title: Computer-aided design of aptamers for cytochrome p450.
abstract: Aptamers are short single-stranded DNA or RNA oligonucleotides that can bind to their targets with high affinity and specificity. Usually, they are experimentally selected using the SELEX method. Here, we describe an approach toward the in silico selection of aptamers for proteins. This approach involves three steps: finding a potential binding site, designing the recognition and structural parts of the aptamers and evaluating the experimental affinity. Using this approach, a set of 15-mer aptamers for cytochrome P450 51A1 was designed using docking and molecular dynamics simulation. An experimental evaluation of the synthesized aptamers using SPR biosensor showed that these aptamers interact with cytochrome P450 51A1 with Kd values in the range of 10(-6)-10(-7) M.
authors.affiliation: Institute of Biomedical Chemistry RAMS, Pogodinskaya str., 10, Moscow 119121, Russia. Electronic address: amid.dima@gmail.com.
authors.forename: Dmitrii S
authors.initials: DS
authors.lastname: Shcherbinin
authors.affiliation: Institute of Biomedical Chemistry RAMS, Pogodinskaya str., 10, Moscow 119121, Russia.
authors.forename: Oksana V
authors.initials: OV
authors.lastname: Gnedenko
authors.affiliation: Institute of Biomedical Chemistry RAMS, Pogodinskaya str., 10, Moscow 119121, Russia.
authors.forename: Svetlana A
authors.initials: SA
authors.lastname: Khmeleva
authors.affiliation: Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus, Kuprevich str., 5/2, Minsk 220141, Belarus.
authors.forename: Sergey A
authors.initials: SA
authors.lastname: Usanov
authors.affiliation: Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus, Kuprevich str., 5/2, Minsk 220141, Belarus.
authors.forename: Andrei A
authors.initials: AA
authors.lastname: Gilep
authors.affiliation: Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus, Kuprevich str., 5/2, Minsk 220141, Belarus.
authors.forename: Aliaksei V
authors.initials: AV
authors.lastname: Yantsevich
authors.affiliation: Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus, Kuprevich str., 5/2, Minsk 220141, Belarus.
authors.forename: Tatsiana V
authors.initials: TV
authors.lastname: Shkel
authors.affiliation: Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus, Kuprevich str., 5/2, Minsk 220141, Belarus.
authors.forename: Ivan V
authors.initials: IV
authors.lastname: Yushkevich
authors.affiliation: Institute of Biomedical Chemistry RAMS, Pogodinskaya str., 10, Moscow 119121, Russia.
authors.forename: Sergey P
authors.initials: SP
authors.lastname: Radko
authors.affiliation: Institute of Biomedical Chemistry RAMS, Pogodinskaya str., 10, Moscow 119121, Russia.
authors.forename: Alexis S
authors.initials: AS
authors.lastname: Ivanov
authors.affiliation: Institute of Biomedical Chemistry RAMS, Pogodinskaya str., 10, Moscow 119121, Russia.
authors.forename: Alexander V
authors.initials: AV
authors.lastname: Veselovsky
authors.affiliation: Institute of Biomedical Chemistry RAMS, Pogodinskaya str., 10, Moscow 119121, Russia.
authors.forename: Alexander I
authors.initials: AI
authors.lastname: Archakov
mesh_terms: D052157:Aptamers, Nucleotide / Q000737:chemistry*; D001665:Binding Sites; D003577:Cytochrome P-450 Enzyme System / Q000737:chemistry*; D008958:Models, Molecular; D062105:Molecular Docking Simulation / Q000379:methods; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D017434:Protein Structure, Tertiary; D013329:Structure-Activity Relationship
chemical_list: D052157:Aptamers, Nucleotide; D003577:Cytochrome P-450 Enzyme System
keywords: Aptamer; Bioinformatics; Cytochrome P450 51A1; Molecular docking; Molecular dynamics; Rational design; SELEX