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BR-112018070934-B1 - ICOS-BINDING POLYPEPTIDE (ICOSL) VARIANT, FUSION PROTEIN, CONJUGATE, METHOD FOR ENGINEERING A CELL, INFECTIOUS AGENT, PHARMACEUTICAL COMPOSITION AND USE THEREOF

BR112018070934B1BR 112018070934 B1BR112018070934 B1BR 112018070934B1BR-112018070934-B1

Abstract

The present invention relates to immunomodulatory proteins comprising ICOSL variants and nucleic acids encoding such proteins. The immunomodulatory proteins provide therapeutic utility for a variety of immunological and oncological conditions. Compositions and methods for the production and use of such proteins are provided.

Inventors

  • Ryan Swanson
  • Michael Kornacker

Assignees

  • ALPINE IMMUNE SCIENCES, INC

Dates

Publication Date
20260310
Application Date
20170414
Priority Date
20160415

Claims (20)

  1. 1. ICOS-binding polypeptide (ICOSL) variant, characterized in that it comprises an IgV domain, wherein the ICOSL variant polypeptide comprises SEQ ID NO:32 comprising an N52H amino acid substitution or a portion thereof comprising the IgV domain, wherein the IgV domain is amino acids 19-129 of SEQ ID NO:5, wherein: the ICOSL variant polypeptide comprises an amino acid sequence that is the result of amino acid substitution in SEQ ID NO:32 or a portion of SEQ ID NO:32 comprising the IgV domain; and the ICOSL variant polypeptide specifically binds to the ectodomain of human CD28 with higher affinity compared to unmodified ICOSL.
  2. 2. ICOSL polypeptide variant according to claim 1, characterized in that the unmodified ICOSL comprises (i) the amino acid sequence shown in SEQ ID NO:32, or (ii) a portion thereof comprising an IgV domain or an IgC domain or both.
  3. 3. A variant ICOSL polypeptide according to claim 1 or 2, characterized in that the variant ICOSL comprises up to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 amino acid substitutions; and/or the variant ICOSL comprises an amino acid sequence that is the result of amino acid substitution in SEQ ID NO:32 or the portion thereof comprising the IgV domain.
  4. 4. A variant ICOSL polypeptide according to any one of claims 1 to 3, characterized in that one or more amino acid modifications are selected from N52D, N52Q, N52S, N52Y, N52K, N57D, N57Y, Q100R, Q100K, Q100P, M10V, M10I, V11E, S13G, E16V, S18R, A20V, S25G, F27S, F27C, N30D, Y33del, Q37R, K42E, T43A, Y47H, R61S, R61C, Y62F, L67P, A71T, G72R, L74Q, R75Q, D77G, F78L, L80P, N84Q, E90A, K92R, F93L, H94E, H94D, L96F, L96I, V97A, L98F, S99G, L102R, G103E, V107A, V107I, S109G, S109N, V110D, V110N, V110A, E111del, T113E,H115Q, H115R, V116A, A117T, N119Q, F120I, F120S, S121G, V122A, V122M, S126T, S126R, H129P, S130G,S132F, Q133H, E135K, F138L, T139S, C140del, S142F,I143V, I143T, N144D, Y146C, V151A, Y152C, Y152H, W153R, I154F, N155H, N155Q, K156M, D158G, L161P, L161M, L166Q, N168Q, F172S, L173S, M175T, T190A, T190S, S192G, V193M, N194D, C198R, N201S, L203P, L203F, N207Q, L208P, V210A, S212G, D217V, I218T, I218N, E220G, R221G, R221I, I224V, T225A, N227K or an amino acid substitution conservative of the same.
  5. 5. Variant ICOSL polypeptide according to any one of claims 1 to 4, characterized in that the variant ICOSL polypeptide comprises amino acid substitutions selected from N52H/N57Y/Q100P, N52H/C198R, N52H/C140D/T225A, N52H/C198R/T225A, N52H/K92R, N52H/S99G, N52H/L161P/C198R, N52H/I143T, F120S/Y152H/N201S, N52H/F78L/Q100R, N52H/N57Y/Q100R/V110D, N52H/N57Y/R75Q/Q100R/V110D, N52H/N57Y/Q100R,N52H/N57Y/L74Q/Q100R/V110D, N52H/Q100R, N52H/S121G,A20V/N52H/N57Y/Q100R/S109G, N52H/N57Y/R61S/Q100R/V110D/L173S, N52H/N57Y/Q100R/V122A,N52H/N57Y/Q100R/F172S, N52H/N57Y,N52H/N57Y/Q100R/V110D/S132F/M175T, E16V/N52H/N57Y/Q100R/V110D/H115R/Y152C/K156M/C198R, Q37R/N52H/N57Y/Q100R/V110N/S142F/C198R/D217V/R221G, N52H/N57Y/Q100R/V110D/C198R, N52H/N57Y/Q100R/V110D/V116A/L161M/F172S/S192G/C198R, F27S/N52H/N57Y/V110N,V11E/N30D/N52H/N57Y/H94E/L96I/L98F/N194D/V210A/I218T, N52H/N57Y/H94E/L96I/F120I/S126T/W153R/I218N,N52H/N57Y/Q100R/V110D/A117T/T190S/C198R, N52H/N57Y/Q100R/V110D/F172S/C198R,S25G/F27C/N52H/N57Y/Q100R/V110D/E135K/L173S/C198R, N52H/N57Y/V110A/C198R/R221I,M10I/S13G/N52H/N57Y/D77G/V110A/H129P/I143V/F172S/V193M/C1 98R N52H/N57Y/R61C/Y62F/Q100R/V110N/F120S/C198R,N52H/N57Y/Q100R/V110D/H115R/C198R,N52H/N57Y/Q100R/V110D/N144D/F172S/C198R, N52H/N57Y/Q100R/V110D/C198R/S212G, N52H/N57Y/Q100R/C198R,N52H/N57Y/Q100R/L102R/V110D/H115R/C198R, N52H/C140del/T225A,N52H/F78L/Q100R/C198R,N52H/N57Y/R75Q/Q100P/V110D,N52H/N57Y/L74Q/V110D/S192G, N52H/S121G/C198R,T43A/N52H/N57Y/L74Q/D89G/V110D/F172S,N52H/N57Y/Q100R/V107I/V110D/I154F/C198R/R221G,N52H/N84Q/N119Q, N52H/N84Q, N52H/N84Q/N168Q/N207Q,N52H/N57Y/Q100R/H115R/C198R,N52H/N57Y/Q100R/F172S/C198R,N52H/N57Y/Q100R/H115R/F172S/C198R, N52H/N57Y/Q100R/H115R/I143V/F172S/C198R, N52H/N57Y/Q100R/L102R/H115R/F172S/C198R,N52H/V122A/F172S/C198R,N52H/N57Y/Q10 0R/H115R/F172S/N194D,N52H/N57Y/H115R/F172S/C198R,N52H/N57Y/Q100R/H115R/C198R, N52H/N57Y/H115R,N52H/N57Y/Q100R/H115R, N52H/N57Y/Q100R/H115R/F172S/I224V,N52H/N57Y/Q100R/H115R/F172S, N52H/Q100R/H115R/I143T/F172S, N52H/N57Y/Q100P/H115R/F172S,E16V/N52H/N57Y/Q100R/V110D/H115R/C198R, E16V/N52H/N57Y/Q100R/V110D/H115R/Y152C/K156M/F172S/C198R, N52H/N57Y/Q100P/C198R, N52H/N57Y/Q100PH115R/F172S/C198R, N52H/N57Y/Q100P/F172S/C198R,N52H/N57Y/Q100P/H115R, N52H/N57Y/Q100P/H115R/C198R,N52H/Q100R/C198R, N52H/Q100R/H115R/F172S,N52H/Q100R/F172S/C198R, N52H/Q100R/H115R/F172S/C198R,N52H/N57Y/Q100R/F172S/C198R,N52H/N57Y/Q100P/H115R/F172S/C198R, N52H/Q100R/H115X/F172S/C198R,N52H/N57Y/Q100R/V107I/V110D/S132F/I154F/C198R/R221G, Q37R/ N52H/N57Y/Q100R/V110N/S142F/C198R/D217V/R221G, F27S/N52H/N57Y/V110N, V11E/N30D/N52H/N57Y/H94E/L96I/L98F/N194D/V210A/I218T, S25G/F27C/N52H/N57Y/Q100R/V110D/E135K/L173S/C198R, or A20V/N52H/N57Y/Q100R/S109G.
  6. 6. A variant ICOSL polypeptide according to any one of claims 1 to 5, characterized in that the variant ICOSL polypeptide comprises N52H/N57Y/Q100R amino acid substitutions.
  7. 7. Variant ICOSL polypeptide according to any one of claims 1 to 6, characterized in that: the variant ICOSL polypeptide comprises the IgV domain and the IgC domain; or the IgV domain is the only immunoglobulin superfamily domain of the variant ICOSL polypeptide.
  8. 8. A variant ICOSL polypeptide according to any one of claims 1 to 7, characterized in that it comprises the amino acid sequence shown in any one of the following SEQ ID NOS: 110, 113, 115, 117-119, 128, 135, 280, 283, 285, 287, 289-292, 300-302, 304, 308, 310, 315-318, 321, 364, 365, 367, 372, 375, 376, 381, 435-439, 441-450, 452, 453, 461-470; or that it contains the amino acid substitution N52H; or the amino acid sequence shown in any of the SEQ ID NOS: 198, 201-203, 326-334, 337, 386, and which contains the amino acid substitution N52H.
  9. 9. Variant ICOSL polypeptide according to any one of claims 1 to 8, characterized in that the variant ICOSL polypeptide binds specifically to the ectodomain of human ICOS and the ectodomain of human CD28 with increased affinity compared to the binding of unmodified ICOSL to the ectodomain of human ICOS or human CD28, respectively.
  10. 10. A variant ICOSL polypeptide according to any one of claims 1 to 9, characterized in that: the increased affinity of the human CD28 ectodomain is increased more than 1.2 times, 1.5 times, 2 times, 3 times, 4 times, 5 times, 6 times, 7 times, 8 times, 9 times, 10 times, 20 times, 30 times, 40 times, 50 times or 60 times compared to unmodified ICOSL; and/or the increased affinity of the human ICOS ectodomain is increased more than 1.2 times, 1.5 times, 2 times, 3 times, 4 times, 5 times, 6 times, 7 times, 8 times, 9 times, 10 times, 20 times, 40 times, 50 times, 60 times or 70 times compared to unmodified ICOSL.
  11. 11. A variant ICOSL polypeptide, according to any one of claims 1 to 10, characterized in that it is a soluble protein.
  12. 12. Fusion protein, characterized in that it comprises the ICOSL variant polypeptide as defined in any one of claims 1 to 11 and the Fc domain or its variant, wherein the Fc domain or its variant comprises the amino acid sequence presented in SEQ ID NO:226 or SEQ ID NO:227.
  13. 13. Fusion protein according to claim 12, characterized in that the Fc domain comprises one or more amino acid modifications selected from E233P, L234A, L234V, L235A, L235E, G236del, G237A, S267K, R292C, N297G and V302C, each numbered EU.
  14. 14. Fusion protein according to claim 12 or 13, characterized in that the Fc domain comprises the C220S amino acid modification by EU numbering.
  15. 15. Fusion protein, characterized in that it comprises the variant ICOSL polypeptide as defined in any one of claims 1 to 11 and an Fc domain, wherein the Fc domain comprises the amino acid sequence presented in any one of the SEQ ID NOS: 474, 476, 477, 478 and exhibits reduced effector function.
  16. 16. Fusion protein according to any one of claims 12 to 15, characterized in that the variant ICOSL polypeptide is linked to the Fc domain indirectly via a linker.
  17. 17. Fusion protein according to claim 16, characterized in that the ligand is a G4S ligand.
  18. 18. Fusion protein according to any one of claims 12 to 17, characterized in that the immunomodulatory protein is a homodimer.
  19. 19. Conjugate, characterized in that it comprises a variant ICOSL polypeptide as defined in any one of claims 1 to 11 or a fusion protein as defined in any one of claims 12 to 18, linked to a target moiety that specifically binds to a molecule on the surface of a cell, optionally an immune cell or a tumor cell.
  20. 20. Conjugate according to claim 19, characterized in that the target portion is an antibody or antigen-binding fragment.

Description

CROSS-REFERENCE TO RELATED REQUESTS [001] This application claims priority over U.S. Provisional Patent Application No. 62/323,608 filed April 15, 2016, entitled "ICOS Ligand Variant Immunomodulatory Proteins and Uses Thereof", U.S. Provisional Patent Application No. 62/394,745 filed September 14, 2016, entitled "ICOS Ligand Variant Immunomodulatory Proteins and Uses Thereof", U.S. Provisional Patent Application No. 62/410,842 filed October 20, 2016, entitled "ICOS Ligand Variant Immunomodulatory Proteins and Uses Thereof", U.S. Provisional Patent Application No. 62/472,568 filed March 16, 2017, entitled "ICOS Ligand Variant Immunomodulatory Proteins and Uses Thereof" and U.S. Provisional Patent Application No. 62/475,162 filed March 22, 2017, entitled "ICOS Ligand Variant Immunomodulatory Proteins and Uses Thereof," the contents of each are incorporated herein by reference in their entirety. INCORPORATION FOR REFERENCE PURPOSES IN SEQUENCE LISTING [002] This application is being filed together with a Sequence Listing in electronic format. The Sequence Listing is provided as a file entitled 761612000340SeqList.txt, created on April 13, 2017, which is 979,474 bytes in size. The information in electronic format of the Sequence Listing is incorporated herein by reference in its entirety. FIELD [003] The present invention relates to therapeutic compositions for modulating the immune response in the treatment of cancer and immunological diseases. In some respects, the present invention relates to particular variants of ICOS ligand (ICOSL) that exhibit improved binding affinity with one or both of the cognate binding counterpart proteins ICOS and CD28. BACKGROUND [004] Modulation of the immune response through intervention in the processes occurring at the immunological synapse (IS) formed by and between antigen-presenting cells (APCs) or target cells and lymphocytes is of great medical interest. Mechanistically, cell surface proteins at the IS can involve the coordinated and often simultaneous interaction of multiple protein targets with a single protein to which they bind. IS interactions occur in close association with the junction of two cells, and a single protein in this structure can interact with both a protein on the same cell (cis) as well as a protein on the associated cell (trans), probably at the same time. Although therapeutic agents that can modulate the IS are known, improved therapeutic agents are needed. Immunotherapeutic proteins, including soluble proteins or transmembrane immunomodulatory proteins capable of being expressed on cells, are available to meet these needs. SUMMARY [005] In some embodiments, a variant ICOS-binding polypeptide (ICOSL) is provided herein comprising an IgV domain or specific binding fragment thereof, an IgC domain or specific binding fragment thereof, or both, wherein the variant ICOSL polypeptide contains one or more amino acid substitutions in an unmodified ICOSL or a specific binding fragment thereof corresponding to the selected position(s) of 10, 11, 13, 16, 18, 20, 25, 27, 30, 33, 37, 38, 42, 43, 47, 52, 54, 57, 61, 62, 67, 71, 72, 74, 75, 77, 78, 80, 84, 89, 90, 92, 93, 94, 96, 97, 98, 99, 100, 102, 103, 107, 109, 110, 111, 113, 115, 116, 117, 119, 120, 121, 122, 126, 129, 130, 132, 133, 135, 138, 139, 140, 142, 143, 144, 146, 148, 151, 152, 153, 154, 155, 156, 158, 161, 164, 166, 168, 172, 173, 175, 190, 192, 193, 194 198, 201, 203, 207, 208, 210, 212, 217, 218, 220, 221, 224, 225, or 227 with reference to SEQ ID NO:32. In some embodiments, the unmodified ICOSL is a mammalian ICOSL or a specific linking fragment thereof. In some embodiments, the unmodified ICOSL is a human ICOSL or a specific linking fragment thereof. In some embodiments, the unmodified ICOSL includes (i) the amino acid sequence shown in SEQ ID NO: 32, (ii) an amino acid sequence that has at least 95% sequence identity with SEQ ID NO: 32; or (iii) a portion thereof comprising an IgV domain or IgC domain or specific linking fragments thereof, or both. [006] In some embodiments of any of the ICOSL variant polypeptides described above, the specific binding fragment of the IgV domain or IgC domain has a length of at least 50, 60, 70, 80, 90, 100, 110 or more amino acids; or the specific binding fragment of the IgV domain includes a length that is at least 80% of the length of the IgV domain defined as amino acids 19-129 of SEQ ID NO: 5 and/or the specific binding fragment of the IgC domain includes a length that is at least 80% of the length of the IgC domain defined as amino acids 141-227 of SEQ ID NO: 5. In some embodiments, the variant ICOSL polypeptide includes up to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 amino acid modifications, optionally amino acid substitutions, insertions and/or deletions. In some embodiments, the ICOSL variant includes an amino acid sequence that exhibits at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 9