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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Mironov, Vladimir, Shchugoreva I. A., Artyushenko P. V., Morozov D. I., Borbone N., Oliviero G., Zamay T. N., Moryachkov R. V., Kolovskaya, ., Lukyanenko K. A., Song Y. L., Merkuleva I. A., Zabluda V. N., Peters G., Koroleva L. S., Veprintsev D. V., Glazyrin Y. E., Volosnikova E. A., Belenkaya S. V., Esina T. I., Isaeva A. A., Nesmeyanova, ., Shanshin D. V., Berlina A. N., Komova N. S., Svetlichnyi V. A., Silnikov V. N., Shcherbakov D. N., Zamay G. S., Zamay S. S., Smolyarova T. E., Tikhonova E. P., Chen U. S., Jeng G., Condorelli V., Franciscis G., Groenhof C. Y., Yang A. A., Moskovsky D. G., Fedorov F. N., Tomilin F. N., Tan Y., Alexeev M. V., Berezovski A. S., Kichkailo A.S.
Заглавие : Structure- and interaction-based design of anti-SARS-CoV-2 Aptamers
Коллективы : Aptamerlab LCC; U.S. Department of Energy, Office of ScienceUnited States Department of Energy (DOE) [DE-AC02-06CH11357]; European UnionEuropean Commission [H2020-INFRAEDI-02-2018-823830, H2020-EINFRA-2015-1-675728, 872391, PRISAR2 872860]; CSC-IT center in Espoo, Finland; PRACE; Russian Foundation for Basic ResearchRussian Foundation for Basic Research (RFBR) [19-03-00043]; Ministry of Science and Higher Education of Russian Federation (state assignment of the Research Center of Biotechnology RAS); Italian Ministry of Education and ResearchMinistry of Education, Universities and Research (MIUR) [FISR2020 _00177]; Canadian Institutes of Health ResearchCanadian Institutes of Health Research (CIHR) [OV1-170353]; Russian Science FoundationRussian Science Foundation (RSF) [21-73-20240]
Место публикации : Chem. - Eur. J. - 2022. - Vol. 28, Is. 12. - Ст.e202104481. - ISSN 0947-6539, DOI 10.1002/chem.202104481. - ISSN 1521-3765(eISSN)
Примечания : Cited References: 85. - The authors are grateful to JCSS Joint Super Computer Center of the Russian Academy of Sciences – Branch of Federal State Institution “Scientific Research Institute for System Analysis of the Russian Academy of Sciences” for providing supercomputers for computer simulations. The authors thank the RSC Group (www.rscgroup.ru) and personally Mr. Oleg Gorbachev for the constant support and establishment of “The Good Hope Net Project” (www.thegoodhope.net) multifunctional non-profit anti-CoVID research project. The authors also thank the Helicon Company (www.helicon.ru) and personally Olesya Kucenko, Alexander Kolobov, Leonid Klimov for instrumental support and help with conducting fluorescence polarization assays, which were performed on a demo instrument Clariostar Plus microplate reader (BMG LABTECH, Germany). We thank Dr. Yong-Zhen Zhang for providing the genome sequence of 2019-nCoV and Dr. Xinquan Wang for providing the crystal structure of the binding domain of the SARS-2 Spike protein. The authors are grateful to Aptamerlab LCC financial support (www.aptamerlab.com). Y.A.’s work at Argonne National Laboratory was supported by the U.S. Department of Energy, Office of Science, under contract DE-AC02-06CH11357. The work of D.M. and G.G. has been done as part of the BioExcel CoE (www.bioexcel.eu), a project funded by the European Union contracts H2020-INFRAEDI-02-2018-823830 and H2020-EINFRA-2015-1-675728. D.M. and G.G. also thank the CSC-IT center in Espoo, Finland, as well as PRACE for awarding access to resource Curie-Rome based in France at GENCI. V.M. thanks Russian Foundation for Basic Research (project number 19-03-00043). A.B.’s and N.K.’s work was supported by the Ministry of Science and Higher Education of Russian Federation (state assignment of the Research Center of Biotechnology RAS). V. deF. G.C., N.B and G.O. are grateful to FISR2020 _00177 Shield, Italian Ministry of Education and Research, for funding. GC is grateful to the European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement: cONCReTE 872391; PRISAR2 872860. Use of the 13 A BioSAXS beamtime at the Taiwan Photon Source is acknowledged. The work of M.V.B was funded by the Canadian Institutes of Health Research grant OV1-170353. SAXS measurements and PIEDA analyses were funded by the Russian Science Foundation (project No 21-73-20240 for A.S.K.)
Предметные рубрики: BIOLOGICAL MACROMOLECULES
SOLUTION SCATTERING
BINDING
SPIKE
Аннотация: 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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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Cazacu, Nicoleta, Chilom, Claudia G., Iftimie, Sorina, Balasoiu, Maria, Ladygina, Valentina P., Stolyar S. V., Orelovich, Oleg L., Kovalev, Yuriy S., Rogachev, Andrey V.
Заглавие : Biogenic ferrihydrite nanoparticles produced by Klebsiella oxytoca: Characterization, physicochemical properties and bovine serum albumin interactions
Место публикации : Nanomaterials. - 2022. - Vol. 12, Is. 2. - Ст.249. - ISSN 2079-4991(eISSN), DOI 10.3390/nano12020249
Примечания : Cited References: 59. - This research was funded by JINR Themes 02-1-1107-2011/2021, 04-5-1131-2017/2021 and 04-4-1133-2018/2023 and with the financial support of the RO-JINR Projects Nos. 366/11.05.2021 (items 7, 86, 97) and 365/11.05.2021 (items 8, 87 and 98). This work also benefited from the use of the SasView application, originally developed under NSF Award DMR-0520547. SasView also contains the code developed with funding from the EU Horizon 2020 program under the SINE2020 project Grant No 654000. The APC was funded by JINR Theme 02-1-1107-2011/2021, Project No. 366/11.05.2021, item 7. This study used the infrastructure of the Applied Genetics Resource Facility of MIPT (Suport Grant 075-15-2021-684)
Предметные рубрики: MAGNETIC-PROPERTIES
REDUCTION
MOSSBAUER
FERRITIN
DOCKING
BINDING
Аннотация: The synthesis of nanoparticles inside microorganisms is an economical alternative to chemical and physical methods of nanoparticle synthesis. In this study, ferrihydrite nanoparticles synthesized by Klebsiella oxytoca bacterium in special conditions were characterized by scanning electron microscopy (SEM), energy-dispersive X-ray analysis (EDS), small-angle X-ray (SAXS), UV-Vis spectroscopy, fluorescence, fluorescence resonance energy transfer (FRET), and molecular docking. The morphology and the structure of the particles were characterized by means of SEM and SAXS. The elemental content was determined by means of the EDS method. The absorption properties of the ferrihydrite nanoparticles were investigated by UV-Vis spectroscopy. The binding mechanism of the biogenic ferrihydrite nanoparticles to Bovine Serum Albumin (BSA) protein, studied by fluorescence, showed a static and weak process, combined with FRET. Protein denaturation by temperature and urea in the presence of the ferrihydrite nanoparticles demonstrated their influence on the unfolding process. The AutoDock Vina and UCSF Chimera programs were used to predict the optimal binding site of the ferrihydrite to BSA and to find the location of the hydrophobic cavities in the sub-domain IIA of the BSA structure.
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