Natural Products from Red Algal Genus Laurencia as Potential Inhibitors of RdRp and nsp15 Enzymes of SARS-CoV-2: An In Silico Perspective
Электронный научный архив УРФУ
Информация об архиве | Просмотр оригинала| Поле | Значение | |
| Заглавие |
Natural Products from Red Algal Genus Laurencia as Potential Inhibitors of RdRp and nsp15 Enzymes of SARS-CoV-2: An In Silico Perspective
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| Автор |
Pokharkar, O.
Anumolu, H. Zyryanov, G. V. Tsurkan, M. V. |
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| Тематика |
ANTI-VIRAL
COVID-19 ENDORIBONUCLEASE LAURENCIA NATURAL PRODUCTS NSP12 NSP15 RDRP RED ALGAE SARS-COV-2 1 METHYL 2 3 5 TRIBROMOINDOLE 10S 10 BROMO 9 HYDROXYCHAMIGRA 2 7 14 DIENE 15 HYDROXYLAURENE 15 OXOLAURENE 6,8-CYCLOEUDESMAN 7 HYDROXYLAURENE 8 10 DIBROMOISOAPLYSIN 9 DEOXYELATOL ALDINGENIN C ALKALOID ALMADIOXIDE ANTIVIRUS AGENT APLYSIOLIC ACID ARISTOLANE AROMADENDRENE AXINYSONE B BOSSEOPENTANOIC ACID BROMOCUPARENE BROMOPHYCOLIDE CAESPITAN CAESSPITENONE CALLOPHYCOIC ACID CHINZALLENE CHOLEST 5 EN 3 ALPHA OL COMPOSITACIN C GAMMA INTERFERON GELATINASE B IMMUNOGLOBULIN ENHANCER BINDING PROTEIN ISODIHYDROLAURENE ISOLAURALLENE ISOLAUREATIN ITOMANINDOLE A LAUREFURENYNE B LAURENCOMPOSIDIENE LAURENENYNE LAURENISOL LAURENOKOMARIN LAUREPINNACIN LAUREPOXYENE LUZOFURAN LUZONDIOL LUZONENONE MAILIONE MAJAPOLENE A NONSTRUCTURAL PROTEIN 12 NONSTRUCTURAL PROTEIN 15 OCTADECANEDIOIC ACID ORGANIC COMPOUND PACIFENOL PANNOSANE PERFORENONE A PROTEIN RHODOPHYTIN RNA DIRECTED RNA POLYMERASE UNCLASSIFIED DRUG ACUTE TOXICITY ANTIBACTERIAL ACTIVITY ANTIFUNGAL ACTIVITY ANTIINFLAMMATORY ACTIVITY ANTINEOPLASTIC ACTIVITY ARTICLE BINDING AFFINITY COMPUTER MODEL CORONAVIRUS DISEASE 2019 CYTOKINE RELEASE DRUG BIOAVAILABILITY ELECTRON MICROSCOPY EYE IRRITATION EYE TOXICITY HUMAN HYDROGEN BOND IMMUNOTOXICITY LAURENCIA LD50 LIVER TOXICITY MOLECULAR DOCKING MOLECULAR DYNAMICS PHARMACOKINETICS RESPIRATORY DISTRESS SYNDROME SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS 2 SIMULATION SKIN SENSITIZATION SKIN TOXICITY THREE-DIMENSIONAL IMAGING TOXICITY TESTING WATER SOLUBILITY X RAY DIFFRACTION |
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| Описание |
The genus Laurencia, a category of marine red algae, is well recognized for producing a large variety of natural products (NPs) that are both chemically intriguing and structurally distinct. The aim of this research was to identify NPs with potential anti-SARS-CoV-2 activity. The crystals of the proteins RdRp and nsp15 were obtained from the RCSB protein database. About 300 NPs were discovered using the PubChem, ChemSpider, and CMNPD databases. The program Autodock Vina was used to conduct the molecular docking procedure once the proteins and ligands were prepared. Before running MD simulations using the CABS-flex 2.0 website, binding affinity assessments and interactions between amino acids were carefully reviewed. Only nine NPs were shortlisted to be examined further. Bromophycolide R, S, and bromophycoic acid C show the tendency to inhibit RdRp by β-hairpin motif binding at the N-terminal known as Active site 2 (AS2), whereas the other four NPs, bromophycolide E, H, P, and thyrsenol A, may effectively inhibit RdRp through interactions via C-terminal, also known as the Active site 1 (AS1). For the enzyme nsp15, bromophycoic B, C, and floridoside showed plausible interactions. In conclusion, out of nine, seven candidates shortlisted for RdRp exhibited strong interactions with the key residues in the AS1 and AS2 regions. Bromophycoic acid C may work as a dual inhibitor due to its favorable interactions with the nsp15 protein and RdRp’s N-terminal, with affinities of −8.5 and −8.2 kcal/mol, respectively. © 2023 by the authors.
Ministry of Education and Science of the Russian Federation, Minobrnauka: 075-15-2022-1118 This research was funded by the Ministry of Science and Higher Education of the Russian Federation (Reference # 075-15-2022-1118, dated 29 June 2022). |
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| Дата |
2024-04-05T16:34:23Z
2024-04-05T16:34:23Z 2023 |
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| Тип |
Article
Journal article (info:eu-repo/semantics/article) |info:eu-repo/semantics/publishedVersion |
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| Идентификатор |
Pokharkar, O, Anumolu, H, Zyryanov, GV & Tsurkan, MV 2023, 'Natural Products from Red Algal Genus Laurencia as Potential Inhibitors of RdRp and nsp15 Enzymes of SARS-CoV-2: An In Silico Perspective', Microbiology Research, Том. 14, № 3, стр. 1020-1048. https://doi.org/10.3390/microbiolres14030069
Pokharkar, O., Anumolu, H., Zyryanov, G. V., & Tsurkan, M. V. (2023). Natural Products from Red Algal Genus Laurencia as Potential Inhibitors of RdRp and nsp15 Enzymes of SARS-CoV-2: An In Silico Perspective. Microbiology Research, 14(3), 1020-1048. https://doi.org/10.3390/microbiolres14030069 2036-7473 Final All Open Access, Gold, Green https://www.scopus.com/inward/record.uri?eid=2-s2.0-85173569279&doi=10.3390%2fmicrobiolres14030069&partnerID=40&md5=9ba8f6dbc697b99b31142471288cf8d1 https://www.mdpi.com/2036-7481/14/3/69/pdf?version=1690791510 http://elar.urfu.ru/handle/10995/130849 10.3390/microbiolres14030069 85173569279 001076183800001 |
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| Язык |
en
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| Права |
Open access (info:eu-repo/semantics/openAccess)
cc-by https://creativecommons.org/licenses/by/4.0/ |
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| Формат |
application/pdf
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| Издатель |
Multidisciplinary Digital Publishing Institute (MDPI)
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| Источник |
Microbiology Research
Microbiology Research |
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