# US 10,501,545 B2 · Anti-CLL-1 antibodies and methods of use > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 10,501,545 B2 - Document ID: US10501545B2 - Status: Granted - Kind: B2 - Application number: 15/182,327 - Filed: 2016-06-14 - Published: 2016-12-22 - Granted: 2019-12-10 - Earliest claimed: 2015-06-16 - Assignees: Genentech, Inc. - Applicants: Genentech, Inc. - Inventors: Robert F. Kelley; Steven R. Leong; Wei-Ching Liang; Mary Mathieu; Andrew G. Polson; Bing Zheng; Xiaocheng Chen; Cecilia Pui Chi Chiu; Mark S. Dennis; Allen Ebens; Yan Wu - Web page: https://patentgrep.com/patent/US10501545B2 ## CPC - C07K 16/2851: {against the lectin superfamily, e.g. CD23, CD72} - A61K 39/3955: {against proteinaceous materials, e.g. enzymes, hormones, lymphokines} - A61K 45/06: Mixtures of active ingredients without chemical characterisation, e.g. antiphlogistics and cardiaca - A61P 35/00: Antineoplastic agents - A61P 35/02: specific for leukemia - A61P 37/02: Immunomodulators - A61P 37/04: Immunostimulants - C07K 16/2803: {against the immunoglobulin superfamily} - C07K 16/2809: {against the T-cell receptor (TcR)-CD3 complex} - C07K 16/2827: {against B7 molecules, e.g. CD80, CD86} - C07K 16/3061: {Blood cells} - A61K 2039/505: {comprising antibodies} - A61K 2039/507: {Comprising a combination of two or more separate antibodies} - A61K 2039/57: {characterised by the type of response, e.g. Th1, Th2} - C07K 2317/14: Specific host cells or culture conditions, e.g. components, pH or temperature - C07K 2317/24: containing regions, domains or residues from different species, e.g. chimeric, humanized or veneered - C07K 2317/31: multispecific - C07K 2317/33: Crossreactivity, e.g. for species or epitope, or lack of said crossreactivity - C07K 2317/34: Identification of a linear epitope shorter than 20 amino acid residues or of a conformational epitope defined by amino acid residues - C07K 2317/40: characterized by post-translational modification - C07K 2317/41: Glycosylation, sialylation, or fucosylation - C07K 2317/52: Constant or Fc region; Isotype - C07K 2317/526: CH3 domain - C07K 2317/55: Fab or Fab' - C07K 2317/56: variable (Fv) region, i.e. VH and/or VL - C07K 2317/73: Inducing cell death, e.g. apoptosis, necrosis or inhibition of cell proliferation - C07K 2317/76: Antagonist effect on antigen, e.g. neutralization or inhibition of binding - C07K 2317/77: Internalization into the cell - C07K 2317/90: characterized by (pharmaco)kinetic aspects or by stability of the immunoglobulin - C07K 2317/92: Affinity (KD), association rate (Ka), dissociation rate (Kd) or EC50 value - C07K 2317/94: Stability, e.g. half-life, pH, temperature or enzyme-resistance - C07K: PEPTIDES (peptides in foodstuffs A23; obtaining protein compositions for foodstuffs, working-up proteins for foodstuffs A23J; preparations for medicinal purposes A61K; peptides containing beta-lactam rings C07D; cyclic dipeptides not having in their molecule any other peptide link than those which form their ring, e.g. piperazine-2,5-diones, C07D; ergot alkaloids of the cyclic peptide type C07D519/02; macromolecular compounds having statistically distributed amino acid units in their molecules, i.e. when the preparation does not provide for a specific; but for a random sequence of the amino acid units, homopolyamides and block copolyamides derived from amino acids C08G69/00; macromolecular products derived from proteins C08H1/00; preparation of glue or gelatine C09H; single cell proteins, enzymes C12N; genetic engineering processes for obtaining peptides C12N15/00; compositions for measuring or testing processes involving enzymes C12Q; investigation or analysis of biological material G01N33/00) - A61K: PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES (devices or methods specially adapted for bringing pharmaceutical products into particular physical or administering forms A61J3/00; chemical aspects of, or use of materials for deodorisation of air, for disinfection or sterilisation, or for bandages, dressings, absorbent pads or surgical articles A61L; soap compositions C11D) - A61P: SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS ## Abstract The present invention relates to anti-CLL-1 antibodies including anti-CLL-1 antibodies comprising a CLL-1 binding domain and a CD3 binding domain (e.g., anti-CLL-1/CD3 T cell dependent bispecific (TDB) antibody) and methods of using the same. ## Claims ### Claim 1 An isolated anti-CLL-1 antibody, wherein the antibody comprises: (a) a CLL-1 binding domain, wherein the CLL-1 binding domain comprises six hypervariable regions (HVRs) as follows: (i) an HVR-L1 comprising the amino acid sequence of SEQ ID NO: 5, an HVR-L2 comprising the amino acid sequence of SEQ ID NO: 6, an HVR-L3 comprising the amino acid sequence of SEQ ID NO: 7, an HVR-H1 comprising the amino acid sequence of SEQ ID NO: 8, an HVR-H2 comprising the amino acid sequence of SEQ ID NO: 45 and an HVR-H3 comprising the amino acid sequence of SEQ ID NO: 10; or (ii) an HVR-L1 comprising the amino acid sequence of SEQ ID NO: 12, an HVR-L2 comprising the amino acid sequence of SEQ ID NO: 13, an HVR-L3 comprising the amino acid sequence of SEQ ID NO: 14, an HVR-H1 comprising the amino acid sequence of SEQ ID NO: 15, an HVR-H2 comprising the amino acid sequence of SEQ ID NO: 16 and an HVR-H3 comprising the amino acid sequence of SEQ ID NO: 17; or (iii) an HVR-L1 comprising the amino acid sequence of SEQ ID NO: 18, an HVR-L2 comprising the amino acid sequence of SEQ ID NO: 19, an HVR-L3 comprising the amino acid sequence of SEQ ID NO: 20, an HVR-H1 comprising the amino acid sequence of SEQ ID NO: 21, an HVR-H2 comprising the amino acid sequence of SEQ ID NO: 22 and an HVR-H3 comprising the amino acid sequence of SEQ ID NO: 23; or (iv) an HVR-L1 comprising the amino acid sequence of SEQ ID NO: 24, an HVR-L2 comprising the amino acid sequence of SEQ ID NO: 25, an HVR-L3 comprising the amino acid sequence of SEQ ID NO: 26, an HVR-H1 comprising the amino acid sequence of SEQ ID NO: 27, an HVR-H2 comprising the amino acid sequence of SEQ ID NO: 28 and an HVR-H3 comprising the amino acid sequence of SEQ ID NO: 29; and (b) a CD3 binding domain, wherein the CD3 binding domain comprises six HVRs as follows: (i) an HVR-L1 comprising the amino acid sequence of SEQ ID NO: 74, an HVR-L2 comprising the amino acid sequence of SEQ ID NO: 75, an HVR-L3 comprising the amino acid sequence of SEQ ID NO: 76, an HVR-H1 comprising the amino acid sequence of SEQ ID NO: 71, an HVR-H2 comprising the amino acid sequence of SEQ ID NO: 72 and an HVR-H3 comprising the amino acid sequence of SEQ ID NO: 73; or (ii) an HVR-L1 comprising the amino acid sequence of SEQ ID NO: 74, an HVR-L2 comprising the amino acid sequence of SEQ ID NO: 80, an HVR-L3 comprising the amino acid sequence of SEQ ID NO: 76, an HVR-H1 comprising the amino acid sequence of SEQ ID NO: 77, an HVR-H2 comprising the amino acid sequence of SEQ ID NO: 78 and an HVR-H3 comprising the amino acid sequence of SEQ ID NO: 79; or (iii) an HVR-L1 comprising the amino acid sequence of SEQ ID NO: 74, an HVR-L2 comprising the amino acid sequence of SEQ ID NO: 80, an HVR-L3 comprising the amino acid sequence of SEQ ID NO: 81, an HVR-H1 comprising the amino acid sequence of SEQ ID NO: 77, an HVR-H2 comprising the amino acid sequence of SEQ ID NO: 78 and an HVR-H3 comprising the amino acid sequence of SEQ ID NO: 79. ### Claim 2 (depends on 1) The anti-CLL-1 antibody of claim 1, wherein the CLL-1 binding domain comprises the following six hypervariable regions (HVRs): (a) an HVR-H1 comprising the amino acid sequence of SEQ ID NO:8; (b) an HVR-H2 comprising the amino acid sequence of SEQ ID NO:45; (c) an HVR-H3 comprising the amino acid sequence of SEQ ID NO:10; (d) an HVR-L1 comprising the amino acid sequence of SEQ ID NO:5; (e) an HVR-L2 comprising the amino acid sequence of SEQ ID NO:6; and (f) an HVR-L3 comprising the amino acid sequence of SEQ ID NO:7. ### Claim 3 (depends on 2) The anti-CLL-1 antibody of claim 2, wherein the CLL-1 binding domain comprises HVR-H2 comprising the amino acid sequence of SEQ ID NO:9. ### Claim 4 (depends on 2) The anti-CLL-1 antibody of claim 2, wherein the CLL-1 binding domain comprises HVR-H2 comprising the amino acid sequence of SEQ ID NO:47. ### Claim 5 (depends on 4) The anti-CLL-1 antibody of claim 4, wherein the CLL-1 binding domain comprises HVR-H2 comprising the amino acid sequence of SEQ ID NO:11. ### Claim 6 (depends on 4) The anti-CLL-1 antibody of claim 4, wherein the CLL-1 binding domain comprises HVR-H2 comprising the amino acid sequence of SEQ ID NO:43. ### Claim 7 (depends on 4) The anti-CLL-1 antibody of claim 4, wherein the CLL-1 binding domain comprises HVR-H2 comprising the amino acid sequence of SEQ ID NO:44. ### Claim 8 (depends on 2) The anti-CLL-1 antibody of claim 2, wherein the antibody comprises a CLL-1 binding domain comprising: a) a heavy chain variable region comprising the sequence of SEQ ID NO:33 and a light chain variable region comprising the sequence of SEQ ID NO:32; b) a heavy chain variable region comprising the sequence of SEQ ID NO:34 and a light chain variable region comprising the sequence of SEQ ID NO:32; c) a heavy chain variable region comprising the sequence of SEQ ID NO:46 and a light chain variable region comprising the sequence of SEQ ID NO:32; or d) a heavy chain variable region comprising the sequence of SEQ ID NO:48 and a light chain variable region comprising the sequence of SEQ ID NO:32. ### Claim 9 (depends on 1) The anti-CLL-1 antibody of claim 1, wherein the CLL-1 binding domain comprises the following six HVRs: (a) HVR-H1 comprising the amino acid sequence of SEQ ID NO:21; (b) HVR-H2 comprising the amino acid sequence of SEQ ID NO:22; (c) HVR-H3 comprising the amino acid sequence of SEQ ID NO:23; (d) HVR-L1 comprising the amino acid sequence of SEQ ID NO:18; (e) HVR-L2 comprising the amino acid sequence of SEQ ID NO:19; and (f) HVR-L3 comprising the amino acid sequence of SEQ ID NO:20. ### Claim 10 (depends on 9) The anti-CLL-1 antibody of claim 9, wherein the antibody comprises a CLL-1 binding domain comprising: (a) a heavy chain variable region comprising the sequence of SEQ ID NO:40 and (b) a light chain variable region comprising the sequence of SEQ ID NO:39. ### Claim 11 (depends on 1) The anti-CLL-1 antibody of claim 1, wherein the antibody comprises a CLL-1 binding domain having one or more of the following characteristics: a. binds to recombinant human CLL-1; b. binds to recombinant cynomolgus monkey CLL-1; c. binds to endogenous CLL-1 on the surface of human peripheral blood mononucleocytes (PBMCs); d. binds to endogenous CLL-1 on the surface of cynomolgus monkey PBMCs; e. binds to endogenous CLL-1 on the surface of a cancer cell; f. binds to endogenous CLL-1 on the surface of an AML cancer cell; g. binds to endogenous CLL-1 on the surface of HL-60 cells; h. binds to endogenous CLL-1 on the surface of EOL-1 cells; i. binds to CLL-1 comprising a K244Q mutation; j. competes for human CLL-1 binding with R&D clone 687317 antibody; k. binds to endogenous human CLL-1 with a Kd of less than 15 nM; l. binds to recombinant human CLL-1 with a Kd of less than 10 nM; and/or m. binds to recombinant cynomolgus monkey CLL-1 with a Kd of less than 10 nM. ### Claim 12 (depends on 1) The anti-CLL-1 antibody of claim 1, wherein the CD3 binding domain binds a CD3 epitope comprising and/or consisting of Gln1, Asp2, Glu6, and Met7 of human CD3c polypeptide. ### Claim 13 (depends on 1) The anti-CLL-1 antibody of claim 1, wherein the CD3 binding domain comprises (a) HVR-H1 comprising the amino acid sequence of SEQ ID NO:71; (b) HVR-H2 comprising the amino acid sequence of SEQ ID NO:72; (c) HVR-H3 comprising the amino acid sequence of SEQ ID NO:73; (d) HVR-L1 comprising the amino acid sequence of SEQ ID NO: 74; (e) HVR-L2 comprising the amino acid sequence of SEQ ID NO:75; and (f) HVR-L3 comprising the amino acid sequence of SEQ ID NO:76. ### Claim 14 (depends on 1) The anti-CLL-1 antibody of claim 1, wherein the CD3 binding domain comprises (a) HVR-H1 comprising the amino acid sequence of SEQ ID NO:77; (b) HVR-H2 comprising the amino acid sequence of SEQ ID NO:78; (c) HVR-H3 comprising the amino acid sequence of SEQ ID NO:79; (d) HVR-L1 comprising the amino acid sequence of SEQ ID NO: 74; (e) HVR-L2 comprising the amino acid sequence of SEQ ID NO:80; and (d) HVR-L1 comprising the amino acid sequence of SEQ ID NO: 76. ### Claim 15 (depends on 1) The anti-CLL-1 antibody of claim 1, wherein the CD3 binding domain comprises an HVR-H1 comprising the amino acid sequence of SEQ ID NO: 77, an HVR-H2 comprising the amino acid sequence of SEQ ID NO: 78 and an HVR-H3 comprising the amino acid sequence of SEQ ID NO: 79; an HVR-L1 comprising the amino acid sequence of SEQ ID NO: 74, an HVR-L2 comprising the amino acid sequence of SEQ ID NO: 80, and (f) HVR-L3 comprising the amino acid sequence of SEQ ID NO:81. ### Claim 16 (depends on 1) The anti-CLL-1 antibody of claim 1, wherein the antibody comprises a CD3 binding domain comprising: a) a heavy chain variable region comprising the sequence of SEQ ID NO:82 and a light chain variable region comprising the sequence of SEQ ID NO:83; b) a heavy chain variable region comprising the sequence of SEQ ID NO:84 and a light chain variable region comprising the sequence of SEQ ID NO:85; or c) a heavy chain variable region comprising the sequence of SEQ ID NO:84 and a light chain variable region comprising the sequence of SEQ ID NO:93. ### Claim 17 (depends on 1) The anti-CLL-1 antibody of claim 1, wherein the anti-CLL-1 antibody is a monoclonal, humanized, or chimeric antibody. ### Claim 18 (depends on 1) The anti-CLL-1 antibody of claim 1, wherein the anti-CLL-1 antibody is an IgG antibody. ### Claim 19 (depends on 1) The anti-CLL-1 antibody of claim 1, wherein the antibody is a bispecific antibody. ### Claim 20 (depends on 1) The anti-CLL-1 antibody of claim 1, wherein the anti-CLL-1 antibody is an antibody fragment that binds CLL-1 and CD3. ### Claim 21 (depends on 20) The anti-CLL-1 antibody of claim 20, wherein the anti-CLL-1 antibody fragment is a Fab, Fab′-SH, Fv, scFv, and/or (Fab′)2 fragment. ### Claim 22 (depends on 1) The anti-CLL-1 antibody of claim 1, wherein the anti-CLL-1 antibody is a full-length antibody. ### Claim 23 (depends on 1) The anti-CLL-1 antibody of claim 1, wherein the anti-CLL-1 antibody comprises an aglycosylation site mutation. ### Claim 24 (depends on 23) The anti-CLL-1 antibody of claim 23, wherein the aglycosylation site mutation is a substitution mutation. ### Claim 25 (depends on 1) The anti-CLL-1 antibody of claim 1, wherein the anti-CLL-1 antibody comprises reduced effector function. ### Claim 26 (depends on 1) The anti-CLL-1 antibody of claim 1, wherein the anti-CLL-1 antibody comprises a substitution mutation is at amino acid residue N297, L234, L235, D265, and/or P329G according to EU numbering. ### Claim 27 (depends on 26) The anti-CLL-1 antibody of claim 26, wherein the substitution mutation is selected from the group consisting of N297G, N297A, L234A, L235A, D265A, and P329G according to EU numbering. ### Claim 28 (depends on 26) The anti-CLL-1 antibody of claim 26, wherein the antibody comprises an N297G substitution mutation at amino acid residue 297 according to EU numbering. ### Claim 29 (depends on 1) The anti-CLL-1 antibody of claim 1, wherein (a) the CD3 binding domain comprises a Fc domain, wherein the Fc domain comprises T366S, L368A, Y407V, and N297G substitution mutations according EU numbering and (b) the CLL-1 binding domain comprises a Fc domain, wherein the Fc domain comprises T366W and N297G substitution mutations according EU numbering. ### Claim 30 (depends on 1) A pharmaceutical composition comprising the anti-CLL-1 antibody of claim 1. ### Claim 31 An isolated anti-CLL-1 antibody, wherein the antibody comprises: (a) a CLL-1 binding domain, wherein the CLL-1 binding domain comprises: (i) a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 31 and a light chain comprising the amino acid sequence of SEQ ID NO: 30; or (ii) a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 33 and a light chain comprising the amino acid sequence of SEQ ID NO: 32; or (iii) a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 34 and a light chain comprising the amino acid sequence of SEQ ID NO: 32; or (iv) a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 36 and a light chain variable region comprising the amino acid sequence of SEQ ID NO: 35; or (v) a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 38 and the light chain variable region comprising the amino acid sequence of SEQ ID NO: 37; or (vi) a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 40 and a light chain comprising the amino acid sequence of SEQ ID NO: 39; or (vii) a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 42 and the light chain variable region comprising the amino acid sequence of SEQ ID NO: 41; or (viii) a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 46 and a light chain comprising the amino acid sequence of SEQ ID NO: 32; and (b) a CD3 binding domain, wherein the CD3 binding domain comprises: (i) a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 82 and the light chain variable region comprising the amino acid sequence of SEQ ID NO: 83; or (ii) a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 84 and the light chain variable region comprising the amino acid sequence of SEQ ID NO: 93; or (iii) a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 84 and the light chain variable region comprising the amino acid sequence of SEQ ID NO: 85.