Patent ID: 8691730
Filing Date: 2014-04-08
Classification: C07K,C40B

Abstract:
1. A library comprising synthetic polynucleotides that encode an antibody heavy chain or alternative scaffold containing at least about 10 6 unique antibody CDRH3 amino acid sequences, wherein each of the polynucleotides encoding the at least about 10 6 unique antibody CDRH3 amino acid sequences has an antibody CDRH3 amino acid sequence represented by the following formula: wherein (i) X is selected from the group consisting of G, D, E and nothing; (ii) N1 is an amino acid sequence selected from the group consisting of G, P, R, A, S, L, T, V, GG, GP, GR, GA, GS, GL, GT, GV, PG, RG, AG, SG, LG, TG, VG, PP, PR, PA, PS, PL, PT, PV, RP, AP, SP, LP, TP, VP, GGG, GPG, GRG, GAG, GSG, GLG, GTG, GVG, PGG, RGG, AGG, SGG, LGG, TGG, VGG, GGP, GGR, GGA, GGS, GGL, GGT, GGV, D, E, F, H, I, K, M, Q, W, Y, AR, AS, AT, AY, DL, DT, EA, EK, FH, FS, HL, HW, IS, KV, LD, LE, LR, LS, LT, NR, NT, QE, QL, QT, RA, RD, RE, RF, RH, RL, RR, RS, RV, SA, SD, SE, SF, SI, SK, SL, SQ, SR, SS, ST, SV, TA, TR, TS, TT, TW, VD, VS, WS, YS, AAE, AYH, DTL, EKR, ISR, NTP, PKS, PRP, PTA, PTQ, REL, RPL, SAA, SAL, SGL, SSE, TGL, WGT; (iii) DH is all of a human CDRH3 DH amino acid sequence, wherein the DH amino acid sequence is selected from the group consisting of ATT, GAT, GIV, IVG, VGA, GATT, GIVG (SEQ ID NO: 624), IVGA (SEQ ID NO: 625), VGAT (SEQ ID NO: 626), GIVGA (SEQ ID NO: 627), IVGAT (SEQ ID NO: 628), VGATT (SEQ ID NO: 629), GIVGAT (SEQ ID NO: 630), IVGATT (SEQ ID NO: 631), GIVGATT (SEQ ID NO: 13), YSG, YSGS (SEQ ID NO: 632), YSGSY (SEQ ID NO: 633), YSGSYY (SEQ ID NO: 14), CSSTSC (SEQ ID NO: 622), CSSTSCY (SEQ ID NO: 620), YCSSTSC (SEQ ID NO: 621), CSSTSCYT (SEQ ID NO: 617), GYCSSTSC (SEQ ID NO: 618), YCSSTSCY (SEQ ID NO: 619), GYCSSTSCY (SEQ ID NO: 615), YCSSTSCYT (SEQ ID NO: 616), GYCSSTSCYT (SEQ ID NO:10), AAM, DIV, IVV, PAA, VPA, VVP, VVV, DIVV (SEQ ID NO: 634), IVVV (SEQ ID NO: 635), PAAM (SEQ ID NO: 636), VPAA (SEQ ID NO: 637), VVPA (SEQ ID NO: 638), VVVP (SEQ ID NO: 639), DIVVV (SEQ ID NO: 640), IVVVP (SEQ ID NO: 641), VPAAM (SEQ ID NO: 642), VVPAA (SEQ ID NO: 643), VVVPA (SEQ ID NO: 644), DIVVVP (SEQ ID NO: 645), IVVVPA (SEQ ID NO: 646), VVPAAM (SEQ ID NO: 647), VVVPAA (SEQ ID NO: 648), DIVVVPA (SEQ ID NO: 649), IVVVPAA (SEQ ID NO: 650), VVVPAAM (SEQ ID NO: 651), DIVVVPAA (SEQ ID NO: 652), IVVVPAAM (SEQ ID NO: 653), DIVVVPAAM (SEQ ID NO: 11), CSGGSC (SEQ ID NO: 654), CSGGSCY (SEQ ID NO: 655), YCSGGSC (SEQ ID NO: 656), CSGGSCYS (SEQ ID NO: 657), GYCSGGSC (SEQ ID NO: 658), YCSGGSCY (SEQ ID NO: 659), GYCSGGSCY (SEQ ID NO: 660), YCSGGSCYS (SEQ ID NO: 661), GYCSGGSCYS (SEQ ID NO: 16), FGV, GVV, IFG, ITI, TIF, VVI, FGVV (SEQ ID NO: 662), GVVI (SEQ ID NO: 663), IFGV (SEQ ID NO: 664), ITIF (SEQ ID NO: 665), TIFG (SEQ ID NO: 666), VVII (SEQ ID NO: 667), FGVVI (SEQ ID NO: 668), GVVII (SEQ ID NO: 669), IFGVV (SEQ ID NO: 670), ITIFG (SEQ ID NO: 671), TIFGV (SEQ ID NO: 672), FGVVII (SEQ ID NO: 673), IFGVVI (SEQ ID NO: 674), ITIFGV (SEQ ID NO: 675), TIFGVV (SEQ ID NO: 676), IFGVVII (SEQ ID NO: 677), ITIFGVV (SEQ ID NO: 678), TIFGVVI (SEQ ID NO: 679), ITIFGVVI (SEQ ID NO: 690), TIFGVVII (SEQ ID NO: 681), ITIFGVVII (SEQ ID NO: 9), ELL, FGE, GEL, LLW, LWF, VLL, WFG, FGEL (SEQ ID NO: 682), GELL (SEQ ID NO: 683), LLWF (SEQ ID NO: 684), LWFG (SEQ ID NO: 685), VLLW (SEQ ID NO: 686), WFGE (SEQ ID NO: 687), FGELL (SEQ ID NO: 688), LLWFG (SEQ ID NO: 689), LWFGE (SEQ ID NO: 690), VLLWF (SEQ ID NO: 691), WFGEL (SEQ ID NO: 692), LLWFGE (SEQ ID NO: 693), LWFGEL (SEQ ID NO: 694), VLLWFG (SEQ ID NO: 695), WFGELL (SEQ ID NO: 696), LLWFGEL (SEQ ID NO: 697), LWFGELL (SEQ ID NO: 698), VLLWFGE (SEQ ID NO: 699), LLWFGELL (SEQ ID NO: 700), VLLWFGEL (SEQ ID NO: 701), VLLWFGELL (SEQ ID NO: 1), GSG, GSY, SGS, SYY, YGS, YYG, YYN, YYY, GSGS (SEQ ID NO: 702), GSYY (SEQ ID NO: 703), SGSY (SEQ ID NO: 704), SYYN (SEQ ID NO: 705), YGSG (SEQ ID NO: 706), YYGS (SEQ ID NO: 707), YYYG (SEQ ID NO: 708), GSGSY (SEQ ID NO: 709), GSYYN (SEQ ID NO: 710), SGSYY (SEQ ID NO: 711), YGSGS (SEQ ID NO: 712), YYGSG (SEQ ID NO: 713), YYYGS (SEQ ID NO: 714), GSGSYY (SEQ ID NO: 715), SGSYYN (SEQ ID NO: 716), YGSGSY (SEQ ID NO: 717), YYGSGS (SEQ ID NO: 718), YYYGSG (SEQ ID NO: 719), GSGSYYN (SEQ ID NO: 720), YGSGSYY (SEQ ID NO: 721), YYGSGSY (SEQ ID NO: 722), YYYGSGS (SEQ ID NO: 723), YGSGSYYN (SEQ ID NO: 724), YYGSGSYY (SEQ ID NO: 725), YYYGSGSY (SEQ ID NO: 726), YYGSGSYYN (SEQ ID NO: 727), YYYGSGSYY (SEQ ID NO: 728), YYYGSGSYYN (SEQ ID NO: 2), GVI, ITM, MVR, RGV, TMV, VII, VRG, GVII (SEQ ID NO: 729), ITMV (SEQ ID NO: 730), MVRG (SEQ ID NO: 731), RGVI (SEQ ID NO: 732), TMVR (SEQ ID NO: 733), VRGV (SEQ ID NO: 734), ITMVR (SEQ ID NO: 735), MVRGV (SEQ ID NO: 736), RGVII (SEQ ID NO: 737), TMVRG (SEQ ID NO: 738), VRGVI (SEQ ID NO: 739), ITMVRG (SEQ ID NO: 740), MVRGVI (SEQ ID NO: 741), TMVRGV (SEQ ID NO: 742), VRGVII (SEQ ID NO: 743), ITMVRGV (SEQ ID NO: 744), MVRGVII (SEQ ID NO: 745), TMVRGVI (SEQ ID NO: 746), ITMVRGVI (SEQ ID NO: 747), TMVRGVII (SEQ ID NO: 748), ITMVRGVII (SEQ ID NO: 3), DSS, GYY, SGY, SSG, YDS, YYD, DSSG (SEQ ID NO: 749), GYYY (SEQ ID NO: 750), SGYY (SEQ ID NO: 751), SSGY (SEQ ID NO: 752), YDSS (SEQ ID NO: 753), YYDS (SEQ ID NO: 754), YYYD (SEQ ID NO: 755), DSSGY (SEQ ID NO: 756), SGYYY (SEQ ID NO: 757), SSGYY (SEQ ID NO: 758), YDSSG (SEQ ID NO: 759), YYDSS (SEQ ID NO: 760), YYYDS (SEQ ID NO: 761), DSSGYY (SEQ ID NO: 762), SSGYYY (SEQ ID NO: 763, YDSSGY (SEQ ID NO: 764), YYDSSG (SEQ ID NO: 765), YYYDSS (SEQ ID NO: 766), DSSGYYY (SEQ ID NO: 767), YDSSGYY (SEQ ID NO: 768), YYDSSGY (SEQ ID NO: 769), YYYDSSG (SEQ ID NO: 770), YDSSGYYY (SEQ ID NO: 771), YYDSSGYY (SEQ ID NO: 772), YYYDSSGY (SEQ ID NO: 773), YYDSSGYYY (SEQ ID NO: 774), YYYDSSGYY (SEQ ID NO: 775), YYYDSSGYYY (SEQ ID NO: 4), DYG, GDY, YGD, DYGD (SEQ ID NO: 613), YGDY (SEQ ID NO: 614), DYGDY (SEQ ID NO: 12), SYG, YGY, YSY, GYSY (SEQ ID NO: 776), SYGY (SEQ ID NO: 777), YSYG (SEQ ID NO: 778), GYSYG (SEQ ID NO: 779), YSYGY (SEQ ID NO: 780), GYSYGY (SEQ ID NO: 15), SSS, SSW, SWY, SSSW (SEQ ID NO: 781), SSWY (SEQ ID NO: 782), YSSS (SEQ ID NO: 783), GYSSS (SEQ ID NO: 784), SSSWY (SEQ ID NO: 785), YSSSW (SEQ ID NO: 786), GYSSSW (SEQ ID NO: 787), YSSSWY (SEQ ID NO: 788), GYSSSWY (SEQ ID NO: 7), GWY, GYS, SGW, YSS, GYSS (SEQ ID NO: 789), SGWY (SEQ ID NO: 790), SSGW (SEQ ID NO: 791), YSSG (SEQ ID NO: 792), GYSSG (SEQ ID NO: 793), SSGWY (SEQ ID NO: 794), YSSGW (SEQ ID NO: 795), GYSSGW (SEQ ID NO: 796), YSSGWY (SEQ ID NO: 797), GYSSGWY (SEQ ID NO: 5), AVA, GIA, IAV, VAG, AVAG (SEQ ID NO: 798), GIAV (SEQ ID NO: 799), LAVA (SEQ ID NO: 800), GIAVA (SEQ ID NO: 801), IAVAG (SEQ ID NO: 802), GIAVAG (SEQ ID NO: 6), AAA, AAG, IAA, AAAG (SEQ ID NO: 803), GIAA (SEQ ID NO: 804), IAAA (SEQ ID NO: 805), GIAAA (SEQ ID NO: 806), IAAAG (SEQ ID NO: 807), and GIAAAG (SEQ ID NO: 8); (iv) N2 is an amino acid sequence selected from the group consisting of G, P, R, A, S, L, T, V, GG, GP, GR, GA, GS, GL, GT, GV, PG, RG, AG, SG, LG, TG, VG, PP, PR, PA, PS, PL, PT, PV, RP, AP, SP, LP, TP, VP, GGG, GPG, GRG, GAG, GSG, GLG, GTG, GVG, PGG, RGG, AGG, SGG, LGG, TGG, VGG, GGP, GGR, GGA, GGS, GGL, GGT, GGV, D, E, F, H, I, K, M, Q, W, Y, AR, AS, AT, AY, DL, DT, EA, EK, FH, FS, HL, HW, IS, KV, LD, LE, LR, LS, LT, NR, NT, QE, QL, QT, RA, RD, RE, RF, RH, RL, RR, RS, RV, SA, SD, SE, SF, SI, SK, SL, SQ, SR, SS, ST, SV, TA, TR, TS, TT, TW, VD, VS, WS, YS, AAE, AYH, DTL, EKR, ISR, NTP, PKS, PRP, PTA, PTQ, REL, RPL, SAA, SAL, SGL, SSE, TGL, WGT; (v) H3-JH is all of a human CDRH3 H3-JH amino acid sequence, wherein the H3-JH amino acid sequence is selected from the group consisting of AEYFQH (SEQ ID NO: 17), EYFQH (SEQ ID NO: 583), YFQH (SEQ ID NO: 584), FQH, QH, H, YWYFDL (SEQ ID NO: 18), WYFDL (SEQ ID NO: 585), YFDL (SEQ ID NO: 586), FDL, DL, L, AFDV (SEQ ID NO: 19), FDV, DV, V, YFDY (SEQ ID NO: 20), FDY, DY, Y, NWFDS (SEQ ID NO: 21), WFDS (SEQ ID NO: 587), FDS, DS, S, YYYYYGMDV (SEQ ID NO: 22), YYYYGMDV (SEQ ID NO: 588), YYYGMDV (SEQ ID NO: 589), YYGMDV (SEQ ID NO: 590), YGMDV (SEQ ID NO: 591), GMDV (SEQ ID NO: 592), and MDV; wherein the diversity of the polynucleotides encoding the at least about 10 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, γB-crystallin/ubiquitin, CTLD