Тип публикации: статья из журнала

Год издания: 2022

Идентификатор DOI: 10.1002/chem.202104481

Ключевые слова: aptamers, fragment molecular orbitals method, molecular dynamics, sars-cov-2, saxs

Аннотация: Aptamer selection against novel infections is a complicated and time-consuming approach. Synergy can be achieved by using computational methods together with experimental procedures. This study aims to develop a reliable methodology for a rational aptamer in silico et vitro design. The new approach combines multiple steps: (1) MoleПоказать полностьюcular design, based on screening in a DNA aptamer library and directed mutagenesis to fit the protein tertiary structure; (2) 3D molecular modeling of the target; (3) Molecular docking of an aptamer with the protein; (4) Molecular dynamics (MD) simulations of the complexes; (5) Quantum-mechanical (QM) evaluation of the interactions between aptamer and target with further analysis; (6) Experimental verification at each cycle for structure and binding affinity by using small-angle X-ray scattering, cytometry, and fluorescence polarization. By using a new iterative design procedure, structure- and interaction-based drug design (SIBDD), a highly specific aptamer to the receptor-binding domain of the SARS-CoV-2 spike protein, was developed and validated. The SIBDD approach enhances speed of the high-affinity aptamers development from scratch, using a target protein structure. The method could be used to improve existing aptamers for stronger binding. This approach brings to an advanced level the development of novel affinity probes, functional nucleic acids. It offers a blueprint for the straightforward design of targeting molecules for new pathogen agents and emerging variants. © 2022 Wiley-VCH GmbH.

Журнал: Chemistry - A European Journal

Выпуск журнала: Vol. 28, Is. 12

Номера страниц: 202104481

ISSN журнала: 09476539

Издатель: John Wiley and Sons Inc

• Mironov V. (Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russian Federation, Department of Chemistry, Kyungpook National University, Daegu, 702-701, South Korea)
• Shchugoreva I.A. (Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center KSC SB RAS, Krasnoyarsk, 660036, Russian Federation, School of Non-Ferrous Metals and Materials Science, Siberian Federal University, Krasnoyarsk, 660041, Russian Federation, Laboratory for Biomolecular and Medical Technologies, Krasnoyarsk State Medical University, Krasnoyarsk, 660022, Russian Federation)
• Artyushenko P.V. (Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center KSC SB RAS, Krasnoyarsk, 660036, Russian Federation, School of Non-Ferrous Metals and Materials Science, Siberian Federal University, Krasnoyarsk, 660041, Russian Federation, Laboratory for Biomolecular and Medical Technologies, Krasnoyarsk State Medical University, Krasnoyarsk, 660022, Russian Federation)
• Morozov D. (Nanoscience Center and Department of Chemistry, University of Jyväskylä, Jyväskylä, 40014, Finland)
• Borbone N. (Department of Pharmacy, University of Naples Federico II, Naples, 80138, Italy)
• Oliviero G. (Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, 80131, Italy)
• Zamay T.N. (Laboratory for Biomolecular and Medical Technologies, Krasnoyarsk State Medical University, Krasnoyarsk, 660022, Russian Federation)
• Moryachkov R.V. (Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center KSC SB RAS, Krasnoyarsk, 660036, Russian Federation, Laboratory of Physics of Magnetic Phenomena, Kirensky Institute of Physics, Krasnoyarsk, 660012, Russian Federation)
• Kolovskaya O.S. (Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center KSC SB RAS, Krasnoyarsk, 660036, Russian Federation, Laboratory for Biomolecular and Medical Technologies, Krasnoyarsk State Medical University, Krasnoyarsk, 660022, Russian Federation)
• Lukyanenko K.A. (Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center KSC SB RAS, Krasnoyarsk, 660036, Russian Federation, Laboratory for Biomolecular and Medical Technologies, Krasnoyarsk State Medical University, Krasnoyarsk, 660022, Russian Federation, School of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, 660041, Russian Federation)
• Song Y. (Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China)
• Merkuleva I.A. (State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, Koltsovo, 630559, Russian Federation)
• Zabluda V.N. (Laboratory of Physics of Magnetic Phenomena, Kirensky Institute of Physics, Krasnoyarsk, 660012, Russian Federation)
• Peters G. (NRC Kurchatov Institute, Moscow, 117 259, Russian Federation)
• Koroleva L.S. (Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russian Federation)
• Veprintsev D.V. (Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center KSC SB RAS, Krasnoyarsk, 660036, Russian Federation)
• Glazyrin Y.E. (Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center KSC SB RAS, Krasnoyarsk, 660036, Russian Federation, Laboratory for Biomolecular and Medical Technologies, Krasnoyarsk State Medical University, Krasnoyarsk, 660022, Russian Federation)
• Volosnikova E.A. (State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, Koltsovo, 630559, Russian Federation)
• Belenkaya S.V. (State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, Koltsovo, 630559, Russian Federation)
• Esina T.I. (State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, Koltsovo, 630559, Russian Federation)
• Isaeva A.A. (State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, Koltsovo, 630559, Russian Federation)
• Nesmeyanova V.S. (State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, Koltsovo, 630559, Russian Federation)
• Shanshin D.V. (State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, Koltsovo, 630559, Russian Federation)
• Berlina A.N. (Laboratory of Immunobiochemistry, A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences Moscow, Moscow, 119071, Russian Federation)
• Komova N.S. (Laboratory of Immunobiochemistry, A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences Moscow, Moscow, 119071, Russian Federation)
• Svetlichnyi V.A. (Laboratory of Advanced Materials and Technology, Tomsk State University, Tomsk, 634050, Russian Federation)
• Silnikov V.N. (Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russian Federation)
• Shcherbakov D.N. (State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, Koltsovo, 630559, Russian Federation, Altai State University, Barnaul, 656049, Russian Federation)
• Zamay G.S. (Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center KSC SB RAS, Krasnoyarsk, 660036, Russian Federation, Laboratory for Biomolecular and Medical Technologies, Krasnoyarsk State Medical University, Krasnoyarsk, 660022, Russian Federation)
• Zamay S.S. (Department of Molecular Electronics, Federal Research Center KSC SB RAS, Krasnoyarsk, 660036, Russian Federation)
• Smolyarova T. (Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center KSC SB RAS, Krasnoyarsk, 660036, Russian Federation, School of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, 660041, Russian Federation)
• Tikhonova E.P. (Department of Infectious Diseases and Epidemiology, Krasnoyarsk State Medical University, Krasnoyarsk, 660022, Russian Federation)
• Chen K.H.C. (Department of Applied Chemistry, National Pingtung University, Pingtung, 900391, Taiwan)
• Jeng U.-S. (National Synchrotron Radiation Research Center, Hsinchu Science Park, Hsinchu, 30076, Taiwan, Department of Chemical Engineering, National Tsing Hua University, Hsinchu, 30013, Taiwan)
• Condorelli G. (Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, 80131, Italy, IRCCS Neuromed-Istituto Neurologico Mediterraneo Pozzilli, Via Atinense 18, Pozzilli, 86077, Italy)
• de Franciscis V. (Institute of Genetic and Biomedical Research (IRGB), Research National Council (CNR), Milan, 09042, Italy)
• Groenhof G. (Nanoscience Center and Department of Chemistry, University of Jyväskylä, Jyväskylä, 40014, Finland)
• Yang C. (Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China, Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China)
• Moskovsky A.A. (Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russian Federation)
• Fedorov D.G. (Research Center for Computational Design of Advanced Functional Materials, National Institute of Advanced Industrial Science and Technology, Tsukuba, 305-8560, Japan)
• Tomilin F.N. (School of Non-Ferrous Metals and Materials Science, Siberian Federal University, Krasnoyarsk, 660041, Russian Federation, Laboratory of Physics of Magnetic Phenomena, Kirensky Institute of Physics, Krasnoyarsk, 660012, Russian Federation)
• Tan W. (Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China)
• Alexeev Y. (Computational Science Division, Argonne National Laboratory, Lemont, IL 60439, United States)
• Berezovski M.V. (Department of Chemistry and Biomolecular Sciences, Ottawa, ON K1N6N5, Canada)
• Kichkailo A.S. (Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center KSC SB RAS, Krasnoyarsk, 660036, Russian Federation, Laboratory for Biomolecular and Medical Technologies, Krasnoyarsk State Medical University, Krasnoyarsk, 660022, Russian Federation)

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