HRP20210498T1 - De novo vezujuća domena koja sadrži polipeptide i njihova upotreba - Google Patents

De novo vezujuća domena koja sadrži polipeptide i njihova upotreba Download PDF

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Publication number
HRP20210498T1
HRP20210498T1 HRP20210498TT HRP20210498T HRP20210498T1 HR P20210498 T1 HRP20210498 T1 HR P20210498T1 HR P20210498T T HRP20210498T T HR P20210498TT HR P20210498 T HRP20210498 T HR P20210498T HR P20210498 T1 HRP20210498 T1 HR P20210498T1
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Croatia
Prior art keywords
target
seq
dbdpp
amino acid
binding
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HRP20210498TT
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English (en)
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David William Lafleur
David M. Hilbert
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Subdomain, Llc
Arcellx, Inc.
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Publication of HRP20210498T1 publication Critical patent/HRP20210498T1/hr

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    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/574—Immunoassay; Biospecific binding assay; Materials therefor for cancer
    • G01N33/57484—Immunoassay; Biospecific binding assay; Materials therefor for cancer involving compounds serving as markers for tumor, cancer, neoplasia, e.g. cellular determinants, receptors, heat shock/stress proteins, A-protein, oligosaccharides, metabolites
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/28—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
    • C07K16/2803—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against the immunoglobulin superfamily
    • C07K16/2827—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against the immunoglobulin superfamily against B7 molecules, e.g. CD80, CD86
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    • A61K38/17—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • A61K38/177—Receptors; Cell surface antigens; Cell surface determinants
    • A61K38/1774—Immunoglobulin superfamily (e.g. CD2, CD4, CD8, ICAM molecules, B7 molecules, Fc-receptors, MHC-molecules)
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    • C—CHEMISTRY; METALLURGY
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    • C07K16/2878—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against the NGF-receptor/TNF-receptor superfamily, e.g. CD27, CD30, CD40, CD95
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    • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
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Claims (40)

1. Polipeptid koji veže cilj koji sadrži sekvencu aminokiseline [image] [image] [image] [image] [image] [image] [image] [image] [image] ili [image] pri čemu (a) Xn je prirodna ili neprirodna aminokiselina; (b) Z1 i Z2 sadrže između 2 do 30 prirodnih ili neprirodnih aminokiselina; (c) polipeptid koji veže cilj specifično veže cilj od interesa, pri čemu je specifično vezanje polipeptida koji veže cilj na cilj od interesa veće od vezanja referentnog polipeptida koji sadrži sekvencu aminokiseline SEQ ID NO:1 na cilj od interesa; i (d) polipeptid koji veže cilj ne sadrži sekvencu aminokiseline SEQ ID NO:50.
2. Polipeptid koji veže cilj prema patentnom zahtjevu 1 naznačen time što sadrži sekvencu aminokiseline SEQ ID NO: 4.
3. Polipeptid koji veže cilj prema patentnom zahtjevu 1 ili zahtjevu 2, naznačen time što Xn nije cistein ili prolin.
4. Polipeptid koji veže cilj prema bilo kojem od patentnih zahtjeva 1 do 3, naznačen time što je cilj od interesa antigen raka, po izboru pri čemu je antigen raka PD-L1, CD137, ili CD123, i po izboru pri čemu (a) cilj od interesa je PD-L1 i polipeptid koji veže cilj sadrži sekvence aminokiseline odabrane iz skupine koju čine SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41, SEQ ID NO:42, SEQ ID NO: 43, i SEQ ID NO:44; (b) cilj od interesa je CD137 i polipeptid koji veže cilj sadrži sekvence aminokiseline odabrane iz skupine koju čine SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO:17, SEQ ID NO:18, i SEQ ID NO:19; (c) cilj od interesa je CD123 i polipeptid koji veže cilj sadrži sekvence aminokiseline odabrane iz skupine koju čine SEQ ID NOS: 92-126 i SEQ ID NO:127; ili (d) cilj od interesa je CD123 i polipeptid koji veže cilj se natječe s polipeptidom koji veže cilj iz (c) za vezanje na CD123.
5. Polipeptid koji veže cilj prema bilo kojem od patentnih zahtjeva 1 do 4, naznačen time što je polipeptid koji veže cilj označen i po izboru, pri čemu je oznaka biotinski dio ili je odabrana iz skupine koja se sastoji od enzimske oznake, fluorescentne oznake, luminiscentne oznake, te bioluminiscentne oznake.
6. Polipeptid koji veže cilj prema bilo kojem od patentnih zahtjeva 1 do 5, naznačen time što je polipeptid koji veže cilj konjugiran s terapijskim ili citotoksičnim sredstvom.
7. Farmaceutski pripravak naznačen time što sadrži polipeptid koji veže cilj prema bilo kojem od patentnih zahtjeva 1 do 6 i nadalje sadrži farmaceutski prihvatljiv nosač.
8. Komplet naznačen time što sadrži polipeptid koji veže cilj prema bilo kojem od patentnih zahtjeva 1 do 6.
9. Izolirana molekula nukleinske kiseline naznačena time što kodira polipeptid koji veže cilj prema bilo kojem od patentnih zahtjeva 1 do 4.
10. Vektor koji sadrži izoliranu molekulu nukleinske kiseline prema patentnom zahtjevu 9, i po izboru nadalje sadrži nukleotidnu sekvencu koja regulira ekspresiju polipeptida koji veže cilj kojeg kodira molekula nukleinske kiseline.
11. Stanica domaćina koja sadrži molekulu nukleinske kiseline prema patentnom zahtjevu 9 ili vektor prema patentnom zahtjevu 10.
12. Stanična linija naznačena time što sadrži polipeptid koji veže cilj prema bilo kojem od patentnih zahtjeva 1 do 4.
13. Kimerni antigenski receptor (CAR), naznačen time što CAR sadrži (a) ciljajuću domenu, (b) transmembransku domenu, i (c) unutarstaničnu signalnu domenu, pri čemu ciljajuća domena obuhvaća polipeptid koji veže cilj prema bilo kojem od patentnih zahtjeva 1 do 4.
14. CAR prema patentnom zahtjevu 13, koji je naznačen time što ima jedno ili više od (a) unutarstanična signalna domena odabrana je iz skupine koju čine humana CD3 zeta domena, 41BB domena, CD28 domena i bilo koja njihova kombinacija, (b) polipeptid koji veže cilj veže se na tumorski antigen povezan s hematološkim zloćudnim tumorom ili solidnim tumorom, (c) polipeptid koji veže cilj veže se za tumorski antigen odabran iz skupine koju čine CD137, PD-L1, CD123, CTLA4, CD47, KIR, DR5, TIM3, PD1, EGFR, TCR, CD19, CD20, CD22, ROR 1, mezotelin, CD33/lL3Ra, cMet, PSMA, Glikolipid F77, EGFRvIII, GD2, NY-ESO- 1, MAGE A3, i njihove kombinacije, (d) unutarstanična signalna domena obuhvaća kostimulacijsku signalnu regiju, i (e) unutarstanična signalna domena obuhvaća kostimulacijsku signalnu regiju koja obuhvaća unutarstaničnu domenu kostimulacijske molekule odabranu iz skupine koju čine CD27, CD28, 4-1BB, OX40, CD30, CD40, PD-1, antigen povezan s funkcijom limfocita 1 (LFA-1), CD2, CD7, LIGHT, NKG2C, B7-H3, ligand koji se specifično veže za CD83, i bilo koju njihovu kombinaciju.
15. Izolirana molekula nukleinske kiseline koja sadrži sekvencu koja kodira CAR prema patentnom zahtjevu 13 ili zahtjevu 14.
16. Stanica koja sadrži molekulu nukleinske kiseline koja sadrži sekvencu koja kodira CAR prema patentnom zahtjevu 13 ili zahtjevu 14, po izboru pri čemu je stanica T stanica ili prirodna stanica ubojica (NK), i po izboru pri čemu stanica pokazuje antitumorski imunitet kada se polipeptid koji veže cilj veže se na njegov odgovarajući tumorski antigen.
17. Imuna stanica koja sadrži CAR prema patentnom zahtjevu 13 ili zahtjevu 14 za uporabu u liječenju raka, po izboru pri čemu imuna stanica je T stanica ili prirodna stanica ubojica (NK).
18. Polipeptid de novo vezujuće domene (DBDpp) koji se sastoji od tri anti-paralelne alfa uzvojnice spojene peptidnim poveznicama, naznačen time što (a) DBDpp je sintetski peptid izveden iz modifikacija sekvence aminokiseline SEQ ID NO:1, pri čemu se modifikacije sastoje od 1 do 30 konzervativnih ili nekonzervativnih supstitucija aminokiselina odabranih iz položaja 1-6, 8-10, 12, 13, 15-17, 19, 20-27, 29, 30, 32-34, 36, 37, 39-41, 43-52, 54, 55, 57-59, 61, 62, 64-66, i 68-73 iz SEQ ID NO: 1; (b) DBDpp specifično veže cilj od interesa, pri čemu je specifično vezanje DBDpp na cilj od interesa veće od vezanja referentnog polipeptida koji sadrži sekvencu aminokiseline SEQ ID NO:1 na cilj od interesa; i (c) DBDpp ne sadrži sekvencu aminokiseline SEQ ID NO:50.
19. Polipeptid de novo vezujuće domene (DBDpp) prema patentnom zahtjevu 18, naznačen time što se modifikacije sastoje od 1 do 30 konzervativnih ili nekonzervativnih supstitucija aminokiselina odabranih iz položaja 2-6, 8-10, 12, 13, 15-17, 19, 20, 29, 30, 32-34, 36, 37, 39-41, 43, 44, 52, 54, 55, 57-59, 61, 62, 64-66, 68, 69, i 70 iz SEQ ID NO: 1.
20. DBDpp prema patentnom zahtjevu 18 ili zahtjevu 19 naznačen time što sadrži sekvencu aminokiseline [image] [image] [image] [image] [image] pri čemu Xn je prirodna ili neprirodna aminokiselina.
21. DBDpp prema bilo kojem od patentnih zahtjeva 18 do 20 koji se specifično veže na protein koji sadrži aminokiseline 19-305 od CD123 (SEQ ID NO: 187) ili protein koji je najmanje 95% identičan sa CD123, po izboru pri čemu DBDpp je naznačen time što ima jedno ili više od (a) DBDpp se veže na protein koji sadrži aminokiseline 19-305 od CD123 (SEQ ID NO: 187) ili protein koji je najmanje 95% identičan sa CD123 s konstantom disocijacije (KD) između 10-4M i 10-12M, (b) DBDpp sadrži sekvencu aminokiseline MGSWX5EFX8X9RLX12AIX15X16RLX19ALGGSEAELAAFEKEIAAFESELQAYKGKGNPEV EX55LRX58X59AAX62IRX65X66LQAYRHN (SEQ ID NO:4), pri čemu Xn je prirodna ili neprirodna aminokiselina, (c) DBDpp sadrži sekvencu aminokiseline MGSWX5EFX8X9RLX12AIX15X16RLX19ALGGSEAELAAFEKEIAAFESELQAYKGKGNPEV EX55LRX58X59AAX62IRX65X66LQAYRHN (SEQ ID NO:4), pri čemu Xn je prirodna ili neprirodna aminokiselina, i pri čemu Xn nije cistein ili prolin, i (d) DBDpp sadrži sekvencu aminokiseline koja je najmanje 85% identična sa sekvencom aminokiseline bilo koje od SEQ ID NO:60 - SEQ ID NO: 136, i (e) DBDpp je sposoban vezati se za tumor.
22. Fuzijski protein koji sadrži prvi i drugi DBDpp prema bilo kojem od patentnih zahtjeva 18-21 naznačen time što prvi i drugi DBDpp pokazuju specifičnost vezanja za tumorski cilj, po izboru pri čemu prvi i drugi DBDpp pokazuju specifičnost vezanja za različite tumorske ciljeve.
23. DBDpp prema bilo kojem od patentnih zahtjeva 18-21, ili fuzijski protein prema patentnom zahtjevu 22, naznačen time što je DBDpp ili fuzijski protein označen i po izboru, pri čemu je oznaka biotinski dio ili je odabrana iz skupine koja se sastoji od enzimske oznake, fluorescentne oznake, luminiscentne oznake, i bioluminiscentne oznake.
24. DBDpp prema bilo kojem od patentnih zahtjeva 18 do 21 i 23, ili fuzijski protein prema patentnom zahtjevu 22 ili zahtjevu 23, naznačen time što polipeptid koji veže cilj, DBDpp, ili fuzijski protein je konjugiran s terapijskim ili citotoksičnim sredstvom.
25. Farmaceutski pripravak naznačen time što sadrži DBDpp prema bilo kojem od patentnih zahtjeva 18 do 21, 23 i 24, ili fuzijski protein prema bilo kojem od patentnih zahtjeva 22 do 24 i nadalje sadrži farmaceutski prihvatljiv nosač.
26. Komplet naznačen time što sadrži DBDpp prema bilo kojem od patentnih zahtjeva 18 do 21, 23 i 24, ili fuzijski protein prema bilo kojem od patentnih zahtjeva 22 do 24.
27. Izolirana molekula nukleinske kiseline naznačena time što kodira DBDpp prema bilo kojem od patentnih zahtjeva 18-21, ili fuzijski protein prema zahtjevu 22.
28. Vektor naznačen time što sadrži izoliranu molekulu nukleinske kiseline prema patentnom zahtjevu 27, i po izboru nadalje sadrži nukleotidnu sekvencu koja regulira ekspresiju DBDpp, ili fuzijski protein kodiran molekulom nukleinske kiseline.
29. Stanica domaćin naznačena time što sadrži molekulu nukleinske kiseline prema patentnom zahtjevu 27 ili vektor prema patentnom zahtjevu 28.
30. Stanična linija naznačena time što sadrži DBDpp prema bilo kojem od patentnih zahtjeva 18-21, ili fuzijski protein prema patentnom zahtjevu 22.
31. Kimerni antigenski receptor (CAR), naznačen time što CAR obuhvaća (a) ciljajuću domenu, (b) transmembransku domenu, i (c) unutarstaničnu signalnu domenu, pri čemu ciljajuća domena obuhvaća DBDpp prema bilo kojem od patentnih zahtjeva 18-21, ili fuzijski protein prema patentnom zahtjevu 22.
32. CAR prema patentnom zahtjevu 32, koji je naznačen time što ima jedno ili više od (a) unutarstanična signalna domena odabrana je iz skupine koju čine humana CD3 zeta domena, 41BB domena, CD28 domena i bilo koja njihova kombinacija, (b) DBDpp, ili fuzijski protein veže se na tumorski antigen povezan s hematološkim zloćudnim tumorom ili solidnim tumorom, (c) DBDpp, ili fuzijski protein veže se na tumorski antigen odabran iz skupine koju čine CD137, PD-L1, CD123, CTLA4, CD47, KIR, DR5, TIM3, PD1, EGFR, TCR, CD19, CD20, CD22, ROR 1, mezotelin, CD33/lL3Ra, cMet, PSMA, Glikolipid F77, EGFRvIII, GD2, NY-ESO- 1, MAGE A3, i njihove kombinacije, (d) unutarstanična signalna domena obuhvaća kostimulacijsku signalnu regiju, i (e) unutarstanična signalna domena obuhvaća kostimulacijsku signalnu regiju koja obuhvaća unutarstaničnu domenu kostimulacijske molekule odabranu iz skupine koju čine CD27, CD28, 4-1BB, OX40, CD30, CD40, PD-1, antigen povezan s funkcijom limfocita 1 (LFA-1), CD2, CD7, LIGHT, NKG2C, B7-H3, ligand koji se specifično veže za CD83 i bilo koju njihovu kombinaciju.
33. Izolirana molekula nukleinske kiseline naznačena time što sadrži sekvencu koja kodira CAR prema patentnom zahtjevu 31 ili zahtjevu 32.
34. Stanica koja sadrži molekulu nukleinske kiseline naznačena time što sadrži sekvencu koja kodira CAR prema patentnom zahtjevu 31 ili zahtjevu 32, po izboru gdje je stanica T stanica ili stanica prirodnog ubojice (NK), i po izboru pri čemu stanica pokazuje antitumorski imunitet kada se DBDpp, ili fuzijski protein veže na njegov odgovarajući tumorski antigen.
35. Imuna stanica koja sadrži CAR prema patentnom zahtjevu 31 ili zahtjevu 32 za uporabu u liječenju raka, po izboru gdje je imuna stanica T stanica ili stanica prirodnog ubojice (NK).
36. T stanica koja sadrži kimerni antigenski receptor (CAR) za uporabu u liječenju raka, naznačena time što CAR sadrži: (a) ciljnu vezujuću domenu koja sadrži polipeptid koji veže cilj koji ima aminokiselinsku sekvencu odabranu iz skupine koja se sastoji od [image] [image] [image] [image] i [image] pri čemu Xn je prirodna ili neprirodna aminokiselina, pri čemu Xn nije cisteinski ili prolinski ostatak, pri čemu polipeptid koji veže cilj specifično veže cilj od interesa izražen pomoću stanice raka, i pri čemu specifično vezanje polipeptida koji veže cilj za cilj od interesa je veće od vezanja polipeptida prema SEQ ID NO:1 na cilj od interesa, (b) transmembransku domenu odabranu između 41BB i CD28, i (c) unutarstaničnu domenu, pri čemu unutarstanična domena sadrži signalnu domenu odabranu između alfa, beta ili zeta lanca receptora T stanica.
37. Imuna stanica prema patentnom zahtjevu 36 naznačena time što je imuna stanica T stanica ili prirodna stanica ubojica (NK).
38. Postupak za transformaciju referentnog polipeptida u polipeptid koji se veže za cilj, koji se može specifično vezati za cilj od interesa, te postupak sadrži: (a) modificiranje mnoštva aminokiselinskih ostataka iz referentnog polipeptida kako bi se dobio veći broj potencijalnih kandidata polipeptida koji se vežu za cilj; pri čemu kandidati za polipeptide koji se vežu za cilj uključuju varijantu sekvence aminokiseline SEQ ID NO: 1, pri čemu kandidati za polipeptide koji se vežu za cilj sadrže tri anti-paralelne alfa uzvojnice spojene veznim peptidima, pri čemu su modificirani aminokiselinski ostaci dostupni otapalu ili nedostupni otapalu, i pri čemu modifikacija obuhvaća jednu ili više konzervativnih ili nekonzervativnih supstitucija aminokiselina i ne uključuje supstituciju s cisteinom ili prolinom; (b) pakiranje mnoštva potencijalnih kandidata polipeptida koji se vežu za cilj u mnoštvo vektora kako bi se stvorila biblioteka kandidata; i (c) probiranje u biblioteci kandidata za potencijalne kandidate polipeptide koji se vežu za cilj koji pokazuju specifično vezanje za cilj od interesa; pri čemu kandidati polipeptidi koji se vežu za cilj uključuju aminokiselinsku sekvencu odabranu iz skupine koja se sastoji od [image] [image] [image] [image] [image] [image] [image] [image] [image] MGSWX5EFX8X9RLX12AIX15X16RLX19ALZ1EAELAX28FEX31X32IAX35FEX38X39LQX42Y Z2NPEVEALX52X53EAX56AIX59X60ELX63AYRHN (SEQ ID NO:11), pri čemu Xn je prirodna ili neprirodna aminokiselina i Z1 i Z2 sadrže između 2 do 30 prirodnih ili neprirodnih aminokiselina.
39. Postupak prema patentnom zahtjevu 38, pri čemu naznačen time što postupak nadalje obuhvaća identificiranje potencijalno imunogenih aminokiselinskih ostataka u kandidatskom polipeptidu koji veže cilj i modificiranje najmanje jednog od potencijalno imunogenih aminokiselinskih ostataka u kandidatskom polipeptidu koji veže cilj, pri čemu modifikacija sadrži supstituciju aminokiseline.
40. Čestice slične virusu (VLP) koje sadrže fuzijski polipeptid koji sadrži DBDpp prema bilo kojem od patentnih zahtjeva 18-21, naznačene time što su VLP prikladne za upotrebu kao imunogeni za stvaranje protutijela, pri čemu su navedena protutijela usmjerena protiv DBDpp.
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