Antibody libraries

• US 10,138,478 B2
• Filed: 05/11/2016
• Issued: 11/27/2018
• 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:
  US15/151,626
• Publication Number:
  US 20160244750A1
• Time in Patent Office: 930 Days
• Field of Search: None
• 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 method of making a library comprising synthetic polynucleotides that encode an antibody heavy chain 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],

the method comprising;

(a) providing a theoretical segment pool containing TN1, DH, N2, and H3-JH segments, wherein, the DH segments are provided according to the following steps;

(i) obtaining a set of polynucleotide sequences of human IGHD genes and alleles;

(ii) progressively deleting one or more nucleotide bases from the polynucleotide sequences of (i) on either or both of the 5′ and

3′

ends;

(iii) systematically adding 0, 1 and/or 2 or more nucleotides to the 5′ and

/or 3′

ends of the polynucleotide sequences from (ii);

(iv) translating the polynucleotide sequences of (iii) and selecting unique amino acid sequences to thereby provide the DH theoretical segment pool;

(b) providing a reference set of preimmune CDRH3 sequences having sequence diversities and length diversities similar to naturally occurring human antibody sequences before these sequences have undergone negative selection and/or hypermutation;

(c) utilizing combinations of the TN1, DH, N2, and H3-JH segments contained in the theoretical segment pool of (a) to identify the closest match(es) to each CDRH3 sequence in the reference set of (b);

(d) selecting segments from the closest match(es) identified in step (c) for inclusion in a library comprising synthetic polynucleotides that encode an antibody heavy chain; and

(e) synthesizing the synthetic polynucleotides that encode an antibody heavy chain;

wherein the diversity of the polynucleotides encoding the at least about 10⁴ unique antibody CDRH3 amino acid sequences is created by polynucleotides having CDRH3 sequences that are different from the CDRH3 sequences of other polynucleotides; and

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.

2. The method of claim 1, wherein the segments selected for inclusion in the synthetic library are selected according to their segment usage weight in the reference set of CDRH3 sequences.

3. The method of claim 1, wherein the segments selected for inclusion in the synthetic library are selected according to one or more physicochemical properties.

4. The method of claim 1, further comprising selecting additional TN1 and N2 segments occurring in the reference set but not in the theoretical segment pool.

5. The method of claim 1, wherein stop codons are reduced or eliminated from the library.

6. The method of claim 1, wherein the unpaired Cys residues, N-linked glycosylation motifs, and deamidation motifs are reduced or eliminated in the translation products of the library.

7. The method of claim 1, wherein the theoretical segment pool contains TN1 segments corresponding to any of the TN1 polypeptides of Tables 10 and 18-26, or a polypeptide produced by translation of any of the TN1-encoding polynucleotides of Tables 25-26.

8. The method of claim 1, wherein the theoretical segment pool contains DH segments 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.

9. The method of claim 1, wherein the theoretical segment pool contains N2 segments 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.

10. The method of claim 1, wherein the theoretical segment pool contains H3-JH segments 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.

11. The method of claim 1, wherein step (ii) includes progressively deleting nucleotide bases until 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 remain.

12. The method of claim 3, wherein step (iii) includes:

A) addition of 0, 1 or 2 nucleotides to the 5′ and

/or 3′

-ends of the polynucleotide sequences from (ii);

B) addition of 1 or 2 nucleotides at both the 5′ and

/or 3′

-ends of the polynucleotide sequences from (ii);

C) addition of 1 nucleotide on the 5′

end combined with 1 or 2 nucleotides on the 3′

end of the polynucleotide sequences from (ii);

D) addition of 1 or 2 nucleotides to the 3′

end only of the polynucleotide sequences from (ii); and

/or

E) addition of 2 nucleotides on the 5′

end combined with 1 or 2 nucleotides on the 3′

end of the polynucleotide sequences from (ii).

13. The method of claim 1, wherein the unique sequences of (iv) do not have stop codons, unpaired Cys residues, deamidation motifs, or Asn in the last or next to last position that can lead to N-linked glycosylation motifs.

14. A method of making a library comprising synthetic polynucleotides that encode an antibody heavy chain 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],

the method comprising;

(a) providing a theoretical segment pool containing TN1, DH, N2, and H3-JH segments, wherein the DH segments are provided according to the following steps;

(i) obtaining a set of polynucleotide sequences of human IGHD genes and alleles;

(ii) translating the polynucleotide sequences of (i), wherein translation of a partial codon containing two untranslated bases is completed to produce a full codon if the two bases encode a single amino acid regardless of the third position;

(iii) progressively deleting amino acid sequences of (ii) at their N- and/or C-termini until at least two amino acids remain; and

(iv) collecting unique sequences from (iii) that contain 2 or more amino acids to thereby provide the DH theoretical segment pool;

(b) providing a reference set of preimmune CDRH3 sequences having sequence diversities and length diversities similar to naturally occurring human antibody sequences before these sequences have undergone negative selection and/or hypermutation;

(c) utilizing combinations of the TN1, DH, N2, and H3-JH segments contained in the theoretical segment pool of (a) to identify the closest match(es) to each CDRH3 sequence in the reference set of (b);

(d) selecting segments from the closest match(es) identified in step (c) for inclusion in a library comprising synthetic polynucleotides that encode an antibody heavy chain; and

(e) synthesizing the synthetic polynucleotides that encode an antibody heavy chain;

wherein the diversity of the polynucleotides encoding the at least about 10⁴ unique antibody CDRH3 amino acid sequences is created by polynucleotides having CDRH3 sequences that are different from the CDRH3 sequences of other polynucleotides; and

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.

15. The method of claim 14, wherein the unique sequences of (iv) do not have a stop codon, unpaired Cys residue, N-linked glycosylation motifs, or deamidation motifs.

16. The method of claim 14, wherein the theoretical segment pool contains DH segments 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.

17. A method of making a library comprising synthetic polynucleotides that encode an antibody heavy chain 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],

the method comprising;

(a) providing a theoretical segment pool containing TN1, DH, N2, and H3-JH segments, wherein 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;

(b) providing a reference set of preimmune CDRH3 sequences having sequence diversities and length diversities similar to naturally occurring human antibody sequences before these sequences have undergone negative selection and/or hypermutation;

(c) utilizing combinations of the TN1, DH, N2, and H3-JH segments contained in the theoretical segment pool of (a) to identify the closest match(es) to each CDRH3 sequence in the reference set of (b);

(d) selecting segments from the closest match(es) identified in step (c) for inclusion in a library comprising synthetic polynucleotides that encode an antibody heavy chain; and

(e) synthesizing the synthetic polynucleotides that encode an antibody heavy chain;

wherein the diversity of the polynucleotides encoding the at least about 10⁴ unique antibody CDRH3 amino acid sequences is created by polynucleotides having CDRH3 sequences that are different from the CDRH3 sequences of other polynucleotides; and

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.