Optimized Fc variants and methods for their generation

• US 10,184,000 B2
• Filed: 05/27/2016
• Issued: 01/22/2019
• Est. Priority Date: 09/27/2002
• Status: Active Grant

• Current Assignee: Xencor, Inc.
• Original Assignee: Xencor, Inc.
• Inventors: Lazar, Gregory Alan, Chirino, Arthur J., Dang, Wei, Desjarlais, John, Doberstein, Stephen K., Hayes, Robert J., Karki, Sher Bahadur, Vafa, Omid
• Primary Examiner(s): Dahle, Chun W
• Application Number:
  US15/167,832
• Publication Number:
  US 20160347825A1
• Time in Patent Office: 970 Days
• Field of Search: None
• CPC Class Codes: A61K 2039/505 comprising antibodies
• CPC Class Codes: A61K 39/395 Antibodies agglutinins A61K38/36 ; as drug carriers A61K47/50; Immunoglobulins; Immune serum, e.g. antilymphocytic serum
• CPC Class Codes: A61K 39/3955 against proteinaceous materials, e.g. enzymes, hormones, lymphokines
• CPC Class Codes: A61K 39/39566 against immunoglobulins, e.g. anti-idiotypic antibodies
• CPC Class Codes: A61P 25/00 Drugs for disorders of the nervous system
• CPC Class Codes: A61P 29/00 Non-central analgesic, antipyretic or antiinflammatory agents, e.g. antirheumatic agents; Non-steroidal antiinflammatory drugs [NSAID]
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: A61P 37/02 Immunomodulators
• CPC Class Codes: A61P 37/04 Immunostimulants
• CPC Class Codes: A61P 9/00 Drugs for disorders of the cardiovascular system
• CPC Class Codes: C07K 16/00 Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies antibodies with enzymatic activity, e.g. abzymes C12N9/0002
• CPC Class Codes: C07K 16/22 against growth factors ; against growth regulators
• CPC Class Codes: C07K 16/283 against Fc-receptors, e.g. CD16, CD32, CD64 CD23 C07K16/2851
• CPC Class Codes: C07K 16/2863 against receptors for growth factors, growth regulators
• CPC Class Codes: C07K 16/2875 against the NGF/TNF superfamily, e.g. CD70, CD95L, CD153, CD154 against NGF C07K16/22, against TNF C07K16/241
• CPC Class Codes: C07K 16/2887 against CD20
• CPC Class Codes: C07K 16/2893 against CD52
• CPC Class Codes: C07K 16/2896 against molecules with a "CD"-designation, not provided for elsewhere
• CPC Class Codes: C07K 16/32 against translation products of oncogenes
• CPC Class Codes: C07K 16/4291 against IgE
• CPC Class Codes: C07K 2317/14 : Specific host cells or culture conditions, e.g. components, pH or temperature
• CPC Class Codes: C07K 2317/21 : from primates, e.g. man
• CPC Class Codes: C07K 2317/24 : containing regions, domains or residues from different species, e.g. chimeric, humanized or veneered
• CPC Class Codes: C07K 2317/33 : Crossreactivity, e.g. for species or epitope, or lack of said crossreactivity
• CPC Class Codes: C07K 2317/34 : Identification of a linear epitope shorter than 20 amino acid residues or of a conformational epitope defined by amino acid residues
• CPC Class Codes: C07K 2317/41 : Glycosylation, sialylation, or fucosylation
• CPC Class Codes: C07K 2317/51 : Complete heavy chain or Fd fragment, i.e. VH + CH1
• CPC Class Codes: C07K 2317/52 : Constant or Fc region; Isotype
• CPC Class Codes: C07K 2317/522 : CH1 domain
• CPC Class Codes: C07K 2317/524 : CH2 domain
• CPC Class Codes: C07K 2317/526 : CH3 domain
• CPC Class Codes: C07K 2317/56 : variable (Fv) region, i.e. VH and/or VL
• CPC Class Codes: C07K 2317/71 : Decreased effector function due to an Fc-modification
• CPC Class Codes: C07K 2317/72 : Increased effector function due to an Fc-modification
• CPC Class Codes: C07K 2317/732 : Antibody-dependent cellular cytotoxicity [ADCC]
• CPC Class Codes: C07K 2317/734 : Complement-dependent cytotoxicity [CDC]
• CPC Class Codes: C07K 2317/76 : Antagonist effect on antigen, e.g. neutralization or inhibition of binding
• CPC Class Codes: C07K 2317/77 : Internalization into the cell
• CPC Class Codes: C07K 2317/92 : Affinity (KD), association rate (Ka), dissociation rate (Kd) or EC50 value
• CPC Class Codes: C07K 2319/30 : Non-immunoglobulin-derived peptide or protein having an immunoglobulin constant or Fc region, or a fragment thereof, attached thereto
• CPC Class Codes: C12P 21/005 : Glycopeptides, glycoproteins
• CPC Class Codes: G16B 15/00 : ICT specially adapted for analysing two-dimensional or three-dimensional molecular structures, e.g. structural or functional relations or structure alignment
• CPC Class Codes: G16B 15/20 : Protein or domain folding
• CPC Class Codes: G16B 30/00 : ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 30/10 : Sequence alignment; Homology search
• CPC Class Codes: G16B 35/00 : ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
• CPC Class Codes: G16B 5/00 : ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks
• CPC Class Codes: G16C 20/60 : In silico combinatorial chemistry

Abstract

The present invention relates to optimized Fc variants, methods for their generation, and antibodies and Fc fusions comprising optimized Fc variants.

Claims

1. A nucleic acid encoding a polypeptide comprising an Fc variant of a parent Fc polypeptide, said Fc variant comprising amino acid substitutions at positions 239 and 332 in the Fc region, wherein numbering is according to the EU index.

2. The nucleic acid according to claim 1, wherein the substitution at position 239 is selected from the group consisting of D and E.

3. The nucleic acid according to claim 1, wherein the substitution at position 332 is selected from the group consisting of D and E.

4. The nucleic acid according to claim 1, wherein the substitution at positions 239 and 332 are selected from the group consisting of 239D/332E, 239D/332D, 239E/332D, and 239E/332E.

5. The nucleic acid according to claim 1, wherein the substitutions at positions 239 and 332 are 239D and 332E.

6. The nucleic acid according to claim 1, wherein the parent Fc polypeptide is a human IgG1 Fc polypeptide.

7. An expression vector comprising the nucleic acid according to claim 1.

8. A host cell comprising a nucleic acid according to claim 1.

9. A host cell comprising an expression vector according to claim 7.

10. A method of producing a polypeptide comprising:

a) culturing a host cell according to claim 8 under conditions wherein said polypeptide is produced; and

b) purifying said polypeptide.

11. A method of producing a polypeptide comprising:

a) culturing a host cell according to claim 9 under conditions wherein said polypeptide is produced; and

b) purifying said polypeptide.

12. A nucleic acid encoding a heavy chain of an antibody comprising an Fc variant of a parent Fc polypeptide, said Fc variant comprising amino acid substitutions at positions 239 and 332 in the Fc region, wherein numbering is according to the EU index.

13. The nucleic acid according to claim 12, wherein the substitution at position 239 is selected from the group consisting of D and E.

14. The nucleic acid according to claim 12, wherein the substitution at position 332 is selected from the group consisting of D and E.

15. The nucleic acid according to claim 12, wherein the substitution at positions 239 and 332 are selected from the group consisting of 239D/332E, 239D/332D, 239E/332D, and 239E/332E.

16. The nucleic acid according to claim 12, wherein the substitutions at positions 239 and 332 are 239D and 332E.

17. The nucleic acid according to claim 12, wherein the parent Fc polypeptide is a human IgG1 Fc polypeptide.

18. The nucleic acid according to claim 12, wherein the antibody is a monoclonal antibody.

19. An expression vector comprising the nucleic acid according to claim 12.

20. A host cell comprising a nucleic acid according to claim 12.

21. A host cell comprising an expression vector according to claim 19.

22. A method of producing a polypeptide comprising:

a) culturing a host cell according to claim 20 under conditions wherein said polypeptide is produced; and

b) purifying said polypeptide.

23. A method of producing a polypeptide comprising:

a) culturing a host cell according to claim 21 under conditions wherein said polypeptide is produced; and

b) purifying said polypeptide.

24. A nucleic acid encoding a polypeptide comprising an Fc variant of a parent Fc polypeptide, said Fc variant comprising amino acid substitutions 239D and 332E in the Fc region, wherein said Fc variant exhibits increased Fcγ

RIIIa binding, and wherein numbering is according to the EU index.

25. The nucleic acid according to claim 24, wherein the parent Fc polypeptide is a human IgG1 Fc polypeptide.

26. An expression vector comprising the nucleic acid according to claim 24.

27. A host cell comprising a nucleic acid according to claim 24.

28. A host cell comprising an expression vector according to claim 26.

29. A method of producing a polypeptide comprising:

a) culturing a host cell according to claim 27 under conditions wherein said polypeptide is produced; and

b) purifying said polypeptide.

30. A method of producing a polypeptide comprising:

a) culturing a host cell according to claim 28 under conditions wherein said polypeptide is produced; and

b) purifying said polypeptide.

31. A nucleic acid encoding a heavy chain of an antibody comprising an Fc variant of a parent Fc polypeptide, said Fc variant comprising amino acid substitutions 239D and 332E in the Fc region, wherein said Fc variant exhibits increased Fcγ

RIIIa binding, and wherein numbering is according to the EU index.

32. The nucleic acid according to claim 31, wherein the parent Fc polypeptide is a human IgG1 Fc polypeptide.

33. The nucleic acid according to claim 31, wherein the antibody is a monoclonal antibody.

34. An expression vector comprising the nucleic acid according to claim 31.

35. A host cell comprising a nucleic acid according to claim 31.

36. A host cell comprising an expression vector according to claim 34.

37. A method of producing a polypeptide comprising:

a) culturing a host cell according to claim 35 under conditions wherein said polypeptide is produced; and

b) purifying said polypeptide.

38. A method of producing a polypeptide comprising:

a) culturing a host cell according to claim 36 under conditions wherein said polypeptide is produced; and

b) purifying said polypeptide.