Nucleic acid compounds for binding to complement component 3 protein
Described herein are aptamers capable of binding to human complement component 3 (C3) protein; compositions comprising a C3 binding aptamer with a C3-Protein; and methods of making and using the same.
1. An aptamer that binds C3 protein, wherein the aptamer comprises a first region and a second region, wherein:
the first region comprises the sequence 5′-PAGPC-3′ (SEQ ID NO: 132) and the second region comprises the sequence 5′-GPAYRPP-3′ (SEQ ID NO: 157), wherein each P is independently, and for each occurrence, a C-5 modified pyrimidine nucleoside; Y is C, U, or T; and R is G or A, wherein each C-5 modified pyrimidine nucleoside is independently selected from: 5-(N-1-naphthylmethylcarboxyamide)-2′-deoxyuridine (NapdU), 5-(N-1-naphthylmethylcarboxyamide)-2′-O-methyluridine, 5-(N-1-naphthylmethylcarboxyamide)-2′-fluorouridine, 5-(N-2-naphthylmethylcarboxyamide)-2′-deoxyuridine (2NapdU), 5-(N-2-naphthylmethylcarboxyamide)-2′-O-methyluridine, 5-(N-2-naphthylmethylcarboxyamide)-2′-fluorouridine, 5-(N-1-naphthylethylcarboxyamide)-2′-deoxyuridine (NEdU), 5-(N-1-naphthylethylcarboxyamide)-2′-O-methyluridine, 5-(N-1-naphthylethylcarboxyamide)-2′-fluorouridine, 5-(N-2-naphthylethylcarboxyamide)-2′-deoxyuridine (2NEdU), 5-(N-2-naphthylethylcarboxyamide)-2′-O-methyluridine, 5-(N-2-naphthylethylcarboxyamide)-2′-fluorouridine, 5-(N-3-benzofuranylethylcarboxyamide)-2′-deoxyuridine (BFdU), 5-(N-3-benzofuranylethylcarboxyamide)-2′-O-methyluridine, 5-(N-3-benzofuranylethylcarboxyamide)-2′-fluorouridine, 5-(N-3-benzothiophenylethylcarboxyamide)-2′-deoxyuridine (BTdU), 5-(N-3-benzothiophenylethylcarboxyamide)-2′-O-methyluridine, and 5-(N-3-benzothiophenylethylcarboxyamide)-2′-fluorouridine, and
wherein the 3′-end of the first region is covalently linked to the 5′-end of the second region by at least one linker.
2. The aptamer of claim 1 , wherein the second region comprises the sequence 5′-GPACGPP-3′ (SEQ ID NO: 133), wherein each P is independently, and for each occurrence, a C-5 modified pyrimidine nucleoside independently selected from: 5-(N-1-naphthylmethylcarboxyamide)-2′-deoxyuridine (NapdU), 5-(N-1-naphthylmethylcarboxyamide)-2′-O-methyluridine, 5-(N-1-naphthylmethylcarboxyamide)-2′-fluorouridine, 5-(N-2-naphthylmethylcarboxyamide)-2′-deoxyuridine (2NapdU), 5-(N-2-naphthylmethylcarboxyamide)-2′-O-methyluridine, 5-(N-2-naphthylmethylcarboxyamide)-2′-fluorouridine, 5-(N-1-naphthylethylcarboxyamide)-2′-deoxyuridine (NEdU), 5-(N-1-naphthylethylcarboxyamide)-2′-O-methyluridine, 5-(N-1-naphthylethylcarboxyamide)-2′-fluorouridine, 5-(N-2-naphthylethylcarboxyamide)-2′-deoxyuridine (2NEdU), 5-(N-2-naphthylethylcarboxyamide)-2′-O-methyluridine, 5-(N-2-naphthylethylcarboxyamide)-2′-fluorouridine, 5-(N-3-benzofuranylethylcarboxyamide)-2′-deoxyuridine (BFdU), 5-(N-3-benzofuranylethylcarboxyamide)-2′-O-methyluridine, 5-(N-3-benzofuranylethylcarboxyamide)-2′-fluorouridine, 5-(N-3-benzothiophenylethylcarboxyamide)-2′-deoxyuridine (BTdU), 5-(N-3-benzothiophenylethylcarboxyamide)-2′-O-methyluridine, and 5-(N-3-benzothiophenylethylcarboxyamide)-2′-fluorouridine.
3. The aptamer of claim 1 , wherein the aptamer comprises a sequence and features of a SEQ ID NO selected from SEQ ID NOs: 4 to 28, 32, 33, 39 to 69, 72, 73, 78 to 118, 121 to 130, and 139 to 151.
4. The aptamer of claim 1 , wherein the aptamer is at least 80% identical to a sequence and features of a SEQ ID NO selected from SEQ ID NOs: 4 to 28, 32, 33, 39 to 69, 72, 73, 78 to 118, 121 to 130, and 139 to 151.
5. The aptamer of claim 1 , wherein the at least one linker is selected from a nucleotide, a substituted or unsubstituted C2-C20 linker, an alkylene glycol, and a polyalkylene glycol.
6. The aptamer of claim 5 , wherein the at least one linker is selected from a nucleotide, a 3-carbon spacer, and a hexaethylene glycol.
7. The aptamer of claim 1 , wherein each C-5 modified pyrimidine nucleoside is independently selected from:
5-(N-1-naphthylmethylcarboxyamide)-2′-deoxyuridine (NapdU), 5-(N-1-naphthylmethylcarboxyamide)-2′-O-methyluridine, and 5-(N-1-naphthylmethylcarboxyamide)-2′-fluorouridine.
8. The aptamer of claim 1 , wherein each C-5 modified pyrimidine nucleoside is 5-(N-naphthylmethylcarboxyamide)-2′-deoxyuridine (NapdU).
9. The aptamer of claim 1 , wherein the aptamer comprises at least one 2′-O-methyl modified nucleotide.
10. The aptamer of claim 1 , wherein the aptamer is 24 to 100 nucleotides in length.
11. The aptamer of claim 1 , wherein the aptamer inhibits cleavage of C3 protein.
12. The aptamer of claim 1 , wherein the C3 protein is human C3 protein.
13. A composition comprising the aptamer of claim 1 and a complement component 3 (C3) protein.
14. The aptamer of claim 2 , wherein each C-5 modified pyrimidine nucleoside is 5-(N-naphthylmethylcarboxyamide)-2′-deoxyuridine (NapdU).
15. The aptamer of claim 5 , wherein each C-5 modified pyrimidine nucleoside is 5-(N-naphthylmethylcarboxyamide)-2′-deoxyuridine (NapdU).
16. The aptamer of claim 6 , wherein each C-5 modified pyrimidine nucleoside is 5-(N-naphthylmethylcarboxyamide)-2′-deoxyuridine (NapdU).
17. The aptamer of claim 8 , wherein the aptamer is 24 to 100 nucleotides in length.
18. The aptamer of claim 17 , wherein the aptamer inhibits cleavage of C3 protein.
19. The aptamer of claim 14 , wherein the aptamer is 24 to 100 nucleotides in length.
20. The aptamer of claim 19 , wherein the aptamer inhibits cleavage of C3 protein.
21. The aptamer of claim 15 , wherein the aptamer is 24 to 100 nucleotides in length.
22. The aptamer of claim 21 , wherein the aptamer inhibits cleavage of C3 protein.
23. The aptamer of claim 16 , wherein the aptamer is 24 to 100 nucleotides in length.
24. The aptamer of claim 23 , wherein the aptamer inhibits cleavage of C3 protein.