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3. Natural Antibodies Produced in Vaccinated Patients and COVID-19 Convalescents Hydrolyze Recombinant RBD and Nucleocapsid (N) Proteins.

Author

Timofeeva, Anna M., Shayakhmetova, Liliya Sh., Nikitin, Artem O., Sedykh, Tatyana A., Matveev, Andrey L., Shanshin, Daniil V., Volosnikova, Ekaterina A., Merkuleva, Iuliia A., Shcherbakov, Dmitriy N., Tikunova, Nina V., Sedykh, Sergey E., and Nevinsky, Georgy A.

Subjects
COVID-19, CYTOSKELETAL proteins, RECOMBINANT proteins, IMMUNOGLOBULINS, SARS-CoV-2
Abstract

Antibodies are protein molecules whose primary function is to recognize antigens. However, recent studies have demonstrated their ability to hydrolyze specific substrates, such as proteins, oligopeptides, and nucleic acids. In 2023, two separate teams of researchers demonstrated the proteolytic activity of natural plasma antibodies from COVID-19 convalescents. These antibodies were found to hydrolyze the S-protein and corresponding oligopeptides. Our study shows that for antibodies with affinity to recombinant structural proteins of the SARS-CoV-2: S-protein, its fragment RBD and N-protein can only hydrolyze the corresponding protein substrates and are not cross-reactive. By using strict criteria, we have confirmed that this proteolytic activity is an intrinsic property of antibodies and is not caused by impurities co-eluting with them. This discovery suggests that natural proteolytic antibodies that hydrolyze proteins of the SARS-CoV-2 virus may have a positive impact on disease pathogenesis. It is also possible for these antibodies to work in combination with other antibodies that bind specific epitopes to enhance the process of virus neutralization. [ABSTRACT FROM AUTHOR]

Published
2024
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4. Pre-Pandemic Cross-Reactive Immunity against SARS-CoV-2 among Siberian Populations

Author

Shaprova, Olga N., primary, Shanshin, Daniil V., additional, Kolosova, Evgeniia A., additional, Borisevich, Sophia S., additional, Soroka, Artem A., additional, Merkuleva, Iuliia A., additional, Nikitin, Artem O., additional, Volosnikova, Ekaterina A., additional, Ushkalenko, Nikita D., additional, Zaykovskaya, Anna V., additional, Pyankov, Oleg V., additional, Elchaninova, Svetlana A., additional, Shcherbakov, Dmitry N., additional, and Ilyicheva, Tatiana N., additional

Published
2023
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5. Corrigendum: The main protease 3CLpro of the SARS-CoV-2 virus: how to turn an enemy into a helper

Author

Belenkaya, Svetlana V., primary, Merkuleva, Iuliia A., additional, Yarovaya, Olga I., additional, Chirkova, Varvara Yu, additional, Sharlaeva, Elena A., additional, Shanshin, Daniil V., additional, Volosnikova, Ekaterina A., additional, Vatsadze, Sergey Z., additional, Khvostov, Mikhail V., additional, Salakhutdinov, Nariman F., additional, and Shcherbakov, Dmitriy, additional

Published
2023
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6. Biochemical Properties of a Promising Milk-Clotting Enzyme, Moose (Alces alces) Recombinant Chymosin

Author

Vladimirovna, Balabova Dina, primary, Alekseevna, Belash Ekaterina, additional, Valeryevna, Belenkaya Svetlana, additional, Nikolayevich, Shcherbakov Dmitry, additional, Nikolayevich, Belov Alexander, additional, Dmitrievich, Koval Anatoly, additional, Vladimirovna, Mironova Anna, additional, Anatolievich, Bondar Alexander, additional, Alexandrovna, Volosnikova Ekaterina, additional, Grigorievich, Arkhipov Sergey, additional, Olegovna, Sokolova Olga, additional, Yurievna, Chirkova Varvara, additional, and Valentinovich, Elchaninov Vadim, additional

Published
2023
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7. The main protease 3CLpro of the SARS-CoV-2 virus: how to turn an enemy into a helper

Author

Belenkaya, Svetlana V., primary, Merkuleva, Iuliia A., additional, Yarovaya, Olga I., additional, Chirkova, Varvara Yu., additional, Sharlaeva, Elena A., additional, Shanshin, Daniil V., additional, Volosnikova, Ekaterina A., additional, Vatsadze, Sergey Z., additional, Khvostov, Mikhail V., additional, Salakhutdinov, Nariman F., additional, and Shcherbakov, Dmitriy N., additional

Published
2023
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8. SARS-CoV-2 RBD Conjugated to Polyglucin, Spermidine, and dsRNA Elicits a Strong Immune Response in Mice

Author

Volosnikova, Ekaterina A., primary, Merkuleva, Iuliia A., additional, Esina, Tatiana I., additional, Shcherbakov, Dmitry N., additional, Borgoyakova, Mariya B., additional, Isaeva, Anastasiya A., additional, Nesmeyanova, Valentina S., additional, Volkova, Natalia V., additional, Belenkaya, Svetlana V., additional, Zaykovskaya, Anna V., additional, Pyankov, Oleg V., additional, Starostina, Ekaterina V., additional, Zadorozhny, Alexey M., additional, Zaitsev, Boris N., additional, Karpenko, Larisa I., additional, Ilyichev, Alexander A., additional, and Danilenko, Elena D., additional

Published
2023
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9. Biochemical Properties of a Promising Milk-Clotting Enzyme, Moose (Alces alces) Recombinant Chymosin.

Author

Balabova, Dina V., Belash, Ekaterina A., Belenkaya, Svetlana V., Shcherbakov, Dmitry N., Belov, Alexander N., Koval, Anatoly D., Mironova, Anna V., Bondar, Alexander A., Volosnikova, Ekaterina A., Arkhipov, Sergey G., Sokolova, Olga O., Chirkova, Varvara Y., and Elchaninov, Vadim V.

Subjects
COAGULANTS, MOOSE, KLUYVEROMYCES marxianus, CHEESEMAKING, PROTEOLYTIC enzymes, AMMONIUM sulfate, THERMAL stability, BLOOD coagulation
Abstract

Moose (Alces alces) recombinant chymosin with a milk-clotting activity of 86 AU/mL was synthesized in the Kluyveromyces lactis expression system. After precipitation with ammonium sulfate and chromatographic purification, a sample of genetically engineered moose chymosin with a specific milk-clotting activity of 15,768 AU/mg was obtained, which was used for extensive biochemical characterization of the enzyme. The threshold of the thermal stability of moose chymosin was 55 °C; its complete inactivation occurred after heating at 60 °C. The total proteolytic activity of moose chymosin was 0.332 A280 units. The ratio of milk-clotting and total proteolytic activities of the enzyme was 0.8. The Km, kcat and kcat/Km values of moose chymosin were 4.7 μM, 98.7 s−1, and 21.1 μM−1 s−1, respectively. The pattern of change in the coagulation activity as a function of pH and Ca2+ concentration was consistent with the requirements for milk coagulants for cheese making. The optimum temperature of the enzyme was 50–55 °C. The introduction of Mg2+, Zn2+, Co2+, Ba2+, Fe2+, Mn2+, Ca2+, and Cu2+ into milk activated the coagulation ability of moose chymosin, while Ni ions on the contrary inhibited its activity. Using previously published data, we compared the biochemical properties of recombinant moose chymosin produced in bacterial (Escherichia coli) and yeast (K. lactis) producers. [ABSTRACT FROM AUTHOR]

Published
2023
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11. Natural IgG against S-Protein and RBD of SARS-CoV-2 Do Not Bind and Hydrolyze DNA and Are Not Autoimmune

Author

Timofeeva, Anna M., primary, Sedykh, Sergey E., additional, Ermakov, Evgeny A., additional, Matveev, Andrey L., additional, Odegova, Eva I., additional, Sedykh, Tatiana A., additional, Shcherbakov, Dmitry N., additional, Merkuleva, Iuliia A., additional, Volosnikova, Ekaterina A., additional, Nesmeyanova, Valentina S., additional, Tikunova, Nina V., additional, and Nevinsky, Georgy A., additional

Published
2022
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14. Antibodies to the Spike Protein Receptor-Binding Domain of SARS-CoV-2 at 4–13 Months after COVID-19

Author

Kolosova, Evgeniia A., primary, Shaprova, Olga N., additional, Shanshin, Daniil V., additional, Nesmeyanova, Valentina S., additional, Merkuleva, Iuliia A., additional, Belenkaya, Svetlana V., additional, Isaeva, Anastasiya A., additional, Nikitin, Artem O., additional, Volosnikova, Ekaterina A., additional, Nikulina, Yuliya A., additional, Nikonorova, Marina A., additional, Shcherbakov, Dmitry N., additional, and Elchaninova, Svetlana A., additional

Published
2022
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15. Are Hamsters a Suitable Model for Evaluating the Immunogenicity of RBD-Based Anti-COVID-19 Subunit Vaccines?

Author

Merkuleva, Iuliia A., primary, Shcherbakov, Dmitry N., additional, Borgoyakova, Mariya B., additional, Isaeva, Anastasiya A., additional, Nesmeyanova, Valentina S., additional, Volkova, Natalia V., additional, Aripov, Vazirbek S., additional, Shanshin, Daniil V., additional, Karpenko, Larisa I., additional, Belenkaya, Svetlana V., additional, Kazachinskaia, Elena I., additional, Volosnikova, Ekaterina A., additional, Esina, Tatiana I., additional, Sergeev, Alexandr A., additional, Titova, Kseniia A., additional, Konyakhina, Yulia V., additional, Zaykovskaya, Anna V., additional, Pyankov, Oleg V., additional, Kolosova, Evgeniia A., additional, Viktorina, Olesya E., additional, Shelemba, Arseniya A., additional, Rudometov, Andrey P., additional, and Ilyichev, Alexander A., additional

Published
2022
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16. Structure‐ and Interaction‐Based Design of Anti‐SARS‐CoV‐2 Aptamers

Author

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

Published
2022
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17. Self-Assembled Particles Combining SARS-CoV-2 RBD Protein and RBD DNA Vaccine Induce Synergistic Enhancement of the Humoral Response in Mice

Author

Borgoyakova, Mariya B., primary, Karpenko, Larisa I., additional, Rudometov, Andrey P., additional, Volosnikova, Ekaterina A., additional, Merkuleva, Iuliia A., additional, Starostina, Ekaterina V., additional, Zadorozhny, Alexey M., additional, Isaeva, Anastasiya A., additional, Nesmeyanova, Valentina S., additional, Shanshin, Daniil V., additional, Baranov, Konstantin O., additional, Volkova, Natalya V., additional, Zaitsev, Boris N., additional, Orlova, Lyubov A., additional, Zaykovskaya, Anna V., additional, Pyankov, Oleg V., additional, Danilenko, Elena D., additional, Bazhan, Sergei I., additional, Shcherbakov, Dmitry N., additional, Taranin, Alexander V., additional, and Ilyichev, Alexander A., additional

Published
2022
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18. Comparative Immunogenicity of the Recombinant Receptor-Binding Domain of Protein S SARS-CoV-2 Obtained in Prokaryotic and Mammalian Expression Systems

Author

Merkuleva, Iuliia A., primary, Shcherbakov, Dmitry N., additional, Borgoyakova, Mariya B., additional, Shanshin, Daniil V., additional, Rudometov, Andrey P., additional, Karpenko, Larisa I., additional, Belenkaya, Svetlana V., additional, Isaeva, Anastasiya A., additional, Nesmeyanova, Valentina S., additional, Kazachinskaia, Elena I., additional, Volosnikova, Ekaterina A., additional, Esina, Tatiana I., additional, Zaykovskaya, Anna V., additional, Pyankov, Oleg V., additional, Borisevich, Sophia S., additional, Shelemba, Arseniya A., additional, Chikaev, Anton N., additional, and Ilyichev, Alexander A., additional

Published
2022
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19. Design and Evaluation of Bispidine-Based SARS-CoV-2 Main Protease Inhibitors

Author

Shcherbakov, Dmitriy, primary, Baev, Dmitriy, additional, Kalinin, Mikhail, additional, Dalinger, Alexander, additional, Chirkova, Varvara, additional, Belenkaya, Svetlana, additional, Khvostov, Aleksei, additional, Krut’ko, Dmitry, additional, Medved’ko, Aleksei, additional, Volosnikova, Ekaterina, additional, Sharlaeva, Elena, additional, Shanshin, Daniil, additional, Tolstikova, Tatyana, additional, Yarovaya, Olga, additional, Maksyutov, Rinat, additional, Salakhutdinov, Nariman, additional, and Vatsadze, Sergey, additional

Published
2021
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20. Delivery of mRNA Vaccine against SARS-CoV-2 Using a Polyglucin:Spermidine Conjugate

Author

Karpenko, Larisa I., primary, Rudometov, Andrey P., additional, Sharabrin, Sergei V., additional, Shcherbakov, Dmitry N., additional, Borgoyakova, Mariya B., additional, Bazhan, Sergei I., additional, Volosnikova, Ekaterina A., additional, Rudometova, Nadezhda B., additional, Orlova, Lyubov A., additional, Pyshnaya, Inna A., additional, Zaitsev, Boris N., additional, Volkova, Natalya V., additional, Azaev, Mamedyar Sh., additional, Zaykovskaya, Anna V., additional, Pyankov, Oleg V., additional, and Ilyichev, Alexander A., additional

Published
2021
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21. Cationic Polymers for the Delivery of the Ebola DNA Vaccine Encoding Artificial T-Cell Immunogen

Author

Karpenko, Larisa I., primary, Apartsin, Evgeny K., additional, Dudko, Sergei G., additional, Starostina, Ekaterina V., additional, Kaplina, Olga N., additional, Antonets, Denis V., additional, Volosnikova, Ekaterina A., additional, Zaitsev, Boris N., additional, Bakulina, Anastasiya Yu., additional, Venyaminova, Aliya G., additional, Ilyichev, Alexander A., additional, and Bazhan, Sergei I., additional

Published
2020
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23. Cover Feature: Structure‐ and Interaction‐Based Design of Anti‐SARS‐CoV‐2 Aptamers (Chem. Eur. J. 12/2022).

Author

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, Yanling, Merkuleva, Iuliia A., Zabluda, Vladimir N., Peters, Georgy, Koroleva, Lyudmila S., Veprintsev, Dmitry V., Glazyrin, Yury E., Volosnikova, Ekaterina A., Belenkaya, Svetlana V., and Esina, Tatiana I.

Subjects
MOLECULAR orbitals, MOLECULAR dynamics, APTAMERS, SMALL-angle X-ray scattering
Abstract

Keywords: aptamers; fragment molecular orbitals method; molecular dynamics; SARS-CoV-2; SAXS EN aptamers fragment molecular orbitals method molecular dynamics SARS-CoV-2 SAXS 1 1 1 02/28/22 20220224 NES 220224 B Digital drug design reveals DNA aptamers binding SARS-CoV-2 b : A hybrid in silico et vitro approach, structure and interaction-based drug design, has been developed to create highly specific DNA aptamers for the receptor-binding domain of the SARS-CoV-2 spike protein. The structure and binding affinity of the aptamers were validated by small-angle X-ray scattering, flow cytometry, and fluorescence polarization. Cover Feature: Structure- and Interaction-Based Design of Anti-SARS-CoV-2 Aptamers (Chem. Eur. J. 12/2022). [Extracted from the article]

Published
2022
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24. 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

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

Author

Mironov V, Shchugoreva IA, Artyushenko PV, Morozov D, Borbone N, Oliviero G, Zamay TN, Moryachkov RV, Kolovskaya OS, Lukyanenko KA, Song Y, Merkuleva IA, Zabluda VN, Peters G, Koroleva LS, Veprintsev DV, Glazyrin YE, Volosnikova EA, Belenkaya SV, Esina TI, Isaeva AA, Nesmeyanova VS, Shanshin DV, Berlina AN, Komova NS, Svetlichnyi VA, Silnikov VN, Shcherbakov DN, Zamay GS, Zamay SS, Smolyarova T, Tikhonova EP, Chen KH, Jeng US, Condorelli G, de Franciscis V, Groenhof G, Yang C, Moskovsky AA, Fedorov DG, Tomilin FN, Tan W, Alexeev Y, Berezovski MV, and Kichkailo AS

Subjects
Humans, Molecular Docking Simulation, Molecular Dynamics Simulation, SARS-CoV-2, SELEX Aptamer Technique, Spike Glycoprotein, Coronavirus, Aptamers, Nucleotide chemistry, COVID-19
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., (© 2022 Wiley-VCH GmbH.)

Published
2022
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