Patent Application
20220098591
Visual impairment is a national and global health concern that has a negative impact on physical and mental health. The number of people with visual impairment and blindness is increasing due to an overall aging population. Visual impairment and blindness can be caused by any one of a large number of eye diseases and disorders affecting people of all ages.
Vascular endothelial growth factor-A (VEGF-A) is thought to be the most significant regulator of angiogenesis in the VEGF family. VEGF-A promotes growth of vascular endothelial cells, which leads to the formation of capillary-like structures and may be necessary for the survival of newly formed blood vessels. VEGF-A is thought to play a role in various ocular diseases and disorders. Previous attempts at developing aptamers that inhibit VEGF-A have proven difficult because such aptamers have been unable to target multiple isoforms and variants of VEGF-A. Therefore, there is an un-met need for pan-variant specific aptamers that demonstrate high specificity and potency towards multiple isoforms and variants of VEGF-A.
These needs may be met by the aptamers provided in the present disclosure.
In one aspect, an aptamer is provided having a nucleic acid sequence, wherein the aptamer comprises a stem-loop secondary structure which specifically binds to and inhibits at least one of VEGF-A121 and VEGF-A110. In some cases, the aptamer comprises up to five loops.
In some cases, the aptamer comprises up to three stems. In some cases, the aptamer comprises up to one terminal stem. In some cases, the aptamer comprises up to two internal stems. In some cases, the aptamer comprises up to two terminal loops. In some cases, the aptamer comprises up to three internal loops. In some cases, the aptamer comprises, in a 5′ to 3′ direction: (i) a first side of a first base paired stem (S1); (ii) optionally, a first loop (L1); (iii) a first side of a second base paired stem (S2); (iv) a second loop (L2); (v) a second side of the second base paired stem (S2′); (vi) a third loop (L3); (vii) a first side of a third base paired stem (S3); (vii) a fourth loop (L4); (viii) a second side of the third base paired stem (S3′); (ix) a fifth loop (L5); and (x) a second side of the first base paired stem (S1′). In some cases, the S1′ forms at least one base pair with the S1. In some cases, the S1′ forms from two to eight contiguous base pairs with the S1. In some cases, the S1′ comprises from one to three nucleotides that are mismatched with the S1. In some cases, a 3′ terminal nucleotide of the S1, and a 5′ terminal nucleotide of the S1′ form a base pair. In some cases, the base pair is C*G. In some cases, the base pair is separated from other base pairs in the S1 and the S1′ by one or more mismatched nucleotides. In some cases, the S1 comprises a consensus nucleic acid sequence of 5′-HNBYHDCC-3′, and the S1′ comprises a consensus nucleic acid sequence of 5′-GKYNKVNW-3′, where H is A, C, or U; N is A, C, G, or U; B is C, G, or U; Y is C or U; D is A, G, or U; K is G or U; V is A, C, or G; and W is A or U. In some cases, the S1 comprises a consensus nucleic acid sequence of 5′-HNBYHDNN-3′, and the S1′ comprises a consensus nucleic acid sequence of 5′-NNYNKVNW-3′, where H is A, C, or U; N is A, C, G, or U; B is C, G, or U; Y is C or U; and D is A, G, or U. In some cases, the L1 comprises up to one nucleotide. In some cases, the L1 comprises a consensus nucleic acid sequence of 5′-N*-3′, wherein N* is A, C, G, U, a 3-carbon non-nucleotidyl spacer, two 3 carbon non-nucleotidyl spacers, a 6-carbon non-nucleotidyl spacer, or a 9-carbon non-nucleotidyl spacer. In some cases, the 3-carbon non-nucleotidyl spacer is 1,3-propanediol. In some cases, the 6-carbon non-nucleotidyl spacer is 1,6-hexanediol. In some cases, the 9-carbon non-nucleotidyl spacer is triethyleneglycol. In some cases, the S2′ forms at least one base pair with the S2. In some cases, the S2′ forms up to two base pairs with the S2. In some cases, the S2 comprises a consensus nucleic acid sequence of 5′-CC-3′, and the S2′ comprises a consensus nucleic acid sequence of 5′-GG-3′. In some cases, the S2 comprises a consensus nucleic acid sequence of 5′-NN-3′, and the S2′ comprises a consensus nucleic acid sequence of 5′-NN-3′, where N is A, C, G, or U. In some cases, the L2 comprises up to four nucleotides. In some cases, the L2 comprises a consensus nucleic acid sequence of 5′-GCGC-3′. In some cases, the L2 comprises a consensus nucleic acid sequence of 5′-KNGC-3′, where K is G or U; and N is A, C, G or U. In some cases, the S3′ forms at least one base pair with the S3. In some cases, the S3′ forms from four to six base pairs with the S3. In some cases, the S3′ forms six base pairs with the S3, and the S3 has one mismatch nucleotide at a 3′ terminal nucleotide of the S3. In some cases, the S3′ forms four base pairs with the S3, and the L4 has six or eight nucleotides. In some cases, the S3′ forms five base pairs with the S3, and the L4 has four or six nucleotides. In some cases, the S3′ forms six base pairs with the S3, and the L4 has four nucleotides. In some cases, the S3′ forms six base pairs with S3, the S3 has one mismatch nucleotide at a 3′ terminal nucleotide, and the L4 has three nucleotides. In some cases, the S3 comprises a consensus nucleic acid sequence of 5′-GRGRWN3′, and the S3′ comprises a consensus nucleic acid sequence of 5′-NHYCYC-3′, where R is A or G; N is A, C, G, or U; W is A or U; and Y is C or U. In some cases, the S3 comprises a consensus nucleic acid sequence of 5′-GGGRUN3′, and the S3′ comprises a consensus nucleic acid sequence of 5′-NWYCCC-3′, where R is A or G; N is A, C, G, or U; W is A or U; and Y is C or U. In some cases, the S3 comprises a consensus nucleic acid sequence of 5′-GGGRUN3′, and the S3′ comprises a consensus nucleic acid sequence of 5′-NAYCCC-3′, where R is A or G; N is A, C, G, or U; and Y is C or U. In some cases, the S3 comprises a consensus nucleic acid sequence of 5′-GGGRUD-3′, and the S3′ comprises a consensus nucleic acid sequence of 5′-HWYCCC-3′, wherein R is A or G; D is A, G, or U; H is A, C, or U; W is A or U; and Y is C or U. In some cases, the S3 comprises a consensus nucleic acid sequence of 5′-GKGN-3′, and the S3′ comprises a consensus nucleic acid sequence of 5′-NSMC-3′, where K is G or U; N is A, C, G or or U and M is A or C. In some cases, the S3 comprises a consensus nucleic acid sequence of 5′-GGGG-3′, and the S3′ comprises a consensus nucleic acid sequence of 5′-CCCC-3′. In some cases, the S3 comprises a consensus nucleic acid sequence of 5′-GGGU-3′, and the S3′ comprises a consensus nucleic acid sequence of 5′-ACCC-3′. In some cases, the S3 comprises a consensus nucleic acid sequence of 5′-GGCU-3′, and the S3′ comprises a consensus nucleic acid sequence of 5′-AGCC-3′. In some cases, the S3 comprises a consensus nucleic acid sequence of 5′-GBBNY-3′, and the S3′ comprises a consensus nucleic acid sequence of 5′-RNBNC-3′, where B is C, G or U; R is A or G; N is A, C, G or U and Y is C or U. In some cases, the S3 comprises a consensus nucleic acid sequence of 5′-GGGRU-3′, and the S3′ comprises a consensus nucleic acid sequence of 5′-AYCCC-3′, where R is A or G; and Y is C or U. In some cases, the S3 comprises a consensus nucleic acid sequence of 5′-SVVVK-, and the S3′ comprises a consensus nucleic acid sequence of 5′-MBBBS-3′, where S is G or C; V is A, C, or G; K is G or U; M is A or C; and B is C, G, or U. In some cases, the S3 comprises a consensus nucleic acid sequence of 5′-GGGGUD-3′, and the S3′ comprises a consensus nucleic acid sequence of 5′-HAUCCC-3′, where D is A, G, or U; and H is A, C, or U. In some cases, the S3 comprises a consensus nucleic acid sequence of 5′-GGGRUUR-3′, and the S3′ comprises a consensus nucleic acid sequence of 5′-UAUCCC-3′, where the underlined U is the single mis-matched nucleotide, and R is A or G. In some cases, the L3 comprises up to one nucleotide. In some cases, the L3 comprises a consensus nucleic acid sequence of 5′-A-3′. In some cases, the L3 comprises a consensus nucleic acid sequence of 5′-W-3′, where W is A or U. In some cases, the L4 has three, four, six, or eight nucleotides. In some cases, the L4 comprises a consensus nucleic acid sequence of 5′-MAU-3′, where M is A or C. In some cases, the L4 comprises a consensus nucleic acid sequence of 5′-CUA-3′. In some cases, the L4 comprises a consensus nucleic acid sequence of 5′-DNAH-3′, where D is A, G, or U; N is A, C, G, or U; and H is A, C, or U; or a consensus nucleic acid sequence of 5′-DNDH-3′, where D is A, G, or U; N is A, C, G, or U; and H is A, C, or U; or a consensus nucleic acid sequence of 5′-DNDN-3′, where D is A, G, or U; N is A, C, G, or U; and H is A, C, or U. In some cases, the L4 comprises a consensus nucleic acid sequence of 5′-UDNDHU-3′, where D is A, G, or U; N is A, C, G, or U; and H is A, C, or U. In some cases, the L4 comprises a consensus nucleic acid sequence of 5′-UDRGBU-3′, where D is A, G, or U; R is A or G, N is A, C, G, or U; and B is G, C, or U. In some cases, the L4 comprises a consensus nucleic acid sequence of 5′-KNNNNW-3′, where K is U or G, N is A, C, G, or U; and W is A, or U. In some cases, the L4 comprises a consensus nucleic acid sequence of 5′-UDUHRKYU-3′, where D is A D, or U; H is A, C or U; R is A or G; K is G or U and Y is C or U. In some cases, the L4 comprises a consensus nucleic acid sequence of 5′-UUUCAUUU-3′. In some cases, the L5 comprises up to four nucleotides. In some cases, the L5 comprises a consensus nucleic acid sequence of 5′-GYUU-3′, where Y is C or U. In some cases, the L5 comprises a consensus nucleic acid sequence of GNNN-3′, where N is A, C, G, or U. In some cases, the L5 comprises a consensus nucleic acid sequence of 5′-GNHW-3′, where N is A, C, G, or U; H is A, C, or U; and W is A or U.
In another aspect, an aptamer is provided comprising a consensus nucleic acid sequence of 5′-HNBYHDCCUCCGCGCGGAGGGRUDDNDHHWYCCCGYUUGKYNKVNW-3′ (SEQ ID NO: 1), where H is A, C, or U; N is A, C, G, or U; B is C, G, or U; Y is C or U; D is A, G, or U; R is A or G; W is A or U; K is G or U; and V is A, C, or G.
In yet another aspect, an aptamer is provided comprising a consensus nucleic acid sequence of 5′-HNBYHDCCUCCGCGCGGAGGGRUUDNDHUAYCCCGYUUGKYNKVNW-3′ (SEQ ID NO: 2), where H is A, C, or U; N is A, C, G, or U; B is C, G, or U; Y is C or U; D is A, G, or U; R is A or G; K is G or U; V is A, C, or G; and W is A or U.
In yet another aspect, an aptamer is provided comprising a consensus nucleic acid sequence of 5′-WNKYHDCCUCCGCGCGGAGGGGUDDNAHHAUCCCGUUUGGYBKMHW-3′ (SEQ ID NO: 3), where W is A or U; N is A, C, G, or U; K is G or U; Y is C or U; H is A, C, or U; D is A, G, or U; B is C, G, or U; and M is A or C.
In yet another aspect, an aptamer is provided comprising a consensus nucleic acid sequence of 5′-AUGCCGCCUCCGCGCGGAGGGGUUUCAUUUCCCCGUUUGGCUGCAU-3′ (SEQ ID NO: 4).
In another aspect, an aptamer is provided comprising a consensus nucleic acid sequence of 5′-HNBYHDNNN*NNKNGCNNWGGGRUNDNDHNWYCCCGNNNNNYNKVNW-3′ (SEQ ID NO: 5), where H is A, C, or U; N is A, C, G, or U; B is C, G, or U; Y is C or U; N* is A, C, G, U, deleted entirely, or a non-nucleotidyl spacer 3 modification, a 6 carbon alkyl linker (1,6-hexanediol), or a spacer 9 (triethyleneglycol) modification: D is A, G, or U; K is G or U; W is A or U; R is A or G; and V is A, C, or G.
In another aspect, an aptamer is provided comprising a consensus nucleic acid sequence of 5′-HNBYHDCCUCCGCGCGGAGDSBHDNNNNHNNBNCGYUUGKYNKVNW-3′ (SEQ ID NO: 436), where H is A, C, or U; N is A, C, G, or U; B is C, G, or U; Y is C or U; D is A, G, or U; R is A or G; W is A or U; K is G or U; and V is A, C, or G.
In another aspect, an aptamer is provided comprising a consensus nucleic acid sequence of 5′-HNBYHDCCUCCGCGCGGAGKBHYDNNNKDBVCGYUUGKYNKVNW-3′ (SEQ ID NO: 437), where H is A, C, or U; N is A, C, G, or U; B is C, G, or U; Y is C or U; D is A, G, or U; R is A or G; W is A or U; K is G or U; and V is A, C, or G.
In another aspect, an aptamer is provided comprising a consensus nucleic acid sequence of 5′-HNBYHDCCUCCGCGCGGAGKSHUDRGBUDSMCGYUUGKYNKVNW-3′ (SEQ ID NO: 438), where H is A, C, or U; N is A, C, G, or U; B is C, G, or U; Y is C or U; D is A, G, or U; R is A or G; W is A or U; K is G or U; M is A or C; and V is A, C, or G.
In some cases, less than 50% of pyrimidines present in the nucleic acid sequence of any aptamer of the preceding comprise a C-5 modified pyrimidine. In some cases, less than 25% of pyrimidines present in the nucleic acid sequence of any aptamer of the preceding comprise a C-5 modified pyrimidine. In some cases, less than 10% of pyrimidines present in the nucleic acid sequence of any aptamer of the preceding comprise a C-5 modified pyrimidine. In some cases, the nucleic acid sequence of any aptamer of the preceding does not comprise any C-5 modified pyrimidines. In some cases, the C-5 modified pyrimidine comprises a C-5 modified cytosine or a C-5 modified uridine. In some cases, the C-5 modified pyrimidine comprises a C-5 hydrophobic modification. In some cases, less than 100% of uridines present in the nucleic acid sequence of any aptamer of the preceding comprise a C-5 modified uridine. In some cases, less than 50% of uridines present in the nucleic acid sequence of any aptamer of the preceding comprise a C-5 modified uridine. In some cases, less than 25% of uridines present in the nucleic acid sequence of any aptamer of the preceding comprise a C-5 modified uridine. In some cases, less than 10% of uridines present in the nucleic acid sequence of any aptamer of the preceding comprise a C-5 modified uridine. In some cases, no uridines present in the nucleic acid sequence of any aptamer of the preceding comprise a C-5 modified uridine. In some cases, the C-5 modified uridine comprises a C-5 hydrophobic modification. In some cases, the C-5 modified uridine is selected from the group consisting of: 5-(N-benzylcarboxyamide)-2′-deoxyuridine (BndU), 5-(N-benzylcarboxyamide)-2′-O-methyluridine, 5-(N-benzylcarboxyamide)-2′-fluorouridine, 5-(N-phenethylcarboxyamide)-2′-deoxyuridine (PEdU), 5-(N-thiophenylmethylcarboxyamide)-2′-deoxyuridine (ThdU), 5-(N-isobutylcarboxyamide)-2′-deoxyuridine (iBudU), 5-(N-tyrosylcarboxyamide)-2′-deoxyuridine (TyrdU), 5-(N-3,4-methylenedioxybenzylcarboxyamide)-2′-deoxyuridine (MBndU), 5-(N-4-fluorobenzylcarboxyamide)-2′-deoxyuridine (FBndU), 5-(N-3-phenylpropylcarboxyamide)-2′-deoxyuridine (PPdU), 5-(N-imidizolylethylcarboxyamide)-2′-deoxyuridine (ImdU), 5-(N-isobutylcarboxyamide)-2′-O-methyluridine, 5-(N-isobutylcarboxyamide)-2′-fluorouridine, 5-(N-tryptaminocarboxyamide)-2′-deoxyuridine (TrpdU), 5-(N—R-threoninylcarboxyamide)-2′-deoxyuridine (ThrdU), 5-(N-tryptaminocarboxyamide)-2′-O-methyluridine, 5-(N-tryptaminocarboxyamide)-2′-fluorouridine, 5-(N-[1-(3-trimethylamonium)propyl]carboxyamide)-2′-deoxyuridine chloride, 5-(N-naphthylmethylcarboxyamide)-2′-deoxyuridine (NapdU), 5-(N-naphthylmethylcarboxyamide)-2′-O-methyluridine, 5-(N-naphthylmethylcarboxyamide)-2′-fluorouridine, 5-(N-[1-(2,3-dihydroxypropyl)]carboxyamide)-2′-deoxyuridine), 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. In some cases, the C-5 modified uridine is 5-(N-naphthylmethylcarboxyamide)-2′-deoxyuridine (NapdU).
In some cases, any aptamer of the preceding selectively binds to a receptor binding face or receptor binding domain of VEGF-A121 or VEGF-A110. In some cases, the receptor binding domain comprises at least one of residues 1-109 of SEQ ID NO: 6-10. In some cases, the receptor binding domain comprises at least one of residues Phe17, Ile43, Ile46, Glu64, Gln79, Ile83, Lys84, Pro85, Arg82, His86, Asp63, and Glu67 of SEQ ID NO: 6-10. In some cases, any aptamer of the preceding inhibits VEGF-A121, VEGF-A110, or both, with an IC50 of less than about 50 nM as measured by a VEGF-A:KDR competition binding assay, a KDR phosphorylation AlphaLISA® assay, or an in vitro model of VEGF-A-induced angiogenesis. In some cases, any aptamer of the preceding inhibits VEGF-A121, VEGF-A110, or both, with an IC50 of less than about 25 nM as measured by a VEGF-A:KDR competition binding assay, a KDR phosphorylation AlphaLISA® assay, or an in vitro model of VEGF-A-induced angiogenesis. In some cases, any aptamer of the preceding inhibits VEGF-A121, VEGF-A110, or both, with an IC50 of less than about 10 nM as measured by a VEGF-A:KDR competition binding assay, a KDR phosphorylation AlphaLISA® assay, or an in vitro model of VEGF-A-induced angiogenesis. In some cases, any aptamer of the preceding inhibits VEGF-A121, VEGF-A110, or both, with an IC50 of less than about 5 nM as measured by a VEGF-A:KDR competition binding assay, a KDR phosphorylation AlphaLISA® assay, or an in vitro model of VEGF-A-induced angiogenesis. In some cases, any aptamer of the preceding inhibits VEGF-A121, VEGF-A110, or both, with an IC50 of less than about 1 nM as measured by a VEGF-A:KDR competition binding assay, a KDR phosphorylation AlphaLISA® assay, or an in vitro model of VEGF-A-induced angiogenesis. In some cases, any aptamer of the preceding binds to VEGF-A121, VEGF-A110, or both, with a Kd of less than about 50 nM as measured by surface plasmon resonance assay. In some cases, any aptamer of the preceding binds to VEGF-A121, VEGF-A110, or both, with a Kd of less than about 25 nM as measured by surface plasmon resonance assay. In some cases, any aptamer of the preceding binds to VEGF-A121, VEGF-A110, or both, with a Kd of less than about 10 nM as measured by surface plasmon resonance assay. In some cases, any aptamer of the preceding aptamer binds to VEGF-A121, VEGF-A110, or both, with a Kd of less than about 5 nM as measured by surface plasmon resonance assay. In some cases, any aptamer of the preceding binds to VEGF-A121, VEGF-A110, or both, with a Kd of less than about 1 nM as measured by surface plasmon resonance assay. In some cases, any aptamer of the preceding selectively binds to and inhibits at least one of VEGF-A165, VEGF-A189, and VEGF-A206. In some cases, any aptamer of the preceding inhibits or reduces an interaction of VEGF-A with KDR. In some cases, any aptamer of the preceding inhibits or reduces VEGF-A-induced KDR phosphorylation.
In some cases, any aptamer of the preceding comprises RNA or sugar-modified RNA. In some cases, any aptamer of the preceding comprises DNA or sugar-modified DNA. In some cases, at least 50% of the nucleic acid sequence of any aptamer of the preceding comprises sugar-modified nucleotides. In some cases, 100% of the nucleic acid sequence of any aptamer of the preceding comprises sugar-modified nucleotides. In some cases, the sugar-modified nucleotides comprise a 2′F-modified nucleotide, a 2′OMe-modified nucleotide, or both. In some cases, the sugar-modified nucleotides are selected from the group consisting of: 2′F-G, 2′OMe-G, 2′OMe-U, 2′OMe-A, 2′OMe-C, and any combination thereof. In some cases, any aptamer of the preceding further comprises a 3′ terminal inverted deoxythymidine. In some cases, any aptamer of the preceding comprises a nuclease-stabilized nucleic acid backbone. In some cases, the nucleic acid sequence of any aptamer of the preceding comprises from about 30 to about 90 nucleotides, wherein the nucleotides are unmodified nucleotides, modified nucleotides, or a combination of modified nucleotides and unmodified nucleotides. In some cases, any aptamer of the preceding is conjugated to a polyethylene glycol (PEG) molecule. In some cases, the PEG molecule has a molecular weight selected from the group consisting of: less than 5 kDa, less than 10 kDa, less than 20 kDa, less than 40 kDa, less than 60 kDa, and less than 80 kDa. In some cases, up to five nucleotides of any aptamer of the preceding comprise a phosphate-backbone modification. In some cases, the phosphate-backbone modification is a phosphorothioate substitution.
In another aspect, an aptamer is provided according to any aptamer described in Table 1 of the specification.
In another aspect, an aptamer is provided having at least 70% sequence identity with any aptamer described in Table 1 of the specification. In some cases, the aptamer has at least 70% modification identity with any aptamer described in Table 1 of the specification.
In some cases, any aptamer of the preceding is provided for use in treating an ocular disease or disorder in a subject in need thereof. In some cases, one or more symptoms of the ocular disease or disorder are treated.
In another aspect, a method is provided for treating an ocular disease or disorder in a subject in need thereof, comprising administering to the subject any aptamer of the preceding, thereby treating the ocular disease or disorder. In some cases, the ocular disease or disorder is selected from the group consisting of: diabetic retinopathy, retinopathy of prematurity, central retinal vein occlusion, macular edema, choroidal neovascularization, neovascular age-related macular degeneration, myopic choroidal neovascularization, punctate inner choroidopathy, ocular histoplasmosis syndrome, familial exudative vitreoretinopathy, and retinoblastoma. In some cases, the ocular disease or disorder exhibits elevated levels of VEGF-A.
In yet another aspect, any aptamer of the preceding is provided for use in a formulation of a medicament for treatment of an ocular disease or disorder.
In yet another aspect, any aptamer of the preceding is provided for use for treatment of an ocular disease or disorder.
In yet another aspect, a method is provided for modulating vascular endothelial growth factor-A (VEGF-A) in a biological system, the method comprising: administering to the biological system any aptamer of the preceding, thereby modulating VEGF-A in the biological system. In some cases, biological system comprises a biological tissue or biological cells. In some cases, the biological system is a subject. In some cases, the subject is a human. In some cases, the modulating comprises inhibiting a function associated with VEGF-A. In some cases, the modulating comprises preventing or reducing an association of VEGF-A with one or more of Flt-1, KDR, or Nrp-1.
All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference in their entireties to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference.
The novel features of the invention are set forth with particularity in the appended claims. A better understanding of the features and advantages of the present invention will be obtained by reference to the following detailed description that sets forth illustrative embodiments, in which the principles of the invention are utilized, and the accompanying drawings of which:
Compounds were tested in a dose-dependent fashion to determine an IC50 against each isoform according to embodiments of the disclosure.
The disclosure herein provides aptamer compositions that selectively bind to and inhibit vascular endothelial growth factor-A (VEGF-A) and methods of using said aptamer compositions. In various aspects, an aptamer composition of the disclosure may comprise an anti-VEGF-A aptamer that binds to one or more isoforms or variants of VEGF-A. In various aspects, an aptamer composition of the disclosure may comprise a pan-variant specific anti-VEGF-A aptamer that binds to each of VEGF-A110, VEGF-A121, VEGF-A165, VEGF-A189, and VEGF-A206. In some cases, the anti-VEGF-A aptamers may bind to the receptor binding face of VEGF-A, or a portion thereof. In some cases, the anti-VEGF-A aptamers may bind to the receptor binding domain (RBD) of VEGF-A, or a portion thereof. In some cases, an aptamer of the disclosure does not bind to the heparin-binding domain (HBD) of VEGF-A. Without wishing to be bound by theory, anti-VEGF-A aptamers of the disclosure may prevent or reduce binding of VEGF-A to a VEGF receptor (VEGFR). For example, an anti-VEGF-A aptamer of the disclosure may prevent or reduce binding of VEGF-A to VEGFR1 (also known as Fms-related tyrosine kinase 1 (Flt1)), VEGFR2 (also known as Kinase insert domain receptor (KDR) or Flk-1), Neuropilin-1 (Nrp-1), or any combination thereof. In some cases, an anti-VEGF-A aptamer of the disclosure may inhibit a function associated with VEGF-A (e.g., engaging a VEGF receptor, a signaling pathway downstream of VEGF-A, or both).
The disclosure herein further provides aptamer compositions having unique stem-loop secondary structures that selectively bind to and inhibit a function associated with one or more isoforms or variants of VEGF-A and methods of using such aptamer compositions. In some cases, the aptamers of the disclosure may have, in a 5′ to 3′ direction, a first side of a first base paired stem (e.g., stem S1); optionally, a first loop (e.g., loop L1); a first side of a second base paired stem (e.g., stem S2); a second loop (e.g., loop L2); a second, complementary side of the second base paired stem (e.g., stem S2′); a third loop (e.g., loop L3); a first side of a third base paired stem (e.g., stem S3), a fourth loop (e.g., loop L4), a second, complementary side of the third base paired stem (e.g., stem S3′), a fifth loop (e.g., loop L5), and a second, complementary side of the first base paired stem (e.g., stem S1′). Put another way, an anti-VEGF-A aptamer of the disclosure may have the following stem and loop structure: 5′-S1-L1-S2-L2-S2′-L3-S3-L4-S3′-L5-S1′-3′. In some cases, an anti-VEGF-A aptamer of the disclosure may have the following stem and loop structure: 5′-S1-S2-L2-S2′-L3-S3-L4-S3′-L5-S1′-3′.
The aptamers disclosed herein may also include one or more further elements (e.g., additional stem(s) or loop(s)). In some cases, additional elements (e.g., additional stem(s), loop(s), one or more nucleotides, etc.) may be located before (e.g., 5′ side) the first side of the first base paired stem, after (e.g., 3′ side) the second, complementary side of the first base paired stem, or both. In some cases, additional elements may be located interspersed between other elements of the aptamer. Additional elements may include additional stem structures, loop structures, non-nucleotidyl linkers, or any number of overhanging, unpaired nucleotides.
In some embodiments, each element may be adjacent to each other. For example, the anti-VEGF-A aptamers of the disclosure may have, in a 5′ to 3′ direction, a first side of a first base paired stem. The 3′ terminal end of the first side of the first base paired stem may be connected to the 5′ terminal end of the first loop. The first loop may be connected at its 5′ terminal end to the 3′ terminal end of the first side of the first base paired stem, and the first loop may be connected at its 3′ terminal end to the 5′ terminal end of the first side of the second base paired stem. The first side of the second base paired stem may be connected at its 5′ terminal end to the 3′ terminal end of the first loop, and the first side of the second base paired stem may be connected at its 3′ terminal end to the 5′ terminal end of the second loop. The second loop may be connected at its 5′ terminal end to the 3′ terminal end of the first side of the second base paired stem, and the second loop may be connected at its 3′ terminal end to the 5′ terminal end of the second, complementary side of the second base paired stem. The second, complementary side of the second base paired stem may be connected at its 5′ terminal end to the 3′ terminal end of the second loop, and the second, complementary side of the second base paired stem may be connected at its 3′ terminal end to the 5′ terminal end of the third loop. The third loop may be connected at its 5′ terminal end to the 3′ terminal end of the second, complementary side of the second base paired stem, and the third loop may be connected at its 3′ terminal end to the 5′ terminal end of the first side of the third base paired stem. The first side of the third base paired stem may be connected at its 5′ terminal end to the 3′ terminal end of the third loop, and the first side of the third base paired stem may be connected at its 3′ terminal end to the 5′ terminal end of the fourth loop. The fourth loop may be connected at its 5′ terminal end to the 3′ terminal end of the first side of the third base paired stem, and the fourth loop may be connected at its 3′ terminal end to the 5′ terminal end of the second, complementary side of the third base paired stem. The second, complementary side of the third base paired stem may be connected at its 5′ terminal end to the 3′ terminal end of the fourth loop, and the second, complementary side of the third base paired stem may be connected at its 3′ terminal end to the 5′ terminal end of the fifth loop. The fifth loop may be connected at its 5′ terminal end to the 3′ terminal end of the second, complementary side of the third base paired stem, and the fifth loop may be connected at its 3′ terminal end to the 5′ terminal end of the second, complementary side of the first base paired stem. The second, complementary side of the first base paired stem may be connected at its 5′ terminal end to the 3′ terminal end of the fifth loop. In some cases, the anti-VEGF-A aptamers of the disclosure may comprise a terminal stem. In some cases, the terminal stem may be the first base paired stem (e.g., S1). In some cases, the anti-VEGF-A aptamers of the disclosure may comprise a plurality of terminal loops. In some cases, a terminal loop may include the second loop (e.g., L2), and/or the fourth loop (e.g., L4). In some cases, the anti-VEGF-A aptamers of the disclosure may comprise a plurality of internal stems. In some cases, an internal stem may include the second base paired stem (e.g., S2), and/or the third base paired stem (e.g., S3). In some cases, the anti-VEGF-A aptamers of the disclosure may comprise a plurality of internal loops. In some cases, an internal loop may include the first loop (e.g., L1), the third loop (e.g., L3), and/or the fifth loop (e.g., L5). Non-limiting examples of stem-loop aptamers that may be used to inhibit VEGF-A are described throughout.
As described above, in some cases, an anti-VEGF-A aptamer of the disclosure may have the following stem and loop structure: 5′-S1-L1-S2-L2-S2′-L3-S3-L4-S3′-L5-S1′-3′. In other cases, an anti-VEGF-A aptamer of the disclosure may have the following stem and loop structure: 5′-S1-S2-L2-S2′-L3-S3-L4-S3′-L5-S1′-3′. In some cases, S1/S1′, S3/S3′, L4, and/or L5 may comprise any combination of nucleotide sequences provided in Tables 10-13.
The disclosure further provides anti-VEGF-A aptamers comprising consensus nucleic acid sequences. In some cases, an anti-VEGF-A aptamer of the disclosure comprises a first side of a first base paired stem having a consensus nucleic acid sequence of 5′-HNBYHDCC-3′, and a second, complementary side of the first base paired stem having a consensus nucleic acid sequence of 5′-GKYNKVNW-3′, where H is A, C, or U; N is A, C, G, or U; B is C, G, or U; Y is C or U; D is A, G, or U; K is G or U; V is A, C, or G, and W is A or U. In some cases, an anti-VEGF-A aptamer of the disclosure comprises a first side of a first base paired stem having a consensus nucleic acid sequence of 5′-HNBYHDNN-3′, and a second, complementary side of the first base paired stem having a consensus nucleic acid sequence of 5′-NNYNKVNW-3′, where H is A, C, or U; N is A, C, G, or U; B is C, G, or U; Y is C or U; D is A, G, or U; K is G or U; V is A, C, or G, and W is A or U. In some cases, an anti-VEGF-A aptamer of the disclosure comprises a first loop having a nucleic acid sequence of 5′-U-3′. In some cases, an anti-VEGF-A aptamer of the disclosure comprises a nucleic acid sequence of 5′-N*-3′, where N is A, C, G, or U, a non-nucleotidyl spacer 3 modification (Sp3), two non-nucleotidyl spacer 3 modifications (Sp3-Sp3), a 6 carbon alkyl linker (1,6-hexanediol), a spacer 9 (triethyleneglycol) modification, or may be deleted. In some cases, the first loop is optional. In such cases, the aptamer may have the following structure: 5′-S1-S2-L2-S2′-L3-S3-L4-S3′-L5-S1′-3′. In some cases, an anti-VEGF-A aptamer of the disclosure comprises a first side of a second base paired stem having a consensus nucleic acid sequence of 5′-CC-3′, and a second, complementary side of a second base paired stem having a consensus nucleic acid sequence of 5′-GG-3′. In some cases, an anti-VEGF-A aptamer of the disclosure comprises a first side of a second base paired stem having a consensus nucleic acid sequence of 5′-NN-3′, and a second, complementary side of a second base paired stem having a consensus nucleic acid sequence of 5′-NN-3′, where N is A, C, G, or U. In some cases, an anti-VEGF-A aptamer of the disclosure comprises a second loop having a nucleic acid sequence of 5′-GCGC-3′. In some cases, an anti-VEGF-A aptamer of the disclosure comprises a second loop having a consensus nucleic acid sequence of 5′-GYGC-3′, where Y is C or U. In some cases, an anti-VEGF-A aptamer of the disclosure comprises a second loop having a consensus nucleic acid sequence of 5′-KNGC-3′, where K is G or U; and N is A, G, C, or U. In some cases, an anti-VEGF-A aptamer of the disclosure comprises a third loop having a nucleic acid sequence of 5′-A-3′. In some cases, an anti-VEGF-A aptamer of the disclosure comprises a third loop having a consensus nucleic acid sequence of 5′-W-3′, where W is A or U.
In some cases, an anti-VEGF-A aptamer of the disclosure comprises a first side of a third base paired stem having a consensus nucleic acid sequence of 5′-GRGRWN-3′, and a second, complementary side of a third base paired stem having a consensus nucleic acid sequence of 5′-NHYCYC-3′, where R is A or G; D is A, G, or U; H is A, C, or U, W is A or U; and Y is C or U. In some cases, an anti-VEGF-A aptamer of the disclosure comprises a first side of a third base paired stem having a nucleic acid sequence of 5′-GKGN-3′, and a second, complementary side of a third base paired stem having a nucleic acid sequence of 5′-NSMC-3′ where K is G or U; N is A, C, G or U and M is A or C. In some cases, an anti-VEGF-A aptamer of the disclosure comprises a first side of a third base paired stem having a nucleic acid sequence of 5′-GBBNY-3′ and a second, complementary side of a third base paired stem having a nucleic acid sequence of 5′-RNBNC-3′, where B is C, G or U; R is A or G; N is A, C, G or U and Y is C or U. In some cases, an anti-VEGF-A aptamer of the disclosure comprises a first side of a third base paired stem having a consensus nucleic acid sequence of 5′-GGGRUD-3′, and a second, complementary side of a third base paired stem having a consensus nucleic acid sequence of 5′-HWYCCC-3′, where R is A or G; D is A, G, or U; H is A, C, or U; W is A or U; and Y is C or U. In some cases, an anti-VEGF-A aptamer of the disclosure comprises a first side of a third base paired stem having a nucleic acid sequence of 5′-GGGG-3′, and a second, complementary side of a third base paired stem having a nucleic acid sequence of 5′-CCCC-3′. In some cases, an anti-VEGF-A aptamer of the disclosure comprises a first side of a third base paired stem having a nucleic acid sequence of 5′-GGGU-3′, and a second, complementary side of a third base paired stem having a nucleic acid sequence of 5′-ACCC-3′. In some cases, an anti-VEGF-A aptamer of the disclosure comprises a first side of a third base paired stem having a nucleic acid sequence of 5′-GGCU-3′, and a second, complementary side of a third base paired stem having a nucleic acid sequence of 5′-AGCC-3′. In some cases, an anti-VEGF-A aptamer of the disclosure comprises a first side of a third base paired stem having a nucleic acid sequence of 5′-GGGRU-3′ and a second, complementary side of a third base paired stem having a nucleic acid sequence of 5′-AYCCC-3′, where R is A or G; and Y is C or U. In some cases, an anti-VEGF-A aptamer of the disclosure comprises a first side of a third base paired stem having a nucleic acid sequence of 5′-GGGGUD-3′, and a second, complementary side of a third base paired stem having a nucleic acid sequence of 5′-HAUCCC-3′, where D is A, G, or U; and H is A, C, or U. In some cases, an anti-VEGF-A aptamer of the disclosure comprises a first side of a third base paired stem having a nucleic acid sequence of 5′-GGGRUUR-3′, and a second, complementary side of a third base paired stem having a nucleic acid sequence of 5′-UAUCCC-3′, where R is A or G. In some cases, an anti-VEGF-A aptamer of the disclosure comprises a first side of a third base paired stem having a consensus nucleic acid sequence of 5′-SVVVK-3′, and a second, complementary side of a third base paired stem having a consensus nucleic acid sequence of 5′-MBBBS-3′, where S is G or C; V is A, C, or G; K is G or U; M is A or C; and B is C, G, or U. In some cases, an anti-VEGF-A aptamer of the disclosure comprises a first side of a third base paired stem having a consensus nucleic acid sequence of 5‘-GGGRUN’-3, and a second, complementary side of a third base paired stem having a consensus nucleic acid sequence of 5′-NWYCCC-3′, where R is A or G; N is A, C, G, or U; W is A or U; and Y is C or U. In some cases, an anti-VEGF-A aptamer of the disclosure comprises a first side of a third base paired stem having a consensus nucleic acid sequence of 5‘-GGGRUN’-3, and a second, complementary side of a third base paired stem having a consensus nucleic acid sequence of 5′-NAYCCC-3′, where R is A or G; N is A, C, G, or U; W is A or U; and Y is C or U.
In some cases, an anti-VEGF-A aptamer of the disclosure comprises a fourth loop having a nucleic acid sequence of 5′-MAU-3′, where M is A or C. In some cases, an anti-VEGF-A aptamer of the disclosure comprises a fourth loop having a nucleic acid sequence of 5′-DNAH-3′, where D is A, G, or U; N is A, C, G, or U; and H is A, C, or U. In some cases, an anti-VEGF-A aptamer of the disclosure comprises a fourth loop having a nucleic acid sequence of 5′-DNDH-3′, where D is A, G, or U; N is A, C, G, or U; and H is A, C, or U. In some cases, an anti-VEGF-A aptamer of the disclosure comprises a fourth loop having a nucleic acid sequence of 5′-UDNDHU-3′, where D is A, G, or U; N is A, C, G, or U; and H is A, C, or U. In some cases, an anti-VEGF-A aptamer of the disclosure comprises a fourth loop having a nucleic acid sequence of 5′-UUUCAUUU-3′. In some cases, an anti-VEGF-A aptamer of the disclosure comprises a fifth loop having a nucleic acid sequence of 5′-GYUU-3′, where Y is C or U. In some cases, an anti-VEGF-A aptamer of the disclosure comprises a fifth loop having a consensus nucleic acid sequence of 5′-GNNN-3′, where N is A, C, G, or U. In some cases, an anti-VEGF-A aptamer of the disclosure comprises a fifth loop having a consensus nucleic acid sequence of 5′-GNHW-3′, where N is A, C, G, or U; H is A, C, or U; and W is A or U. In some cases, an anti-VEGF-A aptamer of the disclosure comprises a consensus nucleic acid sequence of 5′-HNBYHDCCUCCGCGCGGAGGGRUDDNDHHWYCCCGYUUGKYNKVNW-3′ (SEQ ID NO: 1), where H is A, C, or U; N is A, C, G, or U; B is C, G, or U; Y is C or U; D is A, G, or U; R is A or G; W is A or U; K is G or U; and V is A, C, or G. In some cases, an anti-VEGF-A aptamer of the disclosure comprises a consensus nucleic acid sequence of 5′-HNBYHDCCUCCGCGCGGAGGGRUUDNDHUAYCCCGYUUGKYNKVNW-3′ (SEQ ID NO: 2), where H is A, C, or U; N is A, C, G, or U; B is C, G, or U; Y is C or U; D is A, G, or U; R is A or G; K is G or U; V is A, C, or G, and W is A or U. In some cases, an anti-VEGF-A aptamer of the disclosure comprises a consensus nucleic acid sequence of 5′-WNKYHDCCUCCGCGCGGAGGGGUDDNAHHAUCCCGUUUGGYBKMHW-3′ (SEQ ID NO: 3), where W is A or U; N is A, C, G, or U; K is G or U; Y is C or U; H is A, C, or U, D is A, G, or U; B is C, G, or U; and M is A or C. In some cases, an anti-VEGF-A aptamer of the disclosure comprises a nucleic acid sequence of 5′-AUGCCGCCUCCGCGCGGAGGGGUUUCAUUUCCCCGUUUGGCUGCAU-3′ (SEQ ID NO: 4). In some cases, an anti-VEGF-A aptamer of the disclosure comprises a consensus nucleic acid sequence of 5′-HNBYHDNNN*NNKNGCNNWGGGRUNDNDHNWYCCCGNNNNNYNKVNW-3′ (SEQ ID NO: 5), where H is A, C, or U; N is A, C, G, or U; B is C, G, or U; Y is C or U; N* is A, C, G, U, can be deleted entirely, or is a non-nucleotidyl spacer 3 modification, a 6 carbon alkyl linker (1,6-hexanediol), or a spacer 9 (triethyleneglycol) modification; D is A, G, or U; K is G or U; W is A or U; R is A or G; and V is A, C, or G. In some cases, an anti-VEGF-A aptamer of the disclosure comprises a consensus nucleic acid sequence of 5′-HNBYHDCCUCCGCGCGGAGDSBHDNNNNHNNBNCGYUUGKYNKVNW-3′ (SEQ ID NO: 436), where H is A, C, or U; N is A, C, G, or U; B is C, G, or U; Y is C or U; D is A, G, or U; R is A or G; W is A or U; K is G or U; and V is A, C, or G.
In some cases, an anti-VEGF-A aptamer of the disclosure comprises a consensus nucleic acid sequence of 5′-HNBYHDCCUCCGCGCGGAGKBHYDNNNKDBVCGYUUGKYNKVNW-3′ (SEQ ID NO: 437), where H is A, C, or U; N is A, C, G, or U; B is C, G, or U; Y is C or U; D is A, G, or U; R is A or G; W is A or U; K is G or U; and V is A, C, or G. In some cases, an anti-VEGF-A aptamer of the disclosure comprises a consensus nucleic acid sequence of 5′-HNBYHDCCUCCGCGCGGAGKSHUDRGBUDSMCGYUUGKYNKVNW-3′ (SEQ ID NO: 438), where H is A, C, or U; N is A, C, G, or U; B is C, G, or U; Y is C or U; D is A, G, or U; R is A or G; W is A or U; K is G or U; M is A or C; and V is A, C, or G.
The disclosure herein further provides methods for inhibiting VEGF-A (and/or a downstream signaling pathway of VEGF-A). In some cases, the methods include administering an anti-VEGF-A aptamer (or a composition comprising said aptamer) to a biological system (e.g., biological cells, biological tissue, a subject, and the like). The disclosure further provides methods for treating ocular diseases or disorders including administering an anti-VEGF-A aptamer (or a pharmaceutical composition comprising said aptamer) to a subject having, suspected of having, or at risk of developing, an ocular disease or disorder. In some cases, the anti-VEGF-A aptamer is an aptamer having a stem-loop structure as described herein. In some cases, the ocular disease or disorder may be diabetic retinopathy. In some cases, the ocular disease or disorder may be retinopathy of prematurity. In some cases, the ocular disease or disorder may be central retinal vein occlusion. In some cases, the ocular disease or disorder may be macular edema. In some cases, the ocular disease or disorder may be choroidal neovascularization. In some cases, the ocular disease or disorder may be neovascular (or wet) age-related macular degeneration. In some cases, the ocular disease or disorder may be myopic choroidal neovascularization. In some cases, the ocular disease or disorder may be punctate inner choroidopathy. In some cases, the ocular disease or disorder may be presumed ocular histoplasmosis syndrome. In some cases, the ocular disease or disorder may be familial exudative vitreoretinopathy. In some cases, the ocular disease or disorder may be retinoblastoma. In some cases, a subject having, suspected of having, or at risk of developing, an ocular disease or disorder may exhibit elevated levels of one or more variants or isoforms of VEGF-A. For example, a subject having, suspected of having, or at risk of developing, an ocular disease or disorder may exhibit elevated levels of one or more of VEGF-A206, VEGF-A189, VEGF-A165, VEGF-A121, and VEGF-A110.
In some aspects of the disclosure, the methods and compositions may involve the inhibition of a function associated with VEGF-A. In some cases, the methods and compositions may involve preventing or reducing VEGF-A binding to or interaction with one or more VEGF receptors. For example, the methods and compositions may involve preventing or reducing VEGF-A binding to or interaction with Flt-1, KDR, Nrp-1, or any combination thereof. In some cases, the methods and compositions may involve preventing or reducing downstream signaling associated with Flt-1, KDR, Nrp-1, or any combination thereof. In some cases, the methods and compositions may involve the inhibition of a function associated with VEGF-A for the treatment of ocular diseases or disorders. In some cases, the methods and compositions may involve the inhibition of a function associated with VEGF-A for the treatment of diabetic retinopathy. In some cases, the methods and compositions may involve the inhibition of a function associated with VEGF-A for the treatment of retinopathy of prematurity. In some cases, the methods and compositions may involve the inhibition of a function associated with VEGF-A for the treatment of central retinal vein occlusion. In some cases, the methods and compositions may involve the inhibition of a function associated with VEGF-A for the treatment of macular edema. In some cases, the methods and compositions may involve the inhibition of a function associated with VEGF-A for the treatment of choroidal neovascularization. In some cases, the methods and compositions may involve the inhibition of a function associated with VEGF-A for the treatment of neovascular (or wet) age-related macular degeneration. In some cases, the methods and compositions may involve the inhibition of a function associated with VEGF-A for the treatment of myopic choroidal neovascularization. In some cases, the methods and compositions may involve the inhibition of a function associated with VEGF-A for the treatment of punctate inner choroidopathy. In some cases, the methods and compositions may involve the inhibition of a function associated with VEGF-A for the treatment of presumed ocular histoplasmosis syndrome. In some cases, the methods and compositions may involve the inhibition of a function associated with VEGF-A for the treatment of familial exudative vitreoretinopathy. In some cases, the methods and compositions may involve the inhibition of a function associated with VEGF-A for the treatment of retinoblastoma. In some cases, the methods and compositions may involve the inhibition of a function associated with VEGF-A for the treatment of an ocular disease or disorder exhibiting elevated levels of one or more isoforms or variants of VEGF-A.
In various aspects, the compositions may include one or more aptamers that selectively bind to and inhibit a function associated with VEGF-A. In some cases, the compositions may include one or more aptamers that bind to the receptor binding face of VEGF-A. In some cases, the compositions may include one or more aptamers that bind to the receptor binding domain of VEGF-A. In some cases, the compositions may include one or more aptamers that bind to a region of VEGF-A other than the heparin binding domain of VEGF-A. Put another way, the compositions may include one or more aptamers that do not bind to the heparin binding domain of VEGF-A. In some cases, the compositions may include one or more aptamers that bind to one or more variants or isoforms of VEGF-A. For example, the compositions may include one or more aptamers that bind to one or more of VEGF-A206, VEGF-A189, VEGF-A165, VEGF-A121, and VEGF-A110. In some cases, the compositions may include one or more pan-variant specific anti-VEGF-A aptamers. In particular cases, the compositions may include pan-variant specific aptamers that bind to each of VEGF-A110, VEGF-A121, VEGF-A165, VEGF-A189, and VEGF-A206. Generally, a pan-variant specific aptamer disclosed herein may bind to a structural feature of VEGF-A which is shared amongst VEGF-A110, VEGF-A121, VEGF-A165, VEGF-A189, and VEGF-A206. In some cases, the structural feature is the receptor binding face or the receptor binding domain. In some cases, the aptamers have a stem-loop secondary structure as described herein.
In some cases, the compositions may include one or more aptamers that prevent or reduce binding of VEGF-A to Flt-1, KDR, Nrp-1, or any combination thereof. In some cases, the compositions may include one or more aptamers that prevent or reduce downstream signaling pathways associated with Flt-1, KDR, Nrp-1, or any combination thereof. In some cases, the aptamers may be RNA aptamers, DNA aptamers, modified RNA aptamers, or modified DNA aptamers.
In some cases, the aptamers do not contain non-naturally occurring hydrophobic modifications. In some aspects, less than 100% of the pyrimidines (e.g., C, T, or U) present in a nucleic acid sequence of an aptamer herein comprise a C-5 modified pyrimidine. For example, less than 100%, less than 95%, less than 90%, less than 85%, less than 80%, less than 75%, less than 70%, less than 65%, less than 60%, less than 55%, less than 50%, less than 45%, less than 40%, less than 35%, less than 30%, less than 25%, less than 20%, less than 15%, less than 10%, or less than 5% of the pyrimidines present in a nucleic acid sequence of an aptamer herein comprise a C-5 modified pyrimidine. In particular aspects, none of the pyrimidines present in a nucleic acid sequence of an aptamer herein comprise a C-5 modified pyrimidine. In another particular aspect, none of the bases in an aptamer sequence herein comprise a C-5 modification. In some aspects, less than 100% of the uridines present in a nucleic acid sequence of an aptamer herein comprise a C-5 modified uridine. For example, less than 100%, less than 95%, less than 90%, less than 85%, less than 80%, less than 75%, less than 70%, less than 65%, less than 60%, less than 55%, less than 50%, less than 45%, less than 40%, less than 35%, less than 30%, less than 25%, less than 20%, less than 15%, less than 10%, or less than 5% of the uridines present in a nucleic acid sequence of an aptamer herein comprise a C-5 modified uridine. In particular aspects, none of the uridines present in a nucleic acid sequence of an aptamer herein comprise a C-5 modified uridine. In some cases, the C-5 modified pyrimidine or C-5 modified uridine is selected from the group consisting of: 5-(N-benzylcarboxyamide)-2′-deoxyuridine (BndU), 5-(N-benzylcarboxyamide)-2′-O-methyluridine, 5-(N-benzylcarboxyamide)-2′-fluorouridine, 5-(N-phenethylcarboxyamide)-2′-deoxyuridine (PEdU), 5-(N-thiophenylmethylcarboxyamide)-2′-deoxyuridine (ThdU), 5-(N-isobutylcarboxyamide)-2′-deoxyuridine (iBudU), 5-(N-tyrosylcarboxyamide)-2′-deoxyuridine (TyrdU), 5-(N-3,4-methylenedioxybenzylcarboxyamide)-2′-deoxyuridine (MBndU), 5-(N-4-fluorobenzylcarboxyamide)-2′-deoxyuridine (FBndU), 5-(N-3-phenylpropylcarboxyamide)-2′-deoxyuridine (PPdU), 5-(N-imidizolylethylcarboxyamide)-2′-deoxyuridine (ImdU), 5-(N-isobutylcarboxyamide)-2′-O-methyluridine, 5-(N-isobutylcarboxyamide)-2′-fluorouridine, 5-(N-tryptaminocarboxyamide)-2′-deoxyuridine (TrpdU), 5-(N—R-threoninylcarboxyamide)-2′-deoxyuridine (ThrdU), 5-(N-tryptaminocarboxyamide)-2′-O-methyluridine, 5-(N-tryptaminocarboxyamide)-2′-fluorouridine, 5-(N-[1-(3-trimethylamonium)propyl]carboxyamide)-2′-deoxyuridine chloride, 5-(N-naphthylmethylcarboxyamide)-2′-deoxyuridine (NapdU), 5-(N-naphthylmethylcarboxyamide)-2′-O-methyluridine, 5-(N-naphthylmethylcarboxyamide)-2′-fluorouridine, 5-(N-[1-(2,3-dihydroxypropyl)]carboxyamide)-2′-deoxyuridine), 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. In particular aspects, none of the aptamers provided herein comprise NapdU. In other particular cases, the aptamers are not SOMAmers.
In general, “sequence identity” refers to an exact nucleotide-to-nucleotide or amino acid-to-amino acid correspondence of two polynucleotides or polypeptide sequences, respectively.
Typically, techniques for determining sequence identity include determining the nucleotide sequence of a polynucleotide and/or determining the amino acid sequence encoded thereby, and comparing these sequences to a second nucleotide or amino acid sequence. Two or more sequences (polynucleotide or amino acid) can be compared by determining their “percent identity.” The percent identity of two sequences, whether nucleic acid or amino acid sequences, is the number of exact matches between two aligned sequences divided by the length of the longer sequence and multiplied by 100. Percent identity may also be determined, for example, by comparing sequence information using the advanced BLAST computer program, including version 2.2.9, available from the National Institutes of Health. The BLAST program is based on the alignment method of Karlin and Altschul, Proc. Natl. Acad Sci. USA, 87:2264-2268 (1990) and as discussed in Altschul, et al., J. Mol. Biol., 215:403-410 (1990); Karlin And Altschul, Proc. Natl. Acad. Sci. USA, 90:5873-5877 (1993); and Altschul et al., Nucleic Acids Res., 25:3389-3402 (1997). The program may be used to determine percent identity over the entire length of the proteins being compared. Default parameters are provided to optimize searches with short query sequences in, for example, with the blastp program. The program also allows use of an SEG filter to mask-off segments of the query sequences as determined by the SEG program of Wootton and Federhen, Computers and Chemistry 17:149-163 (1993). Ranges of desired degrees of sequence identity are approximately 50% to 100% and integer values therebetween. In general, this disclosure encompasses sequences with at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or at least 98% sequence identity with any sequence provided herein.
In general, “modification identity” refers to two polynucleotides with identical patterns of modifications on a nucleotide-to-nucleotide level. Techniques for determining modification identity may include determining the modifications of a polynucleotide and comparing these modifications to modifications of a second polynucleotide. The percent modification identity of two sequences is the number of exact modification matches between two aligned sequences divided by the length of the longer sequence and multiplied by 100. Ranges of desired degrees of modification identity are generally approximately 50% to 100%, and integer values therebetween. In general, this disclosure encompasses sequences with at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or at least 98% modification identity with any sequence provided herein.
As used herein, “consensus sequence”, when used in reference to a group or series of related nucleic acids, refers to a nucleotide sequence that reflects the most common choice of base at each position in the sequence where the series of related nucleic acids has been subjected to mathematical and/or sequence analysis. Unless otherwise indicated, nucleotide sequences provided herein are represented by standard nucleotide notation, as set forth by the International Union of Pure and Applied Chemistry (IUPAC). For example, the nucleotides typically found in DNA are represented by “A” “C”, “G”, “T”; and the nucleotides typically found in RNA are represented by “A”, “C”, “G”, “U”. Nucleotide sequences provided herein may include one or more degenerate bases. A “degenerate base” generally refers to a position on a nucleotide sequence that can have more than one possible alternative. Degenerate bases are generally represented by a Roman character as set forth by the International Union of Pure and Applied Chemistry (IUPAC). For example, the Roman character “D”, when used in relation to a nucleotide sequence, represents a degenerate base of A, G, or U.
The term “aptamer” as used herein refers to an oligonucleotide and/or nucleic acid analogues that can bind to a specific target molecule. Aptamers can include RNA, DNA, modified RNA, modified DNA, any nucleic acid analogue, and/or combinations thereof.
Aptamers can be single-stranded oligonucleotides. In some cases, aptamers may comprise more than one nucleic acid strand (e.g., two or more nucleic acid strands). Aptamers may bind to a target (e.g., a protein) with high affinity and specificity through non-Watson-Crick base pairing interactions. Generally, the aptamers described herein are non-naturally occurring oligonucleotides (e.g., synthetically produced) that are isolated and used for the treatment of a disorder or a disease. Aptamers can bind to essentially any target molecule including, without limitation, proteins, oligonucleotides, carbohydrates, lipids, small molecules, and even bacterial cells. Aptamers may be monomeric (composed of a single unit) or multimeric (composed of multiple units). Multimeric aptamers can be homomeric (composed of multiple identical units) or heteromeric (composed of multiple non-identical units). Aptamers herein may be described by their primary structures, meaning the linear nucleotide sequence of the aptamer. Aptamer sequences herein are generally described from the 5′ end to the 3′ end, unless otherwise stated. Additionally or alternatively, aptamers herein may be described by their secondary structures which may refer to the combination of single-stranded regions and base-pairing interactions within the aptamer. Whereas many naturally occurring oligonucleotides, such as mRNA, encode information in their linear base sequences, aptamers generally do not encode information in their linear base sequences. Further, aptamers can be distinguished from naturally occurring oligonucleotides in that binding of aptamers to target molecules is dependent upon secondary and tertiary structures of the aptamer. Aptamers may be suitable as therapeutic agents and may be preferable to other therapeutic agents because: 1) aptamers may be fast and economical to produce because aptamers can be developed entirely by in vitro processes; 2) aptamers may have low toxicity and may lack an immunogenic response; 3) aptamers may have high specificity and affinity for their targets; 4) aptamers may have good solubility; 5) aptamers may have tunable pharmacokinetic properties; 6) aptamers may be amenable to site-specific conjugation of PEG and other carriers; and 7) aptamers may be stable at ambient temperatures.
An aptamer may have a secondary structure having at least two complementary regions of the same nucleic acid strand that base-pair to form a double helix (referred to herein as a “stem”). Generally, these complementary regions are complementary when read in the opposite direction. The term “stem” as used herein may refer to either of the complementary nucleotide regions individually or may encompass a base-paired region containing both complementary regions, or a portion thereof. For example, the term “stem” may refer to the 5′ side of the stem, that is, the stem sequence that is closer to the 5′ end of the aptamer; additionally or alternatively, the term “stem” may refer to the 3′ side of the stem, that is, the stem sequence that is closer to the 3′ end of the aptamer. In some cases, the term “stem” may refer to the 5′ side of the stem and the 3′ side of the stem, collectively. The term “base-paired stem” is generally used herein to refer to both complementary stem regions collectively. A base-paired stem may be perfectly complementary meaning that 100% of its base pairs are Watson-Crick base pairs. A base-paired stem may also be “partially complementary.” As used herein, the term “partially complementary stem” refers to a base-paired stem that is not entirely made up of Watson-Crick base pairs but does contain base pairs (either Watson-Crick base pairs or G-U/U-G wobble base pairs) at each terminus. In some cases, a partially complementary stem contains both Watson-Crick base-pairs and G-U/U-G wobble base pairs. In other cases, a partially complementary stem is exclusively made up of G-U/U-G wobble base pairs. A partially complementary stem may contain mis-matched base pairs and/or unpaired bases in the region between the base pairs at each terminus of the stem; but in such cases, the mis-matched base pairs and/or unpaired bases make up at most 50% of the positions between the base pairs at each terminus of the stem.
A stem as described herein may be referred to by the position, in a 5′ to 3′ direction on the aptamer, of the 5′ side of the stem (e.g., the stem sequence closer to the 5′ terminus of the aptamer), relative to the 5′ side of additional stems present on the aptamer. For example, stem 1 (S1) may refer to the stem sequence that is closest to the 5′ terminus of the aptamer, its complementary stem sequence, or both stem sequences collectively. Similarly, stem 2 (S2) may refer to the next stem sequence that is positioned 3′ relative to S1, its complementary stem sequence, or both stem sequences collectively. Each additional stem may be referred to by its position, in a 5′ to 3′ direction, on the aptamer, as described above. For example, S3 may be positioned 3′ relative to S2 on the aptamer, S4 may be positioned 3′ relative to S3 on the aptamer, and so on. In some cases, the term “first stem” is used to refer to a stem in the aptamer, irrespective of its location. For example, a first stem may be S1, S2, S3, S4 or any other stem in the aptamer. A stem may be adjacent to an unpaired region. An unpaired region may be present at a terminus of the aptamer or at an internal region of the aptamer.
As used herein, the term “loop” generally refers to an internal unpaired region of an aptamer. The term “loop” generally refers to any unpaired region of an aptamer that is flanked on both the 5′ end and the 3′ end by a stem region. In some cases, a loop sequence may be adjacent to a single base-paired stem, such that the loop and stem structure together resemble a hairpin. In such cases, generally the primary sequence of the aptamer contains a first stem sequence adjacent to the 5′ end of the loop sequence and a second stem sequence adjacent to the 3′ end of the loop sequence; and the first and second stem sequences are complementary to each other. In some cases, each terminus of a loop is adjacent to first and second stem sequences that are not complementary. In such cases, the primary sequence of the aptamer may contain an additional loop sequence that is bordered at one or both ends by stem sequences that are complementary to the first and/or second stem sequences. In cases where the two loops have different number of nucleotides, the two loops are referred to jointly herein as an “asymmetric loop” or “asymmetric loop pair,” terms that are used herein interchangeably. In cases where the two loops have the same number of nucleotides, they are referred to jointly as a “symmetric loop” or “symmetric loop pair,” terms that are used interchangeably herein.
A loop as described herein may be referred to by its position, in a 5′ to 3′ direction, on the aptamer. For example, loop 1 (L1) may refer to a loop sequence that is positioned most 5′ on the aptamer. Similarly, loop 2 (L2) may refer to a loop sequence that is positioned 3′ relative to L1, and loop 3 (L3) may refer to a loop sequence that is positioned 3′ relative to L2. Each additional loop may be referred to by its position, in a 5′ to 3′ direction, on the aptamer, as described above. For example, L4 may be positioned 3′ relative to L3 on the aptamer, L5 may be positioned 3′relative to L4 on the aptamer, and so on. In some cases, the term “first loop” is used to refer to a loop in the aptamer, irrespective of its location. For example, a first loop may be L1, L2, L3, L4 or any other loop in the aptamer.
The term “stem-loop” as used herein generally refers to the secondary structure of an aptamer of the disclosure having at least one stem and at least one loop. In some cases, a stem-loop secondary structure may include a terminal stem and a terminal loop. In some cases, a stem-loop secondary structure includes structures having more than one stem, and more than one loop, which may include a terminal stem, at least one internal loop, at least one internal stem, and at least one terminal loop. A “terminal stem” as used herein generally refers to a stem that encompasses both the 5′ and the 3′ terminus of the aptamer. In some cases, a “terminal stem” is bordered at one or both termini by a “tail” comprising one or more unpaired nucleotides. For example, a terminal stem present in the aptamer may be bordered by a tail of one or more unpaired nucleotides (or other structures) at its 5′ end. Similarly, a terminal stem present in the aptamer may be bordered by a tail of one or more unpaired nucleotides (or other structures) at its 3′ end. In some cases, a terminal stem present in the aptamer may be bordered by a tail of one or more unpaired nucleotides (or other structures) at both its 5′ end and its 3′ end. A terminal stem may be adjacent to a loop; for example, the 5′ side of a terminal stem (i.e., the terminal stem sequence closest to the 5′ end of the molecule) may be bordered at its 3′ terminus by the 5′ terminus of a loop. Similarly, the 3′ side of a terminal stem (i.e., the terminal stem sequence closest to the 3′ end of the molecule) may be bordered at its 5′ terminus by the 3′ terminus of a loop. In some cases, the 5′ side of a terminal stem (i.e., the terminal stem sequence closest to the 5′ end of the molecule) may be bordered at its 3′ terminus by the 5′ terminus of a loop, and the 3′ side of the terminal stem (i.e., the terminal stem sequence closest to the 3′ end of the molecule) may be bordered at its 5′ terminus by the 3′ terminus of an internal stem. An “internal stem” as used herein may refer to a stem that is bordered at both termini by a loop sequence, or may refer to a stem that is bordered at one terminus by a loop sequence and bordered at the other terminus by a stem sequence. In some cases, a stem-loop secondary structure of the disclosure may include more than one internal stem. A “terminal loop” as used herein generally refers to a loop that is bordered by the same stem at both termini of the loop. For example, a terminal loop may be bordered at its 5′ end by a stem sequence, and may be bordered at its 3′ end by the complementary stem sequence. An “internal loop” as used herein generally refers to a loop that is bordered at both termini by different stems. For example, an internal loop may be bordered at its 5′ end by a first stem sequence, and may be bordered at its 3′ end by a second stem sequence that is not complementary to the first stem sequence. In some cases, a stem-loop secondary structure of the disclosure may include more than one internal loop. In some cases, a stem-loop secondary structure includes structures having more than two stems. Unless otherwise stated, when an aptamer includes more than one stem and/or more than one loop, the stems and loops are numbered consecutively in ascending order from the 5′ end to the 3′ end of the primary nucleotide sequence.
The term “VEGF-A”, as used herein includes any variant or isoform of VEGF-A. Therefore, unless otherwise specified, “VEGF-A” may mean one or more of VEGF-A110, VEGF-A121, VEGF-A165, VEGF-A189, and VEGF-A206.
The term “pan-variant specific aptamer” as used herein refers to an aptamer that selectively binds to at least VEGF-A110, VEGF-Ain, VEGF-A165, VEGF-A189, and VEGF-A206. A pan-variant specific aptamer may, but not necessarily, bind to one or more additional VEGF-A isoforms or variants. Generally, a pan-variant specific aptamer binds to a structural feature of VEGF-A which is common amongst VEGF-A110, VEGF-A121, VEGF-A165, VEGF-A189, and VEGF-A206.
The terms “about” and “approximately” as used herein, generally refer to a range that is 15% greater than or less than a stated numerical value within the context of the particular usage. For example, “about 10” or “approximately 10” would include a range from 8.5 to 11.5.
As used herein, the term “or” is used nonexclusively to encompass “or” and “and.” For example, “A or B” includes “A but not B,” “B but not A,” and “A and B”, unless otherwise indicated.
“A”, “an”, and “the”, as used herein, can include plural referents unless expressly and unequivocally limited to one referent
This disclosure generally provides compositions that bind to vascular endothelial growth factor-A (VEGF-A), and methods of using such compositions to modulate VEGF-A signaling pathways. VEGF-A is thought to be the most significant regulator of angiogenesis in the VEGF family. VEGF-A promotes growth of vascular endothelial cells which leads to the formation of capillary-like structures and may be necessary for the survival of newly formed blood vessels. Vascular endothelial cells are thought to be major effectors of VEGF signaling. Retinal pigment epithelial (RPE) cells may also express VEGF receptors and have been shown to proliferate and migrate upon exposure to VEGF. In addition, VEGF is thought to play roles beyond the vascular system. For example, VEGF may play roles in normal physiological functions, including, but not limited to, bone formation, hematopoiesis, wound healing, and development. In various aspects, the compositions provided herein include aptamers that bind to VEGF-A, thereby inhibiting or reducing angiogenesis, e.g., by inhibiting or preventing growth of vascular endothelial cells, retinal pigment epithelial cells, or both. In some cases, the anti-VEGF-A aptamers provided herein may prevent or reduce binding or association of VEGF-A with a VEGF receptor (e.g., Flt-1, KDR, Nrp-1) expressed on vascular endothelial cells, retinal pigment epithelial cells, or both.
The VEGF family includes VEGF-A, VEGF-B, VEGF-C, VEGF-D, VEGF-E, VEGF-F, and placental growth factor (PIGF). The aptamers disclosed herein primarily bind to variants and isoforms of VEGF-A. In some cases, such aptamers may also bind to one or more of VEGF-B, VEGF-C, VEGF-D, VEGF-E, VEGF-F, and PIGF. Transcription of VEGF mRNA may be upregulated under hypoxic conditions. Furthermore, various growth factors and cytokines have been shown to upregulate VEGF mRNA expression, including, without limitation, epidermal growth factor (EGF), transforming growth factor-alpha (TGF-α), transforming growth factor-beta (TGF-β), keratinocyte growth factor (KGF), insulin-like growth factor-1 (IGF-1), fibroblast growth factor (FGF), platelet-derived growth factor (PDGF), interleukin 1-alpha (IL-1-α), interleukin-6 (IL-6), and interleukin-8 (IL8). VEGF-A is thought to play a role in various ocular diseases and disorders such as, but not limited to, diabetic retinopathy, retinopathy of prematurity, central retinal vein occlusion, macular edema, choroidal neovascularization, neovascular (or wet) age-related macular degeneration, myopic choroidal neovascularization, punctate inner choroidopathy, presumed ocular histoplasmosis syndrome, familial exudative vitreoretinopathy, and retinoblastoma.
In some cases, the aptamers provided herein may be used to treat an ocular disease or disorder involving one or more factors that upregulate VEGF-A expression and/or activity, including, but not limited to, hypoxic conditions; a growth factor such as EGF, TGF-α, TGF-β, KGF, IGF-1, FGF, or PDGF; and a cytokine such as IL-1-α, IL6, and IL8. In some cases, the aptamers provided herein may be used to treat an ocular disease or disorder selected from the group consisting of: diabetic retinopathy, retinopathy of prematurity, central retinal vein occlusion, macular edema, choroidal neovascularization, neovascular (or wet) age-related macular degeneration, myopic choroidal neovascularization, punctate inner choroidopathy, presumed ocular histoplasmosis syndrome, familial exudative vitreoretinopathy, and retinoblastoma.
The gene for human VEGF-A contains eight exons and encodes at least 16 isoforms. The most common isoforms generated by alternative splicing mechanisms are VEGF-A121, VEGF-A165, VEGF-A189, and VEGF-A206. Of these, VEGF-A165, VEGF-A189, and VEGF-A206 each contain a C-terminal heparin binding domain (HBD). In contrast, VEGF-A121 lacks a heparin-binding domain. Furthermore, plasmin activation may result in proteolytic cleavage of VEGF-A165, VEGF-A189, and VEGF-A206, resulting in the release of the soluble VEGF-A110 variant, which also lacks a heparin-binding domain.
In various aspects, the aptamers provided herein may bind to and inhibit a function associated with one or more VEGF-A isoforms or variants. For example, the aptamers provided herein may bind to and inhibit a function associated with one or more of VEGF-A110, VEGF-A121, VEGF-A165, VEGF-A189, and VEGF-A206. In some cases, the aptamers provided herein may be pan-variant specific aptamers. In some cases, a pan-variant specific aptamer may bind to each of VEGF-A110. VEGF-A121, VEGF-A165, VEGF-A189, and VEGF-A206. In some cases, the aptamers provided herein may bind to a structural feature that is common to each of VEGF-A110, VEGF-A121, VEGF-A165, VEGF-A189, and VEGF-A206. For example, the aptamers provided herein may bind to the receptor binding face, or a portion thereof, of each of VEGF-A110, VEGF-A121, VEGF-A165, VEGF-A189, and VEGF-A206. In another example, the aptamers provided herein may bind to the receptor binding domain, or a portion thereof, of each of VEGF-A110, VEGF-A121, VEGF-A165, VEGF-A189, and VEGF-A206. In some cases, the aptamers provided herein may bind to a structural feature of VEGF-A other than the heparin binding domain found in VEGF-A165, VEGF-A189, and VEGF-A206.
VEGF-A is known to interact with the receptor tyrosine kinases VEGFR1 (also known as Flt-1), VEGFR2 (also known as KDR or Flk-1), and Neuropilin-1 (Nrp-1). Nrp-1 is thought to be a co-receptor for KDR. VEGF receptors have been shown to be expressed by endothelial cells, macrophages, hematopoietic cells, and smooth muscle cells. KDR is a class IV receptor tyrosine kinase that binds 2:1 to VEGF-A dimers. Flt-1 is a receptor tyrosine kinase that binds to VEGF-A with a 3-10 fold higher affinity than KDR, and has also been shown to bind to VEGF-B and PlGF. Flt-1 expression may be upregulated by hypoxia, and its affinity for VEGF-A has been proposed as a negative regulator of signaling by KDR by acting as a decoy receptor. An alternative splicing variant of Flt-1 results in a soluble variant of the receptor (sFlt-1) which has been suggested to act as an anti-angiogenic sink for VEGF-A. Association of VEGF-A165 with KDR may be enhanced by the interaction of the heparin binding domain with co-receptor Nrp-1, which may enhance downstream signaling of KDR. Nrp-1 also has strong affinity for Flt-1, which may prevent Nrp-1 association with VEGF-A165 and may be a secondary regulatory mechanism for VEGF-A induced angiogenesis.
In various aspects, aptamers provided herein may bind to one or more isoforms or variants of VEGF-A, and may prevent or reduce binding or association of VEGF-A with a VEGF receptor. For example, aptamers provided herein may prevent or reduce binding of one or more isoforms or variants of VEGF-A with Flt-1, KDR, Nrp-1, or any combination thereof. In some cases, aptamers provided herein may prevent or reduce binding of one or more of VEGF-A110, VEGF-A121, VEGF-A165, VEGF-A189, and VEGF-A206 to one or more of Flt-1, KDR, and Nrp-1.
In particular cases, aptamers provided herein may prevent or reduce binding of one or more isoforms or variants of VEGF-A to KDR. In some aspects, the aptamers are pan-variant specific aptamers that bind to each of VEGF-A110, VEGF-A121, VEGF-A165, VEGF-A189, and VEGF-A206, and reduce or prevent binding or association thereof with one or more of Fit-1, KDR, and Nrp-1.
In one instance, an amino acid sequence of human VEGF-A206 may comprise the following sequence:
In one instance, an amino acid sequence of human VEGF-A189 may comprise the following sequence:
In one instance, an amino acid sequence of human VEGF-A165 may comprise the following sequence:
In one instance, an amino acid sequence of human VEGF-A121 may comprise the following sequence:
In one instance, an amino acid sequence of human VEGF-A110 may comprise the following sequence:
In some cases, the methods and compositions described herein include the use of one or more aptamers for the treatment of an ocular disease or disorder. In some cases, the methods and compositions described herein use one or more aptamers having a secondary structure as described herein for the treatment of an ocular disease or disorder. In some cases, the methods and compositions described herein include the use of one or more aptamers for inhibiting an activity associated with VEGF-A. In some cases, the methods and compositions described herein include the use of one or more aptamers having a secondary structure as described herein for inhibiting an activity associated with VEGF-A.
Aptamers as described herein may include any number of modifications that can affect the function or affinity of the aptamer. For example, aptamers may be unmodified or they may contain modified nucleotides to improve stability, nuclease resistance or delivery characteristics.
Examples of such modifications may include chemical substitutions at the sugar and/or phosphate and/or base positions, for example, at the 2′ position of ribose, the 5 position of pyrimidines, and the 8 position of purines, various 2′-modified pyrimidines and purines and modifications with 2′-amino (2′-NH2), 2′-fluoro (2′-F), and/or 2′-O-methyl (2′-OMe) substituents. In some cases, aptamers described herein comprise a 2′-OMe and/or a 2′F modification to increase in vivo stability. In some cases, the aptamers described herein contain modified nucleotides to improve the affinity and specificity of the aptamers for a target. Examples of modified nucleotides include those modified with guanidine, indole, amine, phenol, hydroxymethyl, or boronic acid. In other cases, pyrimidine nucleotide triphosphate analogs or CE-phosphoramidites may be modified at the 5 position to generate, for example, 5-benzylaminocarbonyl-2′-deoxyuridine (BndU); 5-[N-(phenyl-3-propyl)carboxamide]-2′-deoxyuridine (PPdU); 5-(N-thiophenylmethylcarboxyamide)-2′-deoxyuridine (ThdU); 5-(N-4-fluorobenzylcarboxyamide)-2′-deoxyuridine (FBndU); 5-(N-(1-naphthylmethyl)carboxamide)-2′-deoxyuridine (NapdU); 5-(N-2-naphthylmethylcarboxyamide)-2′-deoxyuridine (2NapdU); 5-(N-1-naphthylethylcarboxyamide)-2′-deoxyuridine (NEdU); 5-(N-2-naphthylethylcarboxyamide)-2′-deoxyuridine (2NEdU); 5-(N-tryptaminocarboxyamide)-2′-deoxyuridine (TrpdU); 5-isobutylaminocarbonyl-2′-deoxyuridine (IbdU); 5-(N-tyrosylcarboxyamide)-2′-deoxyuridine (TyrdU); 5-(N-isobutylaminocarbonyl-2′-deoxyuridine (iBudU): 5-(N-benzylcarboxyamide)-2′-O-methyluridine, 5-(N-benzylcarboxyamide)-2′-fluorouridine, 5-(N-phenethylcarboxyamide)-2′-deoxyuridine (PEdU), 5-(N-3,4-methylenedioxybenzylcarboxyamide)-2′-deoxyuridine (MBndU), 5-(N-imidizolylethylcarboxyamide)-2′-deoxyuridine (ImdU), 5-(N-isobutylcarboxyamide)-2′-O-methyluridine, 5-(N-isobutylcarboxyamide)-2′-fluorouridine, 5-(N—R-threoninylcarboxyamide)-2′-deoxyuridine (ThrdU), 5-(N-tryptaminocarboxyamide)-2′-O-methyluridine, 5-(N-tryptaminocarboxyamide)-2′-fluorouridine, 5-(N-[1-(3-trimethylamonium)propyl]carboxyamide)-2′-deoxyuridine chloride, 5-(N-naphthylmethylcarboxyamide)-2′-O-methyluridine, 5-(N-naphthylmethylcarboxyamide)-2′-fluorouridine, 5-(N-[1-(2,3-dihydroxypropyl)]carboxyamide)-2′-deoxyuridine), 5-(N-2-naphthylmethylcarboxyamide)-2′-O-methyluridine, 5-(N-2-naphthylmethylcarboxyamide)-2′-fluorouridine, 5-(N-1-naphthylethylcarboxyamide)-2′-O-methyluridine, 5-(N-1-naphthylethylcarboxyamide)-2′-fluorouridine, 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, 5-(N-3-benzothiophenylethylcarboxyamide)-2′-fluorouridine; 5-[N-(1-morpholino-2-ethyl)carboxamide]-2′-deoxyuridine (MOEdu); R-tetrahydrofuranylmethyl-2′-deoxyuridine (RTMdU); 3-methoxybenzyl-2′-deoxyuridine (3MBndU); 4-methoxybenzyl-2′-deoxyuridine (4MBndU); 3,4-dimethoxybenzyl-2′-deoxyuridine (3,4DMBndU); S-tetrahydrofuranylmethyl-2′-deoxyuridine (STMdU); 3,4-methylenedioxyphenyl-2-ethyl-2′-deoxyuridine (MPEdU); 4-pyridinylmethyl-2′-deoxyuridine (PyrdU); or 1-benzimidazol-2-ethyl-2′-deoxyuridine (BidU); 5-(amino-1-propenyl)-2′-deoxyuridine; 5-(indole-3-acetamido-1-propenyl)-2′-deoxyuridine; or 5-(4-pivaloylbenzamido-1-propenyl)-2′-deoxyuridine.
Modifications of the aptamers contemplated in this disclosure include, without limitation, those which provide other chemical groups that incorporate additional charge, polarizability, hydrophobicity, hydrogen bonding, electrostatic interaction, and functionality to the nucleic acid aptamer bases or to the nucleic acid aptamer as a whole. Modifications to generate oligonucleotide populations that are resistant to nucleases can also include one or more substitute internucleotide linkages, altered sugars, altered bases, or combinations thereof. Such modifications include, but are not limited to, 2′-position sugar modifications, 5-position pyrimidine modifications, 8-position purine modifications, modifications at exocyclic amines, substitution of 4-thiouridine, substitution of 5-bromo or 5-iodo-uracil; backbone modifications, phosphorothioate, phosphorodithioate, or alkyl phosphate modifications, methylations, and unusual base-pairing combinations such as the isobases isocytidine and isoguanosine.
Modifications can also include 3′ and 5′ modifications such as capping, e.g., addition of a 3′-3′-dT cap to increase exonuclease resistance, or conjugation of a PEG to the 5′ or 3′ end to increase exonuclease and endonuclease resistance.
Aptamers of the disclosure may generally comprise nucleotides having ribose in the β-D-ribofuranose configuration. In some cases, 100% of the nucleotides present in the aptamer have ribose in the β-D-ribofuranose configuration. In some cases, at least 50% of the nucleotides present in the aptamer have ribose in the β-D-ribofuranose configuration. In some cases, at least 10, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, or 100% of the nucleotides present in the aptamer have ribose in the β-D-ribofuranose configuration.
The length of the aptamer can be variable. In some cases, the length of the aptamer is less than 100 nucleotides. In some cases, the length of the aptamer is greater than 10 nucleotides. In some cases, the length of the aptamer is between 10 and 90 nucleotides. The aptamer can be, without limitation, about 10, about 15, about 20, about 25, about 30, about 35, about 40, about 45, about 50, about 55, about 60, about 65, about 70, about 75, about 80, about 85, or about 90 nucleotides in length.
In some instances, a polyethylene glycol (PEG) polymer chain is covalently bound to the aptamer, referred to herein as PEGylation. Without wishing to be bound by theory, PEGylation may increase the half-life and stability of the aptamer in physiological conditions. In some cases, the PEG polymer is covalently bound to the 5′ end of the aptamer. In some cases, the PEG polymer is covalently bound to the 3′ end of the aptamer. In some cases, the PEG polymer is covalently bound to both the 5′ end and the 3 end of the aptamer. In some cases, the PEG polymer is covalently bound to a specific site on a nucleobase within the aptamer, including the 5-position of a pyrimidine or 8-position of a purine. In some cases, the PEG polymer is covalently bound to an abasic site within the aptamer.
In some cases, an aptamer described herein may be conjugated to a PEG having the general formula, H—(O—CH2—CH2)n—OH. In some cases, an aptamer described herein may be conjugated to a methoxy-PEG (mPEG) of the general formula, CH3O—(CH2—CH2—O)n—H. In some cases, the aptamer is conjugated to a linear chain PEG or mPEG. The linear chain PEG or mPEG may have an average molecular weight of up to about 30 kD. Multiple linear chain PEGs or mPEGs can be linked to a common reactive group to form multi-arm or branched PEGs or mPEGs. For example, more than one PEG or mPEG can be linked together through an amino acid linker (e.g., lysine) or another linker, such as glycerine. In some cases, the aptamer is conjugated to a branched PEG or branched mPEG. Branched PEGs or mPEGs may be referred to by their total mass (e.g., two linked 20 kD mPEGs have a total molecular weight of 40 kD).
Branched PEGs or mPEGs may have more than two arms. Multi-arm branched PEGs or mPEGs may be referred to by their total mass (e.g., four linked 10 kD mPEGs have a total molecular weight of 40 kD). In some cases, an aptamer of the present disclosure is conjugated to a PEG polymer having a total molecular weight from about 5 kD to about 200 kD, for example, about 5 kD, about 10 kD, about 20 kD, about 30 kD, about 40 kD, about 50 kD, about 60 kD, about 70 kD, about 80 kD, about 90 kD, about 100 kD, about 110 kD, about 120 kD, about 130 kD, about 140 kD, about 150 kD, about 160 kD, about 170 kD, about 180 kD, about 190 kD, or about 200 kD. In one non-limiting example, the aptamer is conjugated to a PEG having a total molecular weight of about 40 kD.
In some cases, the reagent that may be used to generate PEGylated aptamers is a branched PEG N-Hydroxysuccinimide (mPEG-NHS) having the general formula:
with a 20 kD, 40 kD or 60 kD total molecular weight (e.g., where each mPEG is about 10 kD, 20 kD or about 30 kD). As described above, the branched PEGs can be linked through any appropriate reagent, such as an amino acid (e.g., lysine or glycine residues).
In one non-limiting example, the reagent used to generate PEGylated aptamers is [N2-(monomethoxy 20K polyethylene glycol carbamoyl)-N6-(monomethoxy 20K polyethylene glycol carbamoyl)]-lysine N-hydroxysuccinimide having the formula:
In yet another non-limiting example, the reagent used to generate PEGylated aptamers has the formula:
where X is N-hydroxysuccinimide and the PEG arms are of approximately equivalent molecular weight. Such PEG architecture may provide a compound with reduced viscosity compared to a similar aptamer conjugated to a two-armed or single-arm linear PEG.
In some examples, the reagent used to generate PEGylated aptamers has the formula:
where X is N-hydroxysuccinimide and the PEG arms are of different molecular weights, for example, a 40 kD PEG of this architecture may be composed of 2 arms of 5 kD and 4 arms of 7.5 kD. Such PEG architecture may provide a compound with reduced viscosity compared to a similar aptamer conjugated to a two-armed PEG or a single-arm linear PEG.
In some cases, the reagent that may be used to generate PEGylated aptamers is a non-branched mPEG-Succinimidyl Propionate (mPEG-SPA), having the general formula:
where mPEG is about 20 kD or about 30 kD. In one example, the reactive ester may be —O—CH2—CH2—CO2—NHS.
In some instances, the reagent that may be used to generate PEGylated aptamers may include a branched PEG linked through glycerol, such as the SUNBRIGHT® series from NOF Corporation, Japan. Non-limiting examples of these reagents include:
In another example, the reagents may include a non-branched mPEG Succinimidyl alpha-methylbutanoate (mPEG-SMB) having the general formula:
where mPEG is between 10 and 30 kD. In one example, the reactive ester may be —O—CH2-CH2-CH(CH3)—CO2—NHS.
In other instances, the PEG reagents may include nitrophenyl carbonate-linked PEGs, having the general formula:
Compounds including nitrophenyl carbonate can be conjugated to primary amine containing linkers.
In some cases, the reagents used to generate PEGylated aptamers may include PEG with thiol-reactive groups that can be used with a thiol-modified linker. One non-limiting example may include reagents having the following general structure:
where mPEG is about 10 kD, about 20 kD or about 30 kD.
Another non-limiting example may include reagents having the following general structure:
where each mPEG is about 10 kD, about 20 kD, or about 30 kD and the total molecular weight is about 20 kD, about 40 kD, or about 60 kD, respectively. Branched PEGs with thiol reactive groups that can be used with a thiol-modified linker, as described above, may include reagents in which the branched PEG has a total molecular weight of about 40 kD or about 60 kD (e.g., where each mPEG is about 20 kD or about 30 kD).
In some cases, the reagents used to generated PEGylated aptamers may include reagents having the following structure:
In some cases, the reaction to conjugate the PEG to the aptamer is carried out between about pH 6 and about pH 10, or between about pH 7 and pH 9 or about pH 8.
In some cases, the reagents used to generate PEGylated aptamers may include reagents having the following structure:
In some cases, the reagents used to generate PEGylated aptamers may include reagents having the following structure:
In some cases, the aptamer is associated with a single PEG molecule. In other cases, the aptamer is associated with two or more PEG molecules.
In some cases, the aptamers described herein may be bound or conjugated to one or more molecules having desired biological properties. Any number of molecules can be bound or conjugated to aptamers, non-limiting examples including antibodies, peptides, proteins, carbohydrates, enzymes, polymers, drugs, small molecules, gold nanoparticles, radiolabels, fluorescent labels, dyes, haptens (e.g., biotin), other aptamers, or nucleic acids (e.g., siRNA). In some cases, aptamers may be conjugated to molecules that increase the stability, the solubility or the bioavailability of the aptamer. Non-limiting examples include polyethylene glycol (PEG) polymers, carbohydrates and fatty acids. In some cases, molecules that improve the transport or delivery of the aptamer may be used, such as cell penetrating peptides. Non-limiting examples of cell penetrating peptides can include peptides derived from Tat, penetratin, polyarginine peptide Arg8 sequence, Transportan, VP22 protein from Herpes Simplex Virus (HSV), antimicrobial peptides such as Buforin I and SynB, polyproline sweet arrow peptide molecules, Pep-1 and MPG. In some embodiments, the aptamer is conjugated to a lipophilic compound such as cholesterol, dialkyl glycerol, diacyl glycerol, or a non-immunogenic, high molecular weight compound or polymer such as polyethylene glycol (PEG) or other water-soluble pharmaceutically acceptable polymers including, but not limited to, polyaminoamines (PAMAM) and polysaccharides such as dextran, or polyoxazolines (POZ).
The molecule to be conjugated can be covalently bonded or can be associated through non-covalent interactions with the aptamer of interest. In one example, the molecule to be conjugated is covalently attached to the aptamer. The covalent attachment may occur at a variety of positions on the aptamer, for example, to the exocyclic amino group on the base, the 5-position of a pyrimidine nucleotide, the 8-position of a purine nucleotide, the hydroxyl group of the phosphate, or a hydroxyl group or other group at the 5′ or 3′ terminus. In one example, the covalent attachment is to the 5′ or 3′ hydroxyl group of the aptamer.
In some cases, the aptamer can be attached to another molecule directly or with the use of a spacer or linker. For example, a lipophilic compound or a non-immunogenic, high molecular weight compound can be attached to the aptamer using a linker or a spacer. Various linkers and attachment chemistries are known in the art. In a non-limiting example, 6-(trifluoroacetamido)hexanol (2-cyanoethyl-N,N-diisopropyl)phosphoramidite can be used to add a hexylamino linker to the 5′ end of the synthesized aptamer. This linker, as with the other amino linkers provided herein, once the group protecting the amine has been removed, can be reacted with PEG-NHS esters to produce covalently linked PEG-aptamers. Other non-limiting examples of linker phosphoramidites may include: TFA-amino C4 CED phosphoramidite having the structure:
5′-amino modifier C3 TFA having the structure:
MMT amino modifier C6 CED phosphoramidite having the structure:
5′-amino modifier 5 having the structure:
5′-amino modifier C12 having the structure:
5′ thiol-modifier C6 having the structure:
5′ thiol-modifier C6 having the structure:
and 5′ thiol-modifier C6 having the structure:
The 5′-thiol modified linker may be used, for example, with PEG-maleimides, PEG-vinylsulfone, PEG-iodoacetamide and PEG-orthopyridyl-disulfide. In one example, the aptamer may be bonded to the 5′-thiol through a maleimide or vinyl sulfone functionality.
In some cases, the aptamer formulated according to the present disclosure may also be modified by encapsulation within or displayed on the surface of a liposome. In other cases, the aptamer formulated according to the present disclosure may also be modified by encapsulation within or displayed on the surface of a micelle. Liposomes and micelles may be comprised of any lipids, and in some cases the lipids may be phospholipids, including phosphatidylcholine. Liposomes and micelles may also contain or be comprised in part or in total of other polymers and amphipathic molecules including PEG conjugates of poly lactic acid (PLA), poly DL-lactic-co-glycolic acid (PLGA), or poly caprolactone (PCL).
In some cases, the aptamers described herein may be designed to inhibit a function associated with VEGF-A. In some cases, the aptamers described herein may be designed to bind the receptor binding face of VEGF-A, or a portion thereof. In some cases, the aptamers described herein may be designed to bind the receptor binding domain of VEGF-A, or a portion thereof. The receptor binding domain of VEGF-A may include any one or more of residues 1-109 as described in SEQ ID NOs: 6-10. In some cases, the aptamers described herein may bind to a structural feature of VEGF-A other than the heparin binding domain of VEGF-A. The heparin binding domain of VEGF-A may include any one or more of residues 111-165 as described in SEQ ID NOs: 6-8. In some cases, the aptamers described herein may block or reduce binding of one or more isoforms or variants of VEGF-A to one or more of Flk-1, KDR, and Nip-1.
In some instances, an aptamer is isolated or purified. “Isolated” (used interchangeably with “substantially pure” or “purified”) as used herein means an aptamer that is synthesized chemically, or has been separated from other aptamers.
In some cases, an aptamer of the disclosure may comprise one of the following sequences described in Table 1.
In some aspects, an aptamer of the disclosure may have a primary nucleic acid sequence according to any one of the aptamer sequences described in Table 1, or may have a primary nucleic acid sequence that shares at least 500% sequence identity to any one of the aptamer sequences described in Table 1. In some aspects, an aptamer of the disclosure may have a primary nucleic acid sequence consisting of any one of the aptamer sequences described in Table 1, or may have a nucleic acid sequence that shares at least 50% sequence identity to a primary nucleic acid sequence that consists of any one of the aptamer sequences described in Table 1. In some cases, the nucleic acid sequence may comprise one or more modified nucleotides. In some cases, at least 50%, of said nucleic acid sequence may comprise the one or more modified nucleotides. In some cases, the one or more modified nucleotides may comprise a 2′F-modified nucleotide, a 2′OMe-modified nucleotide, or a combination thereof. In some cases, the one or more modified nucleotides may be selected from the group consisting of; 2′F-G, 2′OMe-G, 2′OMe-U, 2′OMe-A, 2′OMe-C, an inverted deoxythymidine at the 3′ terminus, and any combination thereof. In some cases, the aptamer may comprise a nucleic acid sequence comprising modified nucleotides as described in Table 1. In some cases, the aptamer is any aptamer described in Table 1. For example, the aptamer may be any one of Aptamers 4.2, 26-32, 47-76, 108, 109, 112-117, 119-185, 187-199, 201, 213-241, and 276-300. In some cases, the aptamer may be conjugated to a polyethylene glycol (PEG) molecule. In some cases, the PEG molecule may have a molecular weight of 80 kDa or less (e.g., 40 kDa).
In some cases, an aptamer of the disclosure may have at least 50%, 55%, 600%, 65%, 70%, 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity with any aptamer described herein. For example, an anti-VEGF-A aptamer of the disclosure may have at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity with any aptamer described in Table 1.
In some cases, an anti-VEGF-A aptamer of the disclosure may have at least 50% sequence identity with any one of the aptamer sequences described in Table 1. In some cases, an anti-VEGF-A aptamer of the disclosure may have at least 55% sequence identity with any one of the aptamer sequences described in Table 1. In some cases, an anti-VEGF-A aptamer of the disclosure may have at least 60% sequence identity with any one of the aptamer sequences described in Table 1. In some cases, an anti-VEGF-A aptamer of the disclosure may have at least 65% sequence identity with any one of the aptamer sequences described in Table 1. In some cases, an anti-VEGF-A aptamer of the disclosure may have at least 70% sequence identity with any one of the aptamer sequences described in Table 1. In some cases, an anti-VEGF-A aptamer of the disclosure may have at least 75% sequence identity with any one of the aptamer sequences described in Table 1. In some cases, an anti-VEGF-A aptamer of the disclosure may have at least 80% sequence identity with any one of the aptamer sequences described in Table 1.
In some cases, an anti-VEGF-A aptamer of the disclosure may have at least 85% sequence identity with any one of the aptamer sequences described in Table 1. In some cases, an anti-VEGF-A aptamer of the disclosure may have at least 90% sequence identity with any one of the aptamer sequences described in Table 1. In some cases, an anti-VEGF-A aptamer of the disclosure may have at least 95% sequence identity with any one of the aptamer sequences described in Table 1.
In some cases, an aptamer of the disclosure may have a primary nucleotide sequence that shares at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, at least 28, at least 29, at least 30, at least 31, at least 32, at least 33, at least 34, at least 35, at least 36, at least 37, at least 38, at least 39, or at least 40 contiguous nucleotides with a nucleotide sequence described in Table 1.
In such cases where specific nucleotide modifications have been recited, it should be understood that any number and type of nucleotide modifications may be substituted. For example, 2′OMe-G may be substituted for 2′F-G. Non-limiting examples of nucleotide modifications have been provided herein. In some instances, all of the nucleotides of an aptamer are modified. In some instances, at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% of the nucleotides of an aptamer of the disclosure may be modified. In some aspects, an aptamer of the disclosure has the modified nucleotide sequence of any aptamer sequence described in Table 1.
In some cases, an aptamer of the disclosure may have a modified nucleotide sequence. In some cases, an aptamer of the disclosure may have a modified nucleotide sequence as described in Table 1. In some cases, an aptamer of the disclosure may have a primary nucleotide sequence according to any aptamer described in Table 1, and a modified nucleotide sequence that is different than that described in Table 1. In such cases, an aptamer of the disclosure may have a modified nucleotide sequence that shares at least 10% modification identity with any modified nucleotide sequence described in Table 1. For example, an aptamer of the disclosure may have a modified nucleotide sequence that shares at least 10%, at least 15%, at least 20%, at least 25%, at least 300%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% modification identity with any modified nucleotide sequence described in Table 1.
In some cases, an aptamer of the disclosure may have a primary nucleotide sequence of any aptamer sequence described in Table 1, and a modified nucleotide sequence in which at least 10% of the C nucleotides are modified (e.g., 2′OMe-C). For example, an aptamer of the disclosure may have a modified nucleotide sequence in which at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 99%, or 100% of the C nucleotides are modified (e.g., 2′OMe-C). In some cases, an aptamer of the disclosure may have a modified nucleotide sequence wherein at least 10%, at least 15%, at least 20%, at least 25%, at least 300%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 99%, or 100% of the C nucleotides (C) are modified according to Table 1.
In some cases, an aptamer of the disclosure may have a primary nucleotide sequence of any aptamer sequence described in Table 1, and a modified nucleotide sequence in which at least 10% of the A nucleotides are modified (e.g., 2′OMe-A). For example, an aptamer of the disclosure may have a modified nucleotide sequence in which at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 99%, or 100% of the A nucleotides are modified (e.g., 2′OMe-A). In some cases, an aptamer of the disclosure may have a modified nucleotide sequence wherein at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 99%, or 100% of the A nucleotides are modified according to Table 1.
In some cases, an aptamer of the disclosure may have a primary nucleotide sequence of any aptamer sequence described in Table 1, and a modified nucleotide sequence in which at least 10% of the U nucleotides are modified (e.g., 2′OMe-U). For example, an aptamer of the disclosure may have a modified nucleotide sequence in which at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 99%, or 100% of the U nucleotides are modified (e.g., 2′OMe-U). In some cases, an aptamer of the disclosure may have a modified nucleotide sequence wherein at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 99%, or 100% of the U nucleotides are modified according to Table 1.
In some cases, an aptamer of the disclosure may have a primary nucleotide sequence of any aptamer sequence described in Table 1, and a modified nucleotide sequence in which at least 10% of the G nucleotides are modified (e.g., 2′F-G, 2′OMe-G). For example, an aptamer of the disclosure may have a modified nucleotide sequence in which at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90° %, at least 95%, at least 99%, or 100% of the G nucleotides are modified (e.g., 2′F-G, 2′OMe-G). In some cases, an aptamer of the disclosure may have a modified nucleotide sequence wherein at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 900%, at least 95%, at least 99%, or 100% of the G nucleotides are modified according to Table 1.
In some cases, an anti-VEGF-A aptamer of the disclosure may comprise a stem-loop secondary structure. In some cases, the aptamers of the disclosure may comprise, in a 5′ to 3′ direction, a first side of a first base paired stem; optionally, a first loop; a first side of a second base paired stem; a second loop; a second, complementary side of the second base paired stem; a third loop; a first side of a third base paired stem; a fourth loop; a second, complementary side of the third base paired stem; a fifth loop; and a second, complementary side of the first base paired stem.
In some embodiments, each element may be adjacent to each other. For example, the anti-VEGF-A aptamers of the disclosure may comprise, in a 5′ to 3′ direction, a first side of a first base paired stem. The 3′ terminal end of the first side of the first base paired stem may be connected to the 5′ terminal end of the first loop. The first loop may be connected at its 5′ terminal end to the 3′ terminal end of the first side of the first base paired stem, and the first loop may be connected at its 3′ terminal end to the 5′ terminal end of the first side of the second base paired stem. The first side of the second base paired stem may be connected at its 5′ terminal end to the 3′ terminal end of the first loop, and the first side of the second base paired stem may be connected at its 3′ terminal end to the 5′ terminal end of the second loop. The second loop may be connected at its 5′ terminal end to the 3′ terminal end of the first side of the second base paired stem, and the second loop may be connected at its 3′ terminal end to the 5′ terminal end of a second, complementary side of the second base paired stem. The second, complementary side of the second base paired stem may be connected at its 5′ terminal end to the 3′ terminal end of the second loop, and the second, complementary side of the second base paired stem may be connected at its 3′ terminal end to the 5′ terminal end of a third loop. The third loop may be connected at its 5′ terminal end to the 3′ terminal end of the second, complementary side of the second base paired stem, and the third loop may be connected at its 3′ terminal end to the 5′ terminal end of a first side of a third base paired stem. The first side of the third base paired stem may be connected at its 5′ terminal end to the 3′ terminal end of the third loop, and the first side of the third base paired stem may be connected at its 3′ terminal end to the 5′ terminal end of the fourth loop. The fourth loop may be connected at its 5′ terminal end to the 3′ terminal end of the first side of the third base paired stem, and the fourth loop may be connected at its 3′ terminal end to the 5′ terminal end of the second, complementary side of the third base paired stem. The second, complementary side of the third base paired stem may be connected at its 5′ terminal end to the 3′ terminal end of the fourth loop, and the second, complementary side of the third based paired stem may be connected at its 3′ terminal end to the 5′ terminal end of a fifth loop. The fifth loop may be connected at its 5′ terminal end to the 3′ terminal end of the second, complementary side of the third base paired stem, and the fifth loop may be connected at its 3′ terminal end to the 5′ terminal end of a second, complementary side of the first base paired stem. The second, complementary side of the first base paired stem may be connected at its 5′ terminal end to the 3′ terminal end of the fifth loop. In some cases, the anti-VEGF-A aptamers of the disclosure may comprise a terminal stem. In some cases, the terminal stem may be the first base paired stem (e.g., S1/S1′). In some cases, the anti-VEGF-A aptamers of the disclosure may comprise a plurality of terminal loops. In some cases, the terminal loops may include the second loop (e.g., L2) and/or the fourth loop (e.g., L4). In some cases, the anti-VEGF-A aptamers of the disclosure may comprise a plurality of internal stems. In some cases, the internal stems may include the second stem (e.g., S2/S2′), and/or the third stem (e.g., S3/S3′). In some cases, the anti-VEGF-A aptamers of the disclosure may comprise a plurality of internal loops. In some cases, the internal loops may include the first loop (e.g., L1), the third loop (e.g., L3), and/or the fifth loop (e.g., L5).
In a particular aspect, an anti-VEGF-A aptamer of the disclosure may have a stem-loop secondary structure comprising: (i) a first side of Stem 1 (S1); (ii) optionally, Loop 1 (L1) connected to the 3′ terminal end of S1 and the 5′ terminal end of a first side of Stem 2 (S2); (iii) S2 connected to the 3′ terminal end of L1 (or, when L1 is absent, the 3′ terminal end of S1) and the 5′ terminal end of Loop 2 (L2); (iv) L2 connected to the 3′ terminal end of S2 and the 5′ terminal end of a second, complementary side of Stem 2 (S2′); (v) S2′ connected to the 3′ terminal end of L2 and the 5′ terminal end of Loop 3 (L3); (vi) L3 connected to the 3′ terminal end of S2′ and the 5′ terminal end of a first side of Stem 3 (S3); (vii) S3 connected to the 3′ terminal end of L3 and the 5′ terminal end of Loop 4 (L4); (vi) L4 connected to the 3′ terminal end of S3 and the 5′ terminal end of a second, complementary side of Stem 3 (S3′); (vii) S3′ connected to the 3′ terminal end of L4 and the 5′ terminal end of Loop 5 (L5); (viii) L5 connected to the 3′ terminal end of S3′ and the 5′ terminal end of a second, complementary side of Stem 1 (S1′); and (ix) S1′ connected to the 3′ terminal end of L5. In particular aspects, an anti-VEGF-A aptamer of the disclosure may have the following stem-loop secondary structure: 5′-S1-L1-S2-L2-S2′-L3-S3-L4-S3′-L5-S1′. In other particular aspects, an anti-VEGF-A aptamer of the disclosure may have the following stem-loop secondary structure: 5′-S1-S2-L2-S2′-L3-S3-L4-S3′-L5-S1′.
In some cases, Stem 1 (S1) may comprise from two to eight contiguous base pairs. For example, S1 may comprise two, three, four, five, six, seven, or eight contiguous base pairs. In some cases, S1 may comprise one or more mismatched nucleotides. For example, S1 may comprise one, two, or three mismatched nucleotides. In some cases, the mismatched nucleotides may be adjacent to each other. In other cases, the mismatched nucleotides may be separated by one, two, or three base pairs. In some cases, the 3′ terminal nucleotide of the first side of S1 (e.g., nucleotide position 8), and the 5′ terminal nucleotide of the second, complementary side of S1, may form a base pair (e.g., nucleotide position 39). In some cases, this base pair may be C*G. In some cases, the base pair between the 3′ terminal nucleotide of the first side of S1, and the 5′ terminal nucleotide of the second, complementary side of S1 may be separated from other S1 base pairs by mismatched nucleotides (e.g., at positions 7 and 40). In some cases, S1 may comprise a mismatch at nucleotide positions 5 and 42. In some cases, S1 may be truncated. In some cases, the first side of S1 may comprise a consensus nucleic acid sequence of 5′-HNBYHDCC-3′, and the second, complementary side of S1 may comprise a consensus nucleic acid sequence of 5′-GKYNKVNW-3′, where H is A, C, or U; N is A, C, G, or U; B is C, G, or U; Y is C or U; D is A, G, or U; K is G or U; V is A, C, or G; and W is A or U. In some cases, the first side of S1 may comprise a consensus nucleic acid sequence of 5′-HNBYHDNN-3′, and the second, complementary side of S1 may comprise a consensus nucleic acid sequence of 5′-NNYNKVNW-3′, where H is A, C, or U; N is A, C, G, or U; B is C, G, or U; Y is C or U; and D is A, G, or U.
In some cases, L1 may be optional. In cases in which L1 is present, L1 may comprise one nucleotide. In some cases, when L1 is present, L1 has a nucleic acid sequence of 5′-U-3′. In some cases, when L1 is present, L1 has a nucleic acid sequence of 5′-A-3′. In some cases, when L1 is present, L1 has a nucleic acid sequence of 5′-C-3′. In some cases, when L1 is present, L1 has a nucleic acid sequence of 5′-G-3′. In some cases, L1 may comprise a single non-nucleotidyl spacer 3 modification (e.g., 1,3-propanediol). In some cases, L1 may comprise two non-nucleotidyl spacer 3 modifications. In some cases, L1 may comprise a 6-carbon spacer (e.g., 1,6-hexanediol). In some cases, L1 may comprise a 9-carbon spacer (e.g., triethyleneglycol).
In some cases, S2 may comprise two base pairs. In some cases, S2 may comprise more than one base pair. In some cases, S2 may comprise less than three base pairs. In some cases, a first side of S2 may comprise a consensus nucleic acid sequence of 5′-CC-3′, and a second, complementary side of S2 may comprise a consensus nucleic acid sequence of 5′-GG-3′. In some cases, the first side of S2 may comprise a consensus nucleic acid sequence of 5′-NN-3′, and the second, complementary side of S2 may comprise a consensus nucleic acid sequence of 5′-NN-3′, where N is A, C, G, or U.
In some cases, L2 may comprise four nucleotides. In some cases, L2 may have more than three nucleotides. In some cases, L2 may have less than five nucleotides. In some cases, L2 may comprise a consensus nucleic acid sequence of 5′-GCGC-3′. In some cases, L2 may comprise a consensus nucleic acid sequence of 5′-GYGC-3′, where Y is C or U. In some cases, L2 may comprise a consensus nucleic acid sequence of 5′-KNGC-3′, where K is G or U; and N is A, C, G, or U.
In some cases, S3 may comprise from four to six base pairs. For example, S3 may comprise four base pairs, five base pairs, or six base pairs. In some cases, S3 may comprise less than seven base pairs. In some cases, S3 may comprise more than three base pairs. In some cases, when S3 comprises six base pairs, a first side of S3 may be seven nucleotides in length. In such cases, the 3′ terminal nucleotide of the first side of S3 may form a single mismatch. In some cases, the length of S3 may be directly related to the length of L4. In some cases, when S3 is four base pairs in length, L4 is eight nucleotides in length. In some cases, when S3 is four base pairs in length, L4 is six nucleotides in length. In some cases, when S3 is five base pairs in length, L4 is six nucleotides in length. In some cases, when S3 is five base pairs in length, L4 is four nucleotides in length. In some cases, when S3 is six base pairs in length, L4 is four nucleotides in length. In some cases, when S3 comprises six base pairs and a single mismatched nucleotide, L4 is three nucleotides in length. In some cases, a first side of S3 may comprise a consensus nucleic acid sequence of 5′-GRGRWN-3′, and the second, complementary side of S3 may comprise a consensus nucleic acid sequence of 5′-NHYCYC-3′, where R is A or G; N is A, C, G, or U; W is A or U; and Y is C or U. In some cases, a first side of S3 may comprise a consensus nucleic acid sequence of 5′-GGGRUN3′, and the second, complementary side of S3 may comprise a consensus nucleic acid sequence of 5′-NWYCCC-3′, where R is A or G; N is A, C, G, or U; W is A or U; and Y is C or U. In some cases, a first side of S3 may comprise a consensus nucleic acid sequence of 5′-GGGRUN3′, and the second, complementary side of S3 may comprise a consensus nucleic acid sequence of 5′-NAYCCC-3′, where R is A or G; N is A, C, G, or U; and Y is C or U. In some cases, a first side of S3 comprises a consensus nucleic acid sequence of 5′-GGGRUD-3′, and a second, complementary side of S3 comprises a consensus nucleic acid sequence of 5′-HWYCCC-3′, wherein R is A or G; D is A, G, or U; H is A, C, or U; W is A or U; and Y is C or U. In some cases, when S3 is four base pairs in length, the first side of S3 may comprise a consensus nucleic acid sequence of 5′-GKGN-3′, and the second, complementary side of S3 may comprise a consensus nucleic acid sequence of 5′-NSMC-3′, where K is G or U; N is A, C, G or U and M is A or C. In some cases, when S3 is four base pairs in length, the first side of S3 may comprise a consensus nucleic acid sequence of 5′-GGGG-3′, and the second, complementary side of S3 may comprise a consensus nucleic acid sequence of 5′-CCCC-3′. In some cases, when S3 is four base pairs in length, the first side of S3 may comprise a consensus nucleic acid sequence of 5′-GGGU-3′, and the second, complementary side of S3 may comprise a consensus nucleic acid sequence of 5′-ACCC-3′. In some cases, when S3 is four base pairs in length, the first side of S3 may comprise a consensus nucleic acid sequence of 5′-GGCU-3′, and the second, complementary side of S3 may comprise a consensus nucleic acid sequence of 5′-AGCC-3′. In some cases, when S3 is five base pairs in length, the first side of S3 may comprise a consensus nucleic acid sequence of 5′-GBBNY-3′, and the second, complementary side of S3 may comprise a consensus nucleic acid sequence of 5′-RNBNC-3′, where R is A or G; and Y is C or U. In some cases, when S3 is five base pairs in length, the first side of S3 may comprise a consensus nucleic acid sequence of 5′-GGGRU-3′, and the second, complementary side of S3 may comprise a consensus nucleic acid sequence of 5′-AYCCC-3′, where R is A or G; and Y is C or U. In some cases, when S3 is five base pairs in length, the first side of S3 may comprise a consensus nucleic acid sequence of 5′-SVVVK-, and the second, complementary side of S3 may comprise a consensus nucleic acid sequence of 5′-MBBBS-3′, where S is G or C; V is A, C, or G: K is G or U; M is A or C; and B is C, G, or U. In some cases, when S3 is six base pairs in length, the first side of S3 may comprise a consensus nucleic acid sequence of 5′-GGGGUD-3′, and the second, complementary side of S3 may comprise a consensus nucleic acid sequence of 5′-HAUCCC-3′, where D is A, G, or U; and H is A, C, or U. In some cases, when S3 comprises six base pairs and a single mis-matched nucleotide, the first side of S3 may comprise a consensus nucleic acid sequence of 5′-GGGRUUR-3′, and the second, complementary side of S3 may comprise a consensus nucleic acid sequence of 5′-UAUCCC-3′, where the underlined U is the single mis-matched nucleotide, and R is A or G.
In some cases, L3 may comprise one nucleotide. In some cases, L3 may comprise less than two nucleotides. In some cases, L3 may comprise a consensus nucleic acid sequence of 5′-A-3′. In some cases, L3 may comprise a consensus nucleic acid sequence of 5′-W-3′, where W is A or U.
In some cases, L4 may comprise eight, six, four, or three nucleotides. In some cases, the variation between the number of nucleotides in loop L4 may directly relate to the variation in the length of S3 (e.g., as described above). In some cases, when L4 is three nucleotides in length, L4 may comprise a consensus nucleic acid sequence of 5′-MAU-3′, where M is A or C. In some cases, when L4 is three nucleotides in length, L4 may comprise a consensus nucleic acid sequence of 5′-CUA-3′. In some cases, when L4 is four nucleotides in length, L4 may comprise a consensus nucleic acid sequence of 5′-DNAH-3′, where D is A, G, or U; N is A, C, G, or U; and H is A, C, or U. In some cases, when L4 is four nucleotides in length, L4 may comprise a consensus nucleic acid sequence of 5′-DNDH-3′, where D is A, G, or U; N is A, C, G, or U; and H is A, C, or U. In some cases, when L4 is four nucleotides in length, L4 may comprise a consensus nucleic acid sequence of 5′-DNDN-3′, where D is A, G, or U; N is A, C, G, or U; and N is A, C, G or U. In some cases, when L4 is six nucleotides in length, L4 may comprise a consensus nucleic acid sequence of 5′-UDNDHU-3′, where D is A, G, or U; N is A, C, G, or U; and H is A, C, or U. In some cases, the L4 comprises a consensus nucleic acid sequence of 5′-UDRGBU-3′, where D is A, G, or U; R is A or G, N is A, C, G, or U; and B is G, C, or U. In some cases, the L4 comprises a consensus nucleic acid sequence of 5′-KNNNNW-3′, where K is U or G, N is A, C, G, or U; and W is A, or U. In some cases, the L4 comprises a consensus nucleic acid sequence of 5′-UDUHRKYU-3′, where D is A D, or U; H is A, C or U; R is A or G; K is G or U and Y is C or U. In some cases, when L4 is eight nucleotides in length, L4 may comprise a consensus nucleic acid sequence of 5′-UUUCAUUU-3′.
In some cases, L5 may comprise four nucleotides. In some cases, L5 may comprise less than five nucleotides. In some cases, L5 may comprise more than three nucleotides. In some cases, L5 may comprise a consensus nucleic acid sequence of 5′-GYUU-3′, where Y is C or U.
In some cases, L5 may comprise a consensus nucleic acid sequence of GNNN-3′, where N is A, C, G, or U. In some cases, L5 may comprise a consensus nucleic acid sequence of 5′-GNHW-3′, where N is A, C, G, or U; H is A, C, or U; and W is A or U.
In some cases, an anti-VEGF-A aptamer of the disclosure may comprise a consensus nucleic acid sequence of 5′-HNBYHDCCUCCGCGCGGAGGGRUDDNDHHWYCCCGYUUGKYNKVNW-3′ (SEQ ID NO: 1), where H is A, C, or U; N is A, C, G, or U; B is C, G, or U; Y is C or U; D is A, G, or U; R is A or G; W is A or U; K is G or U; and V is A, C, or G. In some cases, when S3 is five base pairs in length and L4 is six nucleotides in length, an anti-VEGF-A aptamer of the disclosure may comprise a consensus nucleic acid sequence of 5′-HNBYHDCCUCCGCGCGGAGGGRUUDNDHUAYCCCGYUUGKYNKVNW-3′ (SEQ ID NO: 2), where H is A, C, or U; N is A, C, G, or U; B is C, G, or U; Y is C or U; D is A, G, or U; R is A or G; K is G or U; V is A, C, or G; and W is A or U. In some cases, when S3 is six base pairs in length and L4 is 4 nucleotides in length, an anti-VEGF-A aptamer of the disclosure may comprise a consensus nucleic acid sequence of 5′-WNKYHDCCUCCGCGCGGAGGGGUDDNAHHAUCCCGUUUGGYBKMHW-3′ (SEQ ID NO: 3), where W is A or U; N is A, C, G, or U; K is G or U; Y is C or U; H is A, C, or U; D is A, G, or U; B is C, G, or U; and M is A or C. In some cases, when S3 is four base pairs in length and L4 is eight nucleotides in length, an anti-VEGF-A aptamer of the disclosure may comprise a consensus nucleic acid sequence of 5′-AUGCCGCCUCCGCGCGGAGGGGUUUCAUUUCCCCGUUUGGCUGCAU-3′ (SEQ ID NO: 4). In some cases, an anti-VEGF-A aptamer of the disclosure comprises a consensus nucleic acid sequence of 5′-HNBYHDCCUCCGCGCGGAGDSBHDNNNNHNNBNCGYUUGKYNKVNW-3′ (SEQ ID NO: 436), where H is A, C, or U; N is A, C, G, or U; B is C, G, or U; Y is C or U; D is A, G, or U; R is A or G; W is A or U; K is G or U; and V is A, C, or G.
In some cases, an anti-VEGF-A aptamer of the disclosure comprises a consensus nucleic acid sequence of 5′-HNBYHDCCUCCGCGCGGAGKBHYDNNNKDBVCGYUUGKYNKVNW-3′ (SEQ ID NO: 437), where H is A, C, or U; N is A, C, G, or U; B is C, G, or U; Y is C or U; D is A, G, or U; R is A or G; W is A or U; K is G or U; and V is A, C, or G. In some cases, an anti-VEGF-A aptamer of the disclosure comprises a consensus nucleic acid sequence of 5′-HNBYHDCCUCCGCGCGGAGKSHUDRGBUDSMCGYUUGKYNKVNW-3′ (SEQ ID NO: 438), where H is A, C, or U; N is A, C, G, or U; B is C, G, or U; Y is C or U; D is A, G, or U; R is A or G; W is A or U; K is G or U; M is A or C; and V is A, C, or G.
In some cases, an anti-VEGF-A aptamer of the disclosure may comprise a consensus nucleic acid sequence of 5′-HNBYHDNNN*NNKNGCNNWGGGRUNDNDHNWYCCCGNNNNNYNKVNW-3′ (SEQ ID NO: 5), where H is A, C, or U; N is A, C, G, or U; B is C, G, or U; Y is C or U; N* is A, C, G, U, can be deleted entirely, or is a non-nucleotidyl spacer 3 modification, a 6 carbon alkyl linker (1,6-hexanediol), or a spacer 9 (triethyleneglycol) modification; D is A, G, or U; K is G or U; W is A or U; R is A or G; and V is A, C, or G
In some aspects, the disclosure provides anti-VEGF-A compositions that inhibit a function associated with VEGF-A. The anti-VEGF-A compositions may include one or more anti-VEGF-A aptamers that bind to specific regions of VEGF-A with high specificity and high affinity. In some cases, the anti-VEGF-A compositions may include one or more anti-VEGF-A aptamers that bind to a region of VEGF-A that includes the receptor binding face of VEGF-A.
In some cases, the anti-VEGF-A compositions may include one or more anti-VEGF-A aptamers that bind to a region of VEGF-A which includes the receptor binding domain of VEGF-A, or a portion thereof. The receptor binding domain of VEGF-A may include any one or more of residues 1-109 as described in SEQ ID NOs: 6-10. In some cases, the anti-VEGF-A compositions may include one or more anti-VEGF-A aptamers that prevent or reduce binding of one or more isoforms or variants of VEGF-A with Flt-1, KDR, Nrp-1, or any combination thereof.
In some aspects, anti-VEGF-A aptamers of the disclosure may block or reduce the interaction of VEGF-A with Flt-1, may block or reduce the interaction of VEGF-A with KDR, may block or reduce the interaction of VEGF-A with Nrp-1, or any combination thereof.
In some aspects, anti-VEGF-A aptamers of the disclosure bind to structural features that are common to VEGF-A110, VEGF-A121, VEGF-A165, VEGF-A189, and VEGF-A206. In some cases, anti-VEGF-A aptamers of the disclosure bind to regions of VEGF-A other than the heparin binding domain present in VEGF-A165, VEGF-A189, and VEGF-A206. The heparin binding domain may include residues 111-165 as described by SEQ ID NOs: 6-8. Without wishing to be bound by theory, the cationic heparin binding domain of VEGF-A is thought to be the dominant epitope for aptamer recognition due to the anionic nature of the oligonucleotide sugar phosphate backbone. Therefore, selection of aptamers to regions of VEGF-A other than the heparin binding domain have proven difficult. For example, pegaptanib (brand name Macugen®) is an oligonucleotide inhibitor of VEGF-A which binds to the heparin binding domain. Because VEGF-A121 and VEGF-A110 lack the heparin binding domain, pegaptanib does not bind to or inhibit VEGF-A121 and VEGF-A110, thereby providing inferior VEGF-A suppression as compared to an inhibitor that binds to the receptor binding domain of VEGF-A.
Similarly, additional aptamer inhibitors of VEGF-A have been described which bind to the heparin binding domain of VEGF-A. For example, a DNA aptamer specific for VEGF-A165, but not VEGF-A121 has been described (Hasegawa, Hijiri, Koji Sode, and Kazunori Ikebukuro. “Selection of DNA aptamers against VEGF165 using a protein competitor and the aptamer blotting method.” Biotechnology letters 30.5 (2008): 829-834; Kaur, Harleen, and Lin-Yue Lanry Yung. “Probing high affinity sequences of DNA aptamer against VEGF165.” PLoS One 7.2 (2012): e31196.). Additionally, a 2′-O-Methyl aptamer has been described that binds to VEGF-A165, but not VEGF-A121 (Burmeister, Paula E., et al. “Direct in vitro selection of a 2′-O-methyl aptamer to VEGF.” Chemistry & biology 12.1 (2005): 25-33.). Similarly, DNA aptamers with an expanded 6-base nucleotide alphabet have been described that recognize VEGF-A165, but not VEGF-A121 (Kimoto, Michiko, et al. “Generation of high-affinity DNA aptamers using an expanded genetic alphabet.” Nature biotechnology 31.5 (2013): 453.). Furthermore, aptamer selections against other proteins that contain heparin binding domains tend to generate aptamers to those epitopes. For example, RNA aptamers that bind to the heparin binding domain have been described for thrombin (Jeter, Martha L., et al. “RNA aptamer to thrombin binds anion□ binding exosite□2 and alters protease inhibition by heparin□binding serpins.” FEBS letters 568.1-3 (2004): 10-14; Long, Stephen B., et al. “Crystal structure of an RNA aptamer bound to thrombin.” RNA (2008)), basic fibroblast growth factor (Jellinek, D., et al. “High-affinity RNA ligands to basic fibroblast growth factor inhibit receptor binding.” Proceedings of the National Academy of Sciences 90.23 (1993): 11227-11231.), interleukin-8 (Sung, Ho Jin, et al. “Inhibition of human neutrophil activity by an RNA aptamer bound to interleukin-8.” Biomaterials 35.1 (2014): 578-589.), and Plasmodium falciparum erythrocyte membrane protein 1 (Barfod, Anders, Tina Persson, and Johan Lindh. “In vitro selection of RNA aptamers against a conserved region of the Plasmodium falciparum erythrocyte membrane protein 1.” Parasitology research 105.6 (2009): 1557-1566.).
In some cases, anti-VEGF-A aptamers of the disclosure may bind to a region of VEGF-A that includes the receptor-binding face of any isoform or variant of VEGF-A, or portions thereof. The receptor-binding face of VEGF-A may include strands β2, β5, and β6, and loops β1 to β2 of one monomer, and the N-terminal a helix and loop β3 to β4 of a second monomer. The receptor-binding face of VEGF-A may be as described by Muller et al. “The crystal structure of vascular endothelial growth factor (VEGF) refined to 1.93 Å resolution: multiple copy flexibility and receptor binding.” Structure 5.10 (1997): 1325-1338. In some cases, anti-VEGF-A aptamers of the disclosure may bind to one or more amino acid residues of any isoform or variant of VEGF-A, including, without limitation, Phe17, Ile43, Ile46, Glu64, Gln79, Ile83, Lys84, Pro85, Arg82, His86, Asp63, and Glu67 as described by SEQ ID NOs: 6-10. In some cases, anti-VEGF-A aptamers that bind to the receptor-binding face of VEGF-A, or a portion thereof, may prevent or reduce the association of VEGF-A with one or more of Flt-1, KDR, or Nrp-1. In some cases, anti-VEGF-A aptamers that bind to the receptor-binding face of VEGF-A, or a portion thereof, may interact with recombinant bead-bound VEGF-A165, VEGF-A121, or VEGF-A110 as measured by flow cytometry or may interact with recombinant surface-bound VEGF-A165, VEGF-A121, or VEGF-A110 as measured by surface plasmon resonance (see Examples 1 and 2, respectively). In some cases, anti-VEGF-A aptamers that bind to the receptor-binding face of VEGF-A, or a portion thereof, may inhibit or reduce the interaction of VEGF-A165, VEGF-A121, or VEGF-A110 with KDR as measured by a reduction in FRET signal (see Example 3). In some cases, anti-VEGF-A aptamers that bind to the receptor-binding face of VEGF-A, or a portion thereof, may inhibit or reduce VEGF-A165, VEGF-A121, or VEGF-A110 induced trans autophosphorylation of the intracellular domain of KDR as measured by phospho-KDR AlphaLISA® (see Example 4). In some cases, anti-VEGF-A aptamers that bind to the receptor-binding face of VEGF-A, or a portion thereof, may inhibit or reduce VEGF-A165, VEGF-A121, or VEGF-A110 induced gene expression of tissue factor in HUVEC cells as measured by qPCR. In some cases, anti-VEGF-A aptamers that bind to the receptor-binding face of VEGF-A, or a portion thereof, may inhibit or reduce VEGF-A165, VEGF-A121, or VEGF-A110 induced tube formation of GFP-HUVECs in co-culture with human dermal fibroblasts cells as measured by change in network length or network area (see Example 5). In some cases, anti-VEGF-A aptamers that bind to the receptor-binding face of VEGF-A, or a portion thereof, may inhibit or reduce vascular leakage in a mouse, rat, rabbit, or primate eye following exogenous VEGF-A165, VEGF-A121, or VEGF-A110 challenge as measured by fluorescein angiography and Evans-blue albumin staining.
In some cases, anti-VEGF-A aptamers of the disclosure may bind to a region of VEGF-A that includes the receptor binding domain of any isoform or variant of VEGF-A, or portions thereof. The receptor binding domain of VEGF-A may include one or more of residues 1-109, as described in SEQ ID NOs: 6-10. In some cases, anti-VEGF-A aptamers of the disclosure may bind to one or more amino acid residues of any isoform or variant of VEGF-A, including, without limitation, Phe17, Tyr21, Tyr25, Ile43, Ile46, Ile83, Asp63, Glu64, Pro85, and His86, as described by SEQ ID NOs: 6-10. In some cases, anti-VEGF-A aptamers of the disclosure may bind to a region within the receptor binding domain of VEGF-A which results in global conformational changes in VEGF-A such that it no longer binds to and activates signaling via KDR. In some cases, anti-VEGF-A aptamers that bind to the receptor binding domain of VEGF-A, or a portion thereof, may prevent or reduce the association of VEGF-A with one or more of Flt-1, KDR, and Nrp-1. In some cases, anti-VEGF-A aptamers that bind to the receptor binding domain of VEGF-A, or a portion thereof, may interact with recombinant bead-bound VEGF-A165, VEGF-A121, or VEGF-A110 as measured by flow cytometry or may interact with recombinant surface-bound VEGF-A165, VEGF-A121, or VEGF-A110 as measured by surface plasmon resonance (see Examples 1 and 2, respectively). In some cases, anti-VEGF-A aptamers that bind to the receptor-binding domain of VEGF-A, or a portion thereof, may inhibit or reduce the interaction of VEGF-A165, VEGF-A121, or VEGF-A110 with KDR as measured by a reduction in FRET signal (see Example 3). In some cases, anti-VEGF-A aptamers that bind to the receptor-binding domain of VEGF-A, or a portion thereof, may inhibit or reduce VEGF-A165, VEGF-A121, or VEGF-A110 induced trans autophosphorylation of the intracellular domain of KDR as measured by phospho-KDR AlphaLISA® (see Example 4). In some cases, anti-VEGF-A aptamers that bind to the receptor binding domain of VEGF-A, or a portion thereof, may inhibit or reduce VEGF-A165, VEGF-A121, or VEGF-A110 induced gene expression of tissue factor in HUVEC cells as measured by qPCR. In some cases, anti-VEGF-A aptamers that bind to the receptor binding domain of VEGF-A, or a portion thereof, may inhibit or reduce VEGF-A165, VEGF-A121, or VEGF-A110 induced tube formation of GFP-HUVECs in co-culture with human dermal fibroblasts cells as measured by change in network length or network area (see Example 5). In some cases, anti-VEGF-A aptamers that bind to the receptor binding domain of VEGF-A, or a portion thereof, may inhibit or reduce vascular leakage in a mouse, rat, rabbit, or primate eye following exogenous VEGF-A165, VEGF-A121, or VEGF-A110 challenge as measured by fluorescein angiography and Evans-blue albumin staining.
The dissociation constant (Kd) can be used to describe the affinity of an aptamer for a target (or to describe how tightly the aptamer binds to the target) or to describe the affinity of an aptamer for a specific epitope of a target. The dissociation constant may be defined as the molar concentration at which half of the binding sites of a target are occupied by the aptamer. Thus, the smaller the Kd, the tighter the binding of the aptamer to its target. In some cases, an anti-VEGF-A aptamer of the disclosure may have a Kd for one or more isoforms or variants of VEGF-A of less than about 1000 nM, for example, less than about 500 nM, less than about 100 nM, less than about 50 nM, less than about 10 nM, less than about 5 nM, less than about 1 nM, less than about 0.5 nM, or less than about 0.1 nM, as measured by a surface plasmon resonance assay (see Example 2). In some cases, an anti-VEGF-A aptamer may have a dissociation constant (Kd) for one or more isoforms or variants of VEGF-A of less than about 50 nM, as measured by a surface plasmon resonance assay (see Example 2). In some cases, an anti-VEGF-A aptamer may have a dissociation constant (Kd) for one or more isoforms or variants of VEGF-A of less than about 25 nM, as measured by a surface plasmon resonance assay (see Example 2). In some cases, an anti-VEGF-A aptamer may have a dissociation constant (Kd) for one or more isoforms or variants VEGF-A of less than about 10 nM, as measured by a surface plasmon resonance assay (see Example 2). In some cases, an anti-VEGF-A aptamer may have a dissociation constant (Kd) for one or more isoforms or variants of VEGF-A of less than about 5 nM, as measured by a surface plasmon resonance assay (see Example 2). In some cases, an anti-VEGF-A aptamer may have a dissociation constant (Kd) for one or more isoforms or variants of VEGF-A of less than about 1 nM, as measured by a surface plasmon resonance assay (see Example 2). In some cases, an anti-VEGF-A aptamer may have a dissociation constant (Kd) for one or more isoforms or variants of VEGF-A of less than about 0.5 nM, as measured by a surface plasmon resonance assay (see Example 2). In some cases, an anti-VEGF-A aptamer may have a dissociation constant (Kd) for one or more isoforms or variants of VEGF-A of less than about 0.1 nM, as measured by a surface plasmon resonance assay (see Example 2). In some cases, the aptamer may be a pan-variant specific aptamer that binds to each of VEGF-A110, VEGF-A121, VEGF-A165, VEGF-A is, and VEGF-A206 with a Kd of less than about 1000 nM, for example, less than about 500 nM, less than about 100 nM, less than about 50 nM, less than about 25 nM, less than about 10 nM, less than about 5 nM, less than about 1 nM, less than about 0.5 nM, or less than about 0.1 nM, as measured by a surface plasmon resonance assay (see Example 2). In some cases, the aptamer may bind to any region of VEGF-A described herein, or a portion thereof, with a Kd of less than about 1000 nM, for example, less than about 500 nM, less than about 100 nM, less than about 50 nM, less than about 25 nM, less than about 10 nM, less than about 5 nM, less than about 1 nM, less than about 0.5 nM, or less than about 0.1 nM, as measured by a surface plasmon resonance assay (see Example 2). In some cases, the aptamer may bind to the receptor-binding face or the receptor binding domain of VEGF-A, or portions thereof, with a Kd of less than about 1000 nM, for example, less than about 500 nM, less than about 100 nM, less than about 50 nM, less than about 25 nM, less than about 10 nM, less than about 5 nM, less than about 1 nM, less than about 0.5 nM, or less than about 0.1 nM, as measured by a surface plasmon assay (see Example 2). In some cases, the anti-VEGF-A aptamer may bind to the receptor-binding face or the receptor binding domain of VEGF-A, or portions thereof, with a Kd from about 0.5 nM to about 25 nM, as measured by a surface plasmon resonance assay (see Example 2).
In some cases, the aptamers disclosed herein may bind to a region of VEGF-A, such as the receptor-binding face of VEGF-A, or the receptor binding domain of VEGF-A, or portions thereof, with a Kd of less than about 50 nM as measured by a surface plasmon assay (see Example 2), and may have an IC50 of less than about 50 nM as measured by a VEGF-A:KDR competition binding assay (see Example 3), a KDR phosphorylation AlphaLISA® assay (see Example 4), or an in vitro model of VEGF-A-induced angiogenesis (see Example 5). In some cases, the aptamers disclosed herein may bind to a region of VEGF-A, such as the receptor binding face of VEGF-A, or the receptor binding domain of VEGF-A, or portions thereof, with a Kd of less than about 50 nM as measured by a surface plasmon resonance assay (see Example 2), and may have an IC50 of less than about 10 nM as measured by a VEGF-A:KDR competition binding assay (see Example 3), a KDR phosphorylation AlphaLISA® assay (see Example 4), or an in vitro model of VEGF-A-induced angiogenesis (see Example 5). In some cases, the aptamers disclosed herein may bind to a region of VEGF-A, such as the receptor binding face of VEGF-A, or the receptor binding domain of VEGF-A, or portions thereof, with a Kd of less than about 50 nM as measured by a surface plasmon resonance assay (see Example 2), and may have an IC50 of less than about 5 nM as measured by a VEGF-A:KDR competition binding assay (see Example 3), a KDR phosphorylation AlphaLISA® assay (see Example 4), or an in vitro model of VEGF-A-induced angiogenesis (see Example 5). In some cases, the aptamers disclosed herein may bind to a region of VEGF-A, such as the receptor binding face of VEGF-A, or the receptor binding domain of VEGF-A, or portions thereof, with a Kd of less than about 50 nM as measured by a surface plasmon resonance assay (see Example 2), and may have an IC50 of less than about 1 nM as measured by a VEGF-A:KDR competition binding assay (see Example 3), a KDR phosphorylation AlphaLISA® assay (see Example 4), or an in vitro model of VEGF-A-induced angiogenesis (see Example 5). In some cases, the aptamers disclosed herein may bind to a region of VEGF-A, such as the receptor binding face of VEGF-A, or the receptor binding domain of VEGF-A, or portions thereof, with a Kd of less than about 50 nM as measured by a surface plasmon resonance assay (see Example 2), and may have an IC50 of less than about 0.5 nM as measured by a VEGF-A:KDR competition binding assay (see Example 3), a KDR phosphorylation AlphaLISA® assay (see Example 4), or an in vitro model of VEGF-A-induced angiogenesis (see Example 5). In some cases, the aptamers disclosed herein may bind to a region of VEGF-A, such as the receptor binding face of VEGF-A, or the receptor binding domain of VEGF-A, or portions thereof, with a Kd of less than about 50 nM as measured by a surface plasmon resonance assay (see Example 2), and may have an IC50 of less than about 0.1 nM as measured by a VEGF-A:KDR competition binding assay (see Example 3), a KDR phosphorylation AlphaLISA® assay (see Example 4), or an in vitro model of VEGF-A-induced angiogenesis (see Example 5).
In some cases, the aptamers disclosed herein may bind to a region of VEGF-A, such as the receptor binding face of VEGF-A, or the receptor binding domain of VEGF-A, or portions thereof, with a Kd of less than about 10 nM as measured by a surface plasmon resonance assay (see Example 2), and may have an IC50 of less than about 50 nM as measured by a VEGF-A:KDR competition binding assay (see Example 3), a KDR phosphorylation AlphaLISA® assay (see Example 4), or an in vitro model of VEGF-A-induced angiogenesis (see Example 5). In some cases, the aptamers disclosed herein may bind to a region of VEGF-A, such as the receptor binding face of VEGF-A, or the receptor binding domain of VEGF-A, or portions thereof, with a Kd of less than about 10 nM as measured by a surface plasmon resonance assay (see Example 2), and may have an IC50 of less than about 10 nM as measured by a VEGF-A:KDR competition binding assay (see Example 3), a KDR phosphorylation AlphaLISA® assay (see Example 4), or an in vitro model of VEGF-A-induced angiogenesis (see, Example 5). In some cases, the aptamers disclosed herein may bind to a region of VEGF-A, such as the receptor binding face of VEGF-A, or the receptor binding domain of VEGF-A, or portions thereof, with a Kd of less than about 10 nM as measured by a surface plasmon resonance assay (see Example 2), and may have an IC50 of less than about 5 nM as measured by a VEGF-A:KDR competition binding assay (see Example 3), a KDR phosphorylation AlphaLISA® assay (see Example 4), or an in vitro model of VEGF-A-induced angiogenesis (see Example 5). In some cases, the aptamers disclosed herein may bind to a region of VEGF-A, such as the receptor binding face of VEGF-A, or the receptor binding domain of VEGF-A, or portions thereof, with a Kd of less than about 10 nM as measured by a surface plasmon resonance assay (see Example 2), and may have an IC50 of less than about 1 nM as measured by a VEGF-A:KDR competition binding assay (see Example 3), a KDR phosphorylation AlphaLISA® assay (see Example 4), or an in vitro model of VEGF-A-induced angiogenesis (see Example 5). In some cases, the aptamers disclosed herein may bind to a region of VEGF-A, such as the receptor binding face of VEGF-A, or the receptor binding domain of VEGF-A, or portions thereof, with a Kd of less than about 10 nM as measured by a surface plasmon resonance assay (see Example 2), and may have an IC50 of less than about 0.5 nM as measured by a VEGF-A:KDR competition binding assay (see Example 3), a KDR phosphorylation AlphaLISA® assay (see Example 4), or an in vitro model of VEGF-A-induced angiogenesis (see Example 5). In some cases, the aptamers disclosed herein may bind to a region of VEGF-A, such as the receptor binding face of VEGF-A, or the receptor binding domain of VEGF-A, or portions thereof, with a K of less than about 10 nM as measured by a surface plasmon resonance assay (see Example 2), and may have an IC50 of less than about 0.1 nM as measured by a VEGF-A:KDR competition binding assay (see Example 3), a KDR phosphorylation AlphaLISA® assay (see Example 4), or an in vitro model of VEGF-A-induced angiogenesis (see Example 5).
In some cases, the aptamers disclosed herein may bind to a region of VEGF-A, such as the receptor binding face of VEGF-A, or the receptor binding domain of VEGF-A, or portions thereof, with a Kd of less than about 5 nM as measured by a surface plasmon resonance assay (see Example 2), and may have an IC50 of less than about 50 nM as measured by a VEGF-A:KDR competition binding assay (see Example 3), a KDR phosphorylation AlphaLISA® assay (see Example 4), or an in vitro model of VEGF-A-induced angiogenesis (see Example 5). In some cases, the aptamers disclosed herein may bind to a region of VEGF-A, such as the receptor binding face of VEGF-A, or the receptor binding domain of VEGF-A, or portions thereof, with a Kd of less than about 5 nM as measured by a surface plasmon resonance assay (see Example 2), and may have an IC50 of less than about 10 nM as measured by a VEGF-A:KDR competition binding assay (see Example 3), a KDR phosphorylation AlphaLISA® assay (see Example 4), or an in vitro model of VEGF-A-induced angiogenesis (see Example 5). In some cases, the aptamers disclosed herein may bind to a region of VEGF-A, such as the receptor binding face of VEGF-A, or the receptor binding domain of VEGF-A, or portions thereof, with a Kd of less than about 5 nM as measured by a surface plasmon resonance assay (see Example 2), and may have an IC50 of less than about 5 nM as measured by a VEGF-A:KDR competition binding assay (see Example 3), a KDR phosphorylation AlphaLISA® assay (see Example 4), or an in vitro model of VEGF-A-induced angiogenesis (see Example 5). In some cases, the aptamers disclosed herein may bind to a region of VEGF-A, such as the receptor binding face of VEGF-A, or the receptor binding domain of VEGF-A, or portions thereof, with a Kd of less than about 5 nM as measured by a surface plasmon resonance assay (see Example 2), and may have an IC50 of less than about 1 nM as measured by a VEGF-A:KDR competition binding assay (see Example 3), a KDR phosphorylation AlphaLISA® assay (see Example 4), or an in vitro model of VEGF-A-induced angiogenesis (see Example 5). In some cases, the aptamers disclosed herein may bind to a region of VEGF-A, such as the receptor binding face of VEGF-A, or the receptor binding domain of VEGF-A, or portions thereof, with a Kd of less than about 5 nM as measured by a surface plasmon resonance assay (see Example 2), and may have an IC50 of less than about 0.5 nM as measured by a VEGF-A:KDR competition binding assay (see Example 3), a KDR phosphorylation AlphaLISA® assay (see Example 4), or an in vitro model of VEGF-A-induced angiogenesis (see Example 5). In some cases, the aptamers disclosed herein may bind to a region of VEGF-A, such as the receptor binding face of VEGF-A, or the receptor binding domain of VEGF-A, or portions thereof, with a Kd of less than about 5 nM as measured by a surface plasmon resonance assay (see Example 2), and may have an IC50 of less than about 0.1 nM as measured by a VEGF-A:KDR competition binding assay (see Example 3), a KDR phosphorylation AlphaLISA® assay (see Example 4), or an in vitro model of VEGF-A-induced angiogenesis (see Example 5).
In some cases, the aptamers disclosed herein may bind to a region of VEGF-A, such as the receptor binding face of VEGF-A, or the receptor binding domain of VEGF-A, or portions thereof, with a Kd of less than about 1 nM as measured by a surface plasmon resonance assay (see Example 2), and may have an IC50 of less than about 50 nM as measured by a VEGF-A:KDR competition binding assay (see Example 3), a KDR phosphorylation AlphaLISA® assay (see Example 4), or an in vitro model of VEGF-A-induced angiogenesis (see Example 5). In some cases, the aptamers disclosed herein may bind to a region of VEGF-A, such as the receptor binding face of VEGF-A, or the receptor binding domain of VEGF-A, or portions thereof, with a Kd of less than about 1 nM as measured by a surface plasmon resonance assay (see Example 2), and may have an IC50 of less than about 10 nM as measured by a VEGF-A:KDR competition binding assay (see Example 3), a KDR phosphorylation AlphaLISA® assay (see Example 4), or an in vitro model of VEGF-A-induced angiogenesis (see Example 5). In some cases, the aptamers disclosed herein may bind to a region of VEGF-A, such as the receptor binding face of VEGF-A, or the receptor binding domain of VEGF-A, or portions thereof, with a Kd of less than about 1 nM as measured by a surface plasmon resonance assay (see Example 2), and may have an IC50 of less than about 5 nM as measured by a VEGF-A:KDR competition binding assay (see Example 3), a KDR phosphorylation AlphaLISA® assay (see Example 4), or an in vitro model of VEGF-A-induced angiogenesis (see Example 5). In some cases, the aptamers disclosed herein may bind to a region of VEGF-A, such as the receptor binding face of VEGF-A, or the receptor binding domain of VEGF-A, or portions thereof, with a Kd of less than about 1 nM as measured by a surface plasmon resonance assay (see Example 2), and may have an IC50 of less than about 1 nM as measured by a VEGF-A:KDR competition binding assay (see Example 3), a KDR phosphorylation AlphaLISA® assay (see Example 4), or an in vitro model of VEGF-A-induced angiogenesis (see Example 5). In some cases, the aptamers disclosed herein may bind to a region of VEGF-A, such as the receptor binding face of VEGF-A, or the receptor binding domain of VEGF-A, or portions thereof, with a Kd of less than about 1 nM as measured by a surface plasmon resonance assay (see Example 2), and may have an IC50 of less than about 0.5 nM as measured by a VEGF-A:KDR competition binding assay (see Example 3), a KDR phosphorylation AlphaLISA® assay (see Example 4), or an in vitro model of VEGF-A-induced angiogenesis (see Example 5). In some cases, the aptamers disclosed herein may bind to a region of VEGF-A, such as the receptor binding face of VEGF-A, or the receptor binding domain of VEGF-A, or portions thereof, with a Kd of less than about 1 nM as measured by a surface plasmon resonance assay (see Example 2), and may have an IC50 of less than about 0.1 nM as measured by a VEGF-A:KDR competition binding assay (see Example 3), a KDR phosphorylation AlphaLISA® assay (see Example 4), or an in vitro model of VEGF-A-induced angiogenesis (see Example 5).
In some cases, the aptamers disclosed herein may bind to a region of VEGF-A, such as the receptor binding face of VEGF-A, or the receptor binding domain of VEGF-A, or portions thereof, with a Kd of less than about 0.5 nM as measured by a surface plasmon resonance assay (see Example 2), and may have an IC50 of less than about 50 nM as measured by a VEGF-A:KDR competition binding assay (see Example 3), a KDR phosphorylation AlphaLISA® assay (see Example 4), or an in vitro model of VEGF-A-induced angiogenesis (see Example 5). In some cases, the aptamers disclosed herein may bind to a region of VEGF-A, such as the receptor binding face of VEGF-A, or the receptor binding domain of VEGF-A, or portions thereof, with a Kd of less than about 0.5 nM as measured by a surface plasmon resonance assay (see Example 2), and may have an IC50 of less than about 10 nM as measured by a VEGF-A:KDR competition binding assay (see Example 3), a KDR phosphorylation AlphaLISA® assay (see Example 4), or an in vitro model of VEGF-A-induced angiogenesis (see Example 5). In some cases, the aptamers disclosed herein may bind to a region of VEGF-A, such as the receptor binding face of VEGF-A, or the receptor binding domain of VEGF-A, or portions thereof, with a Kd of less than about 0.5 nM as measured by a surface plasmon resonance assay (see Example 2), and may have an IC50 of less than about 5 nM as measured by a VEGF-A:KDR competition binding assay (see Example 3), a KDR phosphorylation AlphaLISA® assay (see Example 4), or an in vitro model of VEGF-A-induced angiogenesis (see Example 5). In some cases, the aptamers disclosed herein may bind to a region of VEGF-A, such as the receptor binding face of VEGF-A, or the receptor binding domain of VEGF-A, or portions thereof, with a Kd of less than about 0.5 nM as measured by a surface plasmon resonance assay (see Example 2), and may have an IC50 of less than about 1 nM as measured by a VEGF-A:KDR competition binding assay (see Example 3), a KDR phosphorylation AlphaLISA® assay (see Example 4), or an in vitro model of VEGF-A-induced angiogenesis (see Example 5). In some cases, the aptamers disclosed herein may bind to a region of VEGF-A, such as receptor binding face of VEGF-A, or the receptor binding domain of VEGF-A, or portions thereof, with a Kd of less than about 0.5 nM as measured by a surface plasmon resonance assay (see Example 2), and may have an IC50 of less than about 0.5 nM as measured by a VEGF-A:KDR competition binding assay (see Example 3), a KDR phosphorylation AlphaLISA® assay (see Example 4), or an in vitro model of VEGF-A-induced angiogenesis (see Example 5). In some cases, the aptamers disclosed herein may bind to a region of VEGF-A, such as the receptor binding face of VEGF-A, or the receptor binding domain of VEGF-A, or portions thereof, with a Kd of less than about 0.5 nM as measured by a surface plasmon resonance assay (see Example 2), and may have an IC50 of less than about 0.1 nM as measured by a VEGF-A:KDR competition binding assay (see Example 3), a KDR phosphorylation AlphaLISA® assay (see Example 4), or an in vitro model of VEGF-A-induced angiogenesis (see Example 5).
In some cases, the aptamers disclosed herein may bind to a region of VEGF-A, such as the receptor binding face of VEGF-A, or the receptor binding domain of VEGF-A, or portions thereof, with a Kd of less than about 0.1 nM as measured by a surface plasmon resonance assay (see Example 2), and may have an IC50 of less than about 50 nM as measured by a VEGF-A:KDR competition binding assay (see Example 3), a KDR phosphorylation AlphaLISA® assay (see Example 4), or an in vitro model of VEGF-A-induced angiogenesis (see Example 5). In some cases, the aptamers disclosed herein may bind to a region of VEGF-A, such as the receptor binding face of VEGF-A, or the receptor binding domain of VEGF-A, or portions thereof, with a Kd of less than about 0.1 nM as measured by a surface plasmon resonance assay (see Example 2), and may have an IC50 of less than about 10 nM as measured by a VEGF-A:KDR competition binding assay (see Example 3), a KDR phosphorylation AlphaLISA® assay (see Example 4), or an in vitro model of VEGF-A-induced angiogenesis (see Example 5). In some cases, the aptamers disclosed herein may bind to a region of VEGF-A, such as the receptor binding face of VEGF-A, or the receptor binding domain of VEGF-A, or portions thereof, with a Kd of less than about 0.1 nM as measured by a surface plasmon resonance assay (see Example 2), and may have an IC50 of less than about 5 nM as measured by a VEGF-A:KDR competition binding assay (see Example 3), a KDR phosphorylation AlphaLISA® assay (see Example 4), or an in vitro model of VEGF-A-induced angiogenesis (see Example 5). In some cases, the aptamers disclosed herein may bind to a region of VEGF-A, such as the receptor binding face of VEGF-A, or the receptor binding domain of VEGF-A, or portions thereof, with a Kd of less than about 0.1 nM as measured by a surface plasmon resonance assay (see Example 2), and may have an IC50 of less than about 1 nM as measured by a VEGF-A:KDR competition binding assay (see Example 3), a KDR phosphorylation AlphaLISA® assay (see Example 4), or an in vitro model of VEGF-A-induced angiogenesis (see Example 5). In some cases, the aptamers disclosed herein may bind to a region of VEGF-A, such as the receptor binding face of VEGF-A, or the receptor binding domain of VEGF-A, or portions thereof, with a Kd of less than about 0.1 nM as measured by a surface plasmon resonance assay (see Example 2), and may have an IC50 of less than about 0.5 nM as measured by a VEGF-A:KDR competition binding assay (see Example 3), a KDR phosphorylation AlphaLISA® assay (see Example 4), or an in vitro model of VEGF-A-induced angiogenesis (see Example 5). In some cases, the aptamers disclosed herein may bind to a region of VEGF-A, such as the receptor binding face of VEGF-A, or the receptor binding domain of VEGF-A, or portions thereof, with a Kd of less than about 0.1 nM as measured by a surface plasmon resonance assay (see Example 2), and may have an IC50 of less than about 0.1 nM as measured by a VEGF-A:KDR competition binding assay (see Example 3), a KDR phosphorylation AlphaLISA® assay (see Example 4), or an in vitro model of VEGF-A-induced angiogenesis (see Example 5).
In some aspects, the aptamers disclosed herein may have an improved half-life as compared to other therapeutics, including antibodies. In some cases, the aptamers may have an improved half-life in a biological fluid or solution as compared to an antibody. In some cases, the aptamers may have an improved half-life in vivo as compared to an antibody. In one example, the aptamers may have an improved half-life when injected into the eye (intraocular half-life) as compared to an antibody. In some cases, the aptamers may have an improved intraocular half-life when injected into the eye of a human. In some cases, the aptamers may demonstrate improved stability over antibodies under physiological conditions.
In some cases, the aptamers described herein may have an intraocular half-life of at least 7 days in a human. In some cases, the aptamers described herein may have an intraocular half-life of at least 8 days, at least 9 days, at least 10 days, at least 11 days, at least 12 days, at least 13 days, at least 14 days, at least 15 days, at least 20 days or greater in a human.
In some cases, the aptamers described herein may have an intraocular half-life of at least 1 day in a non-human animal (e.g., rodent/rabbit/monkey/chimpanzee/pig). In some cases, the aptamers described herein may have an intraocular half-life of at least 1 day, at least 2 days, at least 3 days, at least 4 days, at least 5 days, at least 6 days, at least 7 days, at least 8 days, at least 9 days, at least 10 days or greater in a non-human animal such as a rodent, rabbit or monkey.
In some aspects, the aptamers described herein may have a shorter half-life as compared to other therapeutics. For example, an unmodified or unconjugated aptamer may have a lower half-life as compared to a modified or conjugated aptamer, however, the low molecular weight of the unmodified or unconjugated forms may allow for orders of magnitude greater initial concentrations, thereby achieving greater duration/efficacy. In some examples, the aptamer may have an intraocular half-life of less than about 7 days in a human. In some examples, the aptamers described herein may have an intraocular half-life of less than about 6 days, less than about 5 days or even less than about 4 days in a human.
The aptamers disclosed herein may demonstrate high specificity for VEGF-A versus other members of the VEGF family, including VEGF-B, VEGF-C, VEGF-D, VEGF-E, VEGF-F, and PIGF. In some cases, the aptamer may be selected such that the aptamer has high affinity for VEGF-A, but with little to no affinity for VEGF-B, VEGF-C, VEGF-D, VEGF-E, VEGF-F, or PIGF. In some cases, the aptamers of the disclosure may bind to VEGF-A with a specificity of at least 5-fold, at least 10-fold, at least 15-fold, at least 20-fold, at least 50-fold, at least 100-fold, at least 250-fold, at least 500-fold, at least 1,000-fold, at least 5,000-fold, at least 10,000-fold, at least 50,000-fold, or at least 100,000-fold, or greater than 100,000-fold than the aptamers bind to VEGF-B, VEGF-C, VEGF-D, VEGF-E, VEGF-F, or PIGF at relative serum concentrations.
The activity of a therapeutic agent can be characterized by the half maximal inhibitory concentration (IC50). The IC50 may be calculated as the concentration of therapeutic agent in nM at which half of the maximum inhibitory effect of the therapeutic agent is achieved. The IC50 may be dependent upon the assay utilized to calculate the value. In some examples, the IC50 of an aptamer described herein may be less than 100 nM, less than 50 nM, less than 25 nM, less than 10 nM, less than 5 nM, less than 1 nM, less than 0.5 nM, less than 0.1 nM or less than 0.01 nM as measured by a VEGF-A:KDR competition binding assay (see Example 3). In some examples, the IC50 of an aptamer described herein may be less than 100 nM, less than 50 nM, less than 25 nM, less than 10 nM, less than 5 nM, less than 1 nM, less than 0.5 nM, less than 0.1 nM or less than 0.01 nM as measured by a KDR phosphorylation AlphaLISA® assay (see Example 4). In some examples, the IC50 of an aptamer described herein may be less than 100 nM, less than 50 nM, less than 25 nM, less than 10 nM, less than 5 nM, less than 1 nM, less than 0.5 nM, less than 0.1 nM or less than 0.01 nM as measured by an in vitro model of VEGF-A-induced angiogenesis (see Example 5).
Aptamers generally have high stability at ambient temperatures for extended periods of time. The aptamers described herein may demonstrate greater than 70%, greater than 75%, greater than 80%, greater than 85%, greater 90%, greater than 91%, greater than 92%, greater than 93%, greater than 94%, greater than 95%, greater than 96%, greater than 97%, greater than 98%, greater than 99%, greater than 99.5%, or greater than 99.9% activity in solution under physiological conditions at 30 days or later.
In some cases, a composition of the disclosure comprises anti-VEGF-A aptamers, wherein essentially 100% of the anti-VEGF-A aptamers comprise nucleotides having ribose in the β-D-ribofuranose configuration. In other examples, a composition of the disclosure may comprise anti-VEGF-A aptamers, wherein at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, or greater than 90% of the anti-VEGF-A aptamers have ribose in the β-D-ribofuranose configuration.
In some aspects, the methods and compositions provided herein may be suitable for the treatment of ocular diseases or disorders. In some aspects, the methods and compositions provided herein may be suitable for the prevention of ocular diseases or disorders. In some aspects, the methods and compositions provided herein may be suitable to slow or halt the progression of ocular diseases or disorders. In some cases, the ocular disease or disorder is diabetic retinopathy. In some cases, the ocular disease or disorder is retinopathy of prematurity. In some cases, the ocular disease or disorder is central retinal vein occlusion. In some cases, the ocular disease or disorder is macular edema. In some cases, the ocular disease or disorder is choroidal neovascularization. In some cases, the ocular disease or disorder is neovascular (or wet) age-related macular degeneration. In some cases, the ocular disease or disorder is myopic choroidal neovascularization. In some cases, the ocular disease or disorder is punctate inner choroidopathy. In some cases, the ocular disease or disorder is presumed ocular histoplasmosis syndrome. In some cases, the ocular disease or disorder is familial exudative vitreoretinopathy. In some cases, the ocular disease or disorder is retinoblastoma.
Additional examples of ocular diseases or disorders that may be amendable to treatment by the methods and compositions provided herein may include, without limitation, pterygium, inflammatory conjunctivitis, including allergic and giant papillary conjunctivitis, infectious conjunctivitis, vernal keratoconjunctivitis, Stevens-Johnson disease, corneal herpetic keratitis, rhegmatogenous retinal detachment, pseudo-exfoliation syndrome, endophthalmitis, scleritis, corneal ulcers, dry eye syndrome, glaucoma, ischemic retinal disease, corneal transplant rejection, complications related to intraocular surgery such intraocular lens implantation and inflammation associated with cataract surgery, Behcet's disease, Stargardt disease, immune complex vasculitis, Fuch's disease, Vogt-Koyanagi-Harada disease, subretinal fibrosis, keratitis, vitreo-retinal inflammation, ocular parasitic infestation/migration, retinitis pigmentosa, cytomegalovirus retinitis and choroidal inflammation, ectropion, lagophthalmos, blepharochalasis, ptosis, xanthelasma of the eyelid, parasitic infestation of the eyelid, dermatitis of the eyelid, dacryoadenitis, epiphora, dysthyroid exophthalmos, conjunctivitis, scleritis, adenovirus keratitis, corneal ulcer, corneal abrasion, snow blindness, arc eye, Thygeson's superficial punctate keratopathy, corneal neovascularization, Fuchs' dystrophy, keratoconus, keratoconjunctivitis sicca, iritis, sympathetic ophthalmia, cataracts, chorioretinal inflammation, focal chorioretinal inflammation, focal chorioretinitis, focal choroiditis, focal retinitis, focal retinochoroiditis, disseminated chorioretinal inflammation, disseminated chorioretinitis, disseminated choroiditis, disseminated retinitis, disseminated retinochoroiditis, exudative retinopathy, posterior cyclitis, pars planitis, Harada's disease, chorioretinal scars, macula scars of posterior pole, solar retinopathy, choroidal degeneration, choroidal atrophy, choroidal sclerosis, angioid streaks, hereditary choroidal dystrophy, choroideremia, choroidal dystrophy (central arealor), gyrate atrophy (choroid), ornithinaemia, choroidal haemorrhage and rupture, choroidal haemorrhage (not otherwise specified), choroidal haemorrhage (expulsive), choroidal detachment, retinoschisis, retinal artery occlusion, retinal vein occlusion, hypertensive retinopathy, diabetic retinopathy, retinopathy, retinopathy of prematurity, macular degeneration, Bull's Eye maculopathy, epiretinal membrane, peripheral retinal degeneration, hereditary retinal dystrophy, retinitis pigmentosa, retinal haemorrhage, separation of retinal layers, central serous retinopathy, retinal detachment, macular edema, glaucoma-optic neuropathy, glaucoma suspect-ocular hypertension, primary open-angle glaucoma, primary angle-closure glaucoma, floaters, Leber's hereditary optic neuropathy, optic disc drusen, strabismus, ophthalmoparesis, progressive external ophthaloplegia, esotropia, exotropia, disorders of refraction and accommodation, hypermetropia, myopia, astigmastism, anisometropia, presbyopia, internal ophthalmoplegia, amblyopia, Leber's congenital amaurosis, scotoma, anopsia, color blindness, achromatopsia, maskun, nyctalopia, blindness, River blindness, micropthalmia, coloboma, red eye, Argyll Robertson pupil, keratomycosis, xerophthalmia, aniridia, sickle cell retinopathy, ocular neovascularization, retinal neovascularization, subretinal neovascularization; rubeosis iritis inflammatory diseases, chronic posterior and pan uveitis, neoplasms, retinoblastoma, pseudoglioma, neovascular glaucoma; neovascularization resulting following a combined vitrectomy-2 and lensectomy, vascular diseases, retinal ischemia, choroidal vascular insufficiency, choroidal thrombosis, neovascularization of the optic nerve, diabetic macular edema, cystoid macular edema, proliferative vitreoretinopathy, and neovascularization due to penetration of the eye or ocular injury.
In some aspects, the methods and compositions provided herein are suitable for the treatment of diseases that cause one or more ocular symptoms. Non-limiting examples of symptoms which may be amenable to treatment with the methods disclosed herein include, but are not limited to choroidal or vitreal neovascularization, vascular leakage, reduced reading speed, reduced color vision, macular edema, increased retinal thickening, increase in central retinal volume and/or, macular sensitivity, loss of retinal cells, increase in area of retinal atrophy, reduced best corrected visual acuity such as measured by Snellen or ETDRS scales, reduced Best Corrected Visual Acuity under low luminance conditions, impaired night vision, impaired light sensitivity, impaired dark adaptation, impaired contrast sensitivity, worsened patient reported outcomes, and any combination thereof.
In some cases, the methods and compositions provided herein may alleviate or reduce a symptom of a disease. In some cases, treatment with an aptamer provided herein may result in a reduction in the severity of any of the symptoms described herein. In some cases, treatment with an aptamer described herein may slow, halt or reverse the progression of any of the symptoms described herein. In some cases, treatment with an aptamer described herein may prevent the development of any of the symptoms described herein. In some cases, treatment with an aptamer described herein may slow, halt or reverse the progression of a disease, as measured by the number and severity of symptoms experienced. Examples of symptoms and relevant endpoints where the aptamer may have a therapeutic effect include choroidal or retinal neovascularization, vascular leakage, reduced reading speed, reduced color vision, macular edema, increased retinal thickening, increase in central retinal volume and/or, macular sensitivity, loss of retinal cells, increase in area of retinal atrophy, reduced best corrected visual acuity such as measured by Snellen or ETDRS scales, reduced Best Corrected Visual Acuity under low luminance conditions, impaired night vision, impaired light sensitivity, impaired dark adaptation, impaired contrast sensitivity, and worsening patient reported outcomes. In some instances, treatment with an aptamer described herein may have beneficial effects as measured by clinical endpoints including reading speed, choroidal or retinal neovascularization or vascular leakage as measured by fluorescein angiography, retinal thickness as measured by Optical Coherence Tomography or other techniques, central retinal volume, number and density of retinal cells, area of retinal atrophy as measured by Fundus Photography or Fundus Autofluorescence or other techniques, best corrected visual acuity such as measured by Snellen or ETDRS scales, Best Corrected Visual Acuity under low luminance conditions, light sensitivity, dark adaptation, contrast sensitivity, and patient reported outcomes as measured by such tools as the National Eye Institute Visual Function Questionnaire and Health Related Quality of Life Questionnaires.
In some cases, the methods and compositions provided herein may alleviate or reduce a symptom of a neovascular eye disease. In some cases, treatment with an aptamer provided herein may result in a reduction in the severity of any symptoms associated with a neovascular eye disease. In some cases, treatment with an aptamer described herein may slow, halt or reverse the progression of any symptom associated with a neovascular eye disease. In some cases, treatment with an aptamer described herein may prevent the development of any symptom associated with a neovascular eye disease. In some cases, treatment with an aptamer described herein may slow, halt or reverse the progression of a neovascular eye disease, as measured by the number and severity of symptoms experienced. Non-limiting examples of symptoms associated with neovascular eye diseases where the aptamer may have a therapeutic effect include choroidal or retinal neovascularization, vascular leakage within the eye, macular edema, central retinal thickness and visual acuity.
The terms “subject” and “patient” are used interchangeably herein to refer to a vertebrate, preferably a mammal, and more preferably a human. Mammals include, but are not limited to, rodents (e.g., mice, rats, rabbits, etc.) simians, humans, research animals (e.g., beagles, etc.), farm animals (e.g., pigs, horses, cows, llamas, alpacas, etc.), sport animals, and pets. In some cases, the methods described herein may be used on tissues or cells derived from a subject and the progeny of such tissues or cells. For example, aptamers described herein may be used to affect some function in tissues or cells of a subject. The tissues or cells may be obtained from a subject in vivo. In some cases, the tissues or cells are cultured in vitro and contacted with a composition provided herein (e.g., an aptamer).
In some aspects, the methods and compositions provided herein are used to treat a subject in need thereof. In some cases, the subject has, is suspected of having, or is at risk of developing, an ocular disease or disorder. In some cases, the subject is a human. In some cases, the human is a patient at a hospital or a clinic. In some cases, the subject is a non-human animal, for example, a non-human primate, a livestock animal, a domestic pet, or a laboratory animal. For example, a non-human animal can be an ape (e.g., a chimpanzee, a baboon, a gorilla, or an orangutan), an old world monkey (e.g., a rhesus monkey), a new world monkey, a dog, a cat, a bison, a camel, a cow, a deer, a pig, a donkey, a horse, a mule, a lama, a sheep, a goat, a buffalo, a reindeer, a yak, a mouse, a rat, a rabbit, or any other non-human animal.
In cases where the subject is a human, the subject may be of any age. In some cases, the subject has an age-related ocular disease or disorder (e.g., age-related macular degeneration). In some cases, the subject is about 50 years or older. In some cases, the subject is about 55 years or older. In some cases, the subject is about 60 years or older. In some cases, the subject is about 65 years or older. In some cases, the subject is about 70 years or older. In some cases, the subject is about 75 years or older. In some cases, the subject is about 80 years or older. In some cases, the subject is about 85 years or older. In some cases, the subject is about 90 years or older. In some cases, the subject is about 95 years or older. In some cases, the subject is about 100 years or older. In some cases, the subject is about 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100 or greater than 100 years old. In some cases, the subject is about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or greater than 20 years old.
In some aspects, the methods and compositions provided herein may be used to treat a subject having, suspected of having, or at risk of developing ocular symptoms as described herein. In some aspects, the methods and compositions provided herein may be used to treat a subject having, suspected of having, or at risk of developing an ocular disease as provided herein. In some cases, the methods and compositions provided herein may be used to treat a subject having, suspected of having, or at risk of developing an ocular disease or disorder. In some cases, the ocular disease or disorder is diabetic retinopathy. In some cases, the ocular disease or disorder is retinopathy of prematurity. In some cases, the ocular disease or disorder is central retinal vein occlusion. In some cases, the ocular disease or disorder is macular edema. In some cases, the ocular disease or disorder is choroidal neovascularization. In some cases, the ocular disease or disorder is neovascular (or wet) age-related macular degeneration. In some cases, the ocular disease or disorder is myopic choroidal neovascularization. In some cases, the ocular disease or disorder is punctate inner choroidopathy. In some cases, the ocular disease or disorder is presumed ocular histoplasmosis syndrome. In some cases, the ocular disease or disorder is familial exudative vitreoretinopathy. In some cases, the ocular disease or disorder is retinoblastoma. In some cases, the methods and compositions provided herein may be used to treat a subject having, suspected of having, or at risk of developing an ocular disease or disorder exhibiting elevated levels of one or more isoforms or variants of VEGF-A.
Disclosed herein are pharmaceutical compositions or medicaments, used interchangeably, for use in a method of therapy, or for use in a method of medical treatment.
Such use may be for the treatment of ocular diseases or disorders. In some cases, the pharmaceutical compositions can be used for the treatment of an ocular disease or disorder. In some cases, the pharmaceutical compositions comprise one or more anti-VEGF-A aptamers for the treatment of an ocular disease or disorder. In some cases, the ocular disease or disorder is diabetic retinopathy. In some cases, the ocular disease or disorder is retinopathy of prematurity. In some cases, the ocular disease or disorder is central retinal vein occlusion. In some cases, the ocular disease or disorder is macular edema. In some cases, the ocular disease or disorder is choroidal neovascularization. In some cases, the ocular disease or disorder is neovascular (or wet) age-related macular degeneration. In some cases, the ocular disease or disorder is myopic choroidal neovascularization. In some cases, the ocular disease or disorder is punctate inner choroidopathy. In some cases, the ocular disease or disorder is presumed ocular histoplasmosis syndrome. In some cases, the ocular disease or disorder is familial exudative vitreoretinopathy.
In some cases, the ocular disease or disorder is retinoblastoma. In some cases, the pharmaceutical compositions can be used for the treatment of an ocular disease or disorder that exhibits elevated levels of one or more isoforms or variants of VEGF-A.
In some cases, the one or more anti-VEGF-A aptamers may bind to one or more isoforms or variants of VEGF-A. In some cases, the one or more anti-VEGF-A aptamers are pan-variant specific aptamers that bind to each of VEGF-A110, VEGF-A121, VEGF-A165, VEGF-A189, and VEGF-A206. In some cases, the one or more anti-VEGF-A aptamers may bind to the receptor binding face of VEGF-A, or a portion thereof. The receptor binding face of VEGF-A may include strands β2, β5, and β6 and loop β1 and β2 of a first monomer, and the N-terminal a helix and loop β3 to β4 of the second monomer (see Muller, Yves A., et al. “The crystal structure of vascular endothelial growth factor (VEGF) refined to 1.93 Å resolution: multiple copy flexibility and receptor binding.” Structure 5.10 (1997): 1325-1338.). In some cases, anti-VEGF-A aptamers that bind to the receptor binding face of VEGF-A may bind to one or more of residues Phe17, Ile43, Ile46, Glu64, Gln79, Ile83, Lys84, Pro85, Arg82, His86, Asp63, Glu67, as described in SEQ ID NOs: 6-10. In some cases, the one or more anti-VEGF-A aptamers may bind to the receptor binding domain of VEGF-A, or a portion thereof. The receptor binding domain of VEGF-A may include any one or more of residues 1-109, as described in SEQ ID NOs: 6-10. In some cases, the one or more anti-VEGF-A aptamers may prevent or reduce the binding of one or more isoforms or variants of VEGF-A with Flt-1, KDR, or Nrp-1. In some cases, the compositions may include, e.g., an effective amount of the aptamer, alone or in combination, with one or more vehicles (e.g., pharmaceutically acceptable compositions or e.g., pharmaceutically acceptable carriers).
Compositions as described herein may comprise a liquid formulation, a solid formulation or a combination thereof. Non-limiting examples of formulations may include a tablet, a capsule, a gel, a paste, a liquid solution and a cream. The compositions of the present disclosure may further comprise any number of excipients. Excipients may include any and all solvents, coatings, flavorings, colorings, lubricants, disintegrants, preservatives, sweeteners, binders, diluents, and vehicles (or carriers). Generally, the excipient is compatible with the therapeutic compositions of the present disclosure. The pharmaceutical composition may also contain minor amounts of non-toxic auxiliary substances such as wetting or emulsifying agents, pH buffering agents, and other substances such as, for example, sodium acetate, and triethanolamine oleate.
Therapeutic doses of formulations of the disclosure can be administered to a subject in need thereof. In some cases, a formulation is administered to the eye of a subject for the treatment of an ocular disease as described herein. Administration to the eye can be; a) local ocular delivery; or b) systemic. A topical formulation can be applied directly to the eye (e.g., eye drops, contact lens loaded with the formulation) or to the eyelid (e.g., cream, lotion, gel). In some cases, topical administration can be to a site remote from the eye, for example, to the skin of an extremity. This form of administration may be suitable for targets that are not produced directly by the eye. In some cases, a formulation of the disclosure is administered by local ocular delivery. Non-limiting examples of local ocular delivery include intravitreal (IVT), intracamarel, subconjunctival, subtenon, retrobulbar, posterior juxtascleral, and peribulbar. In some cases, a formulation of the disclosure is delivered by intravitreal administration (IVT). Local ocular delivery may generally involve injection of a liquid formulation. In other cases, a formulation of the disclosure is administered systemically. Systemic administration can involve oral administration. In some cases, systemic administration can be intravenous administration, subcutaneous administration, infusion, implantation, and the like.
Other formulations suitable for delivery of the pharmaceutical compositions described herein may include a sustained release gel or polymer formulations by surgical implantation of a biodegradable microsize polymer system, e.g., microdevice, microparticle, or sponge, or other slow release transscleral devices, implanted during the treatment of an ophthalmic disease, or by an ocular delivery device, e.g., polymer contact lens sustained delivery device. In some cases, the formulation is a polymer gel, a self-assembling gel, a durable implant, an eluting implant, a biodegradable matrix or biodegradable polymers. In some cases, the formulation may be administered by iontophoresis using electric current to drive the composition from the surface to the posterior of the eye. In some cases, the formulation may be administered by a surgically implanted port with an intravitreal reservoir, an extra-vitreal reservoir or a combination thereof. Examples of implantable ocular devices can include, without limitation, the Durasert™ technology developed by Bausch & Lomb, the ODTx device developed by On Demand Therapeutics, the Port Delivery System developed by ForSight VISION4 and the Replenish MicroPump™ System developed by Replenish, Inc. In some cases, nanotechnologies can be used to deliver the pharmaceutical compositions including nanospheres, nanoparticles, nanocapsules, liposomes, nanomicelles and dendrimers.
A composition of the disclosure can be administered once or more than once each day.
In some cases, the composition is administered as a single dose (i.e., one-time use). In this example, the single dose may be curative. In other cases, the composition may be administered serially (e.g., taken every day without a break for the duration of the treatment regimen). In some cases, the treatment regime can be less than a week, a week, two weeks, three weeks, a month, or greater than a month. In some cases, the composition is administered over a period of at least 12 weeks, at least 16 weeks, at least 20 weeks, or at least 24 weeks. In other cases, the composition is administered for a day, at least two consecutive days, at least three consecutive days, at least four consecutive days, at least five consecutive days, at least six consecutive days, at least seven consecutive days, at least eight consecutive days, at least nine consecutive days, at least ten consecutive days, or at least greater than ten consecutive days. In some cases, a therapeutically effective amount can be administered one time per week, two times per week, three times per week, four times per week, five times per week, six times per week, seven times per week, eight times per week, nine times per week, 10 times per week, 11 times per week, 12 times per week, 13 times per week, 14 times per week, 15 times per week, 16 times per week, 17 times per week, 18 times per week, 19 times per week, 20 times per week, 25 times per week, 30 times per week, 35 times per week, 40 times per week, or greater than 40 times per week. In some cases, a therapeutically effective amount can be administered one time per day, two times per day, three times per day, four times per day, five times per day, six times per day, seven times per day, eight times per day, nine times per day, 10 times per day, or greater than 10 times per day. In some cases, the composition is administered at least twice a day. In further cases, the composition is administered at least every hour, at least every two hours, at least every three hours, at least every four hours, at least every five hours, at least every six hours, at least every seven hours, at least every eight hours, at least every nine hours, at least every 10 hours, at least every 11 hours, at least every 12 hours, at least every 13 hours, at least every 14 hours, at least every 15 hours, at least every 16 hours, at least every 17 hours, at least every 18 hours, at least every 19 hours, at least every 20 hours, at least every 21 hours, at least every 22 hours, at least every 23 hours, or at least every day.
Aptamers as described herein may be particularly advantageous over antibodies as they may sustain therapeutic intravitreal concentrations of drug for longer periods of time, thus requiring less frequent administration. The aptamers described herein may have a longer intraocular half-life, and/or sustain therapeutic intravitreal concentrations of drug for longer periods of time than an anti-VEGF-A antibody therapy and can be dosed less frequently. In some cases, the aptamers of the disclosure are dosed at least once every 4 weeks (q4w), once every 5 weeks (q5w), once every 6 weeks (q6w), once every 7 weeks (q7w), once every 8 weeks (q8w), once every 9 weeks (q9w), once every 10 weeks (q10w), once every 11 weeks (q11w) once every 12 weeks (q12w), once every 13 weeks (q13w), once every 14 weeks (q14w), once every 15 weeks (q15w), once every 16 weeks (q16w), once every 17 weeks (q17w), once every 18 weeks (q18w), once every 19 weeks (q19w), once every 20 weeks (q20w), once every 21 weeks (q21w), once every 22 weeks (q22w), once every 23 weeks (q23w), once every 24 weeks (q24w), or greater than once every 24 weeks.
In some aspects, a therapeutically effective amount of the aptamer may be administered. A “therapeutically effective amount” or “therapeutically effective dose” are used interchangeably herein and refer to an amount of a therapeutic agent (e.g., an aptamer) that provokes a therapeutic or desired response in a subject. The therapeutically effective amount of the composition may be dependent on the route of administration. In the case of systemic administration, a therapeutically effective amount may be about 10 mg/kg to about 100 mg/kg. In some cases, a therapeutically effective amount may be about 10 μg/kg to about 1000 μg/kg for systemic administration. For intravitreal administration, a therapeutically effective amount can be about 0.01 mg to about 150 mg in about 25 μl to about 100 μl volume per eye.
Disclosed herein are methods for the treatment of ocular diseases or disorders. In some cases, the ocular disease or disorder may be diabetic retinopathy. In some cases, the ocular disease or disorder may be retinopathy of prematurity. In some cases, the ocular disease or disorder may be central retinal vein occlusion. In some cases, the ocular disease or disorder may be macular edema. In some cases, the ocular disease or disorder may be choroidal neovascularization. In some cases, the ocular disease or disorder may be neovascular (or wet) age-related macular degeneration. In some cases, the ocular disease or disorder may be myopic choroidal neovascularization. In some cases, the ocular disease or disorder may be punctate inner choroidopathy. In some cases, the ocular disease or disorder may be presumed ocular histoplasmosis syndrome. In some cases, the ocular disease or disorder may be familial exudative vitreoretinopathy. In some cases, the ocular disease or disorder may be retinoblastoma. In some cases, the ocular disease or disorder may exhibit elevated levels of one or more isoforms or variants of VEGF-A.
In some cases, the method involves administering a therapeutically effective amount of a composition to a subject to treat an ocular disease. In some cases, the composition includes one or more aptamers as described herein. The aptamers may bind to and inhibit a function associated with one or more isoforms or variants of VEGF-A as described herein. The methods can be performed at a hospital or a clinic, for example, the pharmaceutical compositions can be administered by a health-care professional. In other cases, the pharmaceutical compositions can be self-administered by the subject. Treatment may commence with the diagnosis of a subject with an ocular disease. In the event that further treatments are necessary, follow-up appointments may be scheduled for the administration of subsequent doses of the composition, for example, administration every 8, 12, 16, 20, or 24 weeks.
Further disclosed herein are methods of using an anti-VEGF-A composition of the disclosure to inhibit a function associated with VEGF-A. For example, the methods may involve administering a composition of the disclosure, including one or more anti-VEGF-A aptamers, to a biological system (e.g., biological cells, biological tissue, a subject) to inhibit a function associated with VEGF-A. In some cases, the anti-VEGF-A aptamers may bind to the receptor binding face of VEGF-A, or portions thereof. In some cases, the anti-VEGF-A aptamers may bind to the receptor binding domain of VEGF-A. In some cases, the methods may be used to prevent or reduce binding of VEGF-A to Flt-1, KDR, Nrp-1, or any combination thereof. In some cases, the methods may be used to inhibit downstream signaling pathways associated with VEGF-A.
The aptamers described herein can be generated by any method suitable for generating aptamers. In some cases, the aptamers described herein are generated by a process known as Systematic Evolution of Ligands by Exponential Enrichment” (“SELEX™”). The SELEX™ process is described in, e.g., U.S. patent application Ser. No. 07/536,428, filed Jun. 11, 1990, now abandoned, U.S. Pat. No. 5,475,096 entitled “Nucleic Acid Ligands”, and U.S. Pat. No. 5,270,163 (see, also WO 91/19813) entitled “Nucleic Acid Ligands”, each of which are herein incorporated by reference. By performing iterative cycles of selection and amplification, SELEX™ may be used to obtain aptamers with any desired level of target binding affinity.
The SELEX™ method generally relies as a starting point upon a large library or pool of single stranded oligonucleotides comprising randomized sequences. The oligonucleotides can be modified or unmodified DNA, RNA, or DNA/RNA hybrids. In some examples, the pool comprises 100% random or partially random oligonucleotides. In other examples, the pool comprises random or partially random oligonucleotides containing at least one fixed sequence and/or conserved sequence incorporated within randomized sequence. In other examples, the pool comprises random or partially random oligonucleotides containing at least one fixed sequence and/or conserved sequence at its 5′ and/or 3′ end which may comprise a sequence shared by all the molecules of the oligonucleotide pool. Fixed sequences are sequences common to oligonucleotides in the pool which are incorporated for a preselected purpose such as, CpG motifs, hybridization sites for PCR primers, promoter sequences for RNA polymerases (e.g., T3, T4, T7, and SP6), sequences to form stems to present the randomized region of the library within a defined terminal stem structure, restriction sites, or homopolymeric sequences, such as poly A or poly T tracts, catalytic cores, sites for selective binding to affinity columns, and other sequences to facilitate cloning and/or sequencing of an oligonucleotide of interest. Conserved sequences are sequences, other than the previously described fixed sequences, shared by a number of aptamers that bind to the same target.
The oligonucleotides of the pool can include a randomized sequence portion as well as fixed sequences necessary for efficient amplification. Typically the oligonucleotides of the starting pool contain fixed 5′ and 3′ terminal sequences which flank an internal region of 30-50 random nucleotides. The randomized nucleotides can be produced in a number of ways including chemical synthesis and size selection from randomly cleaved cellular nucleic acids. Sequence variation in test nucleic acids can also be introduced or increased by mutagenesis before or during the selection/amplification iterations.
The random sequence portion of the oligonucleotide can be of any length and can comprise ribonucleotides and/or deoxyribonucleotides and can include modified or non-natural nucleotides or nucleotide analogs. Typical syntheses carried out on automated DNA synthesis equipment yield 1014-1016 individual molecules, a number sufficient for most SELEX™ experiments. Sufficiently large regions of random sequence in the sequence design increases the likelihood that each synthesized molecule is likely to represent a unique sequence.
The starting library of oligonucleotides may be generated by automated chemical synthesis on a DNA synthesizer. To synthesize randomized sequences, mixtures of all four nucleotides are added at each nucleotide addition step during the synthesis process, allowing for random incorporation of nucleotides. As stated above, in some cases, random oligonucleotides comprise entirely random sequences; however, in other cases, random oligonucleotides can comprise stretches of nonrandom or partially random sequences. Partially random sequences can be created by adding the four nucleotides in different molar ratios at each addition step.
The starting library of oligonucleotides may be RNA, DNA, substituted RNA or DNA or combinations thereof. In those instances where an RNA library is to be used as the starting library it is typically generated by synthesizing a DNA library, optionally PCR amplifying, then transcribing the DNA library in vitro using phage RNA polymerase or modified phage RNA polymerases, and purifying the transcribed library. The nucleic acid library is then mixed with the target under conditions favorable for binding and subjected to step-wise iterations of binding, partitioning and amplification, using the same general selection scheme, to achieve virtually any desired criterion of binding affinity and selectivity. More specifically, starting with a mixture containing the starting pool of nucleic acids, the SELEX™ method includes steps of: (a) contacting the mixture with the target under conditions favorable for binding; (b) partitioning unbound nucleic acids from those nucleic acids which have bound specifically to target molecules; (c) dissociating the nucleic acid-target complexes; (d) amplifying the nucleic acids dissociated from the nucleic acid-target complexes to yield a ligand-enriched mixture of nucleic acids; and (e) reiterating the steps of binding, partitioning, dissociating and amplifying through as many cycles as desired to yield highly specific, high affinity nucleic acid ligands to the target molecule. In those instances where RNA aptamers are being selected, the SELEX™ method further comprises the steps of: (i) reverse transcribing the nucleic acids dissociated from the nucleic acid-target complexes before amplification in step (d); and (ii) transcribing the amplified nucleic acids from step (d) before restarting the process.
Within a nucleic acid mixture containing a large number of possible sequences and structures, there is a wide range of binding affinities for a given target. Those which have the higher affinity (lower dissociation constants) for the target are most likely to bind to the target. After partitioning, dissociation and amplification, a second nucleic acid mixture is generated, enriched for the higher binding affinity candidates. Additional rounds of selection progressively favor the best ligands until the resulting nucleic acid mixture is predominantly composed of only one or a few sequences. These can then be cloned, sequenced and individually tested as ligands or aptamers for 1) target binding affinity; and 2) ability to effect target function.
Cycles of selection and amplification are repeated until a desired goal is achieved. In the most general case, selection/amplification is continued until no significant improvement in binding strength is achieved on repetition of the cycle. The method is typically used to sample approximately 1014 different nucleic acid species but may be used to sample as many as about 1018 different nucleic acid species. Generally, nucleic acid aptamer molecules are selected in a 3 to 20 cycle procedure.
In some cases, the aptamers of the disclosure are generated using the SELEX™ method as described above. In other cases, the aptamers of the disclosure are generated using any modification or variant of the SELEX™ method.
Further provided herein are methods for generating and screening pan-variant specific anti-VEGF-A aptamers. In some cases, the pan-variant specific aptamers bind to the receptor binding face of VEGF-A, or the receptor binding domain of VEGF-A. Generally, the methods provided herein bias the selection process towards aptamers that selectively bind to the receptor binding face or receptor binding domain of VEGF-A. In some cases, such aptamers do not bind to the heparin binding domain of VEGF-A. In various aspects, the methods may involve incubating an aptamer library with an isoform or variant of VEGF-A which contains a receptor binding domain but does not contain a heparin binding domain. In some cases, the isoform or variant of VEGF-A is VEGF-A121 or VEGF-A110. In various aspects, the methods involve immobilizing the VEGF-A variant on a solid support in a manner that does not preclude access of the library to the receptor binding face or receptor binding domain of VEGF-A. In various aspects, the methods involve performing the selection in the absence of Ca++
In various aspects, methods for screening pan-variant specific anti-VEGF-A aptamers are provided. In some cases, the methods may involve measuring the interaction of a candidate aptamers with recombinant bead-bound VEGF-A165, VEGF-A121, or VEGF-A110 by flow cytometry (see Example 1). In such cases, interaction with each isoform or variant would indicate binding to the receptor binding domain, while only binding to VEGF-A165 would indicate recognition of the heparin binding domain. In some cases, the methods may involve measuring the ability of the candidate aptamer to inhibit or reduce the interaction of VEGF-A165, VEGF-A121, or VEGF-A110 with KDR by a reduction in FRET signal (see Example 3). In such cases, efficacy against each variant would indicate binding to the receptor binding domain, while only inhibiting VEGF-A165 would indicate binding to the heparin binding domain. In some cases, the methods may involve measuring the ability of the candidate aptamer to inhibit or reduce VEGF-A165, VEGF-A121, or VEGF-A110 induced trans autophosphorylation of the intracellular domain of KDR by phospho-KDR AlphaLISA® (see Example 4). In such cases, efficacy against each variant would indicate binding to the receptor binding domain, while only inhibiting VEGF165 would indicate binding to the heparin binding domain. In some cases, the methods may involve measuring the ability of the candidate aptamer to inhibit or reduce VEGF-A165, VEGF-A121, or VEGF-A110 induced gene expression of tissue factor in HUVEC cells as measured by qPCR. In such cases, efficacy against each variant would indicate binding to the receptor binding domain, while only inhibiting VEGF165 would indicate binding to the heparin binding domain. In some cases, the methods may involve measuring the ability of the candidate aptamer to inhibit or reduce VEGF-A165, VEGF-A121, or VEGF-A110 induced tube formation of GFP-HUVECs in co-culture with human dermal fibroblasts cells by change in network length or network area (see Example 5). In such cases, efficacy against each variant would indicate binding to the receptor binding domain, while only inhibiting VEGF-A165 would indicate binding to the heparin binding domain. In some cases, the methods may involve measuring the ability of the candidate aptamer to inhibit or reduce vascular leakage in a mouse, rat, rabbit, or primate eye following exogenous VEGF-A165, VEGF-A121, or VEGF-A110 challenge by fluorescein angiography and Evans-blue albumin staining. In such cases, efficacy against each VEGF isoform or variant would indicate binding to the receptor binding domain, while only inhibiting VEGF-A165 would indicate binding to the heparin binding domain.
The following examples are given for the purpose of illustrating various embodiments of the invention and are not meant to limit the present invention in any fashion. The present examples, along with the methods described herein are presently representative of preferred embodiments, are exemplary, and are not intended as limitations on the scope of the invention.
Changes therein and other uses which are encompassed within the spirit of the invention as defined by the scope of the claims will occur to those skilled in the art.
Anti-VEGF-A (VEGF) aptamers targeting the receptor binding domain (RBD) were identified using an N30 library (N30S) comprised of a 30-nucleotide random region flanked by constant regions containing a built-in stem region as depicted in
The library sequence (underlined sequences represent the built-in stem) and the sequence of oligos used to amplify the library are described in Table 2.
GGCGGCTTTGATACTTGATCGCCCTAGAAGC
The starting library was transcribed from a pool of ˜1014 double-stranded DNA (dsDNA) molecules. The dsDNA library was generated by primer extension using Klenow exo(−) DNA polymerase, the pool forward primer (N30S.F; SEQ ID NO: 429) and synthetic single-stranded DNA (ssDNA) molecules encoding the reverse complement of the library. The dsDNA was subsequently converted to 100% backbone modified RNA via transcription using a mixture of 2′F GTP, 2′OMe ATP/CTP/UTP and a modified phage polymerase in buffer optimized to facilitate efficient transcription. Following transcription, RNAs were treated with DNAse to remove the template dsDNA and purified.
In order to isolate pan-specific aptamer inhibitors of VEGF-A that bind to the RBD and inhibit VEGF-A via directly blocking its interaction with its receptor, KDR (also known as VEGFR-2), and avoid the identification of anti-VEGF-A aptamers that bound exclusively to the heparin binding domain (HBD) of the protein, aptamer selections were performed using a combination of the 121 and 110 variants of VEGF-A (VEGF-A121 or VEGF-A110). Both of these variants lack the HBD but possess the RBD and therefore maintain high affinity for the target receptor, KDR.
Aptamer selection was facilitated by the use of biotin-tagged recombinant human VEGF-A121 or VEGF-A110. To ensure the biotin tag did not interfere with the availability of desired epitopes within the RBD during the selection, biotin was chemically conjugated to the terminal sugars on the glycan. These VEGF-A monomers bear a single N-linked glycosylation site on Asn74, which is located in the center of the RBD, distal to the receptor binding face, making this an ideal site for target immobilization. In brief, VEGF-A glycans were oxidized with 100 μM sodium periodate for 30 minutes, and excess periodate was quenched with 1 mM glycerol. 1 mM biotin-PEG12-alkoxyamine and 10 mM anthranilic acid final were added to the reaction and allowed to incubate for another 2 hours. Reactions were cleaned up by membrane filtration using a 10 kDa cutoff filter.
Biotinylated VEGF-A variants were immobilized on magnetic streptavidin capture beads (Dynal, Strepavidin MyOne™) at a constant ratio of 1 μL beads per 1 μg protein. Briefly, beads were washed three times with binding buffer SB1T(−) (40 mM HEPES, pH 7.5, 125 mM NaCl, 5 mM KCl, 1 mM MgCl2, 0.05% Tween-20) and were resuspended in 50 μL of recombinant VEGF-A in SB1T(−) and incubated at room temperature for 30 minutes. The beads were subsequently blocked with excess biotin for 10 minutes. The amount of target protein varied with each round (Table 3). The beads were washed three times with SB1T(−) buffer to remove any unbound protein.
For the first round of selection, ˜1 nanomole of the Round 0 RNA pool, ˜3× coverage for 2×104 sequences, was used. Prior to each round, the library was thermally equilibrated by heating at 90° C. for 3 minutes and cooled at room temperature for 15 minutes in the presence of a 1.5-fold molar excess of reverse primer (N30S.R; SEQ ID NO: 430) to allow the library to refold. Following renaturation, the final volume of the reaction was adjusted to 50 μL in SB1T(−) supplemented with 1 μg/ml ssDNA and 0.1% BSA.
For the first round, the library was added to VEGF-A110 immobilized on beads and incubated at 37° C. for 30 minutes on a tube rotary. After 30 minutes, the beads were washed three times using 0.5 mL SB1T(−) buffer to remove unbound aptamers. After washing, VEGF-A110-bound aptamers were eluted using 200 μL elution buffer (2M Guanidine-HCl in SB1 T(−) buffer) two times (total volume 400 μL). The eluted aptamers, in 400 μL of elution buffer, were ethanol precipitated. The recovered library was converted to DNA by reverse transcription using Super Script IV reverse transcriptase, and the ssDNA was subsequently amplified by PCR. The resulting dsDNA library was subsequently converted back into modified RNA via transcription as described above. DNased, purified RNA was used for subsequent rounds.
Following the first round, a negative selection step was included in all the subsequent rounds. For the negative selection, the pool was prepared as described before and first incubated with biotin saturated beads (in the absence of target protein) for 30 minutes at 37° C. in SB1T(−) buffer. The beads were pelleted and the supernatant, containing molecules that did not bind to the beads, was incubated with VEGF-A-labeled beads for an additional 30 minutes at 37° C. For rounds 2-4, the input RNA was kept fixed at 25 picomoles, and the protein target was fixed at 0.5 μg.
For rounds 5-7, the target was varied between VEGF-A121 and VEGF-A110 and a solution capture method was implemented. Negative selections were implemented as described above, and positive selection involved incubation with biotinylated target without the presence of beads for 30 minutes at 37° C. For capture, 2 μL of streptavidin beads were washed with 0.5 mL of SB1T(−) and the positive selection was used to re-suspend the bead pellet. After a 5 minute incubation, the beads were washed according to Table 3 prior to elution and precipitation as described above.
Flow cytometry was used to assess the progress of the selection. For these assays, RNA from each round was first hybridized with reverse complement oligonucleotide composed of 2′OMe RNA labeled with Dylight® 650 (Dy650-N30S.R.OMe, sequence identical to N30S.R). Briefly, the library was combined with a 1.5-fold molar excess of Dy650-N30S.R.OMe, heated at 90° C. for 3 minutes and allowed to cool at room temperature for 15 minutes, after which it was incubated with unlabeled “Negative” beads or beads labelled with VEGF-A121 in SB1T(−) buffer supplemented with 0.1% BSA and 1 mg/mL ssDNA final. Following incubation for 30 minutes at 37° C., the beads were washed 3 times with SB1T(−), re-suspended in SB1T(−) buffer, and analyzed by flow cytometry. As shown in
The enriched aptamer population from Round 7 was cloned into a TOPO TA vector, transformed into competent cells, and sequenced by Sanger sequencing. All in silico analyses were performed using Geneious software (Biomatters Inc., Newark N.J., USA). Of the 45 sequences identified, 10 were unique and all fell into a single family with one sequence representing 32 identical reads. The dominant sequence, Aptamer 4.2 (r7-01) was chemically synthesized with 2′-fluoro-G and 2′-O-methyl (2′OMe) A/C/U modified phosphoramidites along with a 3′ inverted deoxythymidine and a 5′ C6 disulfide linker, which was conjugated to Dylight® 650 maleimide (Table 4). The aptamer was purified by reversed phase high-performance liquid chromatography (HPLC) and assayed for activity in the flow cytometry assay described above. A dose response against beads bearing VEGF-A121 or VEGF-A165 demonstrated that Aptamer 4.2 was capable of binding to both isoforms (
In order to gain deeper insight to the progression of the selection, the enriched libraries from Rounds 3-6 were sequenced using next-generation sequencing (NGS) to identify individual functional clones. Data from greater than 100,000 individual sequences per round were processed by trimming the flanking constant regions from the library. Aptamers with identical sequences were de-duplicated into stacks and annotated with frequency. Stacks were ranked by frequency within the libraries and organized into families by clustering aptamers with similar sequence relatedness using the MAFFT alignment algorithm. To a first approximation, the number of times a sequence occurs in a stack directly correlates with its molecular function; more functional molecules typically occur more times. Thus, the rank order of each stack can be thought of as a proxy for fitness. From an analysis of Rounds 5 and 6, clones related to r7-01 were selected for testing, chemically synthesized with 2′-fluoro-G and 2′-O-methyl (2′OMe) A/C/U modified phosphoramidites, purified by reversed phase HPLC, and desalted into nuclease-free H2O via buffer exchange before further analysis (Table 5).
Aptamer function was determined by assessing the ability to inhibit VEGF-A165 and VEGF-A121 induced KDR phosphorylation using a cell-based assay described in detail in Example 3. Of the 7 compounds assayed, 5 were able to inhibit KDR phosphorylation by both VEGF-A165 and VEGF-A121 (Table 5).
To measure binding affinity of the identified aptamer and confirm its pan-specific binding to VEGF-A variants described in Example 1, SPR experiments were conducted against VEGF-A165, VEGF-A121, and VEGF-A110 with Aptamer 26 (Table 5) as compared to a previously described HBD binding aptamer, Aptamer 7 (Table 6) (Ruckman, 1998). Aptamer 26 was identical in sequence to Aptamer 4.2 but contained a hexylamine linker in place of the C6 disulfide linker at the 5′ terminus. Aptamer 7 has been demonstrated to bind directly to the HBD of VEGF-A at an epitope overlapping the binding site of the VEGF-A165 co-receptor neuropilin-1 (Ruckman et al. 1998). Briefly, in the SPR studies, 1.0-2.5 μg/mL of glycan biotinylated VEGF-A165, VEGF-A121, and VEGF-A110 were diluted in HEPES running buffer (10 mM HEPES, 137.5 mM NaCl, 5.7 mM KCl, 1 mM MgCl2, 1 mM CaCl2, and 0.05% Tween20; pH 7.4) and immobilized to a streptavidin dextran chip (GE Healthcare Life Sciences) for 1-2 minutes. The chip was then blocked with 0.2 mg/mL biotin in running buffer, followed by 3 cycles of buffer blanks and regenerated with 50 mM NaOH to equilibrate the chip. This resulted in 200-3000 RIU immobilized. After coating and blocking, samples were screened at 100 nM in duplicate injections at a flow rate of 25 μL/min, with an association time of 3 minutes 20 seconds and a dissociation time of 10 minutes. Regeneration conditions of chips were optimized based on the protein immobilized and effected with either 50 mM NaOH for 30 seconds or 2M guanidine HCl for 2×40 seconds. To determine binding affinities, aptamers were subsequently run in an 11-point, 2-fold dose response with Aptamer 26 starting at a top concentration of 1.0 μM, and Aptamer 7 starting at 500 nM.
Data was fit to a 1:1 kinetic binding model. Binding affinities were calculated based on these fits and are shown in Table 7. Results of the assay demonstrate that Aptamer 26 bound to all three variants of VEGF-A tested, whereas, consistent with the literature, Aptamer 7 only bound to VEGF-A165. The affinity for Aptamer 7 to VEGF-A165 as determined here was consistent with the literature reported value (Ruckman et al. 1998). This result provided further evidence that the selection effectively identified pan-specific anti-VEGF-A aptamers, which recognized an epitope of VEGF-A contained within the RBD. This differentiated the aptamers identified in the selection described herein from previously described aptamers to VEGF-A, such as Aptamer 7, which recognize an epitope of VEGF-A contained within the HBD, and thus do not bind the non-HBD bearing variants VEGF-A110 and VEGF-A121.
The SPR data in Example 2 demonstrated that Aptamer 26 bound to the RBD of VEGF-A. To further define the epitope within the RBD of VEGF-A recognized by Aptamer 26, the mechanism of action of Aptamer 26 was interrogated by testing the ability of Aptamer 26 to directly inhibit KDR binding to either VEGF-A165 or VEGF-A121 as compared to a clone of an anti-VEGF-A antibody (Ferrara 2004 b) known to bind an epitope contained in the RBD that defines the receptor binding face of VEGF-A (SEQ ID NO: 432 and SEQ ID NO: 433, shown in Table 8), and as compared to Aptamer 7.
Briefly, the aptamers were heated at 90° C. for 3 minutes and allowed to cool to room temperature for a minimum of 10 minutes. Aptamers and anti-VEGF-A antibody were serial diluted in a polypropylene plate and 5 μL was transferred to a white low volume 384 well Optiplate (Perkin Elmer). A solution of VEGF-A165 (Acro BioSystems) or VEGF-A121 (Acro BioSystems) that was glycan biotinylated was prepared and added to the assay plate containing aptamers or anti-VEGF-A antibody to yield a final assay concentration of 2 nM. A mixture of human recombinant his-tagged KDR, (Sino Biological), AlphaLISA® nickel chelate acceptor beads (Perkin Elmer), and AlphaScreen® streptavidin donor beads (Perkin Elmer) was then prepared and 10 μL was added to the assay plate. The final concentrations of KDR and beads were 5 nM and 5 ug/mL, respectively. The assay plate was sealed and incubated in the dark for approximately 2 hours, after which it was read on a Biotek CYTATION™ 5 plate reader using the Alpha 384 well optical cube. The low signal control was determined using excess anti-VEGF-A inhibitor and the high signal control was determined by buffer only.
Percent inhibition for each sample was calculated by the following formula:
% inhibition=1−(sample−low control)/(high control−low control)*100
The values were fit by using a four-parameter non-linear fit in GraphPad Prism Version 7.0.
The results (
The data presented in
When the RBD of VEGF-A binds to KDR, the receptor dimerizes leading to trans-autophosphorylation and activation of VEGF-A signaling. To determine if Aptamer 26 binding to the RBD of VEGF-A resulted in inhibition of VEGF-A activity, Aptamer 26 was tested for its ability to inhibit KDR phosphorylation induced by either VEGF-A165 or VEGF-A121 as compared to a clone of an anti-VEGF-A antibody (Ferrara 2004 b) (SEQ ID NO: 432 and SEQ ID NO: 433, shown in Table 8), and as compared to Aptamer 7 for inhibition of VEGF-A165-induced KDR phosphorylation.
Briefly, HEK293 cells engineered to stably overexpress KDR were plated overnight in collagen coated 96 well plates at 50 k cells/well. Aptamers in SB1+ (40 mM HEPES, pH 7.5, 125 mM NaCl, 5 mM KCl, 1 mM MgCl2) were heated to 90° C. for 3 minutes and allowed to cool to room temperature for a minimum of 10 minutes. VEGF-A121 (Biolegend) and VEGF-A165 (R&D Systems) were prepared at 12.5 nM in DMEM+0.8% FBS, a 20× stock for the reaction. 15 μL of VEGF-A was added to 15 μL titrated aptamer in a polypropylene plate and diluted to 300 μL with TS buffer (10 mM Tris pH 7.5; 100 mM NaCl; 5.7 mM KCl; 1 mM MgCl2; 1 mM CaCl2). The aptamer/VEGF-A mixture was incubated at 37° C. for 30 minutes, after which 100 μL was added to the cells for 5 minutes at 37° C. in 5% CO2. Treatments were aspirated from cells, and cells were lysed with 100 μL cold lysis buffer [20 mM Tris-HCl, pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.5 mM sodium orthovanadate (freshly prepared), 1 mM PMSF (freshly prepared), lx protease inhibitor cocktail (freshly prepared)] on ice for 10 minutes. Plates were centrifuged at 4000×g for 10 minutes before transferring the cell lysis to the AlphaLISA® assay plate.
To perform the AlphaLISA® assay, 10 μL of cell lysis was transferred to a white low volume 384 well Optiplate (Perkin Elmer). A mixture of the following components was made in order of which they are listed: 1.25 nM anti-hVEGFR2 polyclonal goat IgG antibody (R&D Systems), 10 μg/ml AlphaLISA® anti-goat IgG acceptor beads (Perkin Elmer), 1.25 nM P-tyrosine biotinylated mouse mAb (Cell Signaling Technology), and 10 μg/ml AlphaScreen® streptavidin donor beads (Perkin Elmer). 10 μL of this reagent mixture was added to the assay plate that contained 10 μL of cell lysate. The assay plate was sealed and incubated in the dark for approximately 2 hours, then was read on a Biotek CYTATION™ 5 plate reader using the Alpha 384 well optical cube. Percent inhibition was calculated by subtracting TS buffer background from each value and normalizing to VEGF-A only controls. The values were fit by using a four-parameter non-linear fit in GraphPad Prism Version 7.0.
The results demonstrated that Aptamer 26 and the anti-VEGF-A mAb achieved full inhibition of the phosphorylation of KDR by inhibiting its interaction with VEGF-A165 or VEGF-A121 (
The potency and complete inhibition of VEGF-A165 or VEGF-A121 induced phosphorylation of KDR by Aptamer 26, and its comparable activity profile to an anti-VEGF-A mAb, was consistent with the ability of Aptamer 26 to bind to the receptor binding face present within the RBD of VEGF-A and directly block the interaction between VEGF-A and KDR. The partial inhibition of VEGF-A165-induced phosphorylation of KDR by Aptamer 7 was consistent with indirect inhibition of KDR phosphorylation via blocking the interaction of neuropilin-1 with VEGF-A165 (Soker, 1998). This result supported the conclusion that binding of Aptamer 26 to the receptor binding face within the RBD of VEGF-A variants confers inhibition of VEGF-A signaling. Further, these results differentiated the mechanism of action of Aptamer 26 from previously described HBD binding aptamers such as Aptamer 7.
To further define the secondary structure of the active aptamer, as well as to potentially identify VEGF-A aptamers with increased potency, secondary selections were performed utilizing a partially randomized library based on Aptamer 26 (85% of the parental sequence+5% of the other three nucleotides at each position within the aptamer). The library sequence and the sequence of oligos used to amplify the library are described in Table 9.
AGGCCGCCTCCGCGCGGAGGGGTTTCATTATCCC
GTTTGGCGGCTT-TGATACTTGATCGCCCTAGAAGC
Six rounds of selection were conducted against VEGF-A110. The progress of the selection was monitored by flow cytometry to ensure the enrichment for function (data not shown).
Library DNA from Round 1 through Round 6 were barcoded, pooled, and sequenced on a MiniSeq high throughput sequencer (Illumina), which yielded approximately 400,000 sequences per round. Sequences were trimmed to remove constant regions from the 5′ and 3′ ends, leaving the core 30 nucleotide region from the library and the terminal 8 base pair stem.
Identical sequences were de-duplicated to form stacks of identical sequences. The resultant stacks were then rank ordered based on the total number of sequences within each stack. To a first approximation, the number of times a sequence occurs in a stack directly correlates with molecular function: more functional molecules typically occur more times. Thus, the rank order of each stack can be thought of as a proxy for fitness.
Alignment of the top 250 stacks for Aptamer 26, which represented ˜185,000 de-duplicated sequences and corresponded to the top performing˜40% of the selected population from Round 6 of the secondary selection, revealed a significant level of conservation in the identity of each nucleotide within the aptamer family. Most positions displayed conservation levels >90% (
Comparison of the top 250 stacks revealed that the enriched sequences readily adopted a stem loop structure consistent with the secondary structure shown in
A comparison of sequences observed in stem S1 are shown in Table 10. These data provide additional support of the formation of Stem 1, as indicated by the sequence covariation in this region. In some cases, stem S1 contained one, two or three mismatched nucleotides. In some cases, the mismatched nucleotides were adjacent to each other. In some cases, the mismatched nucleotides were separated by one, two, or three base pairs. In some cases, stem S1 was composed of two to eight contiguous base pairs that ended in a base pair at positions 8 and 39. As depicted in
In some cases, stem S1 contained a mismatch at positions 5 and 42, demonstrated by a preference for conversion from G in the parent sequence to a U in approximately 69% of the sequences represented in the top 250 stacks (
UU
GCUGCC/GGCUGCUU
U
GGCCGCC/GGCUGCUU
UU
GCUGCC/GGCGGCUU
C
UGCCGCC/GGCGGCAU
C
UGCUGCC/GGCGGCAU
U
UGCUGCC/GGCUGCAU
U
GUCCGCC/GGCGGCUU
CU
GCAGCC/GGCUGCUU
AGUCCACC/GGUGGCUA
AGUCCGCC/GGCGGCUA
UU
GCCGCC/GGCUGCUU
U
UGCUGCC/GGCCGCAU
UU
GCCGCC/GGCGGCUU
CU
GCCGCC/GGCGGCUU
C
UGCUGCC/GGCUGCAU
The identity of loop L1 was found to be 100% conserved across the top 250 stacks of sequences analyzed in the doped selection (
The identity of stem S2 was found to be 100% conserved across the top 250 stacks of sequences analyzed in the doped selection (
The identity of loop L2 was found to be 100% conserved across the top 250 stacks of sequences analyzed in the doped selection (
The identity of loop L3 was found to be 100% conserved across the top 250 stacks of sequences analyzed in the doped selection (
A comparison of sequences observed in stem S3 suggested that the preferred length of stem S3 was four, five, or six base pairs. When stem S3 was six base pairs in length, the 5′ side of the stem may be seven nucleotides in length. As such, the six base pair stem S3 may contain a single mis-match at the penultimate nucleotide in the 5′ side of the stem. These data provided additional support of the formation of stem S3, as indicated by the sequence covariation in this region (Table 11). The variation between four, five, and six base pairs in stem S3 directly related to the variation of loop L4 between eight, six, four and three nucleotides. When stem S3 was four base pairs in length, loop L4 was eight nucleotides in length. When stem S3 was five base pairs in length, loop L4 was six nucleotides in length. When stem S3 was six base pairs in length, loop L4 was four nucleotides in length. When stem S3 was six base pairs in length and contained a mismatch, loop L4 was three nucleotides in length.
Together, these data suggested that the consensus sequence of stem S3 for all variants observed with the top 250 stacks of Aptamer 26 was 5′-GGGRUD-3′ for the 5′ side of stem S3 and 5′-HWYCCC-3′ for the 3′ side of stem S3, where R is A or U; D is A, G, or U; H is A, C, or U; W is A or U; and Y is C or U. In some cases, when stem S3 was four base pairs, the consensus sequence was 5′-GGGG-3′ for the 5′ side of stem S3 and 5′-CCCC-3′ for the 3′ side of stem S3. In some cases, when stem S3 was 5 base pairs, the consensus sequence was 5′-GGGRU-3′ for the 5′ side of stem S3 and 5′-AYCCC-3′ for the 3′ side, where R is A or G; and Y is C or U. In some cases, when stem S3 was six base pairs, the consensus sequence was 5′-GGGGUD-3′ for the 5′ side of stem S3 and 5′-HAUCCC-3′ for the 3′ side, where D is A, G or U; and H is A, C, or U. In some cases, when stem S3 was six base pairs long and contained a single mis-matched nucleotide, the consensus was 5′-GGGRUUR-3′ for the 5′ side of stem S3 and 5′-UAUCCC-3′ for the 3′ side, where the underlined U is the single mis-matched nucleotide; and R is A or G.
A comparison of sequences observed in loop L4 suggested that the preferred length of loop L4 was eight, six, four, or three nucleotides (Table 12). The variation between eight, six, four and three nucleotides in loop L4 directly related to the variation in the length of stem S3 between four, five, six base pairs, or six base pairs and a single mismatch. Together, these data suggested that when loop L4 was three nucleotides in length, the consensus sequence for loop L4 was 5′-MAU-3′, where M is A or C. When loop L4 was four nucleotides in length, the consensus sequence for loop L4 was 5′-DNAH-3′, where D is A, G or U; H is A, C, or U; and N is A, C, G, or U. In some cases, when loop L4 was six nucleotides in length, the consensus sequence for loop L4 was 5′-UDNDHU-3′, where D is A, G or U; H is A, C, or U; and N is A, C, G, or U. In some cases, when loop L4 was eight nucleotides in length, the consensus sequence for loop L4 was 5′-UUUCAUUU-3′.
ACAU
GCAA
AAU
A comparison of sequences observed in loop L5 suggested that the preferred length of loop L5 was four bases (Table 13). Together, these data suggest the consensus sequence for loop L5 was 5′-GYUU-3′, where Y is C or U.
Using the data from the degenerate selection, the consensus sequence for all sequence variants within the top 250 stacks of the Aptamer 26 family of sequence members was 5′-HNBYHDCC-U-CC-GCGC-GG-A-GGGRUD-DNDH-HWYCCC-GYUU-GKYNKVNW-3′ (SEQ ID NO: 1), where H is A, C, or U; N is A, C, G, or U; B is C, G, or U; Y is C or U; D is A, G, or U; R is A or G; W is A or U; K is G or U; and V is A, C, or G; and is represented with a six base pair stem S3 and a four nucleotide loop L4 in
To better understand the nucleotide dependence and secondary structure of Aptamer 26, variants of the parent aptamer were synthesized in which every position from U9 to U38 was replaced, individually, with a non-nucleotide 3-carbon spacer (SP3; 1,3-propanediol) and assayed for activity using a receptor phosphorylation AlphaLISA® and competition TR-FRET (Table 14 and
Briefly, for competition TR-FRET, 2-fold dilutions of thermally equilibrated aptamers were made in TR-FRET Buffer (50 mM MOPS, pH 7.4, 125 mM NaCl, 5 mM KCl, 50 μM CHAPS, 0.1 mg/mL BSA, 1 mM CaCl2, and 1 mM MgCl2). 5 μL of aptamer or control solution was added to a 15 μL mix of glycan biotinylated VEGF-A21 (5 nM final), ALEXA FLUOR® 647-labeled Aptamer (30 nM final), and Streptavidin-Eu (Perkin Elmer; 2.5 nM final) in a black wall low volume 384 well plate (Greiner). For control, 5 μl of 1000-fold excess of unlabeled parent aptamer or 5 μl TR-FRET buffer alone was added to the mix of ALEXA FLUOR® 647-labeled aptamer, biotin-VEGF-A, and Streptavidin-Eu. The plate was covered with a plate seal and subsequently incubated in the dark for 1 hour at room temperature. The plate was read on a Biotek CYTATION™ 5 plate reader. Samples were excited at 330 nm and fluorescent values were collected at 665 nm. Data analysis was performed by subtracting the background value and plotting as percent inhibition, normalized to baseline in the absence of competitor. The values were fit by [Inhibitor] vs. response-Variable slope (four parameters) using GraphPad Prism Version 7.0 and then normalized to aptamer control to obtain an IC50 relative to parent aptamer. Data is presented as log values of relative IC50.
Consistent with the high level of conservation observed during the degenerate selection (
To better understand the sequence requirements and to confirm the stem structures of the Aptamer 26 family as determined from sequence covariation analysis from the secondary (degenerate) selection, a series of variants that included mutations and deletions to the predicted stems were synthesized and screened. Activity of each of these variants were tested using a time resolved competition TR-FRET assay, as described in Example 7, in which a labeled parent was competed with increasing concentrations of unlabeled variants for binding to VEGF-A121.
Replacing the sequence of stem S1 found in Aptamer 26, 5′-AGGCCGCC/GGCGGCUU-3′, with single base pair A/U or U/A covariations in positions 7/40 and 8/39 (Table 15 and
The identity of stem S2 was found to be 100% conserved during the degenerate selection (
A comparison of sequences observed in stem S3 suggested that the preferred length of stem S3 was four, five, or six base pairs and that the variation between four, five, and six base pairs in stem S3 was directly related to the length of loop L4, which varied between eight, six, and four nucleotides, respectively. To confirm the identity of this stem, the effect of alternate base pairings on aptamer function was assessed. For simplicity, replacements were done in the context of Aptamer 26, which had a five base pair stem S3 and six nucleotides in loop L4.
Replacing the G:C base pair formed between positions 19 and 34 within this stem with any other canonical pairing resulted in a complete loss of activity (>100-fold; Table 15 and
These data, when combined with sequence data observed in the primary and degenerate selections, supported the observation that stem S3 can be four, five or six base pairs in length, but expanded the observation that a four base pair stem S3 can be combined with a six or eight nucleotide loop L4. These data also further expanded the consensus for stem S3. When stem S3 was five base pairs long and loop L4 was six nucleotides in length, the consensus sequence was 5′-SVVVK-3′ for the 5 side of the stem and 5′-MBBBS-3′ for the complementary region of stem S3, where S is G or C; V is A, C, or G; K is G or U; M is A or C; and B is C, G, or U.
To better understand the role of loops in the Aptamer 26 sequence family, residues in loop L1, loop L2, loop L3, loop L4, and loop L5 were replaced with alternate base identities and the effects of substitutions on activity were determined.
During the degenerate selection, the identity of loop L1 (position 9) was a highly conserved U (100%;
The identity of loop L2 was found to be 100% conserved during the degenerate selection (
A comparison of sequences observed in loop L4 suggested that positions 24, 25, and 29 within the loop were not highly conserved and remained equal to the composition of the staring library, ˜85%. Positions 26, 27, and 28, on the other hand, were more conserved (97%, 99%, and 96%, respectively). The identity of loop L4 was explored by deletion analysis to assess if all nucleotides in the position were required for function. To this end, when the nucleotides at positions 24 and 29 were removed, only a modest loss in activity was observed (Aptamer 145; approximately 8-fold). Together with data from the primary and degenerate selections, these data further expand the relationship between stem S3 and loop L4. Stem S3 can be four, five or six base pairs in length. When stem S3 is four base pairs in length, loop L4 may be six or eight nucleotides in length. When stem S3 is five base pairs in length, loop L4 may be four or six nucleotides in length and when stem S3 is six base pairs, loop L4 may be four nucleotides in length. When loop L4 is four nucleotides in length, the consensus sequence for loop L4 may be 5′-DNAH-3′, where D is A, G or U; H is A, C, or U; and N is A, C, G, or U. In some cases, when loop L4 is six nucleotides in length, the consensus sequence for loop L4 may be 5′-UDNDHU-3′, where D is A, G or U; H is A, C, or U; and N is A, C, G, or U. In some cases, when loop L4 is eight nucleotides in length, the consensus sequence for loop L4 may be 5′-UUUCAUUU-3′.
A comparison of sequences observed in loop L5 from the degenerate selection suggested a high degree of conservation for all positions in this domain (
Linker scanning analysis (Table 14 and
To characterize the binding affinities of lead aptamers and an anti-VEGF-A mAb to VEGF-A165 and VEGF-A121, a time resolved FRET (TR-FRET) assay was performed. Briefly, ALEXA FLUOR® 647-labeled aptamers were heated to 90° C. for 3 minutes and cooled to room temperature. Titrations of ALEXA FLUOR® 647-labeled aptamers and ALEXA FLUOR® 647-labeled anti-VEGF-A antibody were made in TR-FRET buffer (50 mM MOPS, pH 7.4, 125 mM NaCl, 5 mM KCl, 50 μM CHAPS, 0.1 mg/mL BSA, 1 mM CaCl2, and 1 mM MgCl2) in a polypropylene plate. 5 μL of aptamers or antibody were transferred to the black wall low volume 384 well assay plate (Greiner), followed by 5 μL glycan biotinylated VEGF-A121 (2.5 nM final), and 5 μL Streptavidin-Eu (Perkin Elmer; 2.5 nM final). The plate was covered with a plate seal and subsequently incubated in the dark for 2 hours at room temperature. The plate was read on a Biotek CYTATION™ 5 plate reader. Samples were excited at 330 nm and fluorescent values were collected at 665 nm.
No protein background fluorescent values were averaged and subtracted from test compounds, with data normalized as a fold change to highest concentrations of aptamers and antibody. These values were fit using a four-parameter non-linear fit in GraphPad Prism Version 7.0. Representative binding affinity curves of Aptamers 26, 47, and 141, compared to the anti-VEGF-A mAb described in Table 8, is shown in
The mechanism of action of lead aptamers was characterized by interrogating their ability to inhibit the VEGF-A:KDR interaction with both VEGF-A165 and VEGF-A121. To do this, Aptamers 26, 47, 141 and a comparator anti-VEGF-A mAb were tested and analyzed by an AlphaLISA® assay, as described in Example 3.
Representative curves of Aptamers 26, 47, 141 and comparator anti-VEGF-A mAb is shown in
The data presented in
When the RBD of VEGF-A binds to KDR, the receptor dimerizes leading to trans-autophosphorylation and activation of VEGF-A signaling. To determine if lead aptamers bound to the RBD of VEGF-A and resulted in inhibition of VEGF-A activity, Aptamers 26, 47, and 141 were tested for their ability to inhibit KDR phosphorylation induced by VEGF-A165 as compared to an anti-VEGF-A antibody. This characterization was performed by a KDR phosphorylation AlphaLISA®, as described in Example 4.
Representative curves of Aptamers 26, 47, 141 and comparator anti-VEGF-A mAb is shown in
VEGF-A plays an important role in inducing angiogenesis in both normal tissues and diseased pathologies (Ferrara, 2004). It is therefore of interest to evaluate potential VEGF-A antagonists in an angiogenesis assay. In vitro models have been established to study VEGF-A-stimulated angiogenesis. These models can therefore be used with the selected aptamers to determine their ability to inhibit angiogenesis via binding to either VEGF-A165 or VEGF-A121 and inhibiting VEGF-A induced signal transduction via KDR activation.
Co-culture of fibroblasts and endothelial cells leads to the formation of tubes after stimulation with either VEGF-A165 or VEGF-A121. Briefly, at Day 0, primary human dermal fibroblasts (ATCC) were plated at 20 k cells/well in 100 μL fibroblast growth media (ATCC) and incubated at room temperature for 1 hour. GFP-infected HUVEC cells (Lonza, infected in-house) were then plated at 10 k cells/well with 100 μL HUVEC growth media (without VEGF-A supplement, PromoCell) and incubated at room temperature for 1 hour. The plate was then placed in the IncuCyte® Zoom (Essen Bioscience) set to the default angiogenesis analysis definition with imaging programmed every 4 hours. After 24 hours of incubation (Day 1), old media was removed and replaced with 150 μL/well of IncuCyte® Angiogenesis Prime Kit Optimized Assay Medium (Essen Bioscience). After 24 hours (Day 2), media was changed with fresh media with or without treatment. Treatment included 400 μM VEGF-A165 or 800 pM VEGF-A121 premixed with or without a dilution of aptamer or the anti-VEGF-A mAb. Assays were carried out for 6 days with media changes and subsequent treatments performed on Days 4 and 6.
Network length (mm/mm3) of the tubes formed from the GFP-HUVEC cells was measured as a primary indication of angiogenesis. Percent inhibition was calculated by subtracting assay media background from each value and normalizing to VEGF-A only controls. The values were fit using a four-parameter non-linear fit in GraphPad Prism Version 7.0. IC50 values for VEGF-A165 and VEGF-A121 were calculated at a time point that reflected an EC90-EC100 of the VEGF-A alone induction of tube formation. Representative dose response curves of Aptamers 26, 47, and 141, compared to the anti-VEGF-A mAb described in Table 8, are shown in
2′OMe modifications are known to impart higher duplex stability and have greater coupling efficiency during synthesis compared to 2′F-containing nucleotides. The use of these nucleotides also avoids the potential loss of the 2′F group, which can happen in production during the deprotection step and during exposure to heat. The effect of 2′F-G to 2′OMe-G substitution on target binding was probed, using Aptamer 141, an improved variant of Aptamer 26 that contained a non-nucleotidyl spacer 3 modification, and an A:U base pair at positions 7 and 40 within stem S1.
Starting at position 6, 2′F-G residues were systematically replaced, one at a time, and the activity of the resultant molecule was assessed by competition TR-FRET, as described in Example 7, against the parent molecule, Aptamer 141. As shown in Table 18 and
In addition, an initial attempt at truncating stem S1 of Aptamer 141 to six base pairs resulted in a ˜2-fold increase in activity (Aptamer 199). In the context of Aptamer 199, the replacement of the terminal 2′F-G residues outside of the region systematically examined by Aptamers 188-198 was tested. As shown in Table 18 and
In summary, 2′OMe-G substitution was tolerated at numerous positions throughout the molecule and was particularly well tolerated in all of the positions within stem S1 as well as positions 12, 22, and 39 (Aptamers 189, 196, and 198).
To further probe the relationship between 2′F-G to 2′OMe-G replacement and aptamer length, a series of constructs bearing stem S1 lengths of six, five, four, three, two, and one nucleotide were synthesized and the combinatorial effect of 2′F-G to 2′OMe-G replacements that were previously observed to be permissible were explored (Table 19 and
Aptamer 234, a 2′OMe-G bearing variant of Aptamer 141 with a four base pair stem S1, was used to further explore the effects of various stem S3/loop L4 mutations identified in the degenerate selection on aptamer function. The proposed effect of these substitutions on the stem/loop structure are illustrated in
These data further highlighted the relationship between stem S3 and loop L4. When combined with sequence data observed in the primary and degenerate selections, these data further supported the observation that stem S3 could be four, five, or six base pairs in length. When stem S3 is six base pairs in length, it may contain a single mis-match at the penultimate nucleotide in the 5′ side of the stem. When stem S3 is four base pairs in length, loop L4 may be six or eight nucleotides in length. When stem S3 is five base pairs in length, loop L4 may be four or six nucleotides in length and when stem S3 is six base pairs, loop L4 may be four nucleotides in length. When stem S3 is six base pairs long and contains a single mis-matched nucleotide, the length of loop L4 may be three nucleotides in length.
Together these data expand the consensus sequence of stem S3 for all of the variants observed or tested for Aptamer 26. Stem S3 may be expanded to 5′-GGGRUN3′ for the 5′ side of stem S3 and 5′-NWYCCC-3′ for the 3′ side of stem S3, where R is A or G; N is A, C, G, or U; W is A or U; and Y is C or U. When stem S3 is four base pairs, the consensus sequence may be 5′-GGGG-3′ for the 5′ side of stem S3 and 5′-CCCC-3′ for the 3′ side of stem S3. In some cases, when stem S3 is five base pairs, the consensus sequence may be 5′-GGGRU-3′ for the 5′ side of stem S3 and 5′-AYCCC-3′ for the 3′ side, where R is A or G; and Y is C or U. In some cases, when stem S3 is six base pairs, the consensus sequence may be 5′-GGGRUN-3′ for the 5′ side of stem S3 and 5′-NAYCCC-3′ for the 3′ side, where R is A or G; N is A, C, G, or U; D is A, G, or U; and H is A, C, or U. When stem S3 is six base pairs long and contains a single mis-matched nucleotide, the consensus sequence may be 5′-GGGRUUR-3′ for the 5′ side of stem S3 and 5′-UAUCCC-3′ for the 3′ side, where U is the single mis-matched nucleotide; and R is A or G. When stem S3 is six base pairs long and contains a single mis-matched nucleotide, loop L4 may be three nucleotides long. When loop L4 is three nucleotides long, the sequence may be 5′-CUA-3′.
Aptamer 234 was also used to examine the effects of an alternate pairing at positions 10 and 17 in stem S2 (numbering based on Aptamer 141) and the effect of an additional 2′F-G to 2′OMe substitution at position 12 in loop L2 (numbering based on Aptamer 141) on aptamer function (Aptamers 293, 294, and 295). Consistent with the secondary structure prediction, the C:G pair at positions 10 and 17 could be replaced with an A:U pair with only a modest loss in activity relative to Aptamer 141 (Aptamers 293; approximately 6-fold loss). Interestingly, while the effect of the 2′F-G to 2′OMe substitution at position 12 was well tolerated (Aptamer 294; 1-2 fold loss), the combination of both the base pair substitution and the 2′OMe substitution resulted in a more significant loss of activity (Aptamer 295; 12-fold loss). The data further supported the consensus sequence for stem S2. Stem S2 may be composed of two base pairs with a consensus sequence of 5′-NN-3′ for both the 5′ and 3′ sides of the stem.
Finally, using Aptamer 234, the effects of linker length on loop L1 (position 7; numbering based on Aptamer 141; Aptamers 298-300) was explore. Increasing the length of the non-nucleotidyl linker in loop L1 resulted in a loss in activity relative to Aptamer 141. The longer the linker, the less potent the molecule (compare Aptamers 298, 299, and 300;
In total, when the data from the degenerate selection (Example 6) is combined with the data from our structure activity relationship studies (Examples 7, 8, 9 and 10), the consensus sequences for the Aptamer 26 family of molecules is 5′-HNBYHDNNN*NNKNGCNNWGGGRUNDNDHNWYCCCGNNNNNYNKVNW-3 (SEQ ID NO:5) where H is A, C, or U, N is A, C, G, or U, Bis C, G, or U, Y is C or U; N* is A, C, G, U, can be deleted entirely, or is a non-nucleotidyl spacer 3 modification, a 6 carbon alkyl linker (1,6-hexanediol), or a spacer 9 (triethyleneglycol) modification; D is A, G, or U; K is G or U; W is A or U; R is A or G; and V is A, C, or G; and is represented with a six base pair stem S3 and a four nucleotide loop L4 in
To better understand the roles of S3 and L4 in aptamer function we generated two different randomized libraries based on the sequence and structure of Aptamer 285, in which the non-nucleotidyl linker was replaced with a random nucleotide, N, where N is A, G, U or C, and where the entirety of Stem S3 and Loop L4 (S3-L4) was replaced with a library composed of 16 or 14 random positions. The sequence of the libraries used were: GGGAGAGTCGGTAGCCTCAACGACNCCGCGCGGAN16GTTTGTCGCTATGTGGAAAT GGCGCTGT, GGGAGAGTCGGTAGCCTCAACGACNCCGCGCGGAN14GTTTGTCGCTATGTGGAAAT GGCGCTGT (N16, N14; where N16 is 16 N positions, N14 is 14 N positions and N is A, G, U or C).
Using these libraries, we performed two separate selections targeting human VEGF 121 in a manner similar to that described for the original selection (Example 1). Following 3 rounds of selection, each library was found to demonstrate significant VEGF binding activity (˜10-fold signal over background) as determined by flow cytometry. The libraries were subsequently adapted for sequencing and sequenced on a an Illimuna MiSeq sequencer. Sequence analysis was performed as described previously.
For the S3-L4 N16 library, we analyzed the sequence data from 174,583 reads. An alignment of the sequences corresponding to the top 20 stacks from this library are shown in Table 21. These 20 stacks correspond to the top 44% of the enriched library sequences.
As shown in Table 21, the sequences from these top 20 stacks from the S3-L4 N16 library strongly support the structural and sequence requirements summarized in
U
GGGU UGGAGGUU ACCC
U
GUCCC UAAUUU GGGGC
U
GUCCC UUCAUU GGGGC
U
GGGU UAAUGGCU ACCC
U
GUCCC UGUAAU GGGGC
U
GUCCC UAUUUU GGGGC
U
GAGGAG GUUA CCCCUC
U
GUCCC UUGAUU GGGGC
U
GGGU UACUGGCU ACCC
U
GUCCC UAACAU GGGGC
U
GGGGAG GCAA CUUCCC
U
GUCCC UUUAUU GGGGC
U
GUCCC UACAAU GGGGC
U
GUGCC GUUUGA GGUAC
U
GGGCU GAGGCAAUGCCC
U
GUCCC UACUUU GGGGC
U
GUCCC UCACAU GGGGC
U
GGGU UACAGGCU ACCC
U
GUCCC UUUGUU GGGGC
U
GUCCC UAAAAU GGGGC
For the S3-L4 N14 library, we analyzed the sequence data from 1,644,139 reads. An alignment of the sequences corresponding to the top 20 stacks from this library are shown in Table 22. These 20 stacks correspond to the top 80% of the enriched library sequences.
As sown in Table 22, the sequences from the top 20 stacks from the S3-L4 N14 library strongly support the structural and sequence requirements summarized in
U
GGGU UUGGCU ACCC
U
GGCU UGAGGU AGCC
U
GUCCC ACAU GGGGC
U
GGGA UGAGGU UCCC
U
GGCA UGAGGU UGCC
U
GUGC UGAGGU GCAC
U
GUCCC UAUU GGGGC
U
GGGU UAGGCU ACCC
U
GCUUC GGAU GAGGC
U
GUCCC UCAU GGGGC
U
GUCCC GUAU GGGGC
U
GUCCC AAUU GGGGC
U
GGGU UUGGUU ACCC
U
GUCCC AUUU GGGGC
U
GUCCC ACAA GGGGC
U
GCUUC GGAA GAGGC
U
GUCCC AUUA GGGGC
U
GUGCC AACU GGUAC
U
GUCCC UAUA GGGGC
U
GUCCC UAAU GGGGC
When combined the data both the S3-L4 N16 and S3-L4 N14 further broaden the observed consensus sequences for stem S3 and loop L4. When the data from the N16 selection is combined with data from the primary selection, degenerate selection and SAR analysis broadens the observed consensus when stem S3 is 6 base pairs long expands to 5′-GRGGWN-3′ on the 5′ side and 5′-NHYCYC-3′ on the 3′ side. When stem S3 is 5 base pairs long, the consensus from the outcome of the N16 and N14 selections combined with data from the primary selection, degenerate selection and SAR analysis broadens the observed consensus to 5′-GBBNY-3′ on the 5′ side and 5′-RNBNC-3′ on the 3′ side. When stem S3 is 4 base pairs long, the consensus from the outcome of the N16 and N14 selections combined with data from the primary selection, degenerate selection and SAR analysis broadens the observed consensus to 5′-GKGN-3′ on the 5′ side and 5′-NSMC-3′ on the 3′ side. Similarly, when combined with data from the primary selection, degenerate selection and SAR analysis, when loop L4 is 6 nucleotides long, 5 nucleotides long or 4 nucleotides long the consensus sequences expand to 5′UDUHRKYU-3′, 5′KNNNNW-3′ and 5′DNDN-3′.
While preferred embodiments of the present invention have been shown and described herein, it will be obvious to those skilled in the art that such embodiments are provided by way of example only. Numerous variations, changes, and substitutions will now occur to those skilled in the art without departing from the invention. It should be understood that various alternatives to the embodiments of the invention described herein may be employed in practicing the invention. It is intended that the following claims define the scope of the invention and that methods and structures within the scope of these claims and their equivalents be covered thereby.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/US2020/013192 | 1/10/2020 | WO | 00 |
| Number | Date | Country | |
|---|---|---|---|
| 62791611 | Jan 2019 | US |
