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5 results on '"Berlina, A. N."'

1. LATERAL FLOW TEST STRIPS FOR HG2+ IONS DETECTION BASED ON COMBINATION OF OLIGONUCLEOTIDE-MODIFIED GOLD NANOPARTICLES AND CHELATION BY GLUTATHIONE

Author

Berlina, A. N., Komova, N. S., Zherdev, A. V., and Dzantiev, B. B.

Abstract

The environment requires special attention due to the development of the industry, the transition to industrial automation, battery use and human waste disposal. At the same time, the development of analytical test systems makes it possible to determine the content of various contaminants and regulate their entry into the surrounding world. However, a number of toxic contaminants can accumulate in the environment (water, soil) and cause long-term toxic effects on living organisms, including humans. Therefore, the analytical techniques being developed (colorimetric, electrochemical, chromatographic etc.) and the laboratory methods (ICP-MS, ICP-AES) of their analysis existing in practice are in demand. This work was financially supported by Russian Science Foundation (project # 19-44-02020).

Published
2020

5. Structure‐ and Interaction‐Based Design of Anti‐SARS‐CoV‐2 Aptamers

Author

Vladimir Mironov, Irina A. Shchugoreva, Polina V. Artyushenko, Dmitry Morozov, Nicola Borbone, Giorgia Oliviero, Tatiana N. Zamay, Roman V. Moryachkov, Olga S. Kolovskaya, Kirill A. Lukyanenko, Yanling Song, Iuliia A. Merkuleva, Vladimir N. Zabluda, Georgy Peters, Lyudmila S. Koroleva, Dmitry V. Veprintsev, Yury E. Glazyrin, Ekaterina A. Volosnikova, Svetlana V. Belenkaya, Tatiana I. Esina, Anastasiya A. Isaeva, Valentina S. Nesmeyanova, Daniil V. Shanshin, Anna N. Berlina, Nadezhda S. Komova, Valery A. Svetlichnyi, Vladimir N. Silnikov, Dmitriy N. Shcherbakov, Galina S. Zamay, Sergey S. Zamay, Tatyana Smolyarova, Elena P. Tikhonova, Kelvin H.‐C. Chen, U‐Ser Jeng, Gerolama Condorelli, Vittorio Franciscis, Gerrit Groenhof, Chaoyong Yang, Alexander A. Moskovsky, Dmitri G. Fedorov, Felix N. Tomilin, Weihong Tan, Yuri Alexeev, Maxim V. Berezovski, Anna S. Kichkailo, Mironov, Vladimir, Shchugoreva, Irina A., Artyushenko, Polina V., Morozov, Dmitry, Borbone, Nicola, Oliviero, Giorgia, Zamay, Tatiana N., Moryachkov, Roman V., Kolovskaya, Olga S., Lukyanenko, Kirill A., Song, Yangling, Merkuleva, Iuliia A., Zabluda, Vladimir N., Peters, Georgy, Koroleva, Lyudmila S., Veprintsev, Dmitry V., Glazyrin, Yury E., Volosnikova, Ekaterina A., Belenkaya, Svetlana V., Esina, Tatiana I., Isaeva, Anastasiya A., Nesmeyanova, Valentina S., Shanshin, Daniil V., Berlina, Anna N., Komova, Nadezhda S., Svetlichnyi, Valery A., Silnikov, Vladimir N., Shcherbakov, Dmitriy N., Zamay, Galina S., Zamay, Sergey S., Smolyarova, Tatyana, Tikhonova, Elena P., Chen, Kelvin H. -C., Jeng, U-Ser, Condorelli, Gerolama, de Franciscis, Vittorio, Groenhof, Gerrit, Yang, Chaoyong, Moskovsky, Alexander A., Fedorov, Dmitri G., Tomilin, Felix N., Tan, Weihong, Alexeev, Yuri, Berezovski, Maxim V., and Kichkailo, Anna S

Subjects
oligonukleotidit, aptamers, fragment molecular orbitals method, molecular dynamics, SARS-CoV-2, SAXS, fragment molecular orbitals method, SARS-CoV-2, SELEX Aptamer Technique, Organic Chemistry, aptamers, SARS-CoV-2-virus, COVID-19, SAXS, General Chemistry, Aptamers, Nucleotide, Molecular Dynamics Simulation, laskennallinen kemia, molecular dynamics, Catalysis, lääkesuunnittelu, Molecular Docking Simulation, SARS-CoV-2, белки, Spike Glycoprotein, Coronavirus, Humans, дизайн аптамеров, molekyylidynamiikka, proteiinit
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.

Published
2022

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