Structure‐ and Interaction‐Based Design of Anti‐SARS‐CoV‐2 Aptamers
| العنوان: | Structure‐ and Interaction‐Based Design of Anti‐SARS‐CoV‐2 Aptamers |
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| المؤلفون: | 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 |
| المساهمون: | 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., Kichkailo, Anna S |
| المصدر: | Chemistry-A European journal. 2022. Vol. 28, № 12. P. e202104481 (1-16) Chemistry, vol 28 |
| بيانات النشر: | Wiley, 2022. |
| سنة النشر: | 2022 |
| مصطلحات موضوعية: | 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 |
| الوصف: | 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. |
| وصف الملف: | application/pdf; fulltext |
| تدمد: | 1521-3765 0947-6539 |
| URL الوصول: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b6a4c66c212c1d452a13ece0e2edfec3 https://doi.org/10.1002/chem.202104481 |
| حقوق: | OPEN |
| رقم الأكسشن: | edsair.doi.dedup.....b6a4c66c212c1d452a13ece0e2edfec3 |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 15213765 09476539 |
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