Open Access
Open access
Wiley
Chemistry - A European Journal
,  volume 28 ,  issue 12 ,  publication number e202104481

Structure- and Interaction-Based Design of Anti-SARS-CoV-2 Aptamers

Vladimir Mironov 1, 2, 3, 4
, 
Irina A. Shchugoreva 5, 6, 7, 8, 9, 10
, 
Polina V. Artyushenko 5, 6, 7, 8, 9, 10
, 
Dmitry Morozov 11, 12
, 
Nicola Borbone 13, 14
, 
Giorgia Oliviero 15, 16
, 
Tatiana N. Zamay 7, 10
, 
Roman V Moryachkov 5, 8, 17, 18
, 
Olga S Kolovskaya 5, 7, 8, 10
, 
Kirill A Lukyanenko 5, 7, 8, 10, 19, 20
, 
Yanling Song 21, 22
, 
Iuliia A Merkuleva 23, 24
, 
Vladimir N Zabluda 17, 18
, 
Georgy Peters 25, 26
, 
Lyudmila S Koroleva 27, 28
, 
Dmitry V Veprintsev 5, 8
, 
Yury E Glazyrin 5, 7, 8, 10
, 
Ekaterina A. Volosnikova 23, 24
, 
Svetlana V Belenkaya 23, 24
, 
Tatiana I Esina 23, 24
, 
Anastasiya A. Isaeva 23, 24
, 
Valentina S Nesmeyanova 23, 24
, 
Daniil V Shanshin 23, 24
, 
Anna N Berlina 29, 30
, 
Nadezhda S Komova 29
, 
Valery A Svetlichnyi 31, 32
, 
Vladimir N Sil’nikov 27, 28
, 
Dmitriy N Shcherbakov 23, 24, 33, 34
, 
Galina S Zamay 5, 7, 8, 10
, 
Sergey S Zamay 35, 36
, 
Tatyana Smolyarova 5, 8, 19, 20
, 
Elena P Tikhonova 37, 38
, 
Kelvin H C Chen 39, 40
, 
U-Ser Jeng 41, 42, 43, 44
, 
Gerolama Condorelli 15, 16, 45, 46
, 
Vittorio Franciscis 47
, 
Vittorio de FRANCISCIS 48
, 
Gerrit Groenhof 11, 12
, 
Chaoyong Yang 21, 22, 49, 50
, 
Alexander A Moskovsky 1, 3
, 
Dmitri G. Fedorov 51, 52
, 
Felix N. Tomilin 6, 9, 17, 18
, 
Weihong Tan 49, 50, 53, 54
, 
Yuri Alexeev 55, 56
, 
Maxim V. Berezovski 57, 58
, 
Anna S. Kichkailo 5, 7, 8, 10
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Institute of Genetic and Biomedical Research (IRGB) Research National Council (CNR) Milan 09042 Italy | 
48
 
Institute of Genetic and Biomedical Research (IRGB) Research National Council (CNR) Milan 09042 Italy | 
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Department of Chemistry and Biomolecular Sciences Ottawa Ontario K1N6N5 Canada | 
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Department of Chemistry and Biomolecular Sciences Ottawa Ontario K1N6N5 Canada | 
Publication type: Journal Article
Publication date: 2022-02-09
Wiley
scimago Q1
wos Q2
SJR: 0.981
CiteScore: 6.7
Impact factor: 3.7
ISSN: 09476539, 15213765
General Chemistry
Catalysis
Organic Chemistry
Abstract

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) Molecular 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.

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Mironov V. et al. Structure- and Interaction-Based Design of Anti-SARS-CoV-2 Aptamers // Chemistry - A European Journal. 2022. Vol. 28. No. 12. e202104481
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Mironov V. et al. Structure- and Interaction-Based Design of Anti-SARS-CoV-2 Aptamers // Chemistry - A European Journal. 2022. Vol. 28. No. 12. e202104481
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@article{2022_Mironov,
author = {Vladimir Mironov and Irina A. Shchugoreva and Polina V. Artyushenko and Dmitry Morozov and Nicola Borbone and Giorgia Oliviero and Tatiana N. Zamay and Roman V Moryachkov and Olga S Kolovskaya and Kirill A Lukyanenko and Yanling Song and Iuliia A Merkuleva and Vladimir N Zabluda and Georgy Peters and Lyudmila S Koroleva and Dmitry V Veprintsev and Yury E Glazyrin and Ekaterina A. Volosnikova and Svetlana V Belenkaya and Tatiana I Esina and Anastasiya A. Isaeva and Valentina S Nesmeyanova and Daniil V Shanshin and Anna N Berlina and Nadezhda S Komova and Valery A Svetlichnyi and Vladimir N Sil’nikov and Dmitriy N Shcherbakov and Galina S Zamay and Sergey S Zamay and Tatyana Smolyarova and Elena P Tikhonova and Kelvin H C Chen and U-Ser Jeng and Gerolama Condorelli and Vittorio Franciscis and Vittorio de FRANCISCIS and Gerrit Groenhof and Chaoyong Yang and Alexander A Moskovsky and Dmitri G. Fedorov and Felix N. Tomilin and Weihong Tan and Yuri Alexeev and Maxim V. Berezovski and Anna S. Kichkailo and others},
title = {Structure- and Interaction-Based Design of Anti-SARS-CoV-2 Aptamers},
journal = {Chemistry - A European Journal},
year = {2022},
volume = {28},
publisher = {Wiley},
month = {feb},
url = {https://chemistry-europe.onlinelibrary.wiley.com/doi/10.1002/chem.202104481},
number = {12},
pages = {e202104481},
doi = {10.1002/chem.202104481}
}