Antibody molecule-drug conjugates and uses thereof

Abstract

Antibody molecule-drug conjugates (ADCs) that specifically bind to lipopolysaccharides (LPS) are disclosed. The antibody molecule-drug conjugates can be used to treat, prevent, and/or diagnose bacterial infections and related disorders.

1 . An antibody molecule-drug conjugate (ADC) comprising: a) an antibody molecule that binds to lipopolysaccharide (LPS); and b) an antimicrobial peptide. 
     
     
         2 . The ADC of  claim 1 , wherein:
 (i) the ADC or antibody molecule comprises a heavy chain variable region (VH), wherein the VH comprises three heavy chain complementarity determining regions (HCDR1, HCDR2, and HCDR3), and wherein the VH comprises:
 (a) an HCDR1 comprising the amino acid sequence of SEQ ID NO: 108; an HCDR2 comprising the amino acid sequence of any of SEQ ID NOS: 109, 145, or 146; and an HCDR3 comprising the amino acid sequence of SEQ ID NO: 107, or 
 (b) an HCDR1 comprising the amino acid sequence of SEQ ID NO: 105; an HCDR2 comprising the amino acid sequence of SEQ ID NO: 106; and an HCDR3 comprising the amino acid sequence of SEQ ID NO: 107; or 
   (ii) the ADC or antibody molecule comprises a light chain variable region (VL), wherein VL comprises three light chain complementarity determining regions (LCDR1, LCDR2, and LCDR3), and wherein the VL comprises: an LCDR1 comprising the amino acid sequence of any of SEQ ID NOS: 110, 138, 140, or 144; an LCDR2 comprising the amino acid sequence of any of SEQ ID NOS: 111, 139, 141, 142, or 143; and an LCDR3 comprising the amino acid sequence of any of SEQ ID NO: 112.   
     
     
         3 . (canceled) 
     
     
         4 . The ADC of  claim 1 , wherein the ADC or antibody molecule comprises a VH and a VL, wherein the VH comprises three heavy chain complementarity determining regions (HCDR1, HCDR2, and HCDR3), and the VL comprises three light chain complementarity determining regions (LCDR1, LCDR2, and LCDR3), and wherein the ADC or antibody molecule comprises:
 (a) an HCDR1 comprising the amino acid sequence of SEQ ID NO: 108; an HCDR2 comprising the amino acid sequence of any of SEQ ID NOS: 109, 145, or 146; an HCDR3 comprising the amino acid sequence of SEQ ID NO: 107; an LCDR1 comprising the amino acid sequence of any of SEQ ID NOS: 110, 138, 140, or 144; an LCDR2 comprising the amino acid sequence of any of SEQ ID NOS: 111, 139, 141, 142, or 143; and an LCDR3 comprising the amino acid sequence of any of SEQ ID NO: 112, or   (b) an HCDR1 comprising the amino acid sequence of SEQ ID NO: 105; an HCDR2 comprising the amino acid sequence of SEQ ID NO: 106; an HCDR3 comprising the amino acid sequence of SEQ ID NO: 107; an LCDR1 comprising the amino acid sequence of any of SEQ ID NOS: 110, 138, 140, or 144; an LCDR2 comprising the amino acid sequence of any of SEQ ID NOS: 111, 139, 141, 142, or 143; and an LCDR3 comprising the amino acid sequence of any of SEQ ID NO: 112.   
     
     
         5 . The ADC of  claim 1 , wherein the ADC or antibody molecule comprises a VH and a VL, wherein the VH comprises three heavy chain complementarity determining regions (HCDR1, HCDR2, and HCDR3), and the VL comprises three light chain complementarity determining regions (LCDR1, LCDR2, and LCDR3),
 wherein the VH comprises:   (a)(i) an HCDR1 comprising the amino acid sequence of SEQ ID NO: 108; an HCDR2 comprising the amino acid sequence of SEQ ID NO: 109; and an HCDR3 comprising the amino acid sequence of SEQ ID NO: 107,   (a)(ii) an HCDR1 comprising the amino acid sequence of SEQ ID NO: 108; an HCDR2 comprising the amino acid sequence of SEQ ID NO: 145; and an HCDR3 comprising the amino acid sequence of SEQ ID NO: 107,   (a)(iii) an HCDR1 comprising the amino acid sequence of SEQ ID NO: 108; an HCDR2 comprising the amino acid sequence of SEQ ID NO: 146; and an HCDR3 comprising the amino acid sequence of SEQ ID NO: 107, or   (b) an HCDR1 comprising the amino acid sequence of SEQ ID NO: 105; an HCDR2 comprising the amino acid sequence of SEQ ID NO: 106; and an HCDR3 comprising the amino acid sequence of SEQ ID NO: 107, and/or   wherein the VL comprises:   (i) an LCDR1 comprising the amino acid sequence of SEQ ID NO: 110; an LCDR2 comprising the amino acid sequence of SEQ ID NO: 111; and an LCDR3 comprising the amino acid sequence of any of SEQ ID NO: 112,   (ii) an LCDR1 comprising the amino acid sequence of SEQ ID NO: 138; an LCDR2 comprising the amino acid sequence of SEQ ID NO: 139; and an LCDR3 comprising the amino acid sequence of any of SEQ ID NO: 112,   (iii) an LCDR1 comprising the amino acid sequence of SEQ ID NO: 138; an LCDR2 comprising the amino acid sequence of SEQ ID NO: 111; and an LCDR3 comprising the amino acid sequence of any of SEQ ID NO: 112,   (iv) an LCDR1 comprising the amino acid sequence of SEQ ID NO: 140; an LCDR2 comprising the amino acid sequence of SEQ ID NO: 111; and an LCDR3 comprising the amino acid sequence of any of SEQ ID NO: 112,   (v) an LCDR1 comprising the amino acid sequence of SEQ ID NO: 110; an LCDR2 comprising the amino acid sequence of SEQ ID NO: 141; and an LCDR3 comprising the amino acid sequence of any of SEQ ID NO: 112,   (vi) an LCDR1 comprising the amino acid sequence of SEQ ID NO: 110; an LCDR2 comprising the amino acid sequence of SEQ ID NO: 142; and an LCDR3 comprising the amino acid sequence of any of SEQ ID NO: 112,   (vii) an LCDR1 comprising the amino acid sequence of SEQ ID NO: 138; an LCDR2 comprising the amino acid sequence of SEQ ID NO: 143; and an LCDR3 comprising the amino acid sequence of any of SEQ ID NO: 112,   (viii) an LCDR1 comprising the amino acid sequence of SEQ ID NO: 138; an LCDR2 comprising the amino acid sequence of SEQ ID NO: 139; and an LCDR3 comprising the amino acid sequence of any of SEQ ID NO: 112,   (ix) an LCDR1 comprising the amino acid sequence of SEQ ID NO: 144; an LCDR2 comprising the amino acid sequence of SEQ ID NO: 142; and an LCDR3 comprising the amino acid sequence of any of SEQ ID NO: 112, or   (x) an LCDR1 comprising the amino acid sequence of SEQ ID NO: 138; an LCDR2 comprising the amino acid sequence of SEQ ID NO: 142; and an LCDR3 comprising the amino acid sequence of any of SEQ ID NO: 112.   
     
     
         6 . The ADC of  claim 1 , wherein the ADC or antibody molecule comprises a VH and a VL,
 wherein the VH comprises the amino acid sequence of any of SEQ ID NOS: 103 or 115-118, or comprises an amino acid sequence that differs by no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 amino acid residues from, or has at least 85, 90, 95, 96, 97, 98, 99, or 100% homology with, the amino acid sequence of any of SEQ ID NOS: 103 or 115-118, and/or   wherein the VL comprises the amino acid sequence of any of SEQ ID NOS: 104 or 119-137, or comprises an amino acid sequence that differs by no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 amino acid residues from, or has at least 85, 90, 95, 96, 97, 98, 99, or 100% homology with, the amino acid sequence of any of SEQ ID NOS: 104 or 119-137.   
     
     
         7 . The ADC of  claim 1 , wherein:
 (i) the antibody molecule is a monoclonal antibody molecule, a humanized antibody molecule, an isolated antibody molecule, or a synthetic antibody molecule;   (ii) the ADC or antibody molecule comprises two VHs and two VLs, or comprises a Fab, a F(ab′)2, an Fv, or a single chain Fv fragment (scFv);   (iii) the ADC or antibody molecule further comprises a heavy chain constant region of an IgG1, IgG2, IgG3, or IgG4, and/or a light chain constant region of a kappa or lambda chain; or   (iv) the ADC or antibody molecule binds to a core pentasaccharide region of the LPS, wherein the core pentasaccharide region comprises one or more Kdo residues and one or more Hep residues.   
     
     
         8 - 10 . (canceled) 
     
     
         11 . The ADC of  claim 1 , wherein the ADC or antibody molecule binds to:
 (a) one or more Gram-negative bacteria, or one or more antibiotic-resistant or multidrug-resistant (MDR) bacteria.   (b) a species of Enterobacteriaceae chosen from a species of  Klebsiella, Enterobacter, Shigella, Escherichia, Salmonella, Yersinia , or  Citrobacter , a species of  Pseudomonas , a species of  Acinetobacter , or any combination thereof; or   (c)  Klebsiella pneumonia, Enterobacter cancerogenous, Enterobacter cloacae, Enterobacter hormaechei, Enterobacter asburiae, Shigella boydii, Shigella dysenteriae, Shigella flexneri, Shigella sonnei, Escherichia coli, Escherichia fergusonii, Salmonella choleraesuis, Salmonella enteritidis, Salmonella virchow, Salmonella paratyphi  B,  Salmonella typhimurium, Salmonella paratyphi  A,  Salmonella typhi, Salmonella bongori, Citrobacter sedlakii, Citrobacter braakii, Citrobacter werkmanii, Citrobacter freundii, Citrobacter youngae, Citrobacter amalonaticus, Yersinia enterocolitica, Yersinia frederiksenii, Yersinia pestis, Yersinia pseudotuberculosis, Pseudomonas aeruginosa, Acinetobacter baumannii , or any combination thereof.   
     
     
         12 . The ADC of  claim 1 , wherein:
 (i) the ADC or antibody molecule binds to LPS with a K D  that is less than about 10 nM as measured by an ELISA method, and/or has an opsonophagocytic activity against a bacterium;   (ii) the antibody molecule is fused to the antimicrobial peptide;   (iii) the antibody molecule comprises: (a) a VH fused to the antimicrobial peptide, wherein the VH is N-terminal or C-terminal to the antimicrobial peptide; (b) a VL fused to the antimicrobial peptide, wherein the VL is N-terminal or C-terminal to the antimicrobial peptide; or (c) both (a) and (b); optionally wherein the C-terminus of the VH or VL is fused to the N-terminus of the antimicrobial peptide indirectly via a constant region, a linker, or both;   (iv) the antibody molecule is fused to the antimicrobial peptide by a sortase;   (v) the ADC or antimicrobial peptide comprises the amino acid sequence of any of SEQ ID NOS: 67-80, 94-102, 147-156, 158-159, or 163-164, or comprises an amino acid sequence that differs by no more than 1, 2, 3, 4, or 5 amino acid residues from, or has at least 80, 85, 90, 95, 96, 97, 98, 99, or 100% homology with, the amino acid sequence of any of SEQ ID NOS: 67-80, 94-102, 147-156, 158-159, or 163-164;   (vi) the antimicrobial peptide comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, or more D-amino acids, or at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, or 100%, of the amino acid residues in the antimicrobial peptide are D-amino acids;   (vii) the antimicrobial peptide comprises a first cysteine residue and a second cysteine residue, and wherein the first cysteine residue is cross-linked to the second cysteine residue;   (viii) the ADC comprises at least two, three, or four antimicrobial peptides; or comprising at least two, three, or four identical, or substantially identical, antimicrobial peptides, each of which is fused to a VH or VL indirectly via a constant region, a linker, or both;   (ix) the antimicrobial peptide has an antimicrobial activity against 2, 3, or all of the following: (a) at least one species of Enterobacteriaceae chosen from one or more species of  Klebsiella, Enterobacter, Shigella, Escherichia, Salmonella, Yersinia , or  Citrobacter , (b) at least one species of  Pseudomonas ; or (c) at least one species of  Acinetobacter ; or   (x) the antimicrobial peptide has a PLC to MIC ratio for a Gram-negative bacteria which is greater than 4:1, wherein the PLC is determined by a red blood cell hemolysis assay.   
     
     
         13 - 20 . (canceled) 
     
     
         21 . The ADC of  claim 1 , wherein
 (ii) the ADC has
 (a) a minimum inhibitory concentration (MIC) for a Gram-negative bacterium that is at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 fold lower on a molar basis than the MIC of the antimicrobial peptide alone; 
 (b) a minimum bactericidal concentration (MBC) for a Gram-negative bacterium that is at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 fold lower on a molar basis than the MBC of the antimicrobial peptide alone; or 
 (c) both (a) and (b); 
   (ii) the ADC has
 (d) a MIC for a Gram-negative bacterium that is at least 2, 5, 10, 20, 50, 100, 200, 500, or 1000 fold lower on a molar basis than a MIC for a Gram-positive bacterium; 
 (e) an MBC for a Gram-negative bacterium that is at least 2, 5, 10, 20, 50, 100, 200, 500, or 1000 fold lower on a molar basis than an MBC for a Gram-positive bacterium; or 
 (f) both (d) and (e); or 
   (iii) the antimicrobial peptide has:
 (a) a MIC of less than 100, 90, 80, 70, 60, 50, 40, 30, 20, 10, or 5 μg/ml, for  Escherichia coli, Pseudomonas aeruginosa , or both; 
 (b) an MBC of less than 100, 90, 80, 70, 60, 50, 40, 30, 20, 10, or 5 μg/ml, for  Escherichia coli, Pseudomonas aeruginosa , or both; or 
 (c) both (a) and (b). 
   
     
     
         22 - 25 . (canceled) 
     
     
         26 . A pharmaceutical composition comprising the ADC of  claim 1  and a pharmaceutically acceptable carrier. 
     
     
         27 . A method of treating or preventing a bacterial infection, comprising administering to a subject in need thereof the ADC of  claim 1 , in an amount effective to treat or prevent the bacterial infection. 
     
     
         28 . The method of  claim 27 , wherein:
 (i) the bacterial infection is associated with a Gram-negative bacterium, or is a nosocomial infection or a hospital-acquired infection;   (ii) the ADC is administered at a dose of 1-10 mg/kg, and/or is administered intravenously, subcutaneously, or intranasally or by inhalation;   (iii) the ADC is administered prior to or after onset of a symptom associated with the bacterial infection;   (iv) the method further comprises administering to the subject a second antimicrobial agent or therapy.   
     
     
         29 - 30 . (canceled) 
     
     
         31 . The method of  claim 27 , wherein the subject:
 (a) has one or more of: pneumonia, a urinary tract infection (UTI), septicemia, meningitis, diarrhea, a soft tissue infection, a skin infection, bacteremia, a respiratory system infection, endocarditis, an intra-abdominal infection, septic arthritis, osteomyelitis, a CNS infection, an ophthalmic infection, cholecystitis, cholangitis, meningitis, typhoid fever, food poisoning, gastroenteritis, enteric fever, shigellosis, a blood stream infection, intra-abdominal sepsis, a brain abscess, meningitis, sepsis, a joint infection, a bone infection, a gastrointestinal infection, or a wound infection.   (b) is a human or an animal;   (c) is an immunocompromised patient or a health professional;   (d) has, or is at risk of having, an HIV infection or AIDS, a cancer, a solid organ transplantation, a stem cell transplantation, a sickle cell disease or asplenia, a congenital immune deficiency, a chronic inflammatory condition, a cochlear implant, malnutrition, or a cerebrospinal fluid leak; or   (e) is 18 years old or younger, 15 years old or younger, 12 years old or younger, 9 years old or younger, or 6 years old or younger, or is at least 60 years old, at least 65 years old, at least 70 years old, at least 75 years old, or at least 80 years old.   
     
     
         32 . (canceled) 
     
     
         33 . The method of  claim 28 , wherein the second antimicrobial agent or therapy comprises an antibiotic or a phage therapy, wherein the antibiotic is chosen from:
 (a) an aminoglycoside, an ansamycin, a carbacephem, a carbapenem, a cephalosporin, a glycopeptide, a lincosamide, a lipopeptide, a macrolide, a monobactam, a nitrofuran, an oxazolidinone, a penicillin, a penicillin combination, a polypeptide, a quinolone or fluoroquinolone, a sulfonamide, a tetracycline, or a drug against mycobacteria; or   (b) amikacin, gentamicin, kanamycin, neomycin, netilmicin, tobramycin, paromomycin, streptomycin, spectinomycin, geldanamycin, herbimycin, or rifaximin, loracarbef, ertapenem, doripenem, imipenem/cilastatin, meropenem, cefadroxil, cefazolin, cefalotin, cefalothin, cephalexin, cefaclor, cefamandole, cefoxitin, cefprozil, cefuroxime, cefixime, cefdinir, cefditoren, cefoperazone, cefotaxime, cefpodoxime, ceftazidime, ceftibuten, ceftizoxime, ceftriaxone, cefepime, ceftaroline fosamil, ceftobiprole, teicoplanin, vancomycin, telavancin, dalbavancin, oritavancin, clindamycin, lincomycin, daptomycin, azithromycin, clarithromycin, dirithromycin, erythromycin, roxithromycin, troleandomycin, telithromycin, spiramycin, aztreonam, furazolidone, nitrofurantoin, linezolid, posizolid, radezolid, torezolid, amoxicillin, ampicillin, azlocillin, carbenicillin, cloxacillin, dicloxacillin, flucloxacillin, mezlocillin, methicillin, nafcillin, oxacillin, penicillin g, penicillin v, piperacillin, penicillin g, temocillin, ticarcillin, amoxicillin/clavulanate, ampicillin/sulbactam, piperacillin/tazobactam, ticarcillin/clavulanate, bacitracin, colistin, polymyxin b, ciprofloxacin, enoxacin, gatifloxacin, gemifloxacin, levofloxacin, lomefloxacin, moxifloxacin, nalidixic acid, norfloxacin, ofloxacin, trovafloxacin, grepafloxacin, sparfloxacin, temafloxacin, mafenide, sulfacetamide, sulfadiazine, silver sulfadiazine, sulfadimethoxine, sulfamethizole, sulfamethoxazole, sulfanilimide, sulfasalazine, sulfisoxazole, trimethoprim-sulfamethoxazole (co-trimoxazole), sulfonamidochrysoidine, demeclocycline, doxycycline, minocycline, oxytetracycline, tetracycline, clofazimine, dapsone, capreomycin, cycloserine, ethambutol, ethionamide, isoniazid, pyrazinamide, rifampin, rifabutin, rifapentine, streptomycin, arsphenamine, chloramphenicol, fosfomycin, fusidic acid, metronidazole, mupirocin, platensimycin, quinupristin/dalfopristin, thiamphenicol, tigecycline, tinidazole, or trimethoprim; and/or   wherein the second antimicrobial agent or therapy is administered before the ADC is administered, concurrently with the administration of the ADC, or after the ADC is administered.   
     
     
         34 . (canceled) 
     
     
         35 . A method of inhibiting or reducing a bacterial infection, comprising contacting a cell the ADC of  claim 1  in an amount effective to inhibit or reduce the bacterial infection. 
     
     
         36 . A kit comprising: the ADC of  claim 1  and instructions for use of the ADC. 
     
     
         37 . A container comprising the ADC of  claim 1 . 
     
     
         38 . A nucleic acid molecule encoding the ADC of  claim 1 . 
     
     
         39 . A vector comprising the nucleic acid molecule of  claim 38 . 
     
     
         40 . A cell comprising the nucleic acid molecule of  38 . 
     
     
         41 . A method of producing an ADC, the method comprising culturing the cell of  claim 40  under conditions that allow production of an ADC, thereby producing the ADC. 
     
     
         42 . A method of producing an ADC, the method comprising contacting an antibody molecule that binds to LPS with a peptide comprising an antimicrobial peptide, and optionally, a sortase donor sequence, in the presence of a sortase, under conditions that allow a sortase-mediated reaction to occur, thereby producing the ADC. 
     
     
         43 . An antibody molecule that binds to LPS, wherein:
 (i) the antibody molecule comprises a VH and a VL, wherein the VH comprises three heavy chain complementarity determining regions (HCDR1, HCDR2, and HCDR3), and the VL comprises three light chain complementarity determining regions (LCDR1, LCDR2, and LCDR3), and wherein the ADC or antibody molecule comprises:
 (a) an HCDR1 comprising the amino acid sequence of SEQ ID NO: 108; an HCDR2 comprising the amino acid sequence of any of SEQ ID NOS: 109, 145, or 146; an HCDR3 comprising the amino acid sequence of SEQ ID NO: 107; an LCDR1 comprising the amino acid sequence of any of SEQ ID NOS: 110, 138, 140, or 144; an LCDR2 comprising the amino acid sequence of any of SEQ ID NOS: 111, 139, 141, 142, or 143; and an LCDR3 comprising the amino acid sequence of SEQ ID NO: 112, or 
 (b) an HCDR1 comprising the amino acid sequence of SEQ ID NO: 105; an HCDR2 comprising the amino acid sequence of SEQ ID NO: 106; an HCDR3 comprising the amino acid sequence of SEQ ID NO: 107; an LCDR1 comprising the amino acid sequence of any of SEQ ID NOS: 110, 138, 140, or 144; an LCDR2 comprising the amino acid sequence of any of SEQ ID NOS: 111, 139, 141, 142, or 143; and an LCDR3 comprising the amino acid sequence of SEQ ID NO: 112; or 
   (ii) the VH comprises an amino acid sequence that differs by no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 amino acid residues from, or has at least 85, 90, 95, 96, 97, 98, 99, or 100% homology with, the amino acid sequence of any of SEQ ID NOS: 103 or 115-118, and wherein the VL comprises an amino acid sequence that differs by no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 amino acid residues from, or has at least 85, 90, 95, 96, 97, 98, 99, or 100% homology with, the amino acid sequence of any of SEQ ID NOS: 104 or 119-137.   
     
     
         44 . (canceled) 
     
     
         45 . An antimicrobial peptide that comprises an amino acid sequence that differs by no more than 1, 2, 3, 4, or 5 amino acid residues from, or has at least 80, 85, 90, 95, 96, 97, 98, 99, or 100% homology with, the amino acid sequence of any of SEQ ID NOS: 67-80, 94-102, 147-156, 158-159, or 163-164. 
     
     
         46 . A nucleic acid molecule encoding the antibody molecule of  claim 43 . 
     
     
         47 . A nucleic acid molecule encoding the antimicrobial peptide of  claim 45 . 
     
     
         48 . An antibody molecule that:
 (i) binds to the same epitope, or substantially the same epitope, or   (ii) competes for binding with   the antibody molecule of  claim 43 .   
     
     
         49 . (canceled)