Synthesis, characterization and in vitro activity of thrombin-binding DNA aptamers with triazole internucleotide linkages

• Published in: European journal of medicinal chemistry 2013-09, Vol.67, p.90-97
• Main Authors: Varizhuk, Anna M., Tsvetkov, Vladimir B., Tatarinova, Olga N., Kaluzhny, Dmitry N., Florentiev, Vladimir L., Timofeev, Edward N., Shchyolkina, Anna K., Borisova, Olga F., Smirnov, Igor P., Grokhovsky, Sergei L., Aseychev, Anton V., Pozmogova, Galina E.
• Format: Article
• Language: English
• Subjects: Anticoagulants; Aptamers, Nucleotide - chemical synthesis; Aptamers, Nucleotide - chemistry; Aptamers, Nucleotide - metabolism; Aptamers, Nucleotide - pharmacology; Binding Sites; DNA aptamers; Dose-Response Relationship, Drug; G-Quadruplexes; Molecular Conformation; Molecular Dynamics Simulation; Nucleotides - chemistry; Serine Proteinase Inhibitors - chemistry; Serine Proteinase Inhibitors - metabolism; Serine Proteinase Inhibitors - pharmacology; Structure-Activity Relationship; Thrombin - antagonists & inhibitors; Thrombin - chemistry; Thrombin - metabolism; Thrombin inhibition; Triazole internucleotide linkages; Triazoles - chemistry; Triazoles - pharmacology
• ISSN: 0223-5234; 1768-3254
• DOI: 10.1016/j.ejmech.2013.06.034

A series of DNA aptamers bearing triazole internucleotide linkages that bind to thrombin was synthesized. The novel aptamers are structurally analogous to the well-known thrombin-inhibiting G-quadruplexes TBA15 and TBA31. The secondary structure stability, binding affinity for thrombin and anticoagulant effects of the triazole-modified aptamers were measured. A modification in the central loop of the aptamer quadruplex resulted in increased nuclease resistance and an inhibition efficiency similar to that of TBA15. The likely aptamer-thrombin binding mode was determined by molecular dynamics simulations. Due to their relatively high activity and the increased resistance to nuclease digestion imparted by the triazole internucleotide linkages, the novel aptamers are a promising alternative to known DNA-based anticoagulant agents. [Display omitted] •A series of chemically modified DNA aptamers to thrombin were synthesized.•The modification was shown to enhance aptamer resistance to nucleases.•Several aptamers bound efficiently with thrombin and inhibited blood clotting.