Methods and compositions for making antibodies and antibody derivatives with reduced core fucosylation
The invention provides methods and compositions for preparing antibodies and antibody derivatives with reduced core fucosylation.
1. A population of humanized anti-CD70 antibodies, wherein the antibodies each comprise:
(i) a humanized heavy chain comprising the three CDRs from SEQ ID NO:1 and a variable region framework sequence of human germline V H 1-2 or V H 1-18 and exon J H -6, provided that any of positions H46, H67, H68, H69, H70, H71, H80, H81, H82, H82A and H91 (Kabat numbering) can be occupied by the amino acid occupying the corresponding position from SEQ ID NO:1,
(ii) a humanized light chain comprising the three CDRs from SEQ ID NO:2 and a variable region framework sequence of human germline V κ exon B3 and J κ exon J κ− 1, provided that any of positions L25 and L33 can be occupied by the amino acid occupying the corresponding position from SEQ ID NO:2, and
(iii) an Fc domain, wherein at least 50% of the antibodies in the population of antibodies lack core fucosylation;
wherein one or more of the antibodies in the population of humanized anti-CD70 antibodies comprises a fucose analog, or a metabolite or product of the fucose analog,
wherein the fucose analog is selected from the group consisting of one of the following formulae (I) or (II):
or a biologically acceptable salt or solvate thereof, wherein:
each of formula (I) or (II) can be the alpha or beta anomer or the corresponding aldose form;
each of R 1 -R 4 is independently selected from the group consisting of —OH, —OC(O)H, —OC(O)C 1 -C 10 alkyl, —OC(O)C 2 -C 10 alkenyl, —OC(O)C 2 -C 10 alkynyl, —OC(O)aryl, —OC(O)heterocycle, —OC(O)C 1 -C 10 alkylene(aryl), —OC(O)C 2 -C 10 alkenylene(aryl), OC(O)C 2 -C 10 alkynyl(aryl), —OC(O)C 1 -C 10 alkylene heterocycle, —OC(O)C 2 —C 10 alkenylene(heterocycle), —OC(O)C 2 -C 10 alkynyl heterocycle, —OCH 2 OC(O) alkyl, OCH 2 OC(O)O alkyl, —OCH 2 OC(O) aryl, —OCH 2 OC(O)O aryl, —OC(O)CH 2 O(CH 2 CH 2 O) n CH 3 , —OC(O)CH 2 CH 2 O(CH 2 CH 2 O) n CH 3 , —O—tri—C 1 -C 3 alkyl silyl, and —OC 1 -C 10 alkyl, wherein each n is an integer independently selected from 0-5; and
R 5 is selected from the group consisting of —C≡CH, —C≡CCH 3 , —C(O)OCH 3 , —CH(OAc)CH 3 , —CH 2 CN, and —CH 2 X (wherein X is Br).
2. The population of antibodies of claim 1 , wherein at least 70% of the antibodies in the population of antibodies lack core fucosylation.
3. The population of antibodies of claim 1 , wherein position H46 of the antibodies is occupied by the amino acid occupying the corresponding position from SEQ ID NO:1.
4. The population of antibodies of claim 1 , wherein at least one of positions H46, H67, H68, H69, H70, H71, H80, H81, H82, H82A and H91 (Kabat numbering) in the humanized heavy chain variable region of the antibodies is occupied by the residue occupying the corresponding position in SEQ ID NO:1.
5. The population of antibodies of claim 1 , wherein at least one of positions L25 and L33 in the humanized light chain variable region of the antibodies is occupied by the residue occupying the corresponding position in SEQ ID NO:2.
6. The population of antibodies of claim 1 , wherein the antibodies comprise a human IgG1 constant domain, wherein the humanized heavy chain comprises the amino acid sequence corresponding to positions 20-467 of SEQ ID NO:3 or positions 20-467 of SEQ ID NO:4.
7. The population of antibodies of claim 1 , wherein the antibodies each comprise an antibody effector domain.
8. The population of antibodies of claim 7 , wherein the antibody effector domain mediates ADCP.
9. The population of antibodies of claim 1 , wherein the antibodies are conjugated to therapeutic agents.
10. The population of antibodies of claim 9 , wherein the therapeutic agents are chemotherapeutic agents or immunomodulatory agents.
11. A population of humanized anti-CD70 antibodies, wherein the antibodies each comprise:
(i) a humanized heavy chain variable region comprising the amino acid sequence set forth in SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, or amino acids 20-137 of SEQ ID NO:9,
(ii) a humanized light chain variable region comprising the amino acid sequence of SEQ ID NO:10, and
(iii) an Fc domain, wherein at least 50% of the antibodies in the population of antibodies lack core fucosylation:
wherein one or more of the antibodies in the population of humanized anti-CD70 antibodies comprises a fucose analog, or a metabolite or product of the fucose analog,
wherein the fucose analog is selected from the group consisting of one of the following formulae (I) or (II):
or a biologically acceptable salt or solvate thereof, wherein:
each of formula (I) or (II) can he the alpha or beta anomer or the corresponding aldose form;
each of R 1 -R 4 is independently selected from the group consisting of —OH, —OC(O)H, —OC(O)C 1 -C 10 alkyl, —OC(O)C 2 -C 10 alkynyl, —OC(O)aryl, —OC(O)heterocycle, —OC(O)C 1 -C 10 alkylene(aryl), —OC(O)C 2 -C 10 alkenylene(aryl), —OC(O)C 2 -C 10 alkynyl(aryl), —OC(O)C 1 -C 10 alkylene heterocycle, —OC(O)C 2 -C 10 alkenylene(heterocycle), —OC(O)C 2 -C 10 alkynyl heterocycle, —OCH 2 OC(O)alkyl, —OCH 2 OC(O)O alkyl, —OCH 2 OC(O) aryl, —OCH 2 OC(O)O aryl, —OC(O)CH 2 O(CH 2 CH 2 O) n CH 3 , —OC(O)CH 2 CH 2 O(CH 2 CH 2 O) n CH 3 , —O—tri—C 1 -C 3 alkyl silyl, and —OC 1 -C 10 alkyl, wherein each n is an integer independently selected from 0-5; and
R 5 is selected from the group consisting, of —C≡CH, —C≡CCH 3 , —C(O)OCH 3 , —CH(OAc)CH 3 , —CH 2 CN, and —CH 2 X (wherein X is Br).
12. The population of antibodies of claim 11 , wherein at least 70% of the antibodies in the population of antibodies lack core fucosylation.
13. The population of antibodies of claim 11 , wherein the humanized heavy chain variable region of the antibodies comprise the sequence set forth in SEQ ID NO:7 or SEQ ID NO:8, and the humanized light chain variable region of the antibodies comprise the sequence set forth in SEQ ID NO:10.
14. The population of antibodies of claim 11 , wherein the humanized heavy chain variable region of the antibodies comprise the sequence set forth in SEQ ID NO:7 and the humanized light chain variable region of the antibodies comprise the sequence set forth in SEQ ID NO:10.
15. The population of antibodies of claim 14 , wherein at least 70% of the antibodies in the population of antibodies lack core fucosylation.
16. The population of antibodies of claim 11 , wherein the antibodies are conjugated to therapeutic agents.
17. The population of antibodies of claim 16 , wherein the therapeutic agents are chemotherapeutic agents or immunomodulatory agents.
18. A population of anti-CD70 antibodies wherein at least 50% of the antibodies in the population of antibodies lack core fucosylation:
wherein one or more of the antibodies in the population of humanized anti-CD70 antibodies comprises a fucose analog, or a metabolite or product of the fucose analog,
wherein the fucose analog is selected from the group consisting of one of the following formulae (I) or (II):
or a biologically acceptable salt or solvate thereof, wherein:
each of formula (I) or (II) can be the alpha or beta anomer or the corresponding aldose form;
each of R 1 -R 4 is independently selected from the group consisting of —OH, —OC(O)H, —OC(O)C 1 -C 10 alkyl, —OC(O)C 2 -C 10 alkenyl, —OC(O)C 2 -C 10 alkynyl, —OC(O)aryl, —OC(O)heterocycle, —OC(O)C 1 -C 10 alkylene(aryl), —OC(O)C 2 -C 10 alkenylene(aryl), —OC(O)C 2 -C 10 alkynyl (aryl), —OC(O)C 1 -C 10 alkylene heterocycle, —OC(O)C 2 -C 10 alkenylene(heterocycle), —OC(O)C 2 -C 10 alkynyl heterocycle, —OCH 2 OC(O)alkyl, —OCH 2 OC(O)O alkyl, —OCH 2 OC(O) aryl, —OCH 2 OC(O)O aryl, —OC(O)CH 2 O(CH 2 CH 2 O) n CH 3 , —OC(O)CH 2 CH 2 O(CH 2 CH 2 O) n CH 3 , —O—tri—C 1 -C 3 alkyl silyl, and —OC 1 -C 10 alkyl, wherein each n is an integer independently selected from 0-5; and
R 5 is selected from the group consisting of —C≡CH, —C≡CCH 3 , —C(O)OCH 3 , —CH(OAc)CH 3 , —CH 2 CN, and —CH 2 X (wherein X is Br).
19. The population of antibodies of claim 18 , wherein the antibodies are h1F6.
20. The population of antibodies of claim 19 , wherein at least 70% of the antibodies in the population of antibodies lack core fucosylation.
21. The population of antibodies of claim 19 , wherein the antibodies are conjugated to therapeutic agents.
22. A pharmaceutical composition for the treatment of a CD70-expressing cancer or an immunological disorder, the composition comprising the population of antibodies of claim 1 .
23. A kit comprising the population of antibodies of claim 1 and instructions for using the population of antibodies to detect CD70 protein in a subject or a biological sample.
24. A pharmaceutical composition for the treatment of a CD70-expressing cancer or an immunological disorder, the composition comprising the population of antibodies of claim 11 .
25. A kit comprising the population of antibodies of claim 11 and instructions for using the humanized antibody to detect CD70 protein in a subject or a biological sample.
26. A pharmaceutical composition for the treatment of a CD70-expressing cancer or an immunological disorder, the composition comprising the population of antibodies of claim 19 .
27. A kit comprising the population of antibodies of claim 19 and instructions for using the antibody to detect CD70 protein in a subject or a biological sample.
28. A population of humanized anti-CD 70 antibodies, wherein the antibodies each comprise:
(i) a humanized heavy chain comprising the three CDRs from SEQ ID NO: 1 and a variable region framework sequence of human germline V H 1-2 or V H 1-18 and exon J H -6, provided that any of positions H46, H67, H68, H69, H70, H71, H80, H81, H82, H82A and H91 (Kabat numbering) can be occupied by the amino acid occupying the corresponding position from SEQ ID NO:1,
(ii) a humanized light chain comprising the three CDRs from SEQ ID NO:2 and a variable region framework sequence of human germline V K exon B 3 and J K exon J K -1, provided that any of positions L25 and L33 can be occupied by the amino acid occupying the corresponding position from SEQ ID NO:2, and
(iii) an Fc domain, wherein at least 50% of the antibodies in the population of antibodies lack core fucosylation;
wherein one or more of the antibodies in the population of humanized anti-CD70 antibodies comprises a fucose analog, or a metabolite or product of the fucose analog,
wherein the fucose analog is selected from the group consisting of one of the following formulae (III) or (IV):
or a biologically acceptable salt or solvate thereof, wherein:
each of formula (III) or (IV) can be the alpha or beta anomer or the corresponding aldose form;
each of R 1 -R 4 is independently selected from the group consisting of fluoro, chloro, —OH, —OC(O)H, —OC(O)C 1 -C 10 alkyl, —OC(O)C 2 -C 10 alkenyl, —OC(O)C 2 -C 10 alkynyl, —OC(O)aryl, —OC(O)heterocycle, —OC(O)C 1 -C 10 alkylene(aryl), —OC(O)C 2 -C 10 alkenylene(aryl), —OC(O)C 2 -C 10 alkynyl(aryl), —OC(O)C 1 -C 10 alkylene heterocycle, —OC(O)C 2 -C 10 alkenylene(heterocycle), —OC(O)C 2 -C 10 alkynyl heterocycle, —OCH 2 OC(O) alkyl, —OCH 2 OC(O)O alkyl, —OCH 2 OC(O) aryl, —OCH 2 OC(O)O aryl, —OC(O)CH 2 O(CH 2 CH 2 O) n CH 3 , —OC(O)CH 2 CH 2 O(CH 2 CH 2 O) n CH 3 , —O-tri-C 1 -C 3 alkylsilyl and —OC 1 -C 10 alkyl, wherein each n is an integer independently selected from 0-5;
each of R 2a and R 3a is independently selected from the group consisting of H, F and Cl;
R 5 is selected from the group consisting of —CH 3 , —CHF 2 , —CH═C═CH 2 , —C≡CCH 3 , —CH 2 C≡CH, —C(O)OCH 3 , —CH(OAc)CH 3 , —CN, —CH 2 CN, —CH 2 X (wherein X is Br, Cl or I), and methoxiran; and
wherein when R 5 is other than —CH═C═CH 2 or —CHF 2 , at least one of R 1 , R 2 , R 3 , R 2a and R 3a is fluoro or chloro.
29. The population of antibodies of claim 28 , wherein the fucose analog is formula (III) or a biologically acceptable salt or solvate thereof, wherein:
R 1 is —OH;
R 2 is —F;
R 2a is —H;
R 3 is —OH;
R 3a is —H;
R 4 is —OH; and
R 5 is —CH 3 .
30. The population of antibodies of claim 28 , wherein the fucose analog is 2-deoxy-2-fluorofucose.
31. The population of antibodies of claim 28 , wherein at least 70% of the antibodies in the population of antibodies lack core fucosylation.
32. The population of antibodies of claim 28 , wherein position H46 of the antibodies is occupied by the amino acid occupying the corresponding position from SEQ ID NO:1.
33. The population of antibodies of claim 28 , wherein at least one of positions H46, H67, H68, H69, H70, H71, H80, H81, H82, H82A and H91 (Kabat numbering) in the humanized heavy chain variable region of the antibodies is occupied by the residue occupying the corresponding position in SEQ ID NO:1.
34. The population of antibodies of claim 28 , wherein at least one of positions L25 and L33 in the humanized light chain variable region of the antibodies is occupied by the residue occupying the corresponding position in SEQ ID NO:2.
35. The population of antibodies of claim 28 , wherein the antibodies comprise a human IgG1 constant domain, wherein the humanized heavy chain comprises the amino acid sequence corresponding to positions 20-467 of SEQ ID NO:3 or positions 20-467 of SEQ ID NO:4.
36. The population of antibodies of claim 28 , wherein the antibodies each comprise an antibody effector domain.
37. The population of antibodies of claim 36 , wherein the antibody effector domain mediates ADCP.
38. The population of antibodies of claim 28 , wherein the antibodies are conjugated to therapeutic agents.
39. The population of antibodies of claim 38 , wherein the therapeutic agents are chemotherapeutic agents or immunomodulatory agents.
40. A population of humanized anti-CD70 antibodies, wherein the antibodies each comprise:
(i) a humanized heavy chain variable region comprising the amino acid sequence set forth in SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, or amino acids 20-137 of SEQ ID NO:9,
(ii) a humanized light chain variable region comprising the amino acid sequence of SEQ ID NO:10, and
(iii) an Fc domain, wherein at least 50% of the antibodies in the population of antibodies lack core fucosylation:
wherein one or more of the antibodies in the population of humanized anti-CD70 antibodies comprises a fucose analog, or a metabolite or product of the fucose analog,
wherein the fucose analog is selected from the group consisting of one of the following formulae (III) or (IV):
or a biologically acceptable salt or solvate thereof, wherein:
each of formula (III) or (IV) can be the alpha or beta anomer or the corresponding aldose form;
each of R 1 -R 4 is independently selected from the group consisting of fluoro, chloro, —OH, —OC(O)H, —OC(O)C 1 -C 10 alkyl, —OC(O)C 2 -C 10 alkenyl, —OC(O)C 2 -C 10 alkynyl, —OC(O)aryl, —OC(O)heterocycle, —OC(O)C 1 -C 10 alkylene(aryl), —OC(O)C 2 -C 10 alkenylene(aryl), —OC(O)C 2 -C 10 alkynyl(aryl), —OC(O)C 1 -C 10 alkylene heterocycle, —OC(O)C 2 -C 10 alkenylene(heterocycle), —OC(O)C 2 -C 10 alkynyl heterocycle, —OCH 2 OC(O) alkyl, —OCH 2 OC(O)O alkyl, —OCH 2 OC(O) aryl, —OCH 2 OC(O)O aryl, —OC(O)CH 2 O(CH 2 CH 2 O) n CH 3 , —OC(O)CH 2 CH 2 O(CH 2 CH 2 O) n CH 3 , —O-tri-C 1 -C 3 alkylsilyl and —OC 1 -C 10 alkyl, wherein each n is an integer independently selected from 0-5;
each of R 2a and R 3a is independently selected from the group consisting of H, F and Cl;
R 5 is selected from the group consisting of —CH 3 , —CHF 2 , —CH═C═CH 2 , —C≡CCH 3 , —CH 2 C≡CH, —C(O)OCH 3 , —CH(OAc)CH 3 , —CN, —CH 2 CN, —CH 2 X (wherein X is Br, Cl or I), and methoxiran; and
wherein when R 5 is other than —CH═C═CH 2 or —CHF 2 , at least one of R 1 , R 2 , R 3 , R 2a and R 3a is fluoro or chloro.
41. The population of antibodies of claim 40 , wherein the fucose analog is formula (III) or a biologically acceptable salt or solvate thereof, wherein:
R 1 is —OH;
R 2 is —F;
R 2a is —H;
R 3 is —OH;
R 3a is —H;
R 4 is —OH; and
R 5 is —CH 3 .
42. The population of antibodies of claim 40 , wherein the fucose analog is 2-deoxy-2-fluorofucose.
43. The population of antibodies of claim 40 , wherein at least 70% of the antibodies in the population of antibodies lack core fucosylation.
44. The population of antibodies of claim 40 , wherein the humanized heavy chain variable region of the antibodies comprise the sequence set forth in SEQ ID NO:7 or SEQ ID NO:8, and the humanized light chain variable region of the antibodies comprise the sequence set forth in SEQ ID NO:10.
45. The population of antibodies of claim 40 , wherein the humanized heavy chain variable region of the antibodies comprise the sequence set forth in SEQ ID NO:7 and the humanized light chain variable region of the antibodies comprise the sequence set forth in SEQ ID NO:10.
46. The population of antibodies of claim 45 , wherein at least 70% of the antibodies in the population of antibodies lack core fucosylation.
47. The population of antibodies of claim 40 , wherein the antibodies are conjugated to therapeutic agents.
48. The population of antibodies of claim 47 , wherein the therapeutic agents are chemotherapeutic agents or immunomodulatory agents.
49. A population of anti-CD70 antibodies wherein at least 50% of the antibodies in the population of antibodies lack core fucosylation:
wherein one or more of the antibodies in the population of humanized anti-CD70 antibodies comprises a fucose analog, or a metabolite or product of the fucose analog,
wherein the fucose analog is selected from the group consisting of one of the following formulae (III) or (IV):
or a biologically acceptable salt or solvate thereof, wherein:
each of formula (III) or (IV) can be the alpha or beta anomer or the corresponding aldose form;
each of R 1 -R 4 is independently selected from the group consisting of fluoro, chloro, —OH, —OC(O)H, —OC(O)C 1 -C 10 alkyl, —OC(O)C 2 -C 10 alkenyl, —OC(O)C 2 -C 10 alkynyl, —OC(O)aryl, —OC(O)heterocycle, —OC(O)C 1 -C 10 alkylene(aryl), —OC(O)C 2 -C 10 alkenylene(aryl), —OC(O)C 2 -C 10 alkynyl(aryl), —OC(O)C 1 -C 10 alkylene heterocycle, —OC(O)C 2 -C 10 alkenylene(heterocycle), —OC(O)C 2 -C 10 alkynyl heterocycle, —OCH 2 OC(O) alkyl, —OCH 2 OC(O)O alkyl, —OCH 2 OC(O) aryl, —OCH 2 OC(O)O aryl, —OC(O)CH 2 O(CH 2 CH 2 O) n CH 3 , —OC(O)CH 2 CH 2 O(CH 2 CH 2 O) n CH 3 , —O-tri-C 1 -C 3 alkylsilyl and —OC 1 -C 10 alkyl, wherein each n is an integer independently selected from 0-5;
each of R 2a and R 3a is independently selected from the group consisting of H, F and Cl;
R 5 is selected from the group consisting of —CH 3 , —CHF 2 , —CH═C═CH 2 , —C≡CCH 3 , —CH 2 C≡CH, —C(O)OCH 3 , —CH(OAc)CH 3 , —CN, —CH 2 CN, —CH 2 X (wherein X is Br, Cl or I), and methoxiran; and
wherein when R 5 is other than —CH═C═CH 2 or —CHF 2 , at least one of R 1 , R 2 , R 3 , R 2a and R 3a is fluoro or chloro.
50. The population of antibodies of claim 49 , wherein the antibodies are h1F6.
51. The population of antibodies of claim 49 , wherein the fucose analog is formula (III) or a biologically acceptable salt or solvate thereof, wherein:
R 1 is —OH;
R 2 is —F;
R 2a is —H;
R 3 is —OH;
R 3a is —H;
R 4 is —OH; and
R 5 is —CH 3 .
52. The population of antibodies of claim 49 , wherein the fucose analog is 2-deoxy-2-fluorofucose.
53. The population of antibodies of claim 50 , wherein the fucose analog is formula (III) or a biologically acceptable salt or solvate thereof, wherein:
R 1 is —OH;
R 2 is —F;
R 2a is —H;
R 3 is —OH;
R 3a is —H;
R 4 is —OH; and
R 5 is —CH 3 .
54. The population of antibodies of claim 47 , wherein the fucose analog is 2-deoxy-2-fluorofucose.
55. The population of antibodies of claim 47 , wherein at least 70% of the antibodies in the population of antibodies lack core fucosylation.
56. The population of antibodies of claim 47 , wherein the antibodies are conjugated to therapeutic agents.
57. The population of antibodies of claim 56 , wherein the therapeutic agents are chemotherapeutic agents or immunomodulatory agents.
58. A pharmaceutical composition for the treatment of a CD70-expressing cancer or an immunological disorder, the composition comprising the population of antibodies of claim 28 .
59. A kit comprising the population of antibodies of claim 28 and instructions for using the population of antibodies to detect CD70 protein in a subject or a biological sample.
60. A pharmaceutical composition for the treatment of a CD70-expressing cancer or an immunological disorder, the composition comprising the population of antibodies of claim 40 .
61. A kit comprising the population of antibodies of claim 40 and instructions for using the humanized antibody to detect CD70 protein in a subject or a biological sample.
62. A pharmaceutical composition for the treatment of a CD70-expressing cancer or an immunological disorder, the composition comprising the population of antibodies of claim 50 .
63. A kit comprising the population of antibodies of claim 50 and instructions for using the antibody to detect CD70 protein in a subject or a biological sample.