Open Access

Chemistry - A European Journal, volume 28, issue 12

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

Mironov Vladimir ^{1, 2}

Shchugoreva Irina A. ^{3, 4, 5}

Artyushenko Polina V. ^{3, 4, 5}

Morozov Dmitry ⁶

Borbone Nicola ⁷

Oliviero Giorgia ⁸

Zamay Tatiana N. ⁴

Moryachkov Roman V ^{5, 9}

Kolovskaya Olga S ^{4, 5}

Lukyanenko Kirill A ^{4, 5, 10}

Song Yanling ¹¹

Merkuleva Iuliia A ¹²

Zabluda Vladimir N ⁹

Peters Georgy ¹³

Koroleva Lyudmila S ¹⁴

Veprintsev Dmitry V ⁵

Glazyrin Yury E ^{4, 5}

Volosnikova Ekaterina A. ¹²

Belenkaya Svetlana V ¹²

Esina Tatiana I ¹²

Isaeva Anastasiya A. ¹²

Nesmeyanova Valentina S ¹²

Shanshin Daniil V ¹²

Berlina Anna N ¹⁵

Komova Nadezhda S ¹⁵

Svetlichnyi Valery A ¹⁶

Sil’nikov Vladimir N ¹⁴

Shcherbakov Dmitriy N ^{12, 17}

Zamay Galina S ^{4, 5}

Zamay Sergey S ¹⁸

Smolyarova Tatyana ^{5, 10}

Tikhonova Elena P ¹⁹

Chen Kelvin H C ²⁰

Jeng U-Ser ^{21, 22}

Condorelli Gerolama ^{8, 23}

Franciscis Vittorio ²⁴

Groenhof Gerrit ⁶

Yang Chaoyong ^{11, 25}

Moskovsky Alexander A ¹

Fedorov Dmitri G. ²⁶

Tomilin Felix N. ^{3, 9}

Tan Weihong ^{25, 27}

Alexeev Yuri ²⁸

Berezovski Maxim V. ²⁹

Kichkailo Anna S. ^{4, 5}

Hide authors affiliations Show authors affiliations: 29 affiliations

Department of Chemistry Lomonosov Moscow State University Moscow 119991 Russia |

Department of Chemistry Kyungpook National University Daegu 702-701 South Korea |

School of Non-Ferrous Metals and Materials Science Siberian Federal University Krasnoyarsk 660041 Russia |

⁴

Laboratory for Biomolecular and Medical Technologies Krasnoyarsk State Medical University Krasnoyarsk 660022 Russia |

⁵

Laboratory for Digital Controlled Drugs and Theranostics Federal Research Center KSC SB RAS Krasnoyarsk 660036 Russia |

⁶

Nanoscience Center and Department of Chemistry University of Jyväskylä Jyväskylä 40014 Finland |

⁷

Department of Pharmacy University of Naples Federico II Naples 80138 Italy |

⁸

Department of Molecular Medicine and Medical Biotechnologies University of Naples Federico II Naples 80131 Italy |

⁹

Laboratory of Physics of Magnetic Phenomena Kirensky Institute of Physics 660012 Krasnoyarsk Russia |

¹⁰

School of Fundamental Biology and Biotechnology Siberian Federal University Krasnoyarsk 660041 Russia |

¹¹

Department of Chemical Biology College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 P. R. China |

¹²

State Research Center of Virology and Biotechnology VECTOR Rospotrebnadzor Koltsovo 630559 Russia |

¹³

NRC Kurchatov Institute Moscow 117 259 Russia |

¹⁴

Institute of Chemical Biology and Fundamental Medicine Siberian Branch of the Russian Academy of Sciences Novosibirsk 630090 Russia |

¹⁵

Laboratory of Immunobiochemistry A.N. Bach Institute of Biochemistry Research Center of Biotechnology of the Russian Academy of Sciences Moscow Moscow 119071 Russia

Bach Institute of Biochemistry of the Russian Academy of Sciences

Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences

¹⁶

Laboratory of Advanced Materials and Technology Tomsk State University Tomsk 634050 Russia |

¹⁷

Altai State University Barnaul 656049 Russia |

¹⁸

Department of Molecular Electronics Federal Research Center KSC SB RAS Krasnoyarsk 660036 Russia |

¹⁹

Department of Infectious Diseases and Epidemiology Krasnoyarsk State Medical University Krasnoyarsk 660022 Russia |

²⁰

Department of Applied Chemistry National Pingtung University Pingtung 900391 Taiwan |

²¹

National Synchrotron Radiation Research Center Hsinchu Science Park Hsinchu 30076 Taiwan |

²²

Department of Chemical Engineering National Tsing Hua University Hsinchu 30013 Taiwan |

²³

IRCCS Neuromed-Istituto Neurologico Mediterraneo Pozzilli Via Atinense 18 86077 Pozzilli Italy |

²⁴

Institute of Genetic and Biomedical Research (IRGB) Research National Council (CNR) Milan 09042 Italy |

²⁵

Institute of Molecular Medicine Renji Hospital Shanghai Jiao Tong University School of Medicine Shanghai 200127 P. R. China |

²⁶

Research Center for Computational Design of Advanced Functional Materials National Institute of Advanced Industrial Science and Technology Tsukuba 305-8560 Japan |

²⁷

College of Chemistry and Chemical Engineering Hunan University ChangSha 410082 P. R. China |

²⁸

Computational Science Division Argonne National Laboratory Lemont IL, 60439 USA |

²⁹

Department of Chemistry and Biomolecular Sciences Ottawa Ontario K1N6N5 Canada |

Publication type: Journal Article

Publication date: 2022-02-09

Wiley

Journal: Chemistry - A European Journal

Quartile SCImago

Quartile WOS

Impact factor: 4.3

ISSN: 09476539, 15213765

DOI: 10.1002/chem.202104481

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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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Journal of Chemical Physics	Journal of Chemical Physics, 1, 20% Journal of Chemical Physics 1 publication, 20%
Chemical Papers	Chemical Papers, 1, 20% Chemical Papers 1 publication, 20%
Journal of Chemical Information and Modeling	Journal of Chemical Information and Modeling, 1, 20% Journal of Chemical Information and Modeling 1 publication, 20%
Biophysical Reviews	Biophysical Reviews, 1, 20% Biophysical Reviews 1 publication, 20%
Analytical and Bioanalytical Chemistry	Analytical and Bioanalytical Chemistry, 1, 20% Analytical and Bioanalytical Chemistry 1 publication, 20%
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Springer Nature	Springer Nature, 3, 60% Springer Nature 3 publications, 60%
American Institute of Physics (AIP)	American Institute of Physics (AIP), 1, 20% American Institute of Physics (AIP) 1 publication, 20%
American Chemical Society (ACS)	American Chemical Society (ACS), 1, 20% American Chemical Society (ACS) 1 publication, 20%
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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.

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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.

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RIS Copy

TY - JOUR

DO - 10.1002/chem.202104481

UR - https://doi.org/10.1002%2Fchem.202104481

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

T2 - Chemistry - A European Journal

AU - Shchugoreva, Irina A.

AU - Artyushenko, Polina V.

AU - Zamay, Tatiana N.

AU - Moryachkov, Roman V

AU - Kolovskaya, Olga S

AU - Song, Yanling

AU - Merkuleva, Iuliia A

AU - Zabluda, Vladimir N

AU - Peters, Georgy

AU - Koroleva, Lyudmila S

AU - Veprintsev, Dmitry V

AU - Glazyrin, Yury E

AU - Volosnikova, Ekaterina A.

AU - Belenkaya, Svetlana V

AU - Esina, Tatiana I

AU - Isaeva, Anastasiya A.

AU - Nesmeyanova, Valentina S

AU - Shanshin, Daniil V

AU - Berlina, Anna N

AU - Komova, Nadezhda S

AU - Svetlichnyi, Valery A

AU - Sil’nikov, Vladimir N

AU - Shcherbakov, Dmitriy N

AU - Zamay, Galina S

AU - Zamay, Sergey S

AU - Smolyarova, Tatyana

AU - Tikhonova, Elena P

AU - Chen, Kelvin H C

AU - Jeng, U-Ser

AU - Condorelli, Gerolama

AU - Franciscis, Vittorio

AU - Groenhof, Gerrit

AU - Moskovsky, Alexander A

AU - Mironov, Vladimir

AU - Fedorov, Dmitri G.

AU - Berezovski, Maxim V.

AU - Borbone, Nicola

AU - Oliviero, Giorgia

AU - Lukyanenko, Kirill A

AU - Yang, Chaoyong

AU - Tomilin, Felix N.

AU - Tan, Weihong

AU - Alexeev, Yuri

AU - Kichkailo, Anna S.

AU - Morozov, Dmitry

PY - 2022

DA - 2022/02/09 00:00:00

PB - Wiley

IS - 12

VL - 28

SN - 0947-6539

SN - 1521-3765

ER -

BibTex

Cite this

BibTex Copy

@article{2022_Mironov,

author = {Irina A. Shchugoreva and Polina V. Artyushenko and Tatiana N. Zamay and Roman V Moryachkov and Olga S Kolovskaya 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 Gerrit Groenhof and Alexander A Moskovsky and Vladimir Mironov and Dmitri G. Fedorov and Maxim V. Berezovski and Nicola Borbone and Giorgia Oliviero and Kirill A Lukyanenko and Chaoyong Yang and Felix N. Tomilin and Weihong Tan and Yuri Alexeev and Anna S. Kichkailo and Dmitry Morozov},

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://doi.org/10.1002%2Fchem.202104481},

number = {12},

doi = {10.1002/chem.202104481}

}

Found error?

Publisher

Wiley

Journal

Chemistry - A European Journal

Quartile SCImago

Quartile WOS

Impact factor

4.3

ISSN

09476539 (Print)
15213765 (Electronic)

Labs

Laboratory of Digital Controlled Drugs and Theranostics

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