IP Library › Granted Patent US 12,252,543

Granted Patent B2

US 12,252,543 · App. 16/173,150 · Granted Mar 18, 2025

Multispecific NK engager protein

Inventors: Laurent Gauthier (Marseilles, FR); Nadia Anceriz (Aubagne, FR); Ariane Morel (Marseilles, FR); Benjamin Rossi (Marseilles, FR)

Assignee: INNATE PHARMA

C07K16/2896 A61K39/4613 A61K39/464412 C07K16/2803 C07K16/2809 C07K16/283 C07K16/2866 C07K16/2887 A61K2239/48 C07K2317/31 C07K2317/522 C07K2317/524 C07K2317/526 C07K2317/565 C07K2317/622 C07K2317/71 C07K2317/732 C07K2317/75 C07K2317/92 C07K2319/30

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Quick Facts

Patent No.: US 12,252,543
App. No.: 16/173,150
Granted: Mar 18, 2025
Kind: B2

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Abstract

Multispecific proteins that bind and specifically redirect NK cells to lyse a target cell of interest are provided without non-specific activation of NK cells in absence of target cells. The proteins have utility in the treatment of disease, notably cancer or infectious disease.

Claims (154)

1. A nucleic acid which encodes or nucleic acids which separately or in combination encode a multispecific antigen binding protein comprising:

(a) a first antigen binding domain (ABD) which:

(i) monovalently binds to a human NKp46 polypeptide having the amino acid sequence of SEQ ID NO: 1; and

(ii) comprises a first immunoglobulin heavy chain variable region (VH1) and a first immunoglobulin light chain variable region (VL1);

(b) a second ABD which:

(i) binds to a first antigen of interest other than an internalizing cytokine receptor alpha chain or B-cell maturation antigen (BCMA); and

(ii) comprises a second immunoglobulin heavy chain variable region (VH2) and a second immunoglobulin light chain variable region (VL2); and

or a vector or vectors containing the nucleic acid or nucleic acids.

2. An isolated cell which comprises a nucleic acid which encodes or nucleic acids which separately or in combination encode a multispecific antigen binding protein according to claim 1 .

3. A method of producing a multispecific antigen binding protein comprising culturing an isolated cell according to claim 2 .

4. A nucleic acid which encodes or nucleic acids which separately or in combination encode a multispecific antigen binding protein or a vector or vectors containing the nucleic acid or nucleic acids according to claim 1 , wherein the first antigen of interest is expressed by a solid tumor.

5. A nucleic acid which encodes or nucleic acids which separately or in combination encode a multispecific antigen binding protein or a vector or vectors containing the nucleic acid or nucleic acids according to claim 1 , wherein the first antigen of interest is expressed by a hematological cancer.

6. A nucleic acid or nucleic acids encoding a multispecific antigen binding protein or a vector or vectors containing the nucleic acid or nucleic acids according to claim 1 , wherein the antigen of interest is expressed by an infectious agent.

7. A nucleic acid which encodes or nucleic acids which separately or in combination encode a multispecific antigen binding protein or a vector or vectors containing the nucleic acid or nucleic acids according to claim 1 , wherein:

(i) the dimeric human Fc polypeptide is modified to enhance CD16A binding relative to the corresponding wild-type Fc polypeptide;

(ii) the dimeric human Fc polypeptide is capable of binding to human neonatal Fc receptor (FcRn);

(iii) the multispecific protein binds to the first antigen of interest monovalently;

(iv) the multispecific antigen binding protein mediates lysis of target cells by a combination of NKp46 signaling and CD16A-mediated antibody-dependent cell-mediated cytotoxicity (ADCC);

(v) the multispecific antigen binding protein mediates NKp46-signaling-mediated lysis and CD16-mediated lysis resulting in a synergistic enhancement in the lysis of target cells;

(vi) the multispecific antigen binding protein mediates lysis of target cells by a combination of NKp46-signaling, CD137-signaling and CD16A-mediated ADCC;

(vii) the second ABD comprises a monovalent or bivalent antibody or antibody fragment comprising the VH2 and the VL2;

(viii) (ix) the spacing between the first ABD and the second ABD is less than 80 angstroms;

(ix) the spacing between the first ABD and the second ABD is about 55 angstroms;

(x) the multispecific antigen binding protein is a heterodimeric, or heterotrimeric protein;

(xi) the multispecific antigen binding protein comprises at least one polypeptide chain that comprises an ABD bound to the dimeric human Fc polypeptide by a flexible linker;

(xii) the multispecific antigen binding protein comprises at least one polypeptide chain that comprises an ABD bound to the dimeric human Fc polypeptide by a flexible polypeptide linker;

(xiii)

(xiii-1) the multispecific antigen binding protein comprises: a first polypeptide comprising an immunoglobulin heavy chain variable region (VH) and an immunoglobulin light chain variable region (VL) separated by a polypeptide linker; and a second polypeptide comprising a VH and a VL separated by a polypeptide linker;

(xiii-2) the multispecific antigen binding protein comprises:

a first polypeptide comprising the VH1 and the VL1 separated by a polypeptide linker; and a second polypeptide comprising the VH2 and the VL2 separated by a polypeptide linker;

(xiii-3) the multispecific antigen binding protein comprises: a first polypeptide comprising the VH1 and the VL2; and a second polypeptide comprising the VH2 and the VL1;

(xiii-4) the first ABD comprises a Fab comprising the VH1 and the VL1 or comprises the VH1 and the VL1 separated by a linker, optionally by a polypeptide linker;

(xiii-5) the second ABD comprises a Fab comprising the VH2 and the VL2 or comprises the VH2 and VL2 separated by a linker, optionally by a linker comprising a linear or cyclic peptide;

(xiii-6) the first ABD comprises a Fab comprising the VH1 and the VL1 or comprises the VH1 and the VL1 separated by a linker; and the second ABD comprises a Fab comprising the VH2 and the VL2 or comprises the VH2 and the VL2 separated by a linker;

(xiii-7) the first ABD comprises a Fab comprising the VH1 and the VL1; and the second ABD comprises the VH2 and the VL2 separated by a linker; or

(xiii-8) the first ABD comprises the VH1 and the VL1 separated by a linker; and the second ABD comprises a Fab comprising the VH2 and the VL2;

(xiv) the multispecific antigen binding protein further comprises a third ABD which binds to a second antigen of interest, wherein the second antigen of interest is same as or different from the first antigen of interest and is different from said human NKp46 polypeptide;

(xv) the first antigen of interest comprises a cell surface polypeptide which is, when bound by a full-length IgG1 antibody,

(xv-1) capable of undergoing intracellular internalization or

(xv-2) not capable of undergoing intracellular internalization;

(xvi) the multispecific protein does not substantially increase or induce intracellular internalization of the first antigen of interest on target cells;

(xvii) the multispecific antigen binding protein upregulates CD137 expression on NK cells;

(xviii) the multispecific antigen binding protein elicits the expression of CD137 on the surface of NKp46 + CD16 + NK cells; or

(xix) any combination of the foregoing.

8. A nucleic acid which encodes or nucleic acids which separately or in combination encode a multispecific antigen binding protein or a vector or vectors containing the nucleic acid or nucleic acids according to claim 1 , wherein the dimeric human Fc polypeptide is capable of binding to human FcRn.

9. A nucleic acid which encodes or nucleic acids which separately or in combination encode a multispecific antigen binding protein or a vector or vectors containing the nucleic acid or nucleic acids according to claim 8 , wherein the dimeric human Fc polypeptide comprises one or more amino acid modifications that increase binding affinity for CD16A.

10. A nucleic acid which encodes or nucleic acids which separately or in combination encode a multispecific antigen binding protein or a vector or vectors containing the nucleic acid or nucleic acids according to claim 1 , wherein the multispecific antigen binding protein comprises a first (central) polypeptide chain comprising one variable domain that, together with a complementary variable domain comprised in a second polypeptide chain, forms an antigen binding domain specific for one antigen of interest, and the first (central) polypeptide chain further comprises a second variable domain that is paired with a complementary variable domain to form an antigen binding domain specific for another antigen of interest, wherein the variable domain that is complementary to the second variable domain is comprised in the central polypeptide or in a third polypeptide chain.

11. A nucleic acid which encodes or nucleic acids which separately or in combination encode a multispecific antigen binding protein or a vector or vectors containing the nucleic acid or nucleic acids according to claim 1 , wherein the multispecific antigen binding protein is a hetero-multimeric protein comprising at least:

(a) a first polypeptide chain comprising at least:

(a-1) first variable domain (V1);

(a-2) a first human constant domain (C1) fused to the V1; and

(a-3) a first human Fc domain (Fc1);

(b) a second polypeptide chain comprising at least:

(b-1) a second variable domain (V2);

(b-2) a second human constant domain (C2) fused to the V2; and

(b-3) a second human Fc domain (Fc2),

wherein:

(i) the V1 and the V2 are a VH and a VL, respectively, or are a VL and a VH, respectively; and

(ii) the C1 and the C2 are a CH1 domain and a Cκ domain, respectively, or a Cκ domain and a CH1 domain, respectively,

and wherein the first and second polypeptide chains undergo CH1-Cκ dimerization and are bound to one another by disulfide bonds formed between the C1 and the C2, and by non-covalent bonds between the CH3 domain of the Fc1 and the CH3 domain of the Fc2.

12. A nucleic acid or nucleic acids encoding a multispecific antigen binding protein or a vector or vectors containing the nucleic acid or nucleic acids according to claim 1 , wherein the protein is an isolated heterodimeric polypeptide comprising:

(a) a first polypeptide chain comprising, from N- to C-terminus;

(a-1) a second variable domain (V1-2);

(a-2) a third variable domain (V1-3);

(a-3) a Fc domain or portion thereof;

(a-4) a first variable domain (V1-1); and

(a-5) a first CH1 or Cκ constant region; and

(b) a second polypeptide chain comprising, from N- to C-terminus:

(b-1) a first variable domain (V2-1);

(b-2) a second CH1 or Cκ constant region; and

(b-3) an Fc domain or portion thereof,

wherein the second CH1 or Cκ constant region is selected to be complementary to the first CH1 or Cκ constant region, such that the first and second polypeptides form a CH1-Cκ heterodimer in which: the V1-1 and the V2-1 together form an antigen binding domain; and the V1-2 and the V1-3 together form an antigen binding domain.

13. A nucleic acid which encodes or nucleic acids which separately or in combination encode a multispecific antigen binding protein or a vector or vectors containing the nucleic acid or nucleic acids according to claim 1 , wherein the protein is an isolated heterodimeric polypeptide comprising:

(a) a first polypeptide chain comprising, from N- to C-terminus:

(a-1) a first variable domain (V1-1);

(a-2) a first constant domain (C1);

(a-3) a first human Fc domain (Fc1);

(a-4) a second variable domain (V1-2); and

(a-5) a third variable domain (V1-3); and

(b) a second polypeptide chain comprising, from N- to C-terminus:

(b-1) a first variable domain (V2-1);

(b-2) a second constant domain (C2); and

(b-3) a second human Fc domain (Fc2),

wherein:

(i) the C1 and the C2 are a CH1 domain and a Cκ domain, respectively, or a Cκ domain and a CH1 domain, respectively;

(ii) the first and second polypeptide chains form a CH1-Cκ heterodimer;

(iii) the V1-1 and the V2-1 form an ABD; and

(iv) the V1-2 and the V1-3 form an ABD.

14. A nucleic acid which encodes or nucleic acids which separately or in combination encode a multispecific antigen binding protein or a vector or vectors containing the nucleic acid or nucleic acids according to claim 1 , wherein the protein is a heterodimer and comprises:

(a) a first polypeptide having a domain arrangement:

V a-1 -(CH1 or CK) a -human Fc domain-V a-2 -V b-2 ,

and

(b) a second polypeptide chain having a domain arrangement:

V b-1 -(CH1 or CK) b -human Fc domain,

wherein one of the V a-1 and the V b-1 is a VL and the other is a VH, one of the V a-2 and the V b-2 is a VL, and the other is a VH;

wherein the (CH1 or CK) b dimerizes with the (CH1 or CK) a , and the V b-1 forms an ABD together with the V a-1 , and wherein the V a-2 and the V b-2 together form an ABD.

15. A nucleic acid which encodes or nucleic acids which separately or in combination encode a multispecific antigen binding protein or a vector or vectors containing the nucleic acid or nucleic acids according to claim 14 , wherein the V a-2 and the V b-2 together form the first ABD.

16. A nucleic acid or nucleic acids encoding a multispecific antigen binding protein or a vector or vectors containing the nucleic acid or nucleic acids according to claim 1 , wherein the protein is a heterodimer and comprises a domain arrangement:

wherein:

(a) one of the V a-1 and the V b-1 is a VH and the other is a VL; and

(b) one of the V a-2 and the V b-2 is a VH and the other is a VL,

such that:

(i) the V a-1 and the V b-1 form an ABD which binds to said human NKp46 polypeptide, and the V a-2 and the V b-2 form an ABD which binds to an antigen of interest; or

(ii) the V a-1 and the V b-1 form an ABD which binds to an antigen of interest, and the V a-2 and the V b-2 form an ABD which binds to said human NKp46 polypeptide.

17. A nucleic acid or nucleic acids encoding a multispecific antigen binding protein or a vector or vectors containing the nucleic acid or nucleic acids according to claim 1 , wherein the protein is a heterotrimer comprising a domain arrangement:

wherein: (a) one of the V a-1 and the V b-1 is a VH and the other is a VL such that the V a-1 and the V b-1 form an ABD; and

(b) one of the V a-2 and the V b-2 is a VH and the other is a VL such that the V a-2 and the V b-2 form an ABD,

wherein the chain 1 and the chain 2 associate by CH3-CH3 dimerization and the chain 1 and the chain 3 associate by CH1-C K dimerization.

18. A nucleic acid or nucleic acids encoding a multispecific antigen binding protein or a vector or vectors containing the nucleic acid or nucleic acids according to claim 17 , wherein the chain 2 comprises a domain arrangement:

V b-2 -V a-2 -(C K or CH1)-(hinge or linker)-CH2-CH3.

19. A nucleic acid which encodes or nucleic acids which separately or in combination encode a multispecific antigen binding protein or a vector or vectors containing the nucleic acid or nucleic acids according to claim 1 , wherein the multispecific antigen binding protein comprises a polypeptide comprising:

(a) a CH1 or C K domain;

(b) a hinge domain; and

where in the CH1 or C K domain is separated from the CH2 or Fc domain by the hinge domain, optionally wherein the hinge domain:

(i) comprises a cysteine residue capable of forming an interchain disulfide bond;

(ii) is modified to delete or substitute a cysteine residue; or

(iii) is derived from an IgM isotype antibody.

20. A nucleic acid or nucleic acids which separately or in combination encode a multispecific antigen binding protein or a vector or vectors containing the nucleic acid or nucleic acids according to claim 1 , wherein the first ABD binds to the D2 domain of said human NKp46 polypeptide.

21. A nucleic acid which encodes or nucleic acids which separately or in combination encode a multispecific antigen binding protein or a vector or vectors containing the nucleic acid or nucleic acids according to claim 1 , wherein:

(a) the VH1 comprises HCDR1, 2, and 3; and

(b) the VL1 comprises LCDR1, 2, and 3,

and wherein:

(i) the amino acid sequences of the HCDR1, 2, and 3 are respectively identical to those of the heavy chain variable region of SEQ ID NO: 3, and the amino acid sequences of the LCDR1, 2, and 3 are respectively identical to those of the light chain variable region of SEQ ID NO: 4;

(ii) the amino acid sequences of the HCDR1, 2, and 3 are respectively identical to those of the heavy chain variable region of SEQ ID NO: 5, and the amino acid sequences of the LCDR1, 2, and 3 are respectively identical to those of the light chain variable region of SEQ ID NO: 6;

(iii) the amino acid sequences of the HCDR1, 2, and 3 are respectively identical to those of the heavy chain variable region of SEQ ID NO: 7, and the amino acid sequences of the LCDR1, 2, and 3 are respectively identical to those of the light chain variable region of SEQ ID NO: 8;

(iv) the amino acid sequences of the HCDR1, 2, and 3 are respectively identical to those of the heavy chain variable region of SEQ ID NO: 9, and the amino acid sequences of the LCDR1, 2, and 3 are respectively identical to those of the light chain variable region of SEQ ID NO: 10;

(v) the amino acid sequences of the HCDR1, 2, and 3 are respectively identical to those of the heavy chain variable region of SEQ ID NO: 11, and the amino acid sequences of the LCDR1, 2, and 3 are respectively identical to those of the light chain variable region of SEQ ID NO: 12; or

(vi) the amino acid sequences of the HCDR1, 2, and 3 are respectively identical to those of the heavy chain variable region of SEQ ID NO: 13, and the amino acid sequences of the LCDR1, 2, and 3 are respectively identical to those of the light chain variable region of SEQ ID NO: 14.

22. A nucleic acid which encodes or nucleic acids which separately or in combination encode a multispecific antigen binding protein or a vector or vectors containing the nucleic acid or nucleic acids according to claim 1 , wherein:

(i) at least one of the ABDs comprises framework residues from a human framework region and/or is humanized;

(ii) the first antigen of interest is a cell surface polypeptide capable of undergoing intracellular internalization when bound by a full-length IgG1 antibody; and/or

(iii) the multispecific antigen binding protein does not substantially increase or induce intracellular internalization of the first antigen of interest on target cells.

23. A nucleic acid which encodes or nucleic acids which separately or in combination encode a multispecific antigen binding protein or a vector or vectors containing the nucleic acid or nucleic acids according to claim 1 , wherein the multispecific antigen binding protein is an isolated heterodimeric polypeptide comprising Format 13 as shown in FIG. 2 D .

24. A nucleic acid which encodes or nucleic acids which separately or in combination encode a multispecific antigen binding protein or a vector or vectors containing the nucleic acid or nucleic acids according to claim 14 , wherein: (i) the VH1 comprises the HCDR1, 2, and 3 amino acid sequences according to Kabat of SEQ ID NOS: 15, 18 and 21, respectively; and (ii) the VL1 comprises the LCDR1, 2, and 3 amino acid sequences according to Kabat of SEQ ID NOS: 24, 27 and 28, respectively.

25. A nucleic acid which encodes or nucleic acids which separately or in combination encode a multispecific antigen binding protein or a vector or vectors containing the nucleic acid or nucleic acids, wherein the multispecific antigen binding protein comprises:

(a) a first antigen binding domain (ABD) which:

(i) binds to a human NKp46 polypeptide having the amino acid sequence of SEQ ID NO: 1; and

(ii) comprises a first immunoglobulin heavy chain variable region (VH1) comprising HCDR1, 2, and 3 and a first immunoglobulin light chain variable region (VL1) comprising LCDR1, 2, and 3;

(b) a second ABD which binds to a first antigen of interest other than an internalizing cytokine receptor alpha chain or B-cell maturation antigen (BCMA),

or a vector or vectors containing the nucleic acid or nucleic acids, wherein:

26. A nucleic acid which encodes or nucleic acids which separately or in combination encode a multispecific antigen binding protein according to claim 25 , wherein the multispecific antigen binding protein further comprises a dimeric Fc polypeptide capable of binding to CD16A, optionally wherein:

(i) the dimeric Fc polypeptide is a dimeric human Fc polypeptide, optionally comprising one or more amino acid modifications that increase binding affinity for CD16A relative to the corresponding wild-type Fc polypeptide;

(ii) the first antigen of interest is expressed by a cancer cell, optionally by a hematological cancer or a solid tumor;

(iii) the multispecific antigen binding protein binds to said human NKp46 polypeptide monovalently;

(iv) the multispecific antigen binding protein binds to the first antigen of interest monovalently or bivalently; and/or

(v) the dimeric Fc polypeptide is capable of binding to human FcRn.

Continuity (4)

Division 15190337 · Jun 23, 2016

Continuation In Part PCTEP2015064063 · Jun 23, 2015

Provisional Application 62271459 · Dec 28, 2015

Related Publication 20190055315A1 · Feb 21, 2019

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