Antibody libraries with maximized antibody developability characteristics
Antibody libraries comprising a plurality of heavy chain variable domains and/or a plurality of light chain variable domains, which comprise complementary determining regions (CDRs) found in naturally-occurring human antibodies, and methods of making such antibody libraries. The antibody libraries are free of members that comprise one or more liabilities affecting one or more features of such members. Further, the antibody libraries comprise members having heavy chain and/or light chain CDRs not found in the same naturally-occurring human antibody.
1. A method for producing an antibody library, the method comprising: providing:
(a) a first plurality of nucleic acids encoding amino acid sequences of one or more naturally occurring human antibody heavy chain CDR1 fragments,
(b) a second plurality of nucleic acids encoding amino acid sequences of one or more naturally occurring human antibody heavy chain CDR2 fragments,
(c) a third plurality of nucleic acids encoding amino acid sequences of one or more naturally occurring human antibody heavy chain CDR3 fragments,
(d) a nucleic acid gene encoding amino acid sequences of an antibody heavy chain variable domain comprising a heavy chain CDR1 region, a heavy chain CDR2 region, and a heavy chain CDR3 region,
(e) a fourth plurality of nucleic acids encoding amino acid sequences of one or more naturally occurring human antibody light chain CDR1 fragments,
(f) a fifth plurality of nucleic acids encoding amino acid sequences of one or more naturally occurring human antibody light chain CDR2 fragments,
(g) a sixth plurality of nucleic acids encoding amino acid sequences of one or more naturally occurring human antibody light chain CDR3 fragments, and
(h) a nucleic acid gene encoding amino acid sequences of an antibody light chain variable domain comprising a light chain CDR1 region, a light chain CDR2 region, and a light chain CDR3 region;
inserting the first plurality of nucleic acids, the second plurality of nucleic acids, and the third plurality of nucleic acids into the heavy chain CDR1 region, the heavy chain CDR2 region, and the heavy chain CDR3 region, respectively, of the gene encoding the antibody heavy chain variable domain, thereby producing a population of nucleic acids encoding an antibody heavy chain variable domain library;
inserting the fourth plurality of nucleic acids, the fifth plurality of nucleic acids, and the sixth plurality of nucleic acids into the light chain CDR1 region, the light chain CDR2 region, and the light chain CDR3 region, respectively, of the gene encoding the antibody light chain variable domain, thereby producing a population of nucleic acids encoding an antibody light chain variable domain library; and
combining the population of nucleic acids encoding the antibody heavy chain variable domain library to the population of nucleic acids encoding an antibody light chain variable domain library, thereby producing an antibody library;
wherein the library comprises nucleic acids encoding amino acid sequences of a heavy chain framework region 1, a heavy chain framework region 2, a heavy chain framework region 3, and a heavy chain framework region 4;
wherein the library comprises nucleic acids encoding amino acid sequences of a light chain framework region 1, a light chain framework region 2, a light chain framework region 3, and a light chain framework region 4; and
a plurality of nucleic acids encoding a population of heavy chain domains comprising one or more CDR1s, one or more CDR2s, and one or more CDR3s located at the CDR1 region, the CDR2 region, and the CDR3 region of a heavy chain gene, respectively;
wherein at least 90% of the one or more heavy chain CDR1s and at least 90% of the one or more heavy chain CDR2s are free of amino acid sequence liabilities, wherein the amino acid sequence liabilities are: (i) a glycosylation site comprising the motif NXS, NXT, or NXC, in which X represents any naturally occurring amino acid residue except for proline; (ii) a deamidation site comprising the motif of NG, NS, NT, NN, NA, NH, ND, NQ, NF, NW or NY; (iii) an isomerization site comprising the motif of DT, DH, DS, DG, DN, DR, DY or DD; (iv) any cysteines; (v) net charge greater than 1; (vi) a tripeptide motif containing at least two residues with aromatic side chains comprising F, H, W or Y; (vii) a poly specificity site comprising the motif GG, GGG, RR, VG, W, WV, WW, WWW, YY, or WXW, in which X represents any amino acid residue; (viii) a protease sensitive or hydrolysis prone site comprising the motif of DX, in which X is P, G, S, V, Y, F, Q, K, L, or D; (ix) an integrin binding site comprising RGD, RYD, LDV, or KGD; (x) a lysine glycation site comprising KE, EK, or ED; (xi) a metal catalyzed fragmentation site comprising the motif of HS, SH, KT, HXS, or SXH, in which X represents any amino acid residue; (xii) a polyspecificity aggregation site comprising a motif of X.sub.1X.sub.2X.sub.3, wherein each of X.sub.1, X.sub.2, and X.sub.3 is independently selected from the group consisting of F, I, L, V, W and Y; (xiii) a streptavidin binding motif comprises the motif HPQ, EPDW (SEQ ID NO: 49), PWXWL (SEQ ID NO: 50), in which X represents any amino acid residue, GDWVFI (SEQ ID NO: 51), or PWPWLG (SEQ ID NO: 52); (xiv) one or more arginine residues; (xv) a hydrophobic CDR sequence; and/or (xvi) a CDR mutation that reduces binding to protein A said CDR mutation comprising any mutation in the last amino acid of the CDR2, according to the IMGT definition, to A, G, C, D, E, F, G, H, I, L, M, N, P, Q, S, V, W or Y;
wherein at least 90% of the one or more heavy chain CDR1s, at least 90% of the one or more heavy chain CDR2s, and at least 90% of the one or more heavy chain CDR3s are free of non-functional members; wherein functional members are well folded and can form well folded scFvs or Fabs;
wherein at least two of the heavy chain framework regions 1, 2, 3, and 4 are from a human, humanized or partially humanized heavy chain germline sequence;
wherein each heavy chain framework region and/or light chain framework region can contain up to five amino acid substitutions, and
wherein the nucleic acid sequences encoding the amino acid sequences of the one or more heavy chain CDR3s are from heavy chain CDR3s of human donor lymphocytes.
2. The method of claim 1 , wherein the antibody heavy chain variable domain framework 1, framework 2, framework 3, framework 4 are from a human or humanized VH3-23 (DP-47) sequence.
3. The method of claim 1 , wherein the antibody light chain variable domain framework 1, framework 2, framework 3, framework 4 are from a human or humanized kappa VK1-39 sequence.
4. The method of claim 1 , wherein the antibody library is a fragment antigen-binding (Fab) library.
5. The method of claim 1 , wherein the antibody library is a single-chain variable fragment (scFv) library.
6. The method of claim 1 , wherein the first plurality of nucleic acids, the second plurality of nucleic acids, the third plurality of nucleic acids, the fourth plurality of nucleic acids, the fifth plurality of nucleic acids and the sixth plurality of nucleic acids is produced by a process comprising:
(a) obtaining amino acid sequences of the heavy chain CDR1 regions, heavy chain CDR2 regions, light chain CDR1 regions, light chain CDR2 regions, and light chain CDR3 regions of a population of naturally-occurring human antibodies,
(b) excluding from (a) the heavy chain CDR1 amino acid sequences, the heavy chain CDR2 amino acid sequences, the light chain CDR1 amino acid sequences, light chain CDR2 amino acid sequences, and the light chain CDR3 amino acid sequences that comprise any one or all of (i) to (xiv) to obtain sequence liability-free heavy chain CDR1 sequences, sequence liability-free heavy chain CDR2 sequences, sequence liability-free light chain CDR1 sequences, sequence liability-free light chain CDR2 sequences, and sequence liability-free light chain CDR3 sequences; and
(c) synthesizing the first plurality of nucleic acids that encode the sequence liability-free heavy chain CDR1 regions, the second plurality of nucleic acids that encode the sequence liability-free heavy chain CDR2 regions, the fourth plurality of nucleic acids that encode the sequence liability-free light chain CDR1 regions, the fifth plurality of nucleic acids that encode the sequence liability-free light chain CDR2 regions, and the sixth plurality of nucleic acids that encode the sequence liability-free light chain CDR3 regions.
7. The method of claim 6 , wherein the third plurality of nucleic acids is produced by a process comprising: (a) amplifying the heavy chain CDR3 regions from a population of human B cells; and (b) combining the third plurality of nucleic acids that encode the human heavy chain CDR3 regions obtained in (a) with the remaining CDRs.
8. The method of claim 6 , wherein the processes for producing the first plurality of nucleic acids, the second plurality of nucleic acids, and the third plurality of nucleic acids further comprise isolating functional members from the sequence liability-free heavy chain CDR1 and CDR2 regions, and from the CDR3 regions, wherein:
(i) the functional members of the sequence liability-free heavy chain CDR1 and CDR2 regions or the functional members of the CDR3 regions are isolated by expressing antibodies comprising the sequence liability-free heavy chain CDR1 and CDR2 regions, and the CDR3 regions in host cells in a manner that the antibodies are displayed on surface of the host cells, isolating the host cells that display antibodies on their surfaces, and isolating the CDR1, CDR2, and CDR3 regions in the displayed antibodies, which are functional members of the CDR1, CDR2, and CDR3 regions; or
(ii) the functional members of the sequence liability-free heavy chain CDR1 and CDR2 regions, and the CDR3 regions are isolated by expressing human antibodies comprising the sequence liability-free heavy chain CDR1 and CDR2 regions, and the CDR3 regions in fusion with a folding reporter, which optionally is B lactamase or green fluorescent protein, or fragments thereof, to obtain members with improved folding.