title: New oligonucleotide derivatives as unreactive substrate analogues and potential inhibitors of human apurinic/apyrimidinic endonuclease APE1.
abstract: Human apurinic/apyrimidinic endonuclease APE1 is one of the key enzymes of the base excision DNA repair system. The main biological function of APE1 is the hydrolysis of the phosphodiester bond on the 5'-side of an apurinic/apyrimidinic site (AP-site) to give the 5'-phosphate and 3'-hydroxyl group. It has long been known that AP-sites have mutagenic and cytotoxic effects and their accumulation in DNA is a potential hazard to the cell lifecycle. The structural and biochemical studies of APE1 are complicated by its high catalytic activity towards the AP-site and its cyclic or acyclic analogues. This work has focussed on the design, synthesis and analysis of oligonucleotide derivatives as potentially unreactive APE1 substrates. We have shown that the replacement of oxygen atoms in the phosphate group on the 5'-side from the AP-site analogue tetrahydrofuran (F) considerably decreases the rate of enzymatic hydrolysis of modified oligonucleotides. We have calculated that a N3'-P5' phosphoramidate linkage is hydrolysed about 30 times slower than the native phosphodiester bond while phosphorothioate or primary phosphoramidate linkages are cleaved more than three orders of magnitude slower. The value of IC50 of the oligonucleotide duplex containing a primary phosphoramidate linkage is 2.5 × 10(-7) M, which is in accordance with the APE1 association constant of DNA duplexes containing AP-sites. Thus, it is demonstrated that oligonucleotide duplexes with chemical modifications could be used as unreactive substrates and potential competitive inhibitors of APE1.
authors.affiliation: Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia. fedorova@niboch.nsc.ru and Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia.
authors.forename: Nikita A
authors.initials: NA
authors.lastname: Kuznetsov
authors.affiliation: Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia. fedorova@niboch.nsc.ru.
authors.forename: Maxim S
authors.initials: MS
authors.lastname: Kupryushkin
authors.affiliation: Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia. fedorova@niboch.nsc.ru.
authors.forename: Tatyana V
authors.initials: TV
authors.lastname: Abramova
authors.affiliation: Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia. fedorova@niboch.nsc.ru.
authors.forename: Alexandra A
authors.initials: AA
authors.lastname: Kuznetsova
authors.affiliation: Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia. fedorova@niboch.nsc.ru.
authors.forename: Anastasia D
authors.initials: AD
authors.lastname: Miroshnikova
authors.affiliation: Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia. fedorova@niboch.nsc.ru and Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia.
authors.forename: Dmitry A
authors.initials: DA
authors.lastname: Stetsenko
authors.affiliation: Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia. fedorova@niboch.nsc.ru and Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia.
authors.forename: Dmitrii V
authors.initials: DV
authors.lastname: Pyshnyi
authors.affiliation: Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia. fedorova@niboch.nsc.ru and Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia.
authors.forename: Olga S
authors.initials: OS
authors.lastname: Fedorova
mesh_terms: D002384:Catalysis; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D043603:DNA-(Apurinic or Apyrimidinic Site) Lyase / Q000037:antagonists & inhibitors* / Q000737:chemistry*; D015195:Drug Design; D004791:Enzyme Inhibitors / Q000138:chemical synthesis / Q000737:chemistry* / Q000494:pharmacology*; D006801:Humans; D006868:Hydrolysis; D015394:Molecular Structure; D009841:Oligonucleotides / Q000138:chemical synthesis / Q000737:chemistry* / Q000494:pharmacology*; D010710:Phosphates / Q000737:chemistry; D011485:Protein Binding
chemical_list: D004791:Enzyme Inhibitors; D009841:Oligonucleotides; D010710:Phosphates; D004247:DNA; C085108:APEX1 protein, human; D043603:DNA-(Apurinic or Apyrimidinic Site) Lyase