Natural Products from Marine Actinomycete Genus Salinispora Might Inhibit 3CLpro and PLpro Proteins of SARS-CoV-2: An In Silico Evidence
Электронный научный архив УРФУ
Информация об архиве | Просмотр оригинала| Поле | Значение | |
| Заглавие |
Natural Products from Marine Actinomycete Genus Salinispora Might Inhibit 3CLpro and PLpro Proteins of SARS-CoV-2: An In Silico Evidence
|
|
| Автор |
Pokharkar, O.
Zyryanov, G. V. Tsurkan, M. V. |
|
| Тематика |
3CLPRO
ANTIVIRAL MPRO MARINE DRUGS NATURAL PRODUCTS PLPRO REPURPOSING S. ARENICOLA S. PACIFICA S. TROPICA SALINISPORA SARS-COV-2 27 O DEMETHYL 25 O DESACETYLRIFAMYCIN 3 AMINO 2 METHYL N (1R)-1 (NAPHTHALEN 1 YL) ETHYL BENZAMIDE 7 TRIHYDROXY 2 PHENYL 4H CHROMEN 4 ONE ANTIPROTEALIDE ARENAMIDE A ARENAMIDE B ARENAMIDE C CORONAVIRUS 3C PROTEASE CYCLOMARAZINE A CYCLOMARIN A CYCLOMARIN D DEFEROXAMINE EMERICELLAMIDE IKARUGAMYCIN LOMAIVITICIN LOMAIVITICIN A LOMAIVITICIN D LOMAIVITICIN E LYMPHOSTIN LYMPHOSTINOL MYCALAMIDE A N (3 OXODECANOYL) L HOMOSERINE LACTONE N (3 OXODODECANOYL)HOMOSERINE LACTONE NATURAL PRODUCT NEOLYMPHOSTIN A NEOLYMPHOSTIN B NEOLYMPHOSTIN C NEOLYMPHOSTIN D PACIFICANONE A PACIFICANONE B PAPAIN-LIKE PROTEASE RETIMYCIN A RETIMYCIN B SALINAPHTHOQUINONE B SALINICHELIN B SALINICHELIN C SALINILACTONE A SALINILACTONE B SALINILACTONE C SALINILACTONE D SALINILACTONE E SALINILACTONE F SALINILACTONE G SALINILACTONE H SALINIPOSTIN A SALINIPOSTIN B SALINIPOSTIN C SALINIPOSTIN D SALINIPOSTIN E SALINIPOSTIN F SALINIPOSTIN G SALINIPOSTIN H SALINIPOSTIN K SALINOSPORAMIDE B SALINOSPORAMIDE C SALINOSPORAMIDE D SALINOSPORAMIDE E SALINOSPORAMIDE F SALINOSPORAMIDE G SALINOSPORAMIDE H TIRANDALYDIGIN UNCLASSIFIED DRUG ACTINOBACTERIA ANTIVIRAL ACTIVITY ARTICLE BINDING AFFINITY BIOAVAILABILITY BLOOD BRAIN BARRIER COMPUTER MODEL CONTROLLED STUDY COVALENT BOND CRYSTAL STRUCTURE DYSPNEA HYDROGEN BOND HYDROPHOBICITY IMMUNE RESPONSE MOLECULAR DOCKING MOLECULAR DYNAMICS MUCORMYCOSIS NONHUMAN PHARMACOKINETIC PARAMETERS SALINISPORA SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS 2 SIMULATION THREE-DIMENSIONAL IMAGING TOXICITY TESTING TWO-DIMENSIONAL IMAGING X RAY DIFFRACTION |
|
| Описание |
Among the oldest marine species on the planet, the genus Salinispora is often encountered inhabiting sediments and other marine creatures in tropical and subtropical marine settings. This bacterial genus produces a plethora of natural products. The purpose of this study was to examine the potential for salinispora-based natural products (NPs) to combat the SARS-CoV-2 virus. The RCSB PDB was used to obtain the crystal structures of proteins 3CLpro and PLpro. All 125 NPs were obtained from online databases. Using Autodock Vina software v1.2.0 the molecular docking process was carried out after the proteins and ligands were prepared. Assessments of binding affinities and interacting amino acids were rigorously examined prior to MD simulations. The docking experiments revealed 35 NPs in total for both 3CLpro and PLpro, with high docking scores ranging from −8.0 kcal/mol to −9.0 kcal/mol. However, a thorough binding residue analyses of all docked complexes filtered nine NPs showing strong interactions with HIS: 41 and CYS: 145 of 3CLpro. Whereas, for PLpro, merely six NPs presented good interactions with residues CYS: 111, HIS: 272, and ASP: 286. Further research was conducted on residue–residue and ligand–residue interactions in both the filtered docked complexes and the Apo-protein structures using the Protein Contacts Atlas website. All complexes were found to be stable in CABS-flex 2.0 MD simulations conducted at various time frames (50, 125, 500, and 1000 cycles). In conclusion, salinaphthoquinone B appears to be the most promising metabolite, based on favorable amino acid interactions forming stable confirmations towards 3CLpro and PLpro enzymes, acting as a dual inhibitor. © 2023 by the authors.
Ministry of Science and Higher Education of the Russian Federation: 075-15-2022-1118 O.P. and G.V.Z. are thankful to the Ministry of Science and Education of RF (Agreement # 075-15-2022-1118 dated 29 June 2022) for funding. |
|
| Дата |
2024-04-05T16:38:35Z
2024-04-05T16:38:35Z 2023 |
|
| Тип |
Article
Journal article (info:eu-repo/semantics/article) |info:eu-repo/semantics/publishedVersion |
|
| Идентификатор |
Pokharkar, O, Zyryanov, G & Tsurkan, M 2023, 'Natural Products from Marine Actinomycete Genus Salinispora Might Inhibit 3CLpro and PLpro Proteins of SARS-CoV-2: An In Silico Evidence', Microbiology Research, Том. 14, № 4, стр. 1907-1941. https://doi.org/10.3390/microbiolres14040130
Pokharkar, O., Zyryanov, G., & Tsurkan, M. (2023). Natural Products from Marine Actinomycete Genus Salinispora Might Inhibit 3CLpro and PLpro Proteins of SARS-CoV-2: An In Silico Evidence. Microbiology Research, 14(4), 1907-1941. https://doi.org/10.3390/microbiolres14040130 2036-7473 Final All Open Access, Gold https://www.scopus.com/inward/record.uri?eid=2-s2.0-85180651227&doi=10.3390%2fmicrobiolres14040130&partnerID=40&md5=de82556cb5df0f0ea91eff8ff9536e0d https://www.mdpi.com/2036-7481/14/4/130/pdf?version=1700042435 http://elar.urfu.ru/handle/10995/131079 10.3390/microbiolres14040130 85180651227 001132291400001 |
|
| Язык |
en
|
|
| Права |
Open access (info:eu-repo/semantics/openAccess)
cc-by https://creativecommons.org/licenses/by/4.0/ |
|
| Формат |
application/pdf
|
|
| Издатель |
Multidisciplinary Digital Publishing Institute (MDPI)
|
|
| Источник |
Microbiology Research
Microbiology Research |
|