Libraries of genetic packages comprising novel HC CDR1, CDR2, and CDR3 and novel LC CDR1, CDR2, and CDR3 designs

• US 10,683,342 B2
• Filed: 06/08/2016
• Issued: 06/16/2020
• Est. Priority Date: 04/24/2008
• Status: Active Grant

• Current Assignee: Takeda Pharmaceutical Company Limited
• Original Assignee: Dyax Corporation (Shire plc)
• Inventors: Ladner, Robert Charles
• Primary Examiner(s): Boesen, Christian C
• Application Number:
  US15/177,199
• Publication Number:
  US 20160355571A1
• Time in Patent Office: 1,469 Days
• Field of Search: None
• CPC Class Codes: C07K 16/005 constructed by phage libraries
• CPC Class Codes: C07K 2317/565 Complementarity determining region [CDR]
• CPC Class Codes: C40B 40/02 Libraries contained in or displayed by microorganisms, e.g. bacteria or animal cells; Libraries contained in or displayed by vectors, e.g. plasmids; Libraries containing only microorganisms or vectors
• CPC Class Codes: C40B 40/08 Libraries containing RNA or DNA which encodes proteins, e.g. gene libraries
• CPC Class Codes: C40B 40/10 Libraries containing peptides or polypeptides, or derivatives thereof

Abstract

Provided are compositions and methods for preparing and identifying antibodies having CDR3s that vary in sequence and in length from very short to very long which in certain embodiments may bind to a carbohydrate moiety or the active site of an enzyme. Libraries coding for antibodies with the CDR3s are also provided. The libraries can be provided by modifying a pre-existing nucleic acid library.

Claims

1. A library of vectors or genetic packages, wherein the vectors or genetic packages comprise variegated DNA sequences, each encoding a heavy chain (HC) variable region, which comprises three complementarity determining regions (CDRs) 1-3 and framework regions (FRs) 1-4, arranged from the amino terminus to the carboxy-terminus in an order of FR1-CDR2-FR2-CDR2-FR3-CDR3-FR4, wherein the HC CDR3 region contains 3-35 amino acid residues, and wherein at least 1, 2, 3, 4, 5, 6, 7, or 8 positions in the HC CDR3s encoded by the variegated DNA sequences are varied among Tyr, Gly, Asp, Ser, Arg, and Leu residues.

2. The library of claim 1, wherein the library is a library of genetic packages.

3. The library of claim 2, wherein the genetic packages are bacteriophages.

4. The library of claim 3, wherein the library is a phage display library.

5. The library of claim 1, wherein the library is a library of vectors.

6. The library of claim 5, wherein the vectors are phage vectors or phagemid vectors.

7. The library of claim 1, wherein the last four positions in the HC CDR3s comprise Tyr, Gly, Asp, Ser, and Arg residues.

8. The library of claim 1, wherein the proportions of the Tyr, Gly, Asp, Ser, Arg, and Leu residues are 1.0G, 0.57S, 0.46R, 0.42D, 0.36L, and 0.35Y.

9. The library of claim 1, wherein the HC CDR3 are 10-15 amino acids in length, and wherein each of the first 6, 7, or 8 positions in the HC CDR3s is varied among Gly, Ser, Arg, Asp, Leu, and Tyr.

10. The library of claim 1, wherein the HC CDR3 are 18-20 amino acids in length, and wherein each of the first 4, 5, or 6 positions in the HC CDR3s is varied among Gly, Ser, Arg, Asp, Leu, and Tyr.

11. The library of claim 1, wherein the HC CDR3 are 15-17 amino acids in length, and wherein each of the first 2, 3, or 4 positions in the HC CDR3s is varied among Gly, Ser, Arg, Asp, Leu, and Tyr.

12. The library of claim 1, wherein the HC CDR3 are 11-14 amino acids in length, and wherein each of the first 1 or 2 positions in the HC CDR3s is varied among Gly, Ser, Arg, Asp, Leu, and Tyr.

13. The library of claim 1, wherein the HC CDR3 are 11-14 amino acids in length, and wherein each of the first 1, 2, or 3 positions in the HC CDR3s is varied among Gly, Ser, Arg, Asp, Leu, and Tyr.

14. The library of claim 1, wherein the FRs are of a VH gene selected from the group consisting of VH3-23, VH4-34, VH3-30, VH3-30.3, and VH4-30.

15. The library of claim 14, wherein the FRs are from VH 3-23.

16. The library of claim 1, wherein the library comprises at least 1×

10⁹ members.