURGY
International classification
C12N15/63
CHEMISTRY; METALLURGY
C07K16/28
CHEMISTRY; METALLURGY
Abstract
Provided is a modified Fc region. The Fc region has at least one amino acid mutation with respect to a parent Fc region. The modified Fc region has improved affinity to FcγRIIB with respect to the affinity of the parent Fc region to FcγRIIB Also provided is an antibody containing the modified Fc region, especially an agonistic antibody. The modified Fc region has significant use for optimizing the agonistic activity of the antibody.
Claims
1. A mutant Fc polypeptide fragment, wherein the mutant Fc polypeptide fragment has the following features: (i) said mutant Fc polypeptide fragment has a mutation at position(s) selected from the group consisting of: L328, H268, S267, P271, G327, or a combination thereof, with respect to the wild-type Fc polypeptide fragment of SEQ ID NO: 20, wherein the numbering of all amino acids is based on the IgG Eu numbering; and (ii) the affinity of the mutant Fc polypeptide fragment to FcγRIIB is increased compared to the wild-type Fc polypeptide fragment of SEQ ID NO: 20.
2. A mutant immunoglobulin Fc region, wherein the mutant immunoglobulin Fc region comprises the mutant Fc polypeptide fragment according to claim 1.
3. An antibody, wherein the antibody comprises the mutant Fc polypeptide fragment according to claim 1 or a mutant immunoglobulin Fc region comprising the mutant Fc polypeptide fragment.
4. A fusion protein, wherein the fusion protein comprises the mutant Fc polypeptide fragment according to claim 1, a mutant immunoglobulin Fc region or an antibody comprising the mutant Fc polypeptide fragment.
5. An isolated polynucleotide, wherein the polynucleotide encodes the mutant Fc polypeptide fragment according to claim 1, or encodes a mutant immunoglobulin Fc region, a antibody, or a fusion protein comprising the mutant Fc polypeptide fragment.
6. A vector, wherein the vector comprises the isolated polynucleotide according to claim 5.
7. A host cell, wherein the host cell expresses the mutant Fc polypeptide fragment according to claim 1, or expresses a mutant immunoglobulin Fc region, a antibody, or a fusion protein comprising the mutant Fc polypeptide fragment.
8. A pharmaceutical composition, wherein the pharmaceutical composition comprises: (a) the mutant Fc polypeptide fragment according to claim 1, or a mutant immunoglobulin Fc region, a antibody, or a fusion protein comprising the mutant Fc polypeptide fragment; and (b) a pharmaceutically acceptable carrier.
9. A method of producing a mutant Fc polypeptide fragment, or a mutant immunoglobulin Fc region, an antibody, or a fusion protein comprising the mutant Fc polypeptide fragment, wherein the mutant Fc polypeptide fragment has the following features: (i) said mutant Fc polypeptide fragment has a mutation at position(s) selected from the group consisting of: L328, H268, S267, P271, G327, or a combination thereof, with respect to the wild-type Fc polypeptide fragment of SEQ ID NO: 20, wherein the numbering of all amino acids is based on the IgG Eu numbering; and (ii) the affinity of the mutant Fc polypeptide fragment to FcγRIIB is increased compared to the wild-type Fc polypeptide fragment of SEQ ID NO: 20, wherein the method comprises the steps of: (i) culturing the host cell according to claim 7 under suitable conditions to obtain a culture comprising said mutant Fc polypeptide fragment, said mutant immunoglobulin Fc region, said antibody, or said fusion protein; and (ii) purifying and/or separating said mutant Fc polypeptide fragment, said mutant immunoglobulin Fc region, said antibody, or said fusion protein from the culture obtained in step (i).
10. (canceled)
11. A method of treating a disease, comprising the steps of: administering to a subject in need thereof: the mutant Fc polypeptide fragment according to claim 1; a mutant immunoglobulin Fc region, an antibody, or a fusion protein comprising the mutant Fc polypeptide fragment; an isolated polynucleotide encoding the mutant Fc polypeptide fragment, the mutant immunoglobulin Fc region, the antibody, or the fusion protein; a vector comprising the isolated polynucleotide; or a host cell comprising the vector.
12. A method of treating a disease, comprising the steps of: administering to a subject in need thereof the pharmaceutical composition according to claim 8.
13. The method according to claim 12, wherein the subject comprises a mammal.
14. The method according to claim 12, wherein the disease is selected from the group consisting of: cancer, inflammatory diseases, autoimmune diseases, or combinations thereof.
15. The method according to claim 14, wherein the cancer includes: breast cancer, prostate cancer, colon cancer, throat cancer, brain cancer, blood cancer; basal cell carcinoma, biliary cancer, bladder cancer, bone cancer, brain and central nervous system cancer, cervical cancer, chorionic carcinoma, colorectal cancer, connective tissue cancer, digestive system cancer, endometrial cancer, esophageal cancer, ocular cancer, head and neck cancer, gastric cancer, epithelial neoplasm, renal cancer, throat cancer, liver cancer, lung cancer, lymphoma; melanoma; neuroblastoma; oral cancer; ovarian cancer; pancreatic cancer; retinoblastoma; rhabdomyosarcoma; rectal cancer; respiratory cancer; sarcoma; skin cancer; gastric cancer; testicular cancer; thyroid cancer; uterine cancer; urinary system cancer; and other cancers and sarcoma.
16. The mutant Fc polypeptide fragment according to claim 1, wherein, the mutation at L328 is selected form the group consisting of: L328W, L328E, L328Y, L328F, L328M, L328A, L328G, L328N, L328P, L328R, and L328V; the mutation at H268 is selected form the group consisting of: H268D, H268S, H268E, H268K, and H268N; the mutation at 5267 is selected form the group consisting of: S267E, S267V, S267D, S267M, S267Q, S267A, S267G, S267R, S267N, and S267W; the mutation at P271 is selected form the group consisting of: P271C, P271G, P271V, P271A, P271W, P271Y, P271Q, P271T, P271I, P271L, and P271S; the mutation at G327 is selected form the group consisting of: G327A, G327L, and G327S.
17. The mutant Fc polypeptide fragment according to claim 16, wherein, the mutation at L328 is L328W or L328E; the mutation at H268 is H268D, H268S, or H268E; the mutation at 5267 is S267E, S267V, S267D, or S267M; the mutation at P271 is P271C, P271G, P271V, P271A, P271W, P271Y, P271Q, or P271T; the mutation at G327 is G327A.
18. The mutant Fc polypeptide fragment according to claim 1, wherein, the mutant Fc polypeptide fragment has a mutation selected from the group consisting of L328W, L328E, H268D, H268S, H268E, S267V, S267E, A330S, P233G, P271G, P271C, P271V, P271A, P271W, P271Y, and G327A, or a combination thereof, with respect to the wild-type Fc fragment; wherein the numbering of all amino acids is based on the IgG Eu numbering.
19. The mutant Fc polypeptide fragment according to claim 1, wherein, the mutant Fc polypeptide fragment has a mutation of L328W or L328E, and optionally has a mutation at one or more positions selected from the group consisting of: H268, S267, P271, and G327, with respect to the wild-type Fc fragment; the mutant Fc polypeptide fragment has a mutation of H268D, H268S or H268E, and optionally has a mutation at one or more positions selected from the group consisting of: L328, S267, P271, and G327, with respect to the wild-type Fc fragment; the mutant Fc polypeptide fragment has a mutation of S267V, S267D or S267M, and optionally has a mutation at one or more positions selected from the group consisting of: L328, H268, P271, and G327, with respect to the wild-type Fc fragment; the mutant Fc polypeptide fragment has a mutation of P271C, P271G, P271V, P271A, P271W, P271Y, P271Q or P271T, and optionally has a mutation at one or more positions selected from the group consisting of: L328, H268, 5267, and G327, with respect to the wild-type Fc fragment; or the mutant Fc polypeptide fragment has a mutation of G327A, and optionally has a mutation at one or more positions selected from the group consisting of: L328, H268, S267, and P271, with respect to the wild-type Fc fragment.
20. The mutant Fc polypeptide fragment according to claim 1, wherein, the mutant Fc polypeptide fragment has a mutation in at least one of L328 and H268 with respect to the wild-type Fc fragment, and the specific mutations in the mutant Fc polypeptide fragment are selected from one of the group consisting of: L328W, L328E, H268D, H268S, H268E, H268D/S298L/L328W, S267V/S298L/L328W, V234M/S267E/S298L/L328W, A235W/V266L/S298L/L328W, V234Q/A235G/P238L/S239V/H268D/G327A/L328E/A330S/I332T, S239V/V266L/S298L/L328W, V266L/L328W, V266L/S267D/H268D/E269D/P271Q, S267E/H268 S/E269D, P233F/V266L/S298L/L328W, V266L/S298L/L328W, V234Q/A235G/P238L/S239V/G327A/L328E/A330S/I332T, V266L/S267E/H268S/E269V, V266L/S267E/H268S/E269V/P271C, V266L/S267E/H268S/E269A/P271C, S267V/S298G/L328W, V266L/S267M/H268E/P271Q, V266L/S267E/H268S/E269G/P271T, V234Q/V266L/S267D/H268D/E269D/P271Q, V234Q/A235G/P238L/S239V/S267E/H268S/E269D, V266L/S267E/H268S/P271V, V234Q/A235G/P238L/S239V/S267E/S298L/G327A/L328E/A330S/I332T, V234Q/V266L/S267E/H268S/E269V, and L328E/I332T; wherein the numbering of all amino acids is based on the IgG Eu numbering; or the mutant Fc polypeptide fragment has a mutation at S267 with respect to the wild-type Fc fragment, and the specific mutation in the mutant Fc polypeptide fragment is selected from one of the group consisting of: S267E/A330S, S267E/S298G, P233G/S267E, V234M/S267E/S298G/I332L, P233 G/S267E/S298G, V266L/S267E/E269K/P271G, P238Q/S267E, S267A/P271C, S267A/P271G, S267E/D270H, S267E/P271C, S267E/P271V, S267E/P271W, S267E/P271Y, S267E/S298R, S267M/P271C, S267M/P271G, S267V/S298L, and S267E/P329R; wherein the numbering of all amino acids is based on the IgG Eu numbering; or the mutant Fc polypeptide fragment has a mutation at P271 with respect to the wild-type Fc fragment, and the specific mutation in the mutant Fc polypeptide fragment is selected from one of the group consisting of: V266L/S267E/E269K/P271G, V266A/P271C, V266A/P271G, S267A/P271C, S267A/P271G, S267E/P271C, S267E/P271V, S267E/P271W, S267E/P271Y, S267M/P271C, S267M/P271G, V266G/P271C, P271A/S298R, P271G/G236V, P271G/P329S, P271G/P331C, P271G/P331T, P271G/S298D, P271G/S298E, P271G/S298G, P271G/S298K, P271G/S298L, P271G/S298N, P271G/S298R, P271G/T299A, P271G/T299M, P271G/T299S, P271G/T299W, and P271G/I332L; wherein the numbering of all amino acids is based on the IgG Eu numbering; or the mutant Fc polypeptide fragment has a mutation at G327 with respect to the wild-type Fc fragment, and the specific mutation in the mutant Fc polypeptide fragment is selected from one of the group consisting of: G327A/A330R, G327A/A330V, G327A/I332A, G327A/I332C, and G327A/I332E; wherein the numbering of all amino acids is based on the IgG Eu numbering.
21. The mutant Fc polypeptide fragment according to claim 1, wherein, the specific mutation of the mutant Fc polypeptide fragment with respect to the wild-type Fc fragment is selected from one of the group consisting of: H268D/S298L/L328W, S267V/S298L/L328W, V234M/S267E/S298L/L328W, A235W/V266L/S298L/L328W, and V234Q/A235G/P238L/S239V/H268D/G327A/L328E/A330S/I332T; wherein the numbering of all amino acids is based on the IgG Eu numbering.
Description
BRIEF DESCRIPTION OF DRAWINGS
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DETAILED DESCRIPTION
[0109] Unless otherwise stated, the scientific and technical terms used herein shall be understood as having the meanings as commonly understood. Unless otherwise required, as used herein, terms in singular forms include the meaning of plurality, and vice versa. In general, as used herein, nomenclatures and techniques in the cell and tissue culturing/incubation, molecular biology, immunology, protein and nucleic acid chemistry described herein are those already known and commonly used in the art.
[0110] Methods and techniques used in the present disclosure are generally performed as in conventional practices and as described in general and specialized references cited and discussed in this disclosure, unless otherwise indicated. For example, reference can be made to the followings: Molecular Cloning: A Laboratory Manual, Sambrook et al., the 2.sup.nd Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989; Current Protocols in Molecular Biology, Ausubel et al. Greene Publishing Associates, 1992; Antibodies: A Laboratory Manual, Harlow and Lane, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1990, all being incorporated by reference in their entirety. Enzymatic reactions and purifications are performed by following manufacturers' instructions or as known in the art or as specified in the present disclosure. As used herein, nomenclatures, test methods and techniques in biology, pharmacology, medicine and pharmaceutical chemistry are those already known and commonly used in the art. Chemical synthesis, chemical analysis, pharmaceutical manufacturing, formulation and delivery and patient treatment all follow standard practices.
[0111] Unless otherwise stated, the terms have the meanings as defined below.
[0112] An “antibody” (Ab) should include, but is not limited to, a glycoprotein immunoglobulin or antigen-binding portions thereof. Antibodies In one embodiment bind to corresponding antigens, and each includes at least two heavy (H) chains and two light (L) chains that bind to one another through disulfide bonds. Each heavy chain includes a heavy chain variable region (VH) and a heavy chain constant region. The “heavy chain constant region” or CDs of antibodies include three domains identified as CH1, CH2 and CH3, as well as a hinge region between the CH1 domain and the CH2 domain. Each light chain includes a light chain variable region (VL) and a light chain constant region. The light chain constant region consists of one domain CL. VH and VL can each be subdivided into hypervariable regions called “complementary determining regions (CDRs)” and the interspersed relatively conserved regions called “frame regions (FRs)”. VH and VL are each composed of three CDRs and four FRs as arranged in the following order from the amino end to the carboxyl end: FR1, CDR1, FR2, CDR2, FR3, CDR3, FR4. The heavy chain and the light chain variable regions provide the domains that interact with antigens.
[0113] “Fc region” (crystallizable fragment region) or “Fc domain” or “Fc” refers to the C-terminal portion of the heavy chain, which mediates the binding between the immunoglobulin and host tissues or factors, including the binding to Fc receptors on various immune cells (e.g., effector cells) or to the first component of the classic complement system (C1q). Thus, the Fc region is a polypeptide that forms the part of the antibody heavy chain constant region other than the first constant region immunoglobulin domain (CH1 domain). For the allotypes of IgG, IgA and IgD antibodies, the Fc region is composed of two identical protein fragments from CH2 and CH3 domains of the two heavy chains; and in IgM and IgE, the Fc region includes three heavy chain constant domains (CH2-CH3-CH4 domains) in each polypeptide chain. For IgG, the Fc region contains the hinge region between the immunoglobulin domains CH2 and CH3 and the hinge region between CH1 and CH2. Though boundaries of Fc regions of heavy chains of immunoglobulins are variable, Fc regions in heavy chains of human IgGs are normally defined as the segment spanning position P231 to the carboxyl end of the heavy chains, as numbered according to the EU index, the same as in the Kabat system. The CH2 domain of the human IgG Fc region extends from about amino acid 231 to about amino acid 340, while the CH3 domain is located at the C-terminal of the CH2 domain of the Fc region, i.e., it extends from about amino acid 341 of IgG to about amino acid 447.
[0114] The “Fc polypeptide fragment” refers to a fragment contained in the Fc region. The Fc polypeptide fragment herein refers to a fragment extending from the amino acid 233 to the amino acid 332 in the Fc region, or other fragments within the Fc region containing said fragment, such as the Fc CH2 domain or the Fc region.
[0115] As used herein, “Fc region” or “Fc polypeptide fragment” may be a natural Fc or a modified Fc. In addition, “Fc region” or “Fc polypeptide fragment” may also refer to such area in a separated state, or such area provided in a protein polypeptide comprising Fc, which is also referred to as an “Fc fusion protein” (e.g., an antibody or an immunoadhesin).
[0116] “Fc receptor” or “FcR” is the receptor binding to the Fc region of an immunoglobulin. FcRs binding to IgG antibodies include the FcγR family, including their allelic variants and alternative splicing variants. Members of the human Fcγ receptor family include FcγRI (CD64), FcγRIIA (CD32a), FcγRIIB (CD32b), FcγRIIIA (CD16a), FcγRIIIB (CD16b). Therein, FcγRIIB is the only inhibitory Fcγ receptor, and the rest are all activating Fcγ receptors. Most natural effector cells co-express one or more activating FcγRs and the inhibitory FcγRIIB, while natural killer (NK) cells selectively express an activating Fcγ receptor (FcγRIII in mice, FcγRIIIA in humans), while not the inhibitory FcγRIIB in mice and humans. These Fcγ receptors have different molecular structures and therefore different affinity to subclasses of IgG antibodies. Among these Fcγ receptors, FcγRI is a high-affinity receptor, while FcγRIIA, FcγRIIB and FcγRIIIA are low-affinity receptors. Genetic polymorphism is seen in these different Fcγ receptors, which also influences binding affinity. Most dominant genetic polymorphisms include the R131/H131 in FcγRIIA and the V158/F158 in FcγRIIIA Some of these polymorphisms are found disease-associated. And, responsiveness to certain therapeutic antibodies depends on the presence of certain polymorphisms in Fcγ receptors.
[0117] As used herein, a “sequence” should be understood as encompassing sequences that are substantially identical to a specified one according to the disclosure. The term “substantially identical sequences” refers sequences sharing a sequence identity of at least 70, 75 or 80%, preferably at least 90 or 95%, more preferably at least 97, 98 or 99% in the optimal alignment using, for example, GAP or BESTFIT and the default gap value. In one embodiment, the differential residues are conservative amino acid substitution. The term “conservative amino acid substitution” refers to substitution between amino acid residues having similar chemistry (e.g., charge or hydrophilicity) in the side-chain R group. Generally, conservative amino acid substitution does not substantially change a protein's functional properties. When difference(s) between two or more amino acid sequences reside(s) in conservative substitution(s), the sequence identity percentage or similarity value can be up-adjusted to correct for the conservativeness of substitution. See, for example, Pearson, Methods Mol. Biol. 243: 307-31(1994). Examples of amino acids having side-chains with similar chemistry include: 1) aliphatic side chains, including glycine, alanine, valine, leucine and isoleucine; 2) aliphatic-hydroxy side chains, including serine and threonine; 3) amide-containing side chains, including asparagine and glutamine; 4) aromatic side chains, including phenylalanine, tyrosine and tryptophan; 5) basic side chains, including lysine, arginine and histidine; 6) acidic side chains, including aspartic acid and glutamic acid; and 7) sulfur-containing side chain, including cysteine and methionine. conservative amino acid substitutions include valine-leucine-isoleucine, phenylalanine-tyrosine, lysine-arginine, alanine-valine, glutamate-aspartate, and asparagine-glutamine. As noted above, in addition to the amino acid mutations provided by the present disclosure, the Fc region, the antibody, the Fc fragment or the fusion protein according to the present disclosure may further include other possible modifications not disclosed in the present disclosure as long as the “substantially identical” requirements described above are met.
[0118] Amino acids of the antibody and a fragment or domain thereof according to the disclosure are numbered according to the Eu numbering system for IgGs. The mutant types of some mutants involved in the present disclosure and their nomenclature are shown in Table 1.
[0119] Antibodies usually In one embodiment bind to the corresponding antigens with a high affinity (likewise, the proteins of the disclosure may also In one embodiment bind to their epitope recognition molecules), as indicated by, for example, a dissociation constant (KD) of 10.sup.−5-10.sup.−11 M or less. A KD above about 10.sup.−4 M.sup.−1 is usually understood as indicating a nonspecific binding. In this disclosure, an antibody “In one embodiment binding to” an antigen means that the antibody binds to the antigen or a substantially identical antigen with a high affinity as measured by a KD of 10.sup.−7M or less, preferably 10.sup.−8M or less, more preferably 5×10.sup.−9M or less and most preferably 10.sup.−8-10.sup.−1° M or less, and does not bind to any irrelevant antigen with a significant affinity. An antigen is “substantially identical” to a specified antigen, if they share a high sequence identity, such as a sequence identity of at least 80%, at least 90%, preferably at least 95%, more preferably at least 97%, or even more preferably at least 99%.
[0120] Immunoglobulins may come from any commonly known isoform. IgG isoforms can be subdivided into subclasses in some species: IgG1, IgG2, IgG3 and IgG4 in human, IgG1, IgG2a, IgG2b, and IgG3 in mouse. The term “isotype” refers to antibodies encoded by heavy chain constant region genes (e.g. IgM or IgG1). The “antibodies” include naturally occurring and non-naturally occurring antibodies, monoclonal and polyclonal antibodies, chimeric and humanized antibodies, human and non-human antibodies, wholly synthetic antibodies, and single chain antibodies.
[0121] The “natural IgG” described in the present disclosure refers to those IgG that can be naturally present, the sequences of which are not artificially modified. It should be noted that, due to the polymorphism of the gene, even if the natural IgG may also have different mutants. Any non-artificially modified IgG in the natural state is referred to as natural IgG, whether there is a mutation or not.
[0122] An “agonistic antibody” is an antibody that binds to and activates a receptor. Examples of such agonism include an agonistic antibody that binds to a receptor of a tumor necrosis factor receptor (TNFR) superfamily and induces cell apoptosis expressing a TNF receptor. Assays for determining apoptosis-inducing effects are described in WO98/51793 and WO99/37684, which are particularly incorporated herein by reference. In a specific embodiment of the present disclosure, the anti-CD40 agonistic antibody is capable of enhancing the anti-tumor immune response to indirectly kill tumor cells by binding to the target molecule transmitting the immune activation signal on the immune cell surface and activating the important immune activation signal pathway controlled by the target molecule. Examples of agonistic antibodies that have entered the clinical study stage may be referred to in PCT/CN2017/087620.
[0123] The term “agonistic activity” refers to the activity of inducing certain specific physiological activity changes by binding an antibody to an antigen molecule and exciting the antigen molecule to generate a signal. Antigen molecules include receptor molecules and other molecules with signal or physiological functions. Said specific physiological activities include but are not limited to: proliferation activity, survival activity, differentiation activity, transcriptional activity, membrane transport activity, affinity, protein decomposition activity, phosphorylation/dephosphorization activity, redox activity, transfer activity, nucleic acid decomposition activity, dehydration activity, cell death induction activity, apoptosis induction activity, and the like.
[0124] The term “parent” refers to an object that is modified during protein modification. The parent may be a naturally occurring polypeptide, or a variant or modified version of a naturally occurring polypeptide. In some embodiments, the parental Fc region of the present disclosure is an Fc region of natural IgG.
[0125] A “variant” refers to a protein obtained after modification of a parental protein in a protein modification process. In one embodiment, variants can be proteins that are derived from the parental protein by mutations, deletions and/or additions of amino acids in the parental protein, and retain some or all of the function of the parent. In one embodiment, sequence of a mutant herein has at least about 80% homology to the parent's sequence, most preferably at least about 90% homology, more preferably at least about 95% homology. Accordingly, the term “Fc variant” as used herein refers to an Fc sequence that differs from the parent Fc sequence due to at least one amino acid modification. The Fc variant may include only the Fc region, or may be present in the context of an antibody, Fc fusion, isolated Fc, Fc region, or other polypeptide that is substantially encoded by Fc. The Fc variant may refer to the Fc polypeptide itself, a composition comprising an Fc variant polypeptide, or an amino acid sequence encoding it.
[0126] As used herein, “tumor necrosis factor receptor superfamily” and “TNF receptor superfamily” both refer to receptor polypeptides that bind to cytokines of the TNF family. Generally, these receptors are type I transmembrane receptors comprising one or more cysteine-rich repeats in their extracellular domain. Examples of cytokines of TNF family include tumor necrosis factor-α (TNF-α), tumor necrosis factor-β (TNF-β or lymphotoxin), CD30a ligand, CD27a ligand, CD40a ligand, OX-40a ligand, 4-1BB ligand, Apo-1 ligand (also known as Fas ligand or CD95 ligand), Apo-2 ligand (also known as TRAIL), Apo-3 ligand (also known as TWEAK), osteoprotegerin (OPG), APRIL, RANK ligand (also known as TRANCE) and TALL-1 (also known as BlyS, BAFF or THANK). Examples of receptors of the TNF receptor superfamily include type 1 tumor necrosis factor receptor (TNFR1), type 2 tumor necrosis factor receptor (TNFR2), p75 nerve growth factor receptor (NGFR), B-cell surface antigen CD40, T-cell antigen OX-40, Apo-1 receptor (also known as Fas or CD95), Apo-3 receptor (also known as DR3, sw1-1, TRAMP and LARD), receptors called “transmembrane activator and CAML-interactor” or “TACI”, BCMA protein, DR4, DR5 (also known as Apo-2; TRAIL-R2, TR6, Tango-63, hAPO8, TRICK2 or KILLER), DR6, DcR1 (also known as TRID, LIT or TRAIL-R3), DcR2 (also known as TRAIL-R4 or TRUNDD), OPG, DcR3 (also known as TR6 or M68), CAR1, HVEM (also known as ATAR or TR2), GITR, ZTNFR-5, NTR-1, TNFL1, CD30, lymphotoxin β receptor (LTBr), 4-1BB receptor and TR9 (EP988,371 A1).
[0127] As used herein, the terms “ratio of the affinity to the inhibitory Fcγ receptor to the affinity to the activating Fcγ receptor” and “I/A ratio” both refer to the ratio of the antibody heavy chain constant region's affinity to the inhibitory Fcγ receptor (such as human FcγRIIB) to its highest affinity to the activating Fcγ receptor of the same species, e.g., human FcγRI, FcγRIIA, FcγRIIIA, FcγRIIIB
[0128] The term “affinity” refers to the capability of two molecules binding to each other, as usually measured by a KD value. Affinity herein can also be measured by an enrichment factor (as shown in Table 7) or binding analysis signal (as shown in
[0129] “Human” antibodies refer to such antibodies and the variable regions include FRs and CDRs from human immunoglobulins. And, the antibody may also include a constant region from a human immunoglobulin, if present. A human antibody according to the disclosure may include amino acid residues not encoded by human immunoglobulin sequences, such as mutations introduced by random or site-directed mutagenesis in vitro or somatic mutation in vivo. However, as used herein, the term “human antibody” has no intention to include such antibodies that include non-human mammalian (e.g., mouse) CDR sequences grafted between human frame sequences. The term “human” antibody and “wholly human” antibody are used as synonymous to each other.
[0130] The “antibodies” of the disclosure include naturally occurring and non-naturally occurring antibodies, monoclonal and polyclonal antibodies, chimeric and humanized antibodies, human and non-human antibodies and wholly synthetic antibodies.
[0131] A “humanized” antibody refers to an antibody and some, majority or all of the amino acids outside the non-human CDR domains are replaced by corresponding amino acids from a human immunoglobulin. In an embodiment of a humanized antibody, some, majority or all of the amino acids outside the CDR domains are replaced by corresponding amino acids from a human immunoglobulin, and some, majority or all of the amino acids in one or more of the CDRs remain unchanged. Minor addition, deletion, insertion, substitution or modification of amino acid(s) is tolerable, as long as it does not destroy the antibody's capability of binding to the corresponding antigen. A “humanized” antibody retains the antigen binding specificity of the original antibody.
[0132] A “chimeric antibody” refers to an antibody and the variable region(s) come(s) from a species and the constant region(s) from another, for example, an antibody in which the variable region(s) may come from a mouse antibody and the constant region(s) from a human antibody.
[0133] The disclosure is further illustrated by the specific examples described below. It should be understood that these examples are merely illustrative, and do not limit the scope of the present disclosure. The experimental methods without specifying the specific conditions in the following examples generally used the conventional conditions, such as those described in Sambrook, Molecular Cloning: A Laboratory Manual (New York: Cold Spring Harbor Laboratory Press, 1989), or followed the manufacturer's recommendation. Unless otherwise stated, the percentages and parts are by weight.
TABLE-US-00001 TABLE 1 Mutation types of some mutants involved in the present disclosure and their nomenclature Name IgG2 mutation Mut_1 L328W Mut_2 H268D/S298L/L328W Mut_3 S267V/S298L/L328W Mut_4 V234M/S267E/S298L/L328W Mut_5 A235W/V266L/S298L/L328W Mut_6 V234Q/A235G/P238L/S239V/H268D/G327A/L328E/A330S/ I332T Mut_7 S239V/V266L/S298L/L328W Mut_8 V266L/L328W Mut_9 V266L/S267D/H268D/E269D/P271Q Mut_10 S267E/H268S/E269D Mut_11 S267E/A330S Mut_12 P233F/V266L/S298L/L328W Mut_13 V266L/S298L/L328W Mut_14 V234M/S267E/S298G/I332L Mut_15 V234Q/A235G/P238L/S239V/G327A/L328E/A330S/I332T Mut_16 S267E/S298G Mut_17 V266L/S267E/H268S/E269V Mut_18 P233G/S267E Mut_19 V266L/S267E/H268S/E269V/P271C Mut_20 V266L/S267E/H268S/E269A/P271C Mut_21 S267V/S298G/L328W Mut_22 V266L/S267M/H268E/P271Q Mut_23 V266L/S267E/E269K/P271G Mut_24 V266L/S267E/H268S/E269G/P271T Mut_25 V234Q/V266L/S267D/H268D/E269D/P271Q Mut_26 V234Q/A235G/P238L/S239V/S267E/H268S/E269D Mut_27 V266L/S267E/H268S/P271V Mut_28 P233G/S267E/S298G Mut_29 V234Q/A235G/P238L/S239V/S267E/S298L/G327A/L328E/ A330S/I332T Mut_30 V234Q/V266L/S267E/H268S/E269V
[0134] Materials and Methods
[0135] Construction of Vector for Mammalian Cell Surface Display
[0136] The light and heavy-chain full-length sequences of human IgG2 anti-mouse CD40 antibody are constructed to retrovirus vector MIGRI (Addgene, Pear et al. Blood. 1998 Nov. 15. 92(10):3780-92) by Multi One Step Cloning Kit (Yeasen Biotechnology (Shanghai) Co., Ltd., China). The primers used are shown in Table 2, and the construction is shown in
TABLE-US-00002 TABLE 2 Primers used in construction of antibody- expressing vectors for mammalian cell surface display SEQ ID NO: 1 5MIGR1- CTAGGCGCCGGAATTAGATCTACCA Bg1II-LC TGGAGACAGACAGAC SEQ ID NO: 2 3′LC-P2 GTTTGTTGCGCCGGATCCACACTCT CCCCTGTTGAA SEQ ID NO: 3 5′LC-P2 TTCAACAGGGGAGAGTGTGGATCCG GCGCAACAAAC SEQ ID NO: 4 3′P2-HC GCTGAGCCTGATGTCCATGGGTCCA GGATTCTCTTC SEQ ID NO: 5 5′P2-HC GAAGAGAATCCTGGACCCATGGACA TCAGGCTCAGC SEQ ID NO: 6 3′HC-TM GGATGGAGGAGGCTCGAGTTTACCC GGAGACAGGGA SEQ ID NO: 7 5′HC-TM TCCCTGTCTCCGGGTAAACTCGAGC CTCCTCCATCC SEQ ID NO: 8 3MIGR1- TTCGTTAACCTCGAGAGATCTTCAC Bg1II-TM GCTAGAGAATGAGG
TABLE-US-00003 TABLE 3 DNA sequence of each fragment of the surface displayed antibodies Antibody light chain DNA sequence (SEQ ID NO: 9) ATGGAGACAGACAGACTCCTGCTATGGGTGCTGCTGCTCTGGGTGCCAGG CTCCACTGGTGACACTGTACTGACCCAGTCTCCTGCTTTGGCTGTGTCTC CAGGAGAGAGGGTTACCATCTCCTGTAGGGCCAGTGACAGTGTCAGTACA CTTATGCACTGGTACCAACAGAAACCAGGACAGCAACCCAAACTCCTCAT CTATCTAGCATCACACCTAGAATCTGGGGTCCCTGCCAGGTTCAGTGGCA GTGGGTCTGGGACAGACTTCACCCTCACCATTGATCCTGTGGAGGCTGAT GACACTGCAACCTATTACTGTCAGCAGAGTTGGAATGATCCGTGGACGTT CGGTGGAGGCACCAAGCTGGAATTGAAACGAACTGTGGCTGCACCATCTG TCTTCATCTTCCCGCCATCTGATGAGCAGTTGAAATCTGGAACTGCCTCT GTTGTGTGCCTGCTGAATAACTTCTATCCCAGAGAGGCCAAAGTACAGTG GAAGGTGGATAACGCCCTCCAATCGGGTAACTCCCAGGAGAGTGTCACAG AGCAGGACAGCAAGGACAGCACCTACAGCCTCAGCAGCACCCTGACGCTG AGCAAAGCAGACTACGAGAAACACAAAGTCTACGCCTGCGAAGTCACCCA TCAGGGCCTGAGCTCGCCCGTCACAAAGAGCTTCAACAGGGGAGAGTGT Self-cleaving Linker P2A DNA sequence (SEQ ID NO: 10) GGATCCGGCGCAACAAACTTCTCTCTGCTGAAACAAGCCGGAGATGTCGA AGAGAATCCTGGACCC Antibody heavy chain DNA sequence (SEQ ID NO: 11) ATGGACATCAGGCTCAGCTTGGTTTTCCTTGTCCTTTTCATAAAAGGTGT CCAGTGTGAGGTGCAGCTGGTGGAGTCTGATGGAGGCTTAGTGCAGCCTG GAAGGTCCCTAAAACTCCCCTGTGCAGCCTCAGGATTCACTTTCAGTGAC TATTACATGGCCTGGGTCCGCCAGGCTCCAACGAAGGGGCTGGAGTGGGT CGCAAGCATTAGTTATGATGGTAGTAGCACTTACTATCGAGACTCCGTGA AGGGCCGATTCACTATCTCCAGAGATAATGCAAAAAGCACCCTATACCTG CAAATGGACAGTCTGAGGTCTGAGGACACGGCCACTTATTACTGCGGAAG ACACAGTAGCTACTTTGATTACTGGGGCCAAGGAGTCATGGTCACAGTCT CGAGCGCCTCCACCAAGGGCCCATCGGTCTTCCCCCTGGCGCCCTGCTCC AGGAGCACCTCCGAGAGCACAGCGGCCCTGGGCTGCCTGGTCAAGGACTA CTTCCCCGAACCGGTGACGGTGTCGTGGAACTCAGGCGCTCTGACCAGCG GCGTGCACACCTTCCCAGCTGTCCTACAGTCCTCAGGACTCTACTCCCTC AGCAGCGTGGTGACCGTGCCCTCCAGCAACTTCGGCACCCAGACCTACAC CTGCAACGTAGATCACAAGCCCAGCAACACCAAGGTGGACAAGACAGTTG AGCGCAAATGTTGTGTCGAGTGCCCACCGTGCCCAGCACCACCTGTGGCA GGACCGTCAGTCTTCCTCTTCCCCCCAAAACCCAAGGACACCCTCATGAT CTCCCGGACCCCTGAGGTCACGTGCGTGGTGGTGGACGTGAGCCACGAAG ACCCCGAGGTCCAGTTCAACTGGTACGTGGACGGCGTGGAGGTGCATAAT GCCAAGACAAAGCCACGGGAGGAGCAGTTCAACAGCACGTTCCGTGTGGT CAGCGTCCTCACCGTTGTGCACCAGGACTGGCTGAACGGCAAGGAGTACA AGTGCAAGGTCTCCAACAAAGGCCTCCCAGCCCCCATCGAGAAAACCATC TCCAAAACCAAAGGGCAGCCCCGAGAACCACAGGTGTACACCCTGCCCCC ATCCCGGGAGGAGATGACCAAGAACCAGGTCAGCCTGACCTGCCTGGTCA AAGGCTTCTACCCCAGCGACATCGCCGTGGAGTGGGAGAGCAATGGGCAG CCGGAGAACAACTACAAGACCACACCTCCCATGCTGGACTCCGACGGCTC CTTCTTCCTCTACAGCAAGCTCACCGTGGACAAGAGCAGGTGGCAGCAGG GGAACGTCTTCTCATGCTCCGTGATGCATGAGGCTCTGCACAACCACTAC ACGCAGAAGAGCCTCTCCCTGTCTCCGGGTAAA Transmembrane domain DNA sequence (SEQ ID NO: 12) CTCGAGCCTCCTCCATCCACTGTCTCCAACATGGCGACCGTTGCTGTTCT GGTTGTCCTTGGAGCTGCAATAGTCACTGGAGCTGTGGTGGCTTTTGTGA TGAAGATGAGAAGGAGAAACACAGGTGGAAAAGGAGGGGACTATGCTCTG GCTCCAGGCTCCCAGACCTCTGATCTGTCTCTCCCAGATTGTAAAGTGAT GGTTCATGACCCTCATTCTCTAGCGTGA
TABLE-US-00004 TABLE 4 Amino acid sequence of the surface display antibody and the related Fc region thereof Amino acid sequence of the human IgG2 anti-mouse CD40 surface displayed antibody (SEQ ID NO: 13): METDRLLLWVLLLWVPGSTGDTVLTQSPALAVSPGERVTISCRASDSVST LMHWYQQKPGQQPKLLIYLASHLESGVPARFSGSGSGTDFTLTIDPVEAD DTATYYCQQSWNDPWTFGGGTKLELKRTVAAPSVFIFPPSDEQLKSGTAS VVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTL SKADYEKHKVYACEVTHQGLSSPVTKSFNRGECGSGATNFSLLKQAGDVE ENPGPMDIRLSLVFLVLFIKGVQCEVQLVESDGGLVQPGRSLKLPCAASG FTFSDYYMAWVRQAPTKGLEWVASISYDGSSTYYRDSVKGRFTISRDNAK STLYLQMDSLRSEDTATYYCGRHSSYFDYWGQGVMVTVSSASTKGPSVFP LAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSS GLYSLSSVVTVPSSNFGTQTYTCNVDHKPSNTKVDKTVERKCCVECPPCP APPVAGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVQFNWYVDG VEVHNAKTKPREEQFNSTFRVVSVLTVVHQDWLNGKEYKCKVSNKGLPAP IEKTISKTKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEW ESNGQPENNYKTTPPMLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEA LHNHYTQKSLSLSPGKLEPPPSTVSNMATVAVLVVLGAAIVTGAVVAFVM KMRRRNTGGKGGDYALAPGSQTSDLSLPDCKVMVHDPHSLA Amino acid sequence of the Fc region of the human IgG2 anti-mouse CD40 surface displayed antibody (SEQ ID NO: 14): APPVAGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVQFNWYVDG VEVHNAKTKPREEQFNSTFRVVSVLTVVHQDWLNGKEYKCKVSNKGLPAP IEKTISKTKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEW ESNGQPENNYKTTPPMLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEA LHNHYTQKSLSLSPGK Amino acid sequence of the Fc CH2 domain of the human IgG2 anti-mouse CD40 surface displayed antibody (SEQ ID NO: 15): APPVAGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVQFNWYVDG VEVHNAKTKPREEQFNSTFRVVSVLTVVHQDWLNGKEYKCKVSNKGLPAP IEKTISKTK Amino acid sequence corresponding to the residues 233rd to 332nd of Fc region of IgG2 antibody according to Eu numbering (SEQ ID No: 20): PVAGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVQFNWYVDGVE VHNAKTKPREEQFNSTFRVVSVLTVVHQDWLNGKEYKCKVSNKGLPAPI
[0137] Construction of Fc-Mutant Library
[0138] Point mutation libraries are designed to introduce mutations through degenerate primers, and multiple degenerate primers are designed. For example, the degenerate primer used for the P233 point mutation is CCACCGTGCCCAGCACCANNSGTGGCAGGACCGTCAGTC (SEQ ID NO: 21). The mutant library fragment and the connection vector are obtained by PCR, and ligated by Multi One Step Cloning Kit (Yeasen Biotechnology (Shanghai) Co., Ltd., China) and transformed into DH5a to obtain a mutant library. For each library, 20 colonies were picked for sequencing to confirm whether a mutation was introduced at the target location.
[0139] The method for the combined mutation library is similar. The primers are designed according to the mutation type with enrichment which has been screened according to the point mutation library. The intermediate degenerate primer part is modified to be a primer sequence comprising a codon encoding a specific amino acid or a degenerate codon encoding several amino acids, for example, L328W (TGCAAGGTCTCCAACAAAGGCTGGCCAGCCCCCATCGAGAAAAC, SEQ ID NO: 22), Combine2_1 (ACGTGCGTGGTGGTGGACKNGWBGVASRWSSACCHGGAGGTCCAGTTC AACTGG, SEQ ID NO: 23).
[0140] In addition to the normal base, R in the above primers represents A/G, Y represents C/T, M represents A/C, K represents G/T, S represents G/C, W represents A/T, H represents A/T/C, B represents G/T/C, V represents G/A/C, D represents G/A/T, and N represents A/T/C/G.
[0141] Construction of Stably-Expressing Cell Lines
[0142] The library plasmid and the helper plasmid Phoenix-Eco (molar ratio 2:1) were mixed with transfection reagent PEI (mass ratio 1:5) and added into plated Phoenix cells (confluence 80%), changing fresh culture after 6 hours, and the supernatant containing retrovirus was collected after 48 hours. Plated 3T3 cells with a confluence of 80% prepared in advance were infected by 50% fresh medium plus 50% of the above retrovirus supernatant. The solution was changed after 24 hours. After 48 hours, the cell line stably expressing the antibody can be obtained.
[0143] Flow Cytometry Analysis of the Cell Lines Stably Expressing the Antibody
[0144] 3T3 cells were collected by trypsin digestion, and a single cell suspension was prepared. About 1-5*10.sup.6 cells were re-suspended in 50 μl FACS buffer (1×PBS containing 0.5% FBS and 2 mM EDTA) supplied with PE-F(ab′)2 Fragment Goat Anti-Human IgG (1:500, Jackson ImmunoResearch Laboratories) or Biotin-FcγRIIB (1 μg/ml, Sino Biological) and Streptavidin-APC (1:500, BD Biosciences). The cells were incubated for 15 minutes on ice and then washed twice with FACS buffer and re-suspended in 200 μl FACS buffer and analyzed by flow cytometry.
[0145] Sorting of Cells with High Affinity to FcγRIIB by Flow Cytometry
[0146] The staining system is amplified according to the above-mentioned flow cytometry analysis and staining method, and the cell is re-suspended to the final concentration of ˜1-5*10.sup.7 cells/ml before loading. Cells expressing IgG (strong PE fluorescence signal) and having high affinity to FcγRIIB (strong APC fluorescence signal) are sorted, and the proportion is controlled to be less than 1% of IgG positive cells.
[0147] Magnetic-Activated Sorting of Cells with High Affinity to FcγRIIB and Low Affinity to Activating FcγR (High I/A Ratio)
[0148] 3T3 cells were collected by trypsin digestion, and a single cell suspension was prepared. About 1*10.sup.7 cells were re-suspended in 50 μl MACS buffer (1×PBS containing 0.5% BSA and 2 mM EDTA) supplied with Biotin-FcγRIIB (1 μg/ml, Sino Biological) and activating FcγRs (including FcγRI, FcγRIIA.sup.131H, FcγRIIA.sup.131R, FcγRIIIA.sup.158V, FcγRIIIA.sup.158F, all for 1 μg/ml, Shanghai NOVOPROTEIN SCIENTIFIC INC.). The cells were incubated for 15 minutes on ice and then washed twice with MACS buffer and re-suspended in 100 μl MACS buffer. Twenty-five μl anti-Biotin magnetic beads were added, and the cells were incubated for 15 minutes on ice and then washed once with MACS buffer and re-suspended to 500 μl, and added to the LS column put in the magnetic field. The effluent was collected, washed with 3 mL of MACS buffer and collected; The LS column was then removed out of the magnetic field, and 5 mL of MACS buffer was used to rapidly elute the remaining cells from the sorting column to collect positive cells, which are the high I/A ratio cells.
[0149] High Throughput Sequencing Analysis
[0150] About 0.1-5*10.sup.6 cells of the target cell population were taken and subject to cell lysis genomic DNA extraction, PCR (amplification of Fc fragment). Library construction and high-throughput sequencing (PE 150 or PE 250) were performed, and about 60,000-300,000 sequences were obtained for each sample. The nucleotide sequences of the mutation region were extracted and translated into the corresponding amino acid sequences (http://www.cbs.dtu.dk/services/VirtualRibosome/, Rasmus Wernersson. Nucl. Acids Res. 2006 34: W385-W388). The proportion of each mutation sequence in each sample was calculated, and: the proportion of the mutation sequence=the mutation sequence count/the total sequence count.
[0151] Antibody Expression and Purification
[0152] An advantageous Fc mutant or a new combined mutant according to NGS is constructed into the heavy chain of the anti-human OX40 antibody, which is transiently transfected into HEK293S cells together with the corresponding light chain to express proteins. Protein G purification is performed to obtain different Fc mutant antibodies, and SDS-PAGE is used to confirm that all the antibody structures are intact. The anti-human OX40 antibody DNA sequence and protein sequence are shown in Table 5 and Table 6.
TABLE-US-00005 TABLE 5 DNA sequence of wild-type IgG2 anti-human OX40 antibody Antibody light chain DNA sequence (SEQ ID NO: 16) ATGGAAACCCCAGCGCAGCTTCTCTTCCTCCTGCTACTCTGGCTCCCAGA TACCACCGGAGAAATTGTGTTGACGCAGTCTCCAGGCACCCTGTCTTTGT CTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGC GGCGACTACTTAGCCTGGTACCAGCAGAAACTTGGCCAGGCTCCCAGGCT CCTCATCTATGGTGCATCCATCAGGGCCACTGGCATCCCAGACAGGTTCA GTGGCAGTGGGTCTGGGACAGACTTCACTCTCACCATCAGCAAACTGGAG CCTGAAGATTTTGCAGTGTATTACTGTCAGCAGTATGGTAGCTCACCGCT CACTTTCGGCGGAGGGACCAAGGTGGAGATCAAACGAACTGTGGCTGCAC CATCTGTCTTCATCTTCCCGCCATCTGATGAGCAGTTGAAATCTGGAACT GCCTCTGTTGTGTGCCTGCTGAATAACTTCTATCCCAGAGAGGCCAAAGT ACAGTGGAAGGTGGATAACGCCCTCCAATCGGGTAACTCCCAGGAGAGTG TCACAGAGCAGGACAGCAAGGACAGCACCTACAGCCTCAGCAGCACCCTG ACGCTGAGCAAAGCAGACTACGAGAAACACAAAGTCTACGCCTGCGAAGT CACCCATCAGGGCCTGAGCTCGCCCGTCACAAAGAGCTTCAACAGGGGAG AGTGTTGA Wild-type IgG2 antibody heavy chain DNA sequence (SEQ ID NO: 17) ATGAAACACCTGTGGTTCTTCCTCCTCCTGGTGGCAGCTCCCAGATGGGT CCTGTCTCAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTT CGGGGACCCTGTCACTCACCTGCGCTGTCTCTGGTGGCTCCATCAGCAGT AGTATCTGGTGGAGCTGGGTCCGCCAGCCCCCAGGGAAGGGGCTGGAATG GATTGGGGAAATCCATCATAGTGGGAACACCAACTGCAATCCGTCCCTCA AGAGTCGAGTCACCATATCAATAGACAAGTCCAAGAACCAGTTCTCCCTG AAACTGACCTCTGTGACCGCCGCGGACACGGCCGTATATTATTGTGCGAG AGCGGGAACTGGAACTACGCTTGACTACTGGGGCCAGGGAACCCTGGTCA CCGTCTCGAGCGCCTCCACCAAGGGCCCATCGGTCTTCCCCCTGGCGCCC TGCTCCAGGAGCACCTCCGAGAGCACAGCGGCCCTGGGCTGCCTGGTCAA GGACTACTTCCCCGAACCGGTGACGGTGTCGTGGAACTCAGGCGCTCTGA CCAGCGGCGTGCACACCTTCCCAGCTGTCCTACAGTCCTCAGGACTCTAC TCCCTCAGCAGCGTGGTGACCGTGCCCTCCAGCAACTTCGGCACCCAGAC CTACACCTGCAACGTAGATCACAAGCCCAGCAACACCAAGGTGGACAAGA CAGTTGAGCGCAAATGTTGTGTCGAGTGCCCACCGTGCCCAGCACCACCT GTGGCAGGACCGTCAGTCTTCCTCTTCCCCCCAAAACCCAAGGACACCCT CATGATCTCCCGGACCCCTGAGGTCACGTGCGTGGTGGTGGACGTGAGCC ACGAAGACCCCGAGGTCCAGTTCAACTGGTACGTGGACGGCGTGGAGGTG CATAATGCCAAGACAAAGCCACGGGAGGAGCAGTTCAACAGCACGTTCCG TGTGGTCAGCGTCCTCACCGTTGTGCACCAGGACTGGCTGAACGGCAAGG AGTACAAGTGCAAGGTCTCCAACAAAGGCCTCCCAGCCCCCATCGAGAAA ACCATCTCCAAAACCAAAGGGCAGCCCCGAGAACCACAGGTGTACACCCT GCCCCCATCCCGGGAGGAGATGACCAAGAACCAGGTCAGCCTGACCTGCC TGGTCAAAGGCTTCTACCCCAGCGACATCGCCGTGGAGTGGGAGAGCAAT GGGCAGCCGGAGAACAACTACAAGACCACACCTCCCATGCTGGACTCCGA CGGCTCCTTCTTCCTCTACAGCAAGCTCACCGTGGACAAGAGCAGGTGGC AGCAGGGGAACGTCTTCTCATGCTCCGTGATGCATGAGGCTCTGCACAAC CACTACACGCAGAAGAGCCTCTCCCTGTCTCCGGGTAAATGA
TABLE-US-00006 TABLE 6 Protein sequence of wild-type IgG2 anti-human OX40 antibody Antibody light chain protein sequence (SEQ ID NO: 18) METPAQLLFLLLLWLPDTTGEIVLTQSPGTLSLSPGERATLSCRASQSVS GDYLAWYQQKLGQAPRLLIYGASIRATGIPDRFSGSGSGTDFTLTISKLE PEDFAVYYCQQYGSSPLTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGT ASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC Wild-type IgG2 antibody heavy chain protein sequence (SEQ ID NO: 19) MKHLWFFLLLVAAPRWVLSQVQLQESGPGLVKPSGTLSLTCAVSGGSISS SIWWSWVRQPPGKGLEWIGEIHHSGNTNCNPSLKSRVTISIDKSKNQFSL KLTSVTAADTAVYYCARAGTGTTLDYWGQGTLVTVSSASTKGPSVFPLAP CSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLY SLSSVVTVPSSNFGTQTYTCNVDHKPSNTKVDKTVERKCCVECPPCPAPP VAGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVQFNWYVDGVEV HNAKTKPREEQFNSTFRVVSVLTVVHQDWLNGKEYKCKVSNKGLPAPIEK TISKTKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESN GQPENNYKTTPPMLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHN HYTQKSLSLSPGK
[0153] The Analysis of the Binding Properties of the Mutant Antibody to FcγR by Enzyme-Linked Immunosorbent Assay (ELISA)
[0154] One hundred μl (2 μg/mL) of antibody or mutant thereof were added to the enzyme-linked plate to be coated overnight, then the supernatant was discarded. The plate was blocked with PBS containing 1% BSA for 2 hours, and washed with PBST (PBS containing 0.05% Tween 20). Biotin-labeled FcγR extracellular domain protein (Beijing Sino Biological Co., Ltd) of appropriate concentration was added and incubated at room temperature for 1 hour, then the supernatant was discarded and the plate was washed with PBST. The Biotin-labeled protein was detected by incubating with Streptavidin-HRP (BD BioSciences) at room temperature for 1 hour. The supernatant was removed, and the color-developing solution was added for color development for 20-40 minutes to determine the absorbance of 650 nm (A650).
[0155] Immune Activation Activity Analysis (Promoting T Cell Proliferation) of Anti-Human OX40 Antibody with Different Antibody Fc Mutant In Vitro
[0156] Spleen was isolated from humanized FcγR/OX40 mouse to prepare a single cell suspension after lysing red blood cells. CFSE labeling was performed. Cells were re-suspended in PBS containing 5 μM CFSE to a concentration of 5*10.sup.6/mL and incubated at 37° C. for 15 minutes. Cells were then washed twice with 5% FBS-containing PBS and spun down at 600 g for 5 min, followed by re-suspending the cells with primary cell culture medium (RPMI+10% FBS+1% Pen/Strep+1% HEPES+1% Sodium Pyruvate+0.1% 2ME (final 50 μM)+1% L-glutamine+1% Non-essential A.A.) to a concentration of 3*10.sup.6/ml. Each well was added with 100 μl of cell suspension, i.e., 3*10.sup.5 cells per well. The (anti-hOX40) antibody concentrations were diluted to 2, 0.2 and 0.02 μg/ml, respectively, using the primary cell culture medium containing 0.2 μg/ml anti-CD3. One hundred μl of the prepared antibody mixture was transferred into the wells containing CFSE-labeled humanized FCγR/OX40 spleen cells. Two groups of controls were: CD3 only groups containing CFSE-labeled cells and anti-mouse CD3, but without any other antibodies; and CD3+CD28 groups containing CFSE-labeled cells and anti-mouse CD3 and 2 μg/mL of anti-mouse CD28 antibody (Clone 37.51 (RUO), BD Biosciences) (the final concentrations of anti-mouse CD3 and CD28 were 0.1 μg/ml and 1 μg/ml, respectively). The cells were incubated at 37° C. for 3 days in a 5% CO.sub.2 thermostatic cell incubator. After the culturing was finished, the cells were collected and analyzed for the number and proliferation of CD4.sup.+ and CD8.sup.+ cells by flow cytometry. Proliferation of T cells analyzed by flow cytometry: the cultured cells were transferred to a 96-well U bottom plate, washed twice with PBS, centrifuged at 500 g for 5 minutes, then the supernatant was discarded. The cells were re-suspended in 50 μl of FACS buffer (PBS containing 0.5% FBS, 2 mM EDTA) containing PE anti-Mouse CD4 (Clone: GK1.5, 1:500, BD) and APC anti-Mouse CD8a (Clone: 53-6.7, 1:500, BioLegend), incubated on ice in dark for 15 minutes, then washed twice with PBS buffer and re-suspended in 200 μl of FACS buffer containing DAPI (0.5 μg/ml, Invitrogen) and CountBright Absolute Counting Beads (Life Technologies, 2 μl/sample), and analyzed by flow cytometry.
[0157] The present disclosure mainly provides antibody Fc mutant sequences that enhance human IgG2 interaction with FcγRIIB Meanwhile, the present disclosure also provides a method for screening and obtaining these mutants. As shown in
[0158] Furthermore, screen amino acid mutations that enhance various protein-protein interactions or protein-other molecules interactions according to the above screening method provided by the present disclosure; a general screening method includes:
[0159] 1) providing a parent protein sequence, introducing amino acid mutations in the parent protein sequence by PCR;
[0160] 2) constructing the parent protein and the mutated protein into an expression vector to form a mutation library;
[0161] 3) transfecting the expression vector into mammalian cells, and expressing the parent protein and the mutated protein on the cell surface;
[0162] 4) incubating a labeled interacting protein and the mammalian cell, and selecting labeled mammalian cells by flow cytometry or magnetic-activated cell sorting;
[0163] 5) extracting DNAs from the labeled mammalian cells, sequencing the DNAs, and analyzing the change of the sequence proportions before and after sorting; and, the amino acid mutation in which the proportion after sorting is significantly higher than the proportion before sorting is an amino acid mutation capable of enhancing the binding affinity between the protein and the interacting protein.
Example 1: Construction of Human Antibody IgG2_Fc Point Mutation Library
[0164] Some sites on human IgG2 Fc CH2 are selected, including P233-S239, V266-P271, 5298-T299 and G327-I332 (Eu numbering, see
Example 2: Cell Enrichment after Flow Cytometry Sorting Relative to Before Sorting
[0165] After the plasmid library is successfully constructed, retrovirus is prepared to infect 3T3 cells, to obtain the cell lines stably expressing the libraries. The present disclosure uses flow cytometry sorting techniques to sort cells expressing human IgG2 (detected by anti-human IgG F(ab′)2) and binding human FcγRIIB
[0166] As shown in
Example 3: NGS Analysis of IgG2 Fc Mutation Types with Enhanced FcγRIIB Binding Affinity after Flow Cytometry Sorting
[0167] Mutations with the ratio of the proportion of sequence after sorting to the proportion before sorting increased to be greater than twice that of wild-type human IgG2 (enrichment factor/wild-type enrichment factor >2) are selected, i.e., mutations on human IgG2 which is beneficial to the improvement of the binding affinity of IgG2 to FcγRIIB (at least twice that of the wild-type enrichment factor), see Table 7. For example, the proportion of L328W before sorting is 0.39%, and the proportion after sorting is 12.84%, therefore the enrichment factor is 33.20, which is 22.21 times the wild-type enrichment factor (1.49).
TABLE-US-00007 TABLE 7 Mutations in human IgG2 which is beneficial to the improvement of the binding affinity of IgG2 to FcγRIIB Enrichment factor Increased Percentage factor after Enrichment sorting/ factor/ Before sorting After sorting percentage wild-type Per- Per- before enrichment NO. Mutation count centage Count centage sorting factor Library2 #1 Wild-type 12137 11.34 7266 6.51 0.57 1.00 1 S267Q 410 0.38 3693 3.31 8.64 15.05 2 S267A 744 0.70 2457 2.20 3.17 5.52 3 S267D 513 0.48 1128 1.01 2.11 3.67 4 S267M 794 0.74 1223 1.10 1.48 2.57 5 S267G 10 0.00 27 0.01 1.79 3.50 6 H268E 319 0.30 561 0.50 1.69 2.94 7 H268D 221 0.21 355 0.32 1.54 2.68 8 H268K 421 0.39 581 0.52 1.32 2.31 9 P271C 893 0.83 15969 14.30 17.14 29.87 10 V266A/P271C 5 0.00 220 0.20 42.18 73.50 11 V266A/P271G 3 0.00 27 0.02 8.63 15.03 12 S267A/P271C 3 0.00 117 0.10 37.39 65.14 13 S267A/P271G 2 0.00 11 0.01 5.27 9.19 14 S267E/D270H 2 0.00 89 0.08 42.66 74.33 15 S267E/P271C 2 0.00 2089 1.87 1001.34 1744.71 16 S267E/P271V 2 0.00 46 0.04 22.05 38.42 17 S267E/P271W 2 0.00 50 0.04 23.97 41.76 18 S267E/P271Y 4 0.00 80 0.07 19.17 33.41 19 S267M/P271C 2 0.00 67 0.06 32.12 55.96 20 S267M/P271G 2 0.00 9 0.01 4.31 7.52 21 V266G/P271C 3 0.00 12 0.01 3.83 6.68 Library4 #2 wild-type 14727 16.91 17343 25.27 1.49 1.00 22 G327A 713 0.82 2838 4.13 5.05 3.38 23 L328F 3 0.00 1332 1.94 563.47 377.03 24 L328W 337 0.39 8815 12.84 33.20 22.21 25 L328Y 50 0.06 133 0.19 3.38 2.26 26 G327A/A330R 2 0.00 155 0.23 98.35 65.81 27 G327A/A330V 2 0.00 11 0.02 6.98 4.67 28 G327A/I332A 2 0.00 46 0.07 29.19 19.53 29 G327A/I332C 1 0.00 9 0.01 11.42 7.64 30 G327A/I332E 1 0.00 99 0.14 125.64 84.07 31 L328E/I332T 10 0.01 434 0.63 55.08 36.85 LibraryMix #3 wild-type 91423 29.03 119849 21.72 0.75 1.00 32 S267E 259 0.08 98580 17.86 217.23 290.34 33 S267R 6 0.00 16 0.00 1.52 2.03 34 P271G 1132 0.36 136659 24.77 68.90 92.09 35 P271Q 218 0.07 631 0.11 1.65 2.21 36 S298L 2696 0.86 10298 1.87 2.18 2.91 37 L328M 14 0.00 611 0.11 24.91 33.29 38 S267V/S298L 9 0.00 33 0.01 2.09 2.80 39 S267E/S298R 7 0.00 402 0.07 32.78 43.81 40 P271A/S298R 7 0.00 30 0.01 2.45 3.27 41 P271G/G236V 6 0.00 108 0.02 10.27 13.73 42 P271G/P329S 7 0.00 567 0.10 46.23 61.79 43 P271G/P331C 7 0.00 1717 0.31 139.99 187.11 44 P271G/P331T 12 0.00 680 0.12 32.34 43.23 45 P271G/S298D 8 0.00 95 0.02 6.78 9.06 46 P271G/S298E 10 0.00 5218 0.95 297.81 398.04 47 P271G/S298G 20 0.01 341 0.06 9.73 13.01 48 P271G/S298K 6 0.00 107 0.02 10.18 13.60 49 P271G/S298L 13 0.00 4286 0.78 188.17 251.50 50 P271G/S298N 8 0.00 252 0.05 17.98 24.03 51 P271G/S298R 18 0.01 504 0.09 15.98 21.36 52 P271G/T299A 23 0.01 253 0.05 6.28 8.39 53 P271G/T299M 10 0.00 83 0.02 4.74 6.33 54 P271G/T299S 6 0.00 126 0.02 11.99 16.02 55 P271G/T299W 6 0.00 97 0.02 9.23 12.33 #1-3: Data from the experiments of Library 2 (#1), Library 4 (#2), LibraryMix (#3).
[0168] In addition to single point mutation, some double mutations were also obtained, and the ratios of these amino acid mutations after flow cytometry sorting to that before sorting are increased by more than twice as compared to the wild-type human IgG2. The double mutation combination (V266A/P271C or G, S267A/P271C or G, S267E/D270H, S267E/P271C or V or W or Y, S267E/S298R, S267M/P271C or G, P271A/S298R, P271G/G236V, P271G/G329S, P271G/P331C or T, P271G/S298D or E or G or K or L or N or R, P271G/T299A or M or S or W, G327A/A330R or V, G327A/I332A or C or E, L328E/I332T, etc.) has a higher increased factor (ratio) than any point mutation thereof, indicating that both amino acids in the mutation combination contribute to the increase in the binding affinity to FcγRIIB In addition, mutation combinations such as S267V/S298L provide an increased factor approximately equal to S298L mutation, which has a higher increased factor over S267V, indicating that the improvement of the mutation combination is basically only the contribution of S298L, rather than the other point mutation, as shown in Table 8. Therefore, in addition to the amino acid mutation provided by the present disclosure, the Fc region, the antibody, the Fc fragment or the fusion protein of the present disclosure may further include other possible combinations or modifications.
TABLE-US-00008 TABLE 8 Double mutations on human IgG2 which is beneficial to the improvement of the binding affinity of IgG2 to FcγRIIB Enrichment factor Increased Percentage factor .sup.a after Enrichment sorting/ factor/ percentage wild-type Increased Increased before enrichment factor .sup.b factor 2 .sup.c NO. Mutation sorting factor Site 1 Site 2 Site 1 Site 2 1 V266A/P271C 42.18 73.5 3.1 29.9 24.1 2.5 2 V266A/P271G 8.63 15.03 3.1 4.7 4.9 3.2 3 S267A/P271C 37.39 65.14 5.5 29.9 11.8 2.2 4 S267A/P271G 5.27 9.19 5.5 4.7 1.7 1.9 5 S267E/D270H 42.66 74.33 28.5 1.3 2.6 56.7 6 S267E/P271C 1001.34 1744.71 28.5 29.9 61.2 58.4 7 S267E/P271V 22.05 38.42 28.5 0.7 1.4 52.6 8 S267E/P271W 23.97 41.76 28.5 0.4 1.5 101.9 9 S267E/P271Y 19.17 33.41 28.5 1.0 1.2 33.4 10 S267E/S298R 32.78 43.81 28.5 0.8 1.5 56.2 12 S267M/P271C 32.12 55.96 2.6 29.9 21.8 1.9 13 S267M/P271G 4.31 7.52 2.6 4.7 2.9 1.6 14 P271A/S298R 2.45 3.27 0.1 0.8 54.5 4.2 15 P271G/G236V 10.27 13.73 4.7 0.5 2.9 30.5 16 P271G/P329S 46.23 61.79 4.7 1.2 13.1 52.8 17 P271G/P331C 139.99 187.11 4.7 0.2 39.6 779.6 18 P271G/P331T 32.34 43.23 4.7 0.1 9.1 480.3 19 P271G/S298D 6.78 9.06 4.7 1.6 1.9 5.5 20 P271G/S298E 297.81 398.04 4.7 7.1 84.2 56.0 21 P271G/S298G 9.73 13.01 4.7 1.2 2.8 10.7 22 P271G/S298K 10.18 13.6 4.7 4.4 2.9 3.1 23 P271G/S298L 188.17 251.5 4.7 2.9 53.2 86.4 24 P271G/S298N 17.98 24.03 4.7 2.3 5.1 10.5 25 P271G/S298R 15.98 21.36 4.7 0.8 4.5 27.4 26 P271G/T299A 6.28 8.39 4.7 0.4 1.8 20.5 27 P271G/T299M 4.74 6.33 4.7 1.0 1.3 6.1 28 P271G/T299S 11.99 16.02 4.7 0.6 3.4 25.0 29 P271G/T299W 9.23 12.33 4.7 0.5 2.6 23.3 30 G327A/A330R 98.35 65.81 3.4 0.0 19.5 21936.7 31 G327A/A330V 6.98 4.67 3.4 1.0 1.4 4.8 32 G327A/I332A 29.19 19.53 3.4 16.4 5.8 1.2 33 G327A/I332C 11.42 7.64 3.4 2.7 2.3 2.9 34 G327A/I332E 125.64 84.07 3.4 1.1 24.9 79.3 35 L328E/I332T 55.08 36.85 0.1 1.6 335.0 22.6 .sup.a Ratio of mutant enrichment factor/wild-type enrichment factor after sorting. .sup.b Ratio of mutant enrichment factor/wild-type enrichment factor after sorting regarding the original point mutation. .sup.c Ratio of increase factor of combined mutation/increase factor of one point mutation.
Example 4: Analysis of Favorable Mutant Types by NGS after Magnetic-Activated Sorting
[0169] The high-FcγRIIB-affinity cells obtained from the above flow cytometry sorting are further sorted by magnetic-activated sorting. The cells are incubated with the mixture of Biotin-labeled FcγRIIB and non-labeled activating FcγRs, and then the labeled cells are sorted by anti-Biotin magnetic beads. The enrichment ratios after sorting relative to before sorting are analyzed by NGS. Mutations with a higher I/A ratio can be screened, as shown in Table 9. Mutations are selected according to the following criteria: the ratio of the mutation after sorting to that before sorting is increased by more than twice as compared to the wild-type human IgG2, and the proportion of the mutation is decreased in the sorting portion not binding to magnetic bead (i.e., the outflow liquid passing the LS column).
TABLE-US-00009 TABLE 9 Mutations in human IgG2 leading to the improvement of the binding affinity of human IgG2 to FcγRIIB, and showing lower binding affinity of human IgG2 to the activating FcγRs than that to FcγRIIB Enrichment Increased Comparison before factor factor and after sorting Percentage Mutation Portion not Percentage Percentage after enrichment binding to after before sorting/ factor/ Before sorting magnetic bead After sorting sorting/ sorting/ percentage wild-type Percen- Percen- Percen- unbinding unbinding before enrichment NO. Mutation Count tage Count tage Amount tage percentage percentage sorting factor Library2 #1 Wild- 2838 3.60 5139 5.15 2509 2.98 0.58 0.70 0.83 1.00 type 1 S267N 66 0.08 NA NA 205 0.24 — — 2.91 3.51 2 S267W 89 0.11 4 0 177 0.21 52.49 28.16 1.86 2.25 3 H268N 226 0.29 1 0 558 0.66 661.97 286.03 2.31 2.79 4 P271A 61 0.08 3 0 180 0.21 71.18 25.73 2.77 3.33 5 P271I 311 0.39 NA NA 873 1.04 — — 2.63 3.17 6 P271L 51 0.06 2 0 241 0.29 142.95 32.27 4.43 5.34 7 P271S 64 0.08 10 0.01 187 0.22 22.18 8.1 2.74 3.3 8 P271V 246 0.31 1 0 923 1.1 1094.98 311.35 3.52 4.24 Library4 #2 Wild- 11937 14.33 16838 14.78 13554 12.62 0.85 0.97 0.88 1.00 type 9 G327L 14 0.02 19 0.02 68 0.06 3.8 1.01 3.77 4.28 10 G327S 83 0.1 11 0.01 738 0.69 71.16 10.32 6.9 7.84 11 L328N 109 0.13 8 0.01 384 0.36 50.91 18.63 2.73 3.11 LibraryMix #3 Wild- 14919 19.10 20509 20.31 21855 21.53 1.06 0.94 1.13 1.00 type 12 L328G 12 0.02 NA NA 47 0.05 — — 3.01 2.67 13 L328R 18 0.02 4 0 124 0.12 30.84 5.82 5.3 4.69 14 L328V 17 0.02 2 0 51 0.05 25.37 10.99 2.31 2.04 15 P271G/ 8 0.01 2 0 24 0.02 11.94 5.17 2.31 2.04 S298N 16 H268S 30 0.04 NA NA 306 0.3 — — 7.85 6.95 #4 Wild- 14919 19.10 20860 18.89 18101 17.95 0.95 1.01 0.94 1.00 type 17 P238Q/ 40 0.05 48 0.04 191 0.19 4.36 1.18 3.7 3.93 S267E 18 S267E/ 27 0.03 30 0.03 169 0.17 6.17 1.27 4.85 5.16 P329R 19 P271G/ 28 0.04 7 0.01 102 0.1 15.96 5.66 2.82 3 I332L 20 S267E 13 0.02 1 0 48 0.05 52.56 18.38 2.86 3.04 21 P271G 11 0.01 3 0 52 0.05 18.98 5.18 3.66 3.89 22 L328W 18 0.02 NA NA 99 0.1 — — 4.26 4.53 23 L328A 28 0.04 NA NA 116 0.12 — — 3.21 3.41 24 L328P 29 0.04 3 0 81 0.08 29.57 13.67 2.16 2.3 NA: In the sample of the column, the mutation of the row is not detected. #1-#4: Data from Library 2 (#1), Library 4 (#2), and two experiments of LibraryMix (#3, #4).
[0170] The affinity of human IgG1 to FcγRIIB can be increased by G236D, S239D (Seung Y Chu et al. Molecular Immunology 45 (2008) 3926-3933) and S298A mutation (US20090042291A1). However, in the results of NGS analysis of the present disclosure, the proportion of the IgG2 variant comprising G236D or S298A after sorting is not increased, but decreased (Table 10); the proportion of the human IgG2 variant containing S239D before sorting is 0.026%, and is not detected after sorting. These results demonstrate that G236D, S239D, and S298A mutations do not increase the FcγRIIB binding affinity of human IgG2, see Table 10.
TABLE-US-00010 TABLE 10 The effect of the known mutation on the binding affinity of IgG2 to FcγR cannot be directly predicted according to the effect of the mutation on the binding affinity of IgG1 to FcγR. Enrichment factor Before sorting After sorting Percentage after Percen- Percen- sorting/percentage NO. Mutant Count tage Count tage before sorting 1 S298A 4221 4.05 4205 3.72 0.92 2 S239D 29 0.03 0 NA — 3 G236D 511 0.46 427 0.39 0.84 NA: The mutant of the row is not detected in the experiment of the column, and the percentage and factor cannot be calculated.
Example 5: Amino Acid Mutations in Human IgG2 Fc Polypeptide Fragments which can Enhance the Affinity to FcγRIIB
[0171] Table 11 summarizes the amino acid mutations capable of enhancing affinity to FcγRIIB screened by the point mutation library screening method according to the present disclosure. Compared with patents in the prior art, it has been found that the sites S267G and P271C of the present disclosure are both new mutation types on human IgG2 that can improve the binding affinity to FcγRIIB The sites H268S, L328A and G327A are all new mutation types on human IgG2 that improve the binding affinity to FcγRIIB and show lower affinity to other activating FcγRs than that to FcγRIIB
TABLE-US-00011 TABLE 11 Amino acid mutations in human IgG2 that enhance the affinity to FcγRIIB Mutation site Original (Eu num- amino Amino acid mutation bering) acid enhancing affinity to FcγRIIB 267 S E Q A D M G R V N W 268 H E D K N S 271 P C G Q V W Y A I L S 327 G A L S 328 L F M W Y E A G N P R V
Example 6: Construction of Human Antibody IgG2_Fc Combined Mutation Library
[0172] According to the Fc mutation type capable of increasing the affinity to FcγRIIB (the mutation having a higher enrichment factor by more than 1 time over wild-type) screened by the above point mutation libraries and the high-throughput sequencing results, two types of combined mutation library were designed. Type I: combined point mutations among four regions, i.e., regions P233-V240, V266-P271, S298-T299 and G327-I332 each have 0-1 mutation, and the combined mutation contains 0-4 point mutations. Type II: combined mutation of multiple amino acids in one region, i.e., regions P233-V240, V266-P271, S298-T299 or G327-I332 has combined mutation within each region (respectively 0-7, 0-6, 0-2 and 0-6 combined mutations), as shown in
Example 7: Cell Enrichment Before and After Flow Cytometry Sorting for Combined Mutation Library
[0173] According to point mutation screening and high-throughput sequencing results, Type I and Type II combined mutation libraries are constructed (Example 6), and the cell libraries expressing the combined mutation are obtained. Then flow cytometry is used for sorting the cells with high affinity to FcγRIIB for two to three rounds. As shown in
[0174] As shown in
Example 8: NGS Analysis of IgG2 Fc Combined Mutation Showing Enhanced FcγRIIB Binding Affinity after Flow Cytometry Sorting
[0175] In order to screen the IgG2 Fc combined mutation type with increased binding affinity to FcγRIIB, the combined mutant library constructed in the present disclosure is subjected to flow cytometry sorting to obtain cells with higher binding affinity to FcγRIIB, then the enrichment factor of each mutation type after sorting relative to before sorting is analyzed by NGS. The result is shown in Table 12. The screened mutation has a higher enrichment factor (after the last round of sorting/before sorting), or shows a significant enrichment in at least one round of sorting (after said round of sorting/before said round of sorting), or is only detected after the last round of sorting. For example, the enrichment factor of V266L/S298L/L328W is 21920.33 times of the wild type (after the last round of sorting/before sorting); the enrichment factor of the point mutation L328W is 8.78 times of the wild type (after the last round of sorting/before sorting); the enrichment factors of H268D/S298L/L328W are 43.98 (after the second round of sorting/before the second round of sorting) and 5.95 (after the third round of sorting/before the third round of sorting); the enrichment factor of V234M/S267E/S298L/L328W is 5.13 (after third round sorting/before third round sorting); V234Q/A235G/P238L/S239V/G327A/L328E/A330S/I332T is only detected after the last round of sorting.
TABLE-US-00012 TABLE 12 Mutations on human IgG2 screened from the combined mutation library, which are beneficial to the improvement of the binding affinity of IgG2 to FcγRIIB Enrichment factor Increased factor Percentage Percentage Percentage Mutant after 2nd after 1st after 2nd enrichment Percentage sorting/ sorting/ sorting/ factor/ After After percentage percentage percentage wild-type 2nd 1st Before after before before enrichment NO. sorting sorting sorting 1st sorting sorting sorting factor #1 WT 54.22 61.56 63.83 0.88 0.96 0.85 1.00 1 L328W 1.05 0.25 0.14 4.26 1.75 7.46 8.78 2 S267E/A330S 0.03 0.00 NA 43.11 — — — 3 S267E/S298G 0.25 0.01 0.00 19.16 9.16 175.56 206.66 4 P233G/S267E 0.05 0.01 0.00 5.47 3.31 18.10 21.31 5 P233G/S267E/S298G 0.20 0.01 0.00 38.49 7.13 274.31 322.90 #2 WT 47.81 58.39 56.60 0.82 1.03 0.84 1.00 6 V266L/S267E/ 0.25 NA NA — — — — H268S/P271V 7 V234Q/A235G/ 0.15 NA NA — — — — P238L/S239V/ G327A/L328E/ A330S/I332T 8 V234Q/A235G/ 0.07 NA NA — — — — P238L/S239V/ S267E/H268S/ E269D 9 S267E/H268S/ 5.78 0.07 0.00 83.65 80.49 6733.01 7971.36 E269D Percentage Percentage Percentage Percentage Mutant after 3rd after 2nd after 1st after 3rd enrichment/ sorting/ sorting/ sorting/ sorting/ factor After After After percentage percentage percentage percentage wild-type 3rd 2nd 1st Before after 2nd after 1st before before enrichment sorting sorting sorting sorting sorting sorting sorting sorting factor #3 WT 0.40 1.03 1.32 1.07 0.39 0.78 1.24 0.38 1.00 10 H268D/S298L/ 1.25 0.21 0.00 NA 5.95 43.98 — — — L328W 11 V266L/L328W 1.20 0.22 0.00 0.00 5.53 53.28 4.71 1386.84 3695.56 12 V266L/S298L/ 24.98 4.14 0.06 0.00 6.03 64.77 21.07 8226.06 21920.33 L328W 13 S267V/S298L/ 0.90 0.13 0.00 0.00 7.21 73.61 3.92 2081.88 5547.67 L328W 14 S239V/V266L/ 0.33 0.07 0.00 NA 5.02 39.07 — — — S298L/L328W 15 A235W/V266L/ 0.22 0.05 0.00 NA 4.67 70.06 — — — S298L/L328W 16 P233F/V266L/ 0.29 0.16 0.00 NA 1.79 94.73 — — — S298L/L328W 17 S267V/S298G/ 0.19 0.03 0.00 NA 5.76 47.36 — — — L328W 18 V234M/S267E/ 0.53 0.10 NA NA 5.13 — — — — S298L/L328W 19 V234M/S267E/ 0.30 0.46 0.01 0.00 0.66 64.37 16.47 695.04 1852.11 S298G/I332L #4 WT 12.58 5.25 2.51 8.97 2.40 2.09 0.28 1.40 1.00 20 V266L/S267E/H 6.76 0.95 0.25 0.00 7.11 3.84 60.52 1651.90 1178.72 268S/E269A/P271C 21 V266L/S267E/ 4.15 2.13 0.17 0.00 1.95 12.85 99.90 2501.18 1784.72 H268S/E269V 22 V266L/S267E/ 0.11 0.01 0.00 NA 12.64 6.97 — — — H268S/E269V/ P271C 23 V266L/S267E/ 1.23 0.24 0.03 0.00 5.20 9.34 32.69 1588.00 1133.12 H268S/E269G/ P271T 24 V266L/S267D/ 1.88 0.49 0.12 0.00 3.80 4.07 121.76 1882.93 1343.57 H268D/E269D/ P271Q 25 V266L/S267E/ 1.22 0.42 0.14 0.00 2.94 2.92 214.29 1838.25 1311.69 E269K/P271G 26 V234Q/V266L/ 0.04 0.00 NA NA 15.39 — — — — S267D/H268D/ E269D/P271Q 27 V234Q/V266L/ 0.09 0.01 NA NA 11.37 — — — — S267E/H268S/ E269V 28 V266L/S267M/ 13.35 17.07 2.59 0.01 0.78 6.60 229.11 1182.52 843.79 H268E/P271Q #1-4: Data from the experiments of Libraries IgG2_C01 (#1), IgG2_C02 (#2), Cmix (#3), C2 (#4). NA: In the sample of the column, the mutation of the row is not detected.
Example 9: The Binding Property of Mutant Antibodies to FcγR Analyzed by Enzyme-Linked Immunosorbent Assay (ELISA)
[0176] On the basis of the favored Fc single-point mutation and combined mutation screened above by NGS, new Fc mutation combinations are constructed. Anti-human OX40 antibodies containing these new Fc mutation combinations are expressed and the binding property of the mutant antibody to FcγR are analyzed by Enzyme-linked immunosorbent assay (ELISA).
TABLE-US-00013 TABLE 13 Binding of different IgG2 antibody Fc mutants to FcγR. Relative binding affinity Increased factor of RIIB binding com- pared with wild- Absorbance value RI/ RIIAH/ RIIAR/ RIIB/ type RIIIAF/ RIIIAV/ RIIB/ RI RIIAH RIIAR RIIB RIIIAF RIIIAV G1 G1 G1 G1 IgG2 G1 G1 RIIAR IgG1 2.66 0.57 0.26 0.76 0.19 0.96 IgG2 0.08 0.49 0.08 0.08 0.06 0.05 0.03 0.85 0.29 0.10 1.00 0.30 0.06 0.34 IgG2 0.08 0.04 0.04 0.07 0.06 0.06 0.03 0.08 0.16 0.09 0.93 0.31 0.06 0.57 N297A Mut 1 0.17 0.35 0.22 0.64 0.07 0.09 0.06 0.62 0.83 0.85 8.51 0.38 0.09 1.02 Mut 2 0.14 0.32 0.29 1.00 0.07 0.06 0.05 0.56 1.09 1.33 13.38 0.38 0.06 1.21 Mut 3 0.18 0.34 0.23 0.94 0.08 0.07 0.07 0.60 0.87 1.25 12.57 0.40 0.08 1.44 Mut 4 0.25 0.48 1.44 1.92 0.06 0.05 0.10 0.84 5.51 2.54 25.55 0.32 0.06 0.46 Mut 5 0.38 0.46 0.46 1.18 0.06 0.06 0.14 0.81 1.77 1.56 15.69 0.31 0.07 0.88 Mut 6 0.09 0.05 0.05 0.50 0.06 0.06 0.03 0.08 0.19 0.66 6.63 0.30 0.06 3.52 Mut 7 0.13 0.38 0.23 0.58 0.07 0.06 0.05 0.67 0.87 0.76 7.70 0.38 0.07 0.88 Mut 8 0.14 0.52 0.34 1.07 0.08 0.07 0.05 0.90 1.30 1.42 14.30 0.44 0.07 1.09 Mut 9 0.12 0.20 0.74 1.20 0.07 0.07 0.05 0.34 2.83 1.59 15.99 0.38 0.08 0.56 Mut_10 0.18 0.58 0.43 1.05 0.09 0.09 0.07 1.02 1.64 1.40 14.06 0.48 0.09 0.85 Mut_11 0.13 0.55 0.36 1.01 0.08 0.08 0.05 0.96 1.36 1.33 13.40 0.41 0.08 0.98 Mut_12 0.21 0.39 0.33 0.94 0.06 0.06 0.08 0.68 1.26 1.25 12.57 0.32 0.06 0.99 Mut_13 0.18 0.33 0.26 0.73 0.07 0.08 0.07 0.58 1.01 0.97 9.75 0.37 0.09 0.96 Mut 14 0.12 0.12 0.32 0.70 0.06 0.05 0.04 0.21 1.22 0.93 9.36 0.31 0.06 0.76 Mut_15 0.08 0.04 0.04 0.47 0.06 0.05 0.03 0.07 0.17 0.62 6.21 0.31 0.06 3.67 Mut_16 0.10 0.39 0.50 1.09 0.06 0.06 0.04 0.68 1.92 1.44 14.51 0.32 0.06 0.75 Mut_17 0.14 0.54 0.50 1.19 0.09 0.06 0.05 0.95 1.90 1.58 15.93 0.49 0.06 0.83 Mut_18 0.14 0.38 0.26 0.78 0.09 0.08 0.05 0.67 1.00 1.04 10.43 0.47 0.09 1.03 Mut_19 0.11 0.33 0.28 0.82 0.07 0.07 0.04 0.58 1.08 1.09 10.96 0.38 0.07 1.00 Mut_20 0.12 0.48 0.46 1.13 0.06 0.05 0.05 0.85 1.76 1.50 15.08 0.31 0.06 0.85 Mut_21 0.16 0.09 0.11 0.32 0.06 0.06 0.06 0.16 0.41 0.42 4.23 0.31 0.06 1.03 Mut_22 0.12 0.33 0.31 0.93 0.06 0.07 0.05 0.57 1.17 1.22 12.33 0.33 0.07 1.05 Mut_23 0.11 0.43 0.38 0.97 0.07 0.06 0.04 0.75 1.44 1.29 12.96 0.35 0.06 0.90 Mut_24 0.12 0.48 0.35 1.00 0.08 0.08 0.05 0.84 1.35 1.32 13.33 0.42 0.08 0.98 Mut_25 0.12 0.06 0.30 0.86 0.07 0.05 0.05 0.10 1.13 1.14 11.49 0.36 0.06 1.01 Mut_26 0.19 0.06 0.08 0.55 0.08 0.09 0.07 0.11 0.32 0.72 7.28 0.41 0.09 2.24 Mut_27 0.18 0.48 0.28 0.70 0.09 0.10 0.07 0.84 1.06 0.92 9.29 0.49 0.11 0.87 Mut_28 0.13 0.14 0.35 0.88 0.08 0.08 0.05 0.24 1.35 1.17 11.76 0.44 0.08 0.87 Mut_30 0.12 0.18 0.26 0.80 0.06 0.06 0.05 0.32 1.01 1.06 10.65 0.33 0.07 1.05 Note: RI, RIIAH, RIIAR, RIIB, RIIIAF, RIIIAV respectively represent FcγRI, FcγRIIA.sup.131H, FcγRIIA.sup.131R, FcγRIIB, FcγRIIIA.sup.158F, FcγRIIIA.sup.158V.
Example 10: Beneficial Mutations Support Stronger Immune Activation Activity
[0177] The immune activation activity of the anti-human OX40 antibody (Example 9) containing the beneficial mutation is analyzed in the FCγR/OX40 humanized mouse spleen cells.
TABLE-US-00014 TABLE 14 Immunostimulatory activity analysis of anti-human OX40 antibodies containing different Fc mutations Experiment 2 Average increased factor Experiment 1 of the CFSE CFSE activity fluorescence fluorescence Relative Average over intensity Relative activity intensity activity relative wild-type 1 0.1 0.01 1 0.1 0.01 Average 1 0.1 1 0.1 Average activity IgG2 μg/ μg/ μg/ μg/ μg/ μg/ relative μg/ μg/ μg/ μg/ relative of two of two ml ml ml ml ml ml activity ml ml ml ml activity experiments experiments CD3 + CD28 509 473 491 0.97 1.03 1.00 1.00 965 965 1.00 1.00 1.00 1.00 Mut_1 799 786 894 0.44 0.47 0.27 0.39 1552 2062 0.69 0.42 0.56 0.46 10.48 Mut_2 677 654 685 0.66 0.71 0.65 0.67 1149 1548 0.90 0.69 0.80 0.72 16.51 Mut_3 686 568 761 0.65 0.86 0.51 0.67 1365 1769 0.79 0.58 0.68 0.68 15.47 Mut_4 769 616 695 0.50 0.77 0.63 0.63 1439 1702 0.75 0.61 0.68 0.65 14.91 Mut_5 791 695 859 0.46 0.63 0.33 0.47 1309 1660 0.82 0.63 0.73 0.58 13.14 Mut_6 706 689 766 0.61 0.64 0.50 0.59 1698 1986 0.61 0.46 0.54 0.57 12.94 Mut_7 741 755 850 0.55 0.52 0.35 0.47 1347 1819 0.80 0.55 0.67 0.55 12.66 Mut_8 799 719 844 0.44 0.59 0.36 0.46 1436 1813 0.75 0.55 0.65 0.54 12.32 Mut_9 744 742 849 0.54 0.55 0.35 0.48 1454 1909 0.74 0.50 0.62 0.54 12.27 Mut_10 765 743 788 0.50 0.54 0.46 0.50 1465 2048 0.74 0.43 0.58 0.54 12.23 Mut_11 783 831 782 0.47 0.39 0.47 0.44 1359 1868 0.79 0.52 0.66 0.53 12.10 Mut_12 762 689 906 0.51 0.64 0.25 0.47 1319 2085 0.81 0.41 0.61 0.52 11.99 Mut_13 802 728 899 0.44 0.57 0.26 0.42 1446 1865 0.75 0.53 0.64 0.51 11.62 Mut_14 793 775 839 0.45 0.49 0.37 0.44 1581 1899 0.68 0.51 0.59 0.50 11.40 Mut_15 691 707 837 0.64 0.61 0.37 0.54 1826 2253 0.55 0.32 0.43 0.50 11.37 Mut_16 783 770 853 0.47 0.50 0.35 0.44 1487 2158 0.72 0.37 0.55 0.48 11.01 Mut_17 775 788 841 0.49 0.46 0.37 0.44 1557 2120 0.69 0.39 0.54 0.48 10.95 Mut_18 776 828 838 0.48 0.39 0.37 0.42 1535 2135 0.70 0.38 0.54 0.47 10.65 Mut_19 824 735 880 0.40 0.56 0.30 0.42 1672 2089 0.63 0.41 0.52 0.46 10.46 Mut_20 774 844 828 0.49 0.36 0.39 0.41 1610 2161 0.66 0.37 0.51 0.45 10.37 Mut_21 782 711 920 0.47 0.60 0.22 0.43 1814 2194 0.55 0.35 0.45 0.44 10.08 Mut_22 NA NA NA — — — — 1791 2290 0.56 0.30 0.43 0.43 9.90 Mut_23 843 777 898 0.36 0.48 0.26 0.37 1600 2161 0.67 0.37 0.52 0.43 9.80 Mut_24 816 812 912 0.41 0.42 0.24 0.36 1654 2052 0.64 0.43 0.53 0.43 9.75 Mut_25 779 778 895 0.48 0.48 0.27 0.41 1827 2209 0.55 0.34 0.45 0.42 9.69 Mut_26 753 806 938 0.53 0.43 0.19 0.38 1591 2368 0.67 0.26 0.47 0.42 9.50 Mut_27 834 807 849 0.38 0.43 0.35 0.39 1827 2214 0.55 0.34 0.44 0.41 9.36 Mut_28 862 882 829 0.33 0.29 0.39 0.34 1566 2230 0.68 0.33 0.51 0.41 9.26 Mut_29 NA NA NA — — — — 1581 2611 0.68 0.13 0.40 0.40 9.23 Mut_30 NA NA NA — — — — 1925 2277 0.49 0.31 0.40 0.40 9.17 WTIgG2 1060 1016 1002 −0.03 0.05 0.08 0.03 2610 2885 0.13 -0.01 0.06 0.04 1.00 Ctrl hIgG 1071 1083 1018 −0.05 −0.07 0.05 −0.02 2587 2730 0.15 0.07 0.11 0.03 0.65 CD3 0nly 1051 1037 1044 −0.01 0.01 0.00 0.00 2863 2863 0.00 0.00 0.00 0.00 0.00 NA: Mutant antibody of the row was not subjected to the experiment of the column.
Example 11: The Effect of the Known Mutation on the Binding Ability of IgG2 to FcγR Cannot be Directly Predicted According to the Effect of the Mutation on the Binding Ability of IgG1 to FcγR
[0178] The affinity of human IgG1 to FcγRIIB can be increased by G236D, S239D (Seung Y Chu et al. Molecular Immunology 45 (2008) 3926-3933) and S298A mutation (US20090042291A1). However, in the results of NGS analysis of the present disclosure, the proportion of the IgG2 variant comprising G236D or S298A after sorting is not increased, but decreased (Table 10); the proportion of the human IgG2 variant containing S239D before sorting is 0.026%, and is not detected after sorting. These results demonstrate that G236D, S239D, and S298A mutations do not increase the FcγRIIB binding capacity of human IgG2, see Table 10.
[0179] In addition, we also introduce into IgG2 the V11 mutations (G237D/P238D/H268D/P271G/A330R) capable of significantly improving the binding affinity of IgG1 to FcγRIIB (F Mimoto et al., Protein Engineering, Design & Selection vol. 26 no. 10 pp. 589-598, 2013) to obtain IgG2_M2(H268D/P271G), IgG2_M3(H268D/P271G/A330R), IgG2_M4 (G236D/P238D/H268D/P271G) and IgG2_M5(G236D/P238D/H268D/P271G/A330R), and the mutations of M5 in IgG2 corresponds to the mutations of IgG1 V11. ELISA results of
[0180] Therefore, the effect of the known mutation on the binding ability of IgG2 to FcγR cannot be directly predicted according to the effect of the mutation on the binding ability of IgG1 to FcγR.
[0181] Each reference provided herein is incorporated by reference to the same extent as if each reference was individually incorporated by reference. In addition, it should be understood that based on the above teaching content of the disclosure, various changes or modifications to the disclosure, and these equivalent forms also fall within the scope of the appended claims.