In silico screening of the effectiveness of natural compounds from algae as SARS-CoV-2 inhibitors: molecular docking, ADMT profile and molecular dynamic studies

Marine species are known as rich sources of metabolites largely involved in the pharmaceutical industry. This study aimed to evaluate in silico the effect of natural compounds identified in algae on the SARS-CoV-2 Main protease, RNA-dependent-RNA polymerase activity (RdRp), endoribonuclease (NSP15)...

Full description

Saved in:
Bibliographic Details
Published in:Journal of biomolecular structure & dynamics 2023-05, Vol.41 (7), p.3129-3144
Main Authors: Mohammed Ali, Hani S. H., Altayb, Hisham N., Bayoumi, Ahmed Atef Mohamed, El Omri, Abdelfatteh, Firoz, Ahmad, Chaieb, Kamel
Format: Article
Language:English
Subjects:
ADMT
Algae
antiviral
COVID-19
Humans
in silico study
molecular docking
Molecular Docking Simulation
molecular dynamics
Molecular Dynamics Simulation
RNA-Dependent RNA Polymerase
SARS-CoV-2
Spike Glycoprotein, Coronavirus
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
cited_by cdi_FETCH-LOGICAL-c366t-9d099d966a07ced067869be250079ca3c87f9f180b099338062f94e2f6d748253
cites cdi_FETCH-LOGICAL-c366t-9d099d966a07ced067869be250079ca3c87f9f180b099338062f94e2f6d748253
container_end_page 3144
container_issue 7
container_start_page 3129
container_title Journal of biomolecular structure & dynamics
container_volume 41
creator Mohammed Ali, Hani S. H.
Altayb, Hisham N.
Bayoumi, Ahmed Atef Mohamed
El Omri, Abdelfatteh
Firoz, Ahmad
Chaieb, Kamel
description Marine species are known as rich sources of metabolites largely involved in the pharmaceutical industry. This study aimed to evaluate in silico the effect of natural compounds identified in algae on the SARS-CoV-2 Main protease, RNA-dependent-RNA polymerase activity (RdRp), endoribonuclease (NSP15) as well as on their interaction with viral spike protein. A total of 45 natural compounds were screened for their possible interaction on SARS-CoV-2 target proteins using Maestro interface for molecular docking, molecular dynamic (MD) simulation to estimate compounds binding affinities. Among the algal compounds screened in this study, three (Laminarin, Astaxanthin and 4'-chlorostypotriol triacetate) exhibited the lowest docking energy and best interaction with SARS-CoV-2 viral proteins (Main protease, RdRp, Nsp15, and spike protein). The complex of the main protease with laminarin shows the most stable RMSD during a 150 ns MD simulation time. Which indicates their possible inhibitory activity on SARS-CoV-2. Communicated by Ramaswamy H. Sarma
doi_str_mv 10.1080/07391102.2022.2046640
format article
fullrecord <record><control><sourceid>proquest_pubme</sourceid><recordid>TN_cdi_pubmed_primary_35253618</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>2636876524</sourcerecordid><originalsourceid>FETCH-LOGICAL-c366t-9d099d966a07ced067869be250079ca3c87f9f180b099338062f94e2f6d748253</originalsourceid><addsrcrecordid>eNp9kV1vFCEUhonR2G31J2i49MKpfMww4JWbtWqTGhNbvSUsHFqUgRVmNPtv_KnOZLfGK284CXne8xIehJ5Rck6JJK9IzxWlhJ0zwpajFaIlD9CKdlw2hHXtQ7RamGaBTtBprd8IYZT29DE64R3ruKByhX5fJlxDDDbjagtACukWZ4_HO8DgPdgx_IQEtS6XyYxTMRHbPOzylFzFvuQBm3hrAJuKr9efr5tN_towHNJd2IYxl_oaDzmCnaIp2GX7fS54iddvP97gXck-xDmZ3L_MPpkhWFzHyQWoT9Ajb2KFp8d5hr68u7jZfGiuPr2_3KyvGsuFGBvliFJOCWFIb8ER0UuhtsA6QnplDbey98pTSbYzx7kkgnnVAvPC9a2cf-MMvTjsnV_1Y4I66iFUCzGaBHmqmgkuZC861s5od0BtybUW8HpXwmDKXlOiFzn6Xo5e5OijnDn3_FgxbQdwf1P3NmbgzQEIyecymF-5RKdHs4-5-GKSDVXz_3f8AcTvnro</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2636876524</pqid></control><display><type>article</type><title>In silico screening of the effectiveness of natural compounds from algae as SARS-CoV-2 inhibitors: molecular docking, ADMT profile and molecular dynamic studies</title><source>Taylor and Francis:Jisc Collections:Taylor and Francis Read and Publish Agreement 2024-2025:Science and Technology Collection (Reading list)</source><creator>Mohammed Ali, Hani S. H. ; Altayb, Hisham N. ; Bayoumi, Ahmed Atef Mohamed ; El Omri, Abdelfatteh ; Firoz, Ahmad ; Chaieb, Kamel</creator><creatorcontrib>Mohammed Ali, Hani S. H. ; Altayb, Hisham N. ; Bayoumi, Ahmed Atef Mohamed ; El Omri, Abdelfatteh ; Firoz, Ahmad ; Chaieb, Kamel</creatorcontrib><description>Marine species are known as rich sources of metabolites largely involved in the pharmaceutical industry. This study aimed to evaluate in silico the effect of natural compounds identified in algae on the SARS-CoV-2 Main protease, RNA-dependent-RNA polymerase activity (RdRp), endoribonuclease (NSP15) as well as on their interaction with viral spike protein. A total of 45 natural compounds were screened for their possible interaction on SARS-CoV-2 target proteins using Maestro interface for molecular docking, molecular dynamic (MD) simulation to estimate compounds binding affinities. Among the algal compounds screened in this study, three (Laminarin, Astaxanthin and 4'-chlorostypotriol triacetate) exhibited the lowest docking energy and best interaction with SARS-CoV-2 viral proteins (Main protease, RdRp, Nsp15, and spike protein). The complex of the main protease with laminarin shows the most stable RMSD during a 150 ns MD simulation time. Which indicates their possible inhibitory activity on SARS-CoV-2. Communicated by Ramaswamy H. Sarma</description><identifier>ISSN: 0739-1102</identifier><identifier>EISSN: 1538-0254</identifier><identifier>DOI: 10.1080/07391102.2022.2046640</identifier><identifier>PMID: 35253618</identifier><language>eng</language><publisher>England: Taylor &amp; Francis</publisher><subject>ADMT ; Algae ; antiviral ; COVID-19 ; Humans ; in silico study ; molecular docking ; Molecular Docking Simulation ; molecular dynamics ; Molecular Dynamics Simulation ; RNA-Dependent RNA Polymerase ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus</subject><ispartof>Journal of biomolecular structure &amp; dynamics, 2023-05, Vol.41 (7), p.3129-3144</ispartof><rights>2022 Informa UK Limited, trading as Taylor &amp; Francis Group 2022</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c366t-9d099d966a07ced067869be250079ca3c87f9f180b099338062f94e2f6d748253</citedby><cites>FETCH-LOGICAL-c366t-9d099d966a07ced067869be250079ca3c87f9f180b099338062f94e2f6d748253</cites><orcidid>0000-0002-2635-9383</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784,27924,27925</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/35253618$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Mohammed Ali, Hani S. H.</creatorcontrib><creatorcontrib>Altayb, Hisham N.</creatorcontrib><creatorcontrib>Bayoumi, Ahmed Atef Mohamed</creatorcontrib><creatorcontrib>El Omri, Abdelfatteh</creatorcontrib><creatorcontrib>Firoz, Ahmad</creatorcontrib><creatorcontrib>Chaieb, Kamel</creatorcontrib><title>In silico screening of the effectiveness of natural compounds from algae as SARS-CoV-2 inhibitors: molecular docking, ADMT profile and molecular dynamic studies</title><title>Journal of biomolecular structure &amp; dynamics</title><addtitle>J Biomol Struct Dyn</addtitle><description>Marine species are known as rich sources of metabolites largely involved in the pharmaceutical industry. This study aimed to evaluate in silico the effect of natural compounds identified in algae on the SARS-CoV-2 Main protease, RNA-dependent-RNA polymerase activity (RdRp), endoribonuclease (NSP15) as well as on their interaction with viral spike protein. A total of 45 natural compounds were screened for their possible interaction on SARS-CoV-2 target proteins using Maestro interface for molecular docking, molecular dynamic (MD) simulation to estimate compounds binding affinities. Among the algal compounds screened in this study, three (Laminarin, Astaxanthin and 4'-chlorostypotriol triacetate) exhibited the lowest docking energy and best interaction with SARS-CoV-2 viral proteins (Main protease, RdRp, Nsp15, and spike protein). The complex of the main protease with laminarin shows the most stable RMSD during a 150 ns MD simulation time. Which indicates their possible inhibitory activity on SARS-CoV-2. Communicated by Ramaswamy H. Sarma</description><subject>ADMT</subject><subject>Algae</subject><subject>antiviral</subject><subject>COVID-19</subject><subject>Humans</subject><subject>in silico study</subject><subject>molecular docking</subject><subject>Molecular Docking Simulation</subject><subject>molecular dynamics</subject><subject>Molecular Dynamics Simulation</subject><subject>RNA-Dependent RNA Polymerase</subject><subject>SARS-CoV-2</subject><subject>Spike Glycoprotein, Coronavirus</subject><issn>0739-1102</issn><issn>1538-0254</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2023</creationdate><recordtype>article</recordtype><recordid>eNp9kV1vFCEUhonR2G31J2i49MKpfMww4JWbtWqTGhNbvSUsHFqUgRVmNPtv_KnOZLfGK284CXne8xIehJ5Rck6JJK9IzxWlhJ0zwpajFaIlD9CKdlw2hHXtQ7RamGaBTtBprd8IYZT29DE64R3ruKByhX5fJlxDDDbjagtACukWZ4_HO8DgPdgx_IQEtS6XyYxTMRHbPOzylFzFvuQBm3hrAJuKr9efr5tN_towHNJd2IYxl_oaDzmCnaIp2GX7fS54iddvP97gXck-xDmZ3L_MPpkhWFzHyQWoT9Ajb2KFp8d5hr68u7jZfGiuPr2_3KyvGsuFGBvliFJOCWFIb8ER0UuhtsA6QnplDbey98pTSbYzx7kkgnnVAvPC9a2cf-MMvTjsnV_1Y4I66iFUCzGaBHmqmgkuZC861s5od0BtybUW8HpXwmDKXlOiFzn6Xo5e5OijnDn3_FgxbQdwf1P3NmbgzQEIyecymF-5RKdHs4-5-GKSDVXz_3f8AcTvnro</recordid><startdate>20230503</startdate><enddate>20230503</enddate><creator>Mohammed Ali, Hani S. H.</creator><creator>Altayb, Hisham N.</creator><creator>Bayoumi, Ahmed Atef Mohamed</creator><creator>El Omri, Abdelfatteh</creator><creator>Firoz, Ahmad</creator><creator>Chaieb, Kamel</creator><general>Taylor &amp; Francis</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0002-2635-9383</orcidid></search><sort><creationdate>20230503</creationdate><title>In silico screening of the effectiveness of natural compounds from algae as SARS-CoV-2 inhibitors: molecular docking, ADMT profile and molecular dynamic studies</title><author>Mohammed Ali, Hani S. H. ; Altayb, Hisham N. ; Bayoumi, Ahmed Atef Mohamed ; El Omri, Abdelfatteh ; Firoz, Ahmad ; Chaieb, Kamel</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c366t-9d099d966a07ced067869be250079ca3c87f9f180b099338062f94e2f6d748253</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2023</creationdate><topic>ADMT</topic><topic>Algae</topic><topic>antiviral</topic><topic>COVID-19</topic><topic>Humans</topic><topic>in silico study</topic><topic>molecular docking</topic><topic>Molecular Docking Simulation</topic><topic>molecular dynamics</topic><topic>Molecular Dynamics Simulation</topic><topic>RNA-Dependent RNA Polymerase</topic><topic>SARS-CoV-2</topic><topic>Spike Glycoprotein, Coronavirus</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Mohammed Ali, Hani S. H.</creatorcontrib><creatorcontrib>Altayb, Hisham N.</creatorcontrib><creatorcontrib>Bayoumi, Ahmed Atef Mohamed</creatorcontrib><creatorcontrib>El Omri, Abdelfatteh</creatorcontrib><creatorcontrib>Firoz, Ahmad</creatorcontrib><creatorcontrib>Chaieb, Kamel</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Journal of biomolecular structure &amp; dynamics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Mohammed Ali, Hani S. H.</au><au>Altayb, Hisham N.</au><au>Bayoumi, Ahmed Atef Mohamed</au><au>El Omri, Abdelfatteh</au><au>Firoz, Ahmad</au><au>Chaieb, Kamel</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>In silico screening of the effectiveness of natural compounds from algae as SARS-CoV-2 inhibitors: molecular docking, ADMT profile and molecular dynamic studies</atitle><jtitle>Journal of biomolecular structure &amp; dynamics</jtitle><addtitle>J Biomol Struct Dyn</addtitle><date>2023-05-03</date><risdate>2023</risdate><volume>41</volume><issue>7</issue><spage>3129</spage><epage>3144</epage><pages>3129-3144</pages><issn>0739-1102</issn><eissn>1538-0254</eissn><abstract>Marine species are known as rich sources of metabolites largely involved in the pharmaceutical industry. This study aimed to evaluate in silico the effect of natural compounds identified in algae on the SARS-CoV-2 Main protease, RNA-dependent-RNA polymerase activity (RdRp), endoribonuclease (NSP15) as well as on their interaction with viral spike protein. A total of 45 natural compounds were screened for their possible interaction on SARS-CoV-2 target proteins using Maestro interface for molecular docking, molecular dynamic (MD) simulation to estimate compounds binding affinities. Among the algal compounds screened in this study, three (Laminarin, Astaxanthin and 4'-chlorostypotriol triacetate) exhibited the lowest docking energy and best interaction with SARS-CoV-2 viral proteins (Main protease, RdRp, Nsp15, and spike protein). The complex of the main protease with laminarin shows the most stable RMSD during a 150 ns MD simulation time. Which indicates their possible inhibitory activity on SARS-CoV-2. Communicated by Ramaswamy H. Sarma</abstract><cop>England</cop><pub>Taylor &amp; Francis</pub><pmid>35253618</pmid><doi>10.1080/07391102.2022.2046640</doi><tpages>16</tpages><orcidid>https://orcid.org/0000-0002-2635-9383</orcidid></addata></record>
fulltext fulltext
identifier ISSN: 0739-1102
ispartof Journal of biomolecular structure & dynamics, 2023-05, Vol.41 (7), p.3129-3144
issn 0739-1102
1538-0254
language eng
recordid cdi_pubmed_primary_35253618
source Taylor and Francis:Jisc Collections:Taylor and Francis Read and Publish Agreement 2024-2025:Science and Technology Collection (Reading list)
subjects ADMT
Algae
antiviral
COVID-19
Humans
in silico study
molecular docking
Molecular Docking Simulation
molecular dynamics
Molecular Dynamics Simulation
RNA-Dependent RNA Polymerase
SARS-CoV-2
Spike Glycoprotein, Coronavirus
title In silico screening of the effectiveness of natural compounds from algae as SARS-CoV-2 inhibitors: molecular docking, ADMT profile and molecular dynamic studies
url http://sfxeu10.hosted.exlibrisgroup.com/loughborough?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-29T05%3A23%3A19IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_pubme&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=In%20silico%20screening%20of%20the%20effectiveness%20of%20natural%20compounds%20from%20algae%20as%20SARS-CoV-2%20inhibitors:%20molecular%20docking,%20ADMT%20profile%20and%20molecular%20dynamic%20studies&rft.jtitle=Journal%20of%20biomolecular%20structure%20&%20dynamics&rft.au=Mohammed%20Ali,%20Hani%20S.%20H.&rft.date=2023-05-03&rft.volume=41&rft.issue=7&rft.spage=3129&rft.epage=3144&rft.pages=3129-3144&rft.issn=0739-1102&rft.eissn=1538-0254&rft_id=info:doi/10.1080/07391102.2022.2046640&rft_dat=%3Cproquest_pubme%3E2636876524%3C/proquest_pubme%3E%3Cgrp_id%3Ecdi_FETCH-LOGICAL-c366t-9d099d966a07ced067869be250079ca3c87f9f180b099338062f94e2f6d748253%3C/grp_id%3E%3Coa%3E%3C/oa%3E%3Curl%3E%3C/url%3E&rft_id=info:oai/&rft_pqid=2636876524&rft_id=info:pmid/35253618&rfr_iscdi=true