Antibody libraries

• US 9,354,228 B2
• Filed: 07/14/2011
• Issued: 05/31/2016
• Est. Priority Date: 07/16/2010
• Status: Active Grant

• Current Assignee: Adimab, LLC
• Original Assignee: Adimab, LLC
• Inventors: Vasquez, Maximiliano, Sivasubramanian, Arvind, Feldhaus, Michael
• Primary Examiner(s): BOESEN, CHRISTIAN C
• Application Number:
  US13/810,570
• Publication Number:
  US 20130197201A1
• Time in Patent Office: 1,783 Days
• Field of Search: None
• US Class Current: 1/1
• 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 2317/21 from primates, e.g. man
• CPC Class Codes: C07K 2317/565 Complementarity determining region [CDR]
• CPC Class Codes: C07K 2317/567 Framework region [FR]
• CPC Class Codes: C12N 15/1089 Design, preparation, screening or analysis of libraries using computer algorithms
• CPC Class Codes: C40B 40/08 Libraries containing RNA or DNA which encodes proteins, e.g. gene libraries
• CPC Class Codes: C40B 50/06 Biochemical methods, e.g. using enzymes or whole viable microorganisms
• CPC Class Codes: G01N 33/543 with an insoluble carrier for immobilising immunochemicals
• CPC Class Codes: G16B 35/00 ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
• CPC Class Codes: G16B 35/20 Screening of libraries
• CPC Class Codes: G16C 20/60 In silico combinatorial chemistry

Abstract

The present invention overcomes the inadequacies inherent in the known methods for generating libraries of antibody-encoding polynucleotides by specifically designing the libraries with directed sequence and length diversity.

Claims

1. A library comprising synthetic polynucleotides that encode an antibody heavy chain or alternative scaffold containing at least about 10⁴ unique antibody CDRH3 amino acid sequences, wherein each of the polynucleotides encoding the at least about 10⁴ unique antibody CDRH3 amino acid sequences has an antibody CDRH3 amino acid sequence represented by the following formula:

[TN1]-[DH]-[N2]- [H3-JH], wherein;

TN1 is a polypeptide corresponding to any of the TN1 polypeptides of Tables 10 and 18-26, or a polypeptide produced by translation of any of the TN1 polynucleotides of Tables 25-26;

DH is a polypeptide corresponding to any of the DH polypeptides of Tables 11, 17-25 and 28, or a polypeptide produced by translation of any of the DH-encoding polynucleotides of Tables 16, 25 and 27;

N2 is a polypeptide corresponding to any of the N2 polypeptides of Tables 12, 18-25 and 30, or a polypeptide produced by translation of any of the N2-encoding polynucleotides of Tables 25 and 29;

H3-JH is a polypeptide corresponding to any of the H3-JH polypeptides of Tables 13, 15, 18-25 and 32, or a polypeptide produced by translation of any of the H3-JH-encoding polynucleotides of Tables 14, 25 and 31;

wherein the diversity of the polynucleotides encoding the at least about 10⁴ unique antibody CDRH3 amino acid sequences is created by each of the polynucleotides having a CDRH3 sequence that is different from the CDRH3 sequence of every other polynucleotide;

wherein the antibody heavy chain is a variable domain with framework (FRM) and complementary determining regions (CDR) comprising FRMH1-CDRH1-FRMH2-CDRH2-FRMH3-CDRH3-FRMH4; and

wherein the alternative scaffold is selected from the group consisting of fibronectin, the β

-sandwich, lipocalin, EETI-IFAGRP, BPTIFLAC1-D1/IT1-D2, thioredoxin, protein A, ankyrin repeats, γ

B-crystallin/ubiquitin, CTLD₃ and (LDLR-A module)₃.

2. The library of claim 1, wherein the polynucleotides encode CDRH3 polypeptides produced by the sets of TN1, DH, N2, and H3-JH polypeptides provided in any one of Tables 23-25.

3. The library of claim 1, wherein the polynucleotides encode CDRI-13 polypeptides produced by the set of TN1 polypeptides provided in Table 26, the set of DH polypeptides provided in Table 28, the set of N2 polypeptides provided in Table 30 and the set of H3-JH polypeptides provided in Table 32.

4. The library of claim 1 wherein number of N-linked glycosylation sites, deamidation motifs, and/or Cys residues are reduced or eliminated in comparison to libraries produced by amplification of a repertoire from a biological source.

5. The library of claim 1, further comprising a polynucleotide encoding one or more light chain variable domain polypeptides.

6. The library of claim 5, wherein the polypeptides are expressed as full-length IgGs.

7. The polypeptide expression products of the library of claim 6.

8. An antibody isolated from the polypeptide expression products of claim 7.

9. A vector containing the library of claim 1.

10. A host cell containing the vector of claim 9.

11. The host cell of claim 10, wherein the host cell is a yeast cell.

12. The yeast cell of claim 11, wherein the yeast is Saccharomyces cerevisiae.

13. A kit containing the library of claim 1.