Interleukin-18 variants and methods of use

Abstract

The present invention provides compositions and methods comprising an activator of IL-18 activity for use in therapeutic and non-therapeutic applications. The activator provides IL-18 signaling activity even in the presence of an inhibitory molecule such as IL-18BP.

1 . A composition comprising an IL-18 variant polypeptide or a nucleic acid encoding said IL-18 variant polypeptide, wherein the IL-18 variant polypeptide specifically binds to IL-18 receptor (IL-18R) and wherein, compared to wild type (WT) IL-18, the IL-18 variant polypeptide comprises at least one mutation and exhibits substantially reduced binding to IL-18 binding protein (IL-18BP). 
     
     
         2 . (canceled) 
     
     
         3 . The composition of  claim 1 , wherein the WT IL-18 is human IL-18 comprising the amino acid sequence of SEQ ID NO: 30. 
     
     
         4 . The composition of  claim 1 , wherein the WT IL-18 is murine IL-18 comprising the amino acid sequence of SEQ ID NO: 31. 
     
     
         5 . The composition of  claim 3 , wherein the IL-18 variant polypeptide comprises at least one mutation selected from the group consisting of Y1X, L5X, K8X, M51X, K53X, S55X, Q56X, P57X, G59X, M60X, E77X, Q103X, S105X, D110X, N111X, M113X, V153X, and N155X, relative to SEQ ID NO: 30. 
     
     
         6 . The composition of  claim 3 , wherein the IL-18 variant polypeptide comprises at least one mutation selected from the group consisting of Y1H, Y1R, L5H, L5I, L5Y, K8Q, K8R, M51T, M51K, M51D, M51N, M51E, M51R, K53R, K53G, K53S, K53T, S55K, S55R, Q56E, Q56A, Q56R, Q56V, Q56G, Q56K, Q56L, P57L, P57G, P57A, P57K, G59T, G59A, M60K, M60Q, M60R, M60L, E77D, Q103E, Q103K, Q103P, Q103A, Q103R, S105R, S105D, S105K, S105N, S105A, D110H, D110K, D110N, D110Q, D110E, D110S, D110G, N111H, N111Y, N111D, N111R, N111S, N111G, M113V, M113R, M113T, M113K, V153I, V153T, V153A, N155K, and N155H, relative to SEQ ID NO: 30. 
     
     
         7 . The composition of  claim 3 , wherein the IL-18 variant polypeptide comprises at least 6 mutations selected from: Y1X, L5X, K8X, M51X, K53X, 555X, Q56X, P57X, G59X, M60X, E77X, Q103X, S105X, D110X, N111X, M113X, V153X, and N155X, relative to SEQ ID NO: 30. 
     
     
         8 . The composition of  claim 3 , wherein the IL-18 variant polypeptide comprises mutations at positions M51, K53, Q56 D110, and N111, relative to SEQ ID NO: 30. 
     
     
         9 . The composition of  claim 1 , wherein the IL-18 variant polypeptide comprises the amino acid sequence set forth in any one of SEQ ID NOs.: 34-59, 73-91, 191-193, or a fragment thereof. 
     
     
         10 . The composition of  claim 8 , wherein the IL-18 variant polypeptide comprises the following 5 mutations:
 (1) M51E, M51R, M51K, M51T, M51D, or M51N,   (2) K53G, K53S, K53T, or K53R,   (3) Q56G, Q56R, Q56L, Q56E, Q56A, Q56V, or Q56K,   (4) D110S, D110N, D110G, D110K, D110H, D110Q, or D110E, and   (5) N111G, N111R, N111S, N111D, N111H, or N111Y, relative to SEQ ID NO: 30.   
     
     
         11 . The composition of  claim 8 , wherein the IL-18 variant polypeptide further comprises mutations at positions P57 and M60, relative to SEQ ID NO: 30. 
     
     
         12 . The composition of  claim 1 , wherein the IL-18 variant polypeptide comprises the amino acid sequence set forth in any one of SEQ ID NOs.: 60-72, or a fragment thereof. 
     
     
         13 . The composition of  claim 11 , the IL-18 variant polypeptide comprises the following 7 mutations:
 (1) M51E, M51R, M51K, M51T, M51D, or M51N;   (2) K53G, K53S, K53T, or K53R;   (3) Q56G, Q56R, Q56L, Q56E, Q56A, Q56V, or Q56K;   (4) D110S, D110N, D110G, D110K, D110H, D110Q, or D110E;   (5) N111G, N111R, N111S, N111D, N111H, or N111Y;   (6) P57A, P57L, P57G, or P57K; and   (7) M60L, M60R, M60K, or M600,   relative to SEQ ID NO: 30.   
     
     
         14 . The composition  claim 1 , further comprising one or more agents selected from: (i) an immune checkpoint inhibitor; (ii) an agent that modulates activity of one or more proteins selected from PD-L1, PD1, CTLA4, TIM3, TIGIT, LAG3, B7H3, B7H4, VISTA, ICOS, GITR, 41BB, OX40, and CD40; (iii) a cancer cell opsonizing agent; and (iv) an agent that targets one or more antigens selected from: CD19, CD20, CD22, CD24, CD25, CD30, CD33, CD37, CD38, CD44, CD45, CD47, CD51, CD52, CD56, CD62L, CD70, CD74, CD79, CD80, CD96, CD97, CD99, CD123, CD134, CD138, CD152 (CTLA-4), CD200, CD213A2, CD221, CD248, CD276 (B7-H3), B7-H4, CD279 (PD-1), CD274 (PD-L1), CD319, EGFR, EPCAM, 17-1A, HER1, HER2, HER3, CD117, C-Met, HGFR, PDGFRA, AXL, TWEAKR, PTHR2, HAVCR2 (TIM3), GD2 ganglioside, MUC1, mucin CanAg, mesothelin, endoglin, Lewis-Y antigen, CEA, CEACAM1, CEACAM5, CA-125, PSMA, BAFF, FGFR2, TAG-72, gelatinase B, glypican 3, nectin-4, BCMA, CSF1R, SLAMF7, integrin α v β 3 , TYRP1, GPNMB, CLDN18.2, FOLR1, CCR4, CXCR4, MICA, C242 antigen, DLL3, DLL4, EGFL7, vimentin, fibronectin extra domain-B, TROP-2, LRRC15, FAP, SLITRK6, NOTCH2, NOTCH3, Tenascin-3, STEAP1, and NRP1. 
     
     
         15 . A method of treating or preventing a disease or disorder in a subject in need thereof, comprising administering to the subject the composition of  claim 1 . 
     
     
         16 . The method of  claim 15 , wherein the disease or disorder is cancer; a metabolic disease or disorder; or an infectious disease. 
     
     
         17 . The method of  claim 16 , wherein the disease or disorder is a cancer that is resistant to immune checkpoint inhibitors (ICIs). 
     
     
         18 . The method of  claim 16 , wherein the disease or disorder is a cancer that is associated with a tumor that has lost expression of MHC class I. 
     
     
         19 .- 20 . (canceled) 
     
     
         21 . The method of  claim 16 , wherein the method comprises administering to the subject the IL-18 variant polypeptide and at least one other agent. 
     
     
         22 . The method of  claim 21 , wherein the at least one other agent comprises an immune checkpoint inhibitor. 
     
     
         23 . The method of  claim 22 , wherein the immune checkpoint inhibitor is an agent that modulates activity of PD-L1, PD1, CTLA4, TIM3, TIGIT, LAG3, B7H3, B7H4, VISTA, ICOS, GITR, 41BB, OX40, or CD40, or any combination thereof. 
     
     
         24 . The method of  claim 21 , wherein the at least one other agent comprises a cancer cell opsonizing agent. 
     
     
         25 . The method of  claim 24 , wherein the cancer cell opsonizing agent targets one or more antigens selected from: CD19, CD20, CD22, CD24, CD25, CD30, CD33, CD37, CD38, CD44, CD45, CD47, CD51, CD52, CD56, CD62L, CD70, CD74, CD79, CD80, CD96, CD97, CD99, CD123, CD134, CD138, CD152 (CTLA-4), CD200, CD213A2, CD221, CD248, CD276 (B7-H3), B7-H4, CD279 (PD-1), CD274 (PD-L1), CD319, EGFR, EPCAM, 17-1A, HER1, HER2, HER3, CD117, C-Met, HGFR, PDGFRA, AXL, TWEAKR, PTHR2, HAVCR2 (TIM3), GD2 ganglioside, MUC1, mucin CanAg, mesothelin, endoglin, Lewis-Y antigen, CEA, CEACAM1, CEACAM5, CA-125, PSMA, BAFF, FGFR2, TAG-72, gelatinase B, glypican 3, nectin-4, BCMA, CSF1R, SLAMF7, integrin α v β 3 , TYRP1, GPNMB, CLDN18.2, FOLR1, CCR4, CXCR4, MICA, C242 antigen, DLL3, DLL4, EGFL7, vimentin, fibronectin extra domain-B, TROP-2, LRRC15, FAP, SLITRK6, NOTCH2, NOTCH3, Tenascin-3, STEAP1, and NRP1. 
     
     
         26 . The method of  claim 21 , wherein the at least one other agent is conjugated to the IL-18 variant polypeptide. 
     
     
         27 . The method of  claim 21 , wherein the at least one other agent is an altered T-cell or NK cell. 
     
     
         28 . The method of  claim 21 , wherein the at least one other agent is an oncolytic virus. 
     
     
         29 . The method of  claim 21 , wherein the at least one other agent comprises at least one compound selected from: IL-1, IL-2, IL-10, IL-12, IL-15, IL-18, IL-21, IL-33, Interferon alpha, Interferon beta, Interferon gamma, an agonist of Toll Like Receptor (TLR) 2, an agonist of TLR4, an agonist of TLR5, an agonist of TLR7, an agonist of TLR9, an anti-CTLA4 antibody, an anti-PD-1 antibody, an anti-PD-L1 antibody, a TIGIT antibody, a TIM3 antibody, a LAG3 antibody, a VISTA antibody, a B7H3 antibody, a B7H4 antibody, a CD40 agonist, a 41BB-agonist, an OX-40 agonist, a GITR agonist, a CD47 binding agent, and a SIRPA binding agent. 
     
     
         30 . The method of  claim 21 , wherein the at least one other agent comprises at least one compound selected from: an immunomodulatory agent, a cytokine or cytokine variant, a Toll Like Receptor (TLR) agonist, an inflammasome agonist, an agonist of the STING/cGAS pathway, and an agonist of the RIG-I pathway. 
     
     
         31 . A composition, comprising an IL-18 variant polypeptide or a nucleic acid encoding said IL-18 variant polypeptide, wherein the IL-18 variant polypeptide specifically binds to IL-18 binding protein (IL-18BP) and wherein, compared to wild-type (WT) IL-18, the IL-18 variant polypeptide comprises at least one mutation and exhibits substantially reduced binding to IL-18 receptor (IL-18R). 
     
     
         32 . (canceled) 
     
     
         33 . The composition of  claim 31 , wherein the WT IL-18 is human IL-18 comprising the amino acid sequence of SEQ ID NO: 30, or SEQ ID NO: 31. 
     
     
         34 . (canceled) 
     
     
         35 . The composition of  claim 33 , wherein the IL-18 variant polypeptide comprises at least one mutation selected from the group consisting of Y1X, L5X, D17X, E31X, T34X, D35X, S36X, D37X, D40X, N41X, M51X, Q56X, M60X, Q103X, H109X, M113X, and R131X, relative to SEQ ID NO: 30, or at least one mutation selected from the group consisting of N1X, L5X, D17X, E30X, T33X, D34X, I35X, D36X, M50X, Q102X, R104, H108X, N109X, M111X, D129X, and D130X, relative to SEQ ID NO: 31. 
     
     
         36 . (canceled) 
     
     
         37 . The composition of  claim 33 , wherein the IL-18 variant polypeptide comprises the amino acid sequence set forth in any one of SEQ ID NOs.: 92-125, or a fragment thereof. 
     
     
         38 .- 41 . (canceled) 
     
     
         42 . The composition of  claim 33 , wherein the IL-18 variant polypeptide comprises the amino acid sequence set forth in any one of SEQ ID NOs.: 126-190, or a fragment thereof. 
     
     
         43 . (canceled) 
     
     
         44 . The composition of  claim 31 , further comprising one or more agents selected from: (i) an immune checkpoint inhibitor; (ii) an agent that modulates activity of one or more proteins selected from PD-L1, PD1, CTLA4, TIM3, TIGIT, LAG3, B7H3, B7H4, VISTA, ICOS, GITR, 41BB, OX40, and CD40; (iii) a cancer cell opsonizing agent; and (iv) an agent that targets one or more antigens selected from: CD19, CD20, CD22, CD24, CD25, CD30, CD33, CD37, CD38, CD44, CD45, CD47, CD51, CD52, CD56, CD62L, CD70, CD74, CD79, CD80, CD96, CD97, CD99, CD123, CD134, CD138, CD152 (CTLA-4), CD200, CD213A2, CD221, CD248, CD276 (B7-H3), B7-H4, CD279 (PD-1), CD274 (PD-L1), CD319, EGFR, EPCAM, 17-1A, HER1, HER2, HER3, CD117, C-Met, HGFR, PDGFRA, AXL, TWEAKR, PTHR2, HAVCR2 (TIM3), GD2 ganglioside, MUC1, mucin CanAg, mesothelin, endoglin, Lewis-Y antigen, CEA, CEACAM1, CEACAM5, CA-125, PSMA, BAFF, FGFR2, TAG-72, gelatinase B, glypican 3, nectin-4, BCMA, CSF1R, SLAMF7, integrin α v β 3 , TYRP1, GPNMB, CLDN18.2, FOLR1, CCR4, CXCR4, MICA, C242 antigen, DLL3, DLL4, EGFL7, vimentin, fibronectin extra domain-B, TROP-2, LRRC15, FAP, SLITRK6, NOTCH2, NOTCH3, Tenascin-3, STEAP1, and NRP1. 
     
     
         45 . A method of treating or preventing a disease or disorder in a subject in need thereof, comprising administering to the subject the composition of  claim 31 . 
     
     
         46 .- 58 . (canceled)