Focused libraries of genetic packages

• US 10,604,753 B2
• Filed: 10/30/2017
• Issued: 03/31/2020
• Est. Priority Date: 12/18/2000
• Status: Expired due to Term

• Current Assignee: Takeda Pharmaceutical Company Limited
• Original Assignee: Dyax Corporation (Shire plc)
• Inventors: Ladner, Robert Charles
• Primary Examiner(s): Boesen, Christian C
• Application Number:
  US15/797,927
• Publication Number:
  US 20180291368A1
• Time in Patent Office: 883 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 16/005 constructed by phage libraries
• CPC Class Codes: C07K 2317/565 Complementarity determining region [CDR]
• CPC Class Codes: C12N 15/1037 Screening libraries presented on the surface of microorganisms, e.g. phage display, E. coli display
• 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

Focused libraries of vectors or genetic packages that display, display and express, or comprise a member of a diverse family of antibody peptides, polypeptides or proteins and collectively display, display and express, or comprise at least a portion of the focused diversity of the family. The libraries have length and sequence diversities that mimic that found in native human antibodies.

Claims

1. An antibody library comprising a first set of variegated DNA molecules encoding a first collection of antibody light chains (LC), wherein each light chain comprises an LC CDR1 region, an LC CDR2 region, and an LC CDR3 region, and wherein:

(a) the first collection of antibody light chains are kappa light chains, which comprise a plurality of LC_κ

CDR3 regions selected from the group consisting of;

(1) QQ<

3>

<

1>

<

1>

<

1>

P<

1>

T (SEQ ID NO;

16), wherein <

1>

is a mixture of amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, Y; and

<

3>

is a mixture of amino acid residues Y, A, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, and W;

(2) QQ<

3>

<

3>

<

1>

<

1>

<

1>

P (SEQ ID NO;

103), wherein <

1> and

<

3>

are as defined in (1) above;

(3) QQ<

3>

<

2>

<

1>

<

1>

PP<

1>

T (SEQ ID NO;

17), wherein <

1> and

<

3>

are as defined in (1) above and <

2>

is a mixture of amino acid residues S, A, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, and Y; and

(4) a mixture of any of (1) to (3) set forth above;

or

(b) the first collection of antibody light chains are lambda light chains, which comprise a plurality of LC_λ

CDR3 regions selected from the group consisting of;

(1) <

4>

<

5>

<

4>

<

2>

<

4>

S<

4>

<

4>

<

4>

<

4>

V (SEQ ID NO;

106), wherein <

2>

is a mixture of amino acid residues D, N, A, E, F, G, H, I, K, L, M, P, Q, R, S, T, V, W, and Y;

<

4>

is a mixture of amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, and W; and

<

5>

is a mixture of amino acid residues S, A, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, and Y;

(2) <

5>

SY<

1>

<

5>

S<

5>

<

1>

<

4>

V (SEQ ID NO;

19), wherein <

1>

is a mixture of amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, and Y; and

<

4> and

<

5>

are as defined in (1) above; and

(3) a mixture of (1) and (2) set forth above.

2. The library of claim 1, wherein the first collection of antibody light chains are kappa light chains, which further comprises:

(A) a plurality of LC_κ

CDR1 regions selected from the group consisting of;

(1) RASQ<

1>

V<

2>

<

2>

<

3>

LA (SEQ ID NO;

14), wherein <

1>

is a mixture of amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, and Y;

<

2>

is a mixture of amino acid residues S, A, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, Y; and

<

3>

is a mixture of amino acid residues Y, A, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W and S; and

(2) RASQ<

1>

V<

2>

<

2>

<

2>

<

3>

LA (SEQ ID NO;

15);

wherein <

1>

, <

2>

, and <

3>

are as defined in (1) above; and

(3) a mixture of (1) and (2) set forth above;

(B) a plurality of LC_κ

CDR2 regions <

1>

AS<

2>

R<

4>

<

1>

(SEQ ID NO;

102), wherein <

1>

is a mixture of amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, and Y;

<

2>

is a mixture of amino acid residues S, A, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, and Y; and

<

4>

is a mixture of amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, and Y;

or

both (A) and (B).

3. The library of claim 1, wherein the LC_κ

CDR3s (1), (2) and (3) are present in the library in a ratio of 0.65;

0.1;

0.25.

4. The library of claim 2, wherein the LC_κ

CDR1s (1) and (2) are present in the library in a ratio of 0.68;

0.32.

5. The library of claim 4, wherein the first collection of antibody light chains are kappa light chains, and wherein the library further comprises a second set of variegated DNA molecules encoding a second collection of antibody light chains, which are lambda light chains comprising a plurality of LC_λ

CDR3 regions selected from the group consisting of;

(1) <

4>

<

5>

<

4>

<

2>

<

4>

S<

4>

<

4>

<

4>

<

4>

V (SEQ ID NO;

106), wherein <

2>

is a mixture of amino acid residues D, N, A, E, F, G, H, I, K, L, M, P, Q, R, S, T, V, W, and Y;

<

4>

is a mixture of amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, and W; and

<

5>

is a mixture of amino acid residues S, A, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, and Y;

(2) <

5>

SY<

1>

<

5>

S<

5>

<

1>

<

4>

V (SEQ ID NO;

19), wherein <

1>

is a mixture of amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, and Y; and

<

4> and

<

5>

are as defined in (1) above; and

(3) a mixture of (1) and (2) set forth above.

6. The library of claim 5, wherein the second collection of antibody light chains further comprises:

(A) a plurality of LC_λ

CDR1 regions selected from the group consisting of;

(1) TG<

1>

SS<

2>

VG<

1>

<

3>

<

2>

<

3>

VS (SEQ ID NO;

18), wherein <

1>

is a mixture of amino acid residues T, G, A, D, E, F, H, I, K, L, M, N, P, Q, R, S, V, W, and Y, <

2>

is a mixture of amino acid residues D, N, A, E, F, G, H, I, K, L, M, P, Q, R, S, T, V, W, and Y, and <

3>

is a mixture of amino acid residues Y, A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, and W;

(2) G<

2>

<

4>

L<

4>

<

4>

<

4>

<

3>

<

4>

<

4>

(SEQ ID NO;

104), wherein <

2>

is as defined in (1) above, <

3>

is a mixture of amino acid residues Y, A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, and <

4>

is a mixture of amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, and Y; and

(3) a mixture of (1) and (2) set forth above;

(B) a plurality of LCλ

CDR2 regions <

4>

<

4>

<

4>

<

2>

RPS (SEQ ID NO;

105), wherein <

2>

is a mixture of amino acid residues D, N, A, E, F, G, H, I, K, L, M, P, Q, R, S, T, V, W, and Y, and <

4>

is a mixture of amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, and W;

or

both (A) and (B).

7. The library of claim 6, wherein the LC_λ

CDR3s (1) and (2) are present in the library in an equimolar mixture.

8. The library of claim 6, wherein the LC_λ

CDR1s (1) and (2) are present in the library in a ratio of 0.67;

0.33.

9. The library of claim 1, wherein the first collection of antibody light chains are lambda chains, which further comprise

(A) a plurality of LC_λ

CDR1 regions selected from the group consisting of;

(1) TG<

1>

SS<

2>

VG<

1>

<

3>

<

2>

<

3>

VS (SEQ ID NO;

18), wherein <

1>

is a mixture of amino acid residues T, G, A, D, E, F, H, I, K, L, M, N, P, Q, R, S, V, W, and Y, <

2>

is a mixture of amino acid residues D, N and, A, E, F, G, H, I, K, L, M, P, Q, R, S, T, V, W, and Y, and <

3>

is a mixture of amino acid residues Y, A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, and W;

(2) G<

2>

<

4>

L<

4>

<

4>

<

4>

<

3>

<

4>

<

4>

(SEQ ID NO;

104), wherein <

2>

is as defined in (1) above, <

3>

is a mixture of amino acid residues Y, A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, and <

4>

is a mixture of amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, and Y; and

(3) a mixture of (1) and (2) set forth above;

(B) a plurality of LC_λ

CDR2 regions <

4>

<

4>

<

4>

<

2>

RPS (SEQ ID NO;

105), wherein <

2>

is a mixture of amino acid residues D, N, A, E, F, G, H, I, K, L, M, P, Q, R, S, T, V, W, and Y and <

4>

is a mixture of amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, and W;

or

both (A) and (B).

10. The library of claim 9, wherein the LC_λ

CDR3s (1) and (2) are present in the library in an equimolar mixture.

11. The library of claim 9, wherein the LC_λ

CDR1s (1) and (2) are present in the library in a ratio of 0.67;

0.33.

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

13. The library of claim 12, wherein the vectors are yeast vectors or phagemids.

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

15. The library of claim 14, wherein the genetic packages are cells, spores, or viral particles.

16. The library of claim 15, wherein the genetic packages are phage particles or yeast cells, which display the collection of antibody light chains encoded by the variegated DNA molecules in the library.