CovidV2, Main, Exploration, bibRecord, 000232

The potential chemical structure of anti-SARS-CoV-2 RNA-dependent RNA polymerase.

Identifieur interne : 000232 ( Main/Exploration ); précédent : 000231; suivant : 000233

The potential chemical structure of anti-SARS-CoV-2 RNA-dependent RNA polymerase.

Auteurs : Jrhau Lung [Taïwan] ; Yu-Shih Lin [Taïwan] ; Yao-Hsu Yang [Taïwan] ; Yu-Lun Chou [Taïwan] ; Li-Hsin Shu [Taïwan] ; Yu-Ching Cheng [Taïwan] ; Hung Te Liu [Taïwan] ; Ching-Yuan Wu [Taïwan]

Source :

Journal of medical virology [ 1096-9071 ] ; 2020.

RBID : pubmed:32167173

Abstract

An outbreak of coronavirus disease 2019 (COVID-19) occurred in Wuhan and it has rapidly spread to almost all parts of the world. For coronaviruses, RNA-dependent RNA polymerase (RdRp) is an important protease that catalyzes the replication of RNA from RNA template and is an attractive therapeutic target. In this study, we screened these chemical structures from traditional Chinese medicinal compounds proven to show antiviral activity in severe acute respiratory syndrome coronavirus (SARS-CoV) and the similar chemical structures through a molecular docking study to target RdRp of SARS-CoV-2, SARS-CoV, and Middle East respiratory syndrome coronavirus (MERS-CoV). We found that theaflavin has a lower idock score in the catalytic pocket of RdRp in SARS-CoV-2 (-9.11 kcal/mol), SARS-CoV (-8.03 kcal/mol), and MERS-CoV (-8.26 kcal/mol) from idock. To confirm the result, we discovered that theaflavin has lower binding energy of -8.8 kcal/mol when it docks in the catalytic pocket of SARS-CoV-2 RdRp by using the Blind Docking server. Regarding contact modes, hydrophobic interactions contribute significantly in binding and additional hydrogen bonds were found between theaflavin and RdRp. Moreover, one π-cation interaction was formed between theaflavin and Arg553 from the Blind Docking server. Our results suggest that theaflavin could be a potential SARS-CoV-2 RdRp inhibitor for further study.

DOI: 10.1002/jmv.25761
PubMed: 32167173

Affiliations:

Taïwan

Le document en format XML

<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">The potential chemical structure of anti-SARS-CoV-2 RNA-dependent RNA polymerase.</title>
<author><name sortKey="Lung, Jrhau" sort="Lung, Jrhau" uniqKey="Lung J" first="Jrhau" last="Lung">Jrhau Lung</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Research and Development, Chiayi Chang Gung Memorial Hospital, Chiayi Branch, Putzu, Taiwan.</nlm:affiliation>
<country xml:lang="fr">Taïwan</country>
<wicri:regionArea>Department of Research and Development, Chiayi Chang Gung Memorial Hospital, Chiayi Branch, Putzu</wicri:regionArea>
<wicri:noRegion>Putzu</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Lin, Yu Shih" sort="Lin, Yu Shih" uniqKey="Lin Y" first="Yu-Shih" last="Lin">Yu-Shih Lin</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Pharmacy, Chiayi Chang Gung Memorial Hospital, Chiayi Branch, Putzu, Taiwan.</nlm:affiliation>
<country xml:lang="fr">Taïwan</country>
<wicri:regionArea>Department of Pharmacy, Chiayi Chang Gung Memorial Hospital, Chiayi Branch, Putzu</wicri:regionArea>
<wicri:noRegion>Putzu</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Yang, Yao Hsu" sort="Yang, Yao Hsu" uniqKey="Yang Y" first="Yao-Hsu" last="Yang">Yao-Hsu Yang</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Traditional Chinese Medicine, Chang Gung Memorial Hospital, Chiayi Branch, Putzu, Taiwan.</nlm:affiliation>
<country xml:lang="fr">Taïwan</country>
<wicri:regionArea>Department of Traditional Chinese Medicine, Chang Gung Memorial Hospital, Chiayi Branch, Putzu</wicri:regionArea>
<wicri:noRegion>Putzu</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Chou, Yu Lun" sort="Chou, Yu Lun" uniqKey="Chou Y" first="Yu-Lun" last="Chou">Yu-Lun Chou</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Surgery, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan.</nlm:affiliation>
<country xml:lang="fr">Taïwan</country>
<wicri:regionArea>Department of Surgery, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung</wicri:regionArea>
<wicri:noRegion>Kaohsiung</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Shu, Li Hsin" sort="Shu, Li Hsin" uniqKey="Shu L" first="Li-Hsin" last="Shu">Li-Hsin Shu</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Traditional Chinese Medicine, Chang Gung Memorial Hospital, Chiayi Branch, Putzu, Taiwan.</nlm:affiliation>
<country xml:lang="fr">Taïwan</country>
<wicri:regionArea>Department of Traditional Chinese Medicine, Chang Gung Memorial Hospital, Chiayi Branch, Putzu</wicri:regionArea>
<wicri:noRegion>Putzu</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Cheng, Yu Ching" sort="Cheng, Yu Ching" uniqKey="Cheng Y" first="Yu-Ching" last="Cheng">Yu-Ching Cheng</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Traditional Chinese Medicine, Chang Gung Memorial Hospital, Chiayi Branch, Putzu, Taiwan.</nlm:affiliation>
<country xml:lang="fr">Taïwan</country>
<wicri:regionArea>Department of Traditional Chinese Medicine, Chang Gung Memorial Hospital, Chiayi Branch, Putzu</wicri:regionArea>
<wicri:noRegion>Putzu</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Liu, Hung Te" sort="Liu, Hung Te" uniqKey="Liu H" first="Hung Te" last="Liu">Hung Te Liu</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Traditional Chinese Medicine, Chang Gung Memorial Hospital, Chiayi Branch, Putzu, Taiwan.</nlm:affiliation>
<country xml:lang="fr">Taïwan</country>
<wicri:regionArea>Department of Traditional Chinese Medicine, Chang Gung Memorial Hospital, Chiayi Branch, Putzu</wicri:regionArea>
<wicri:noRegion>Putzu</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Wu, Ching Yuan" sort="Wu, Ching Yuan" uniqKey="Wu C" first="Ching-Yuan" last="Wu">Ching-Yuan Wu</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Traditional Chinese Medicine, Chang Gung Memorial Hospital, Chiayi Branch, Putzu, Taiwan.</nlm:affiliation>
<country xml:lang="fr">Taïwan</country>
<wicri:regionArea>Department of Traditional Chinese Medicine, Chang Gung Memorial Hospital, Chiayi Branch, Putzu</wicri:regionArea>
<wicri:noRegion>Putzu</wicri:noRegion>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PubMed</idno>
<date when="2020">2020</date>
<idno type="RBID">pubmed:32167173</idno>
<idno type="pmid">32167173</idno>
<idno type="doi">10.1002/jmv.25761</idno>
<idno type="wicri:Area/PubMed/Corpus">000560</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000560</idno>
<idno type="wicri:Area/PubMed/Curation">000560</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000560</idno>
<idno type="wicri:Area/PubMed/Checkpoint">000219</idno>
<idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">000219</idno>
<idno type="wicri:Area/Ncbi/Merge">001032</idno>
<idno type="wicri:Area/Ncbi/Curation">001032</idno>
<idno type="wicri:Area/Ncbi/Checkpoint">001032</idno>
<idno type="wicri:Area/Main/Merge">000234</idno>
<idno type="wicri:Area/Main/Curation">000232</idno>
<idno type="wicri:Area/Main/Exploration">000232</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en">The potential chemical structure of anti-SARS-CoV-2 RNA-dependent RNA polymerase.</title>
<author><name sortKey="Lung, Jrhau" sort="Lung, Jrhau" uniqKey="Lung J" first="Jrhau" last="Lung">Jrhau Lung</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Research and Development, Chiayi Chang Gung Memorial Hospital, Chiayi Branch, Putzu, Taiwan.</nlm:affiliation>
<country xml:lang="fr">Taïwan</country>
<wicri:regionArea>Department of Research and Development, Chiayi Chang Gung Memorial Hospital, Chiayi Branch, Putzu</wicri:regionArea>
<wicri:noRegion>Putzu</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Lin, Yu Shih" sort="Lin, Yu Shih" uniqKey="Lin Y" first="Yu-Shih" last="Lin">Yu-Shih Lin</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Pharmacy, Chiayi Chang Gung Memorial Hospital, Chiayi Branch, Putzu, Taiwan.</nlm:affiliation>
<country xml:lang="fr">Taïwan</country>
<wicri:regionArea>Department of Pharmacy, Chiayi Chang Gung Memorial Hospital, Chiayi Branch, Putzu</wicri:regionArea>
<wicri:noRegion>Putzu</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Yang, Yao Hsu" sort="Yang, Yao Hsu" uniqKey="Yang Y" first="Yao-Hsu" last="Yang">Yao-Hsu Yang</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Traditional Chinese Medicine, Chang Gung Memorial Hospital, Chiayi Branch, Putzu, Taiwan.</nlm:affiliation>
<country xml:lang="fr">Taïwan</country>
<wicri:regionArea>Department of Traditional Chinese Medicine, Chang Gung Memorial Hospital, Chiayi Branch, Putzu</wicri:regionArea>
<wicri:noRegion>Putzu</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Chou, Yu Lun" sort="Chou, Yu Lun" uniqKey="Chou Y" first="Yu-Lun" last="Chou">Yu-Lun Chou</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Surgery, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan.</nlm:affiliation>
<country xml:lang="fr">Taïwan</country>
<wicri:regionArea>Department of Surgery, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung</wicri:regionArea>
<wicri:noRegion>Kaohsiung</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Shu, Li Hsin" sort="Shu, Li Hsin" uniqKey="Shu L" first="Li-Hsin" last="Shu">Li-Hsin Shu</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Traditional Chinese Medicine, Chang Gung Memorial Hospital, Chiayi Branch, Putzu, Taiwan.</nlm:affiliation>
<country xml:lang="fr">Taïwan</country>
<wicri:regionArea>Department of Traditional Chinese Medicine, Chang Gung Memorial Hospital, Chiayi Branch, Putzu</wicri:regionArea>
<wicri:noRegion>Putzu</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Cheng, Yu Ching" sort="Cheng, Yu Ching" uniqKey="Cheng Y" first="Yu-Ching" last="Cheng">Yu-Ching Cheng</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Traditional Chinese Medicine, Chang Gung Memorial Hospital, Chiayi Branch, Putzu, Taiwan.</nlm:affiliation>
<country xml:lang="fr">Taïwan</country>
<wicri:regionArea>Department of Traditional Chinese Medicine, Chang Gung Memorial Hospital, Chiayi Branch, Putzu</wicri:regionArea>
<wicri:noRegion>Putzu</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Liu, Hung Te" sort="Liu, Hung Te" uniqKey="Liu H" first="Hung Te" last="Liu">Hung Te Liu</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Traditional Chinese Medicine, Chang Gung Memorial Hospital, Chiayi Branch, Putzu, Taiwan.</nlm:affiliation>
<country xml:lang="fr">Taïwan</country>
<wicri:regionArea>Department of Traditional Chinese Medicine, Chang Gung Memorial Hospital, Chiayi Branch, Putzu</wicri:regionArea>
<wicri:noRegion>Putzu</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Wu, Ching Yuan" sort="Wu, Ching Yuan" uniqKey="Wu C" first="Ching-Yuan" last="Wu">Ching-Yuan Wu</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Traditional Chinese Medicine, Chang Gung Memorial Hospital, Chiayi Branch, Putzu, Taiwan.</nlm:affiliation>
<country xml:lang="fr">Taïwan</country>
<wicri:regionArea>Department of Traditional Chinese Medicine, Chang Gung Memorial Hospital, Chiayi Branch, Putzu</wicri:regionArea>
<wicri:noRegion>Putzu</wicri:noRegion>
</affiliation>
</author>
</analytic>
<series><title level="j">Journal of medical virology</title>
<idno type="eISSN">1096-9071</idno>
<imprint><date when="2020" type="published">2020</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass></textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en">An outbreak of coronavirus disease 2019 (COVID-19) occurred in Wuhan and it has rapidly spread to almost all parts of the world. For coronaviruses, RNA-dependent RNA polymerase (RdRp) is an important protease that catalyzes the replication of RNA from RNA template and is an attractive therapeutic target. In this study, we screened these chemical structures from traditional Chinese medicinal compounds proven to show antiviral activity in severe acute respiratory syndrome coronavirus (SARS-CoV) and the similar chemical structures through a molecular docking study to target RdRp of SARS-CoV-2, SARS-CoV, and Middle East respiratory syndrome coronavirus (MERS-CoV). We found that theaflavin has a lower idock score in the catalytic pocket of RdRp in SARS-CoV-2 (-9.11 kcal/mol), SARS-CoV (-8.03 kcal/mol), and MERS-CoV (-8.26 kcal/mol) from idock. To confirm the result, we discovered that theaflavin has lower binding energy of -8.8 kcal/mol when it docks in the catalytic pocket of SARS-CoV-2 RdRp by using the Blind Docking server. Regarding contact modes, hydrophobic interactions contribute significantly in binding and additional hydrogen bonds were found between theaflavin and RdRp. Moreover, one π-cation interaction was formed between theaflavin and Arg553 from the Blind Docking server. Our results suggest that theaflavin could be a potential SARS-CoV-2 RdRp inhibitor for further study.</div>
</front>
</TEI>
<affiliations><list><country><li>Taïwan</li>
</country>
</list>
<tree><country name="Taïwan"><noRegion><name sortKey="Lung, Jrhau" sort="Lung, Jrhau" uniqKey="Lung J" first="Jrhau" last="Lung">Jrhau Lung</name>
</noRegion>
<name sortKey="Cheng, Yu Ching" sort="Cheng, Yu Ching" uniqKey="Cheng Y" first="Yu-Ching" last="Cheng">Yu-Ching Cheng</name>
<name sortKey="Chou, Yu Lun" sort="Chou, Yu Lun" uniqKey="Chou Y" first="Yu-Lun" last="Chou">Yu-Lun Chou</name>
<name sortKey="Lin, Yu Shih" sort="Lin, Yu Shih" uniqKey="Lin Y" first="Yu-Shih" last="Lin">Yu-Shih Lin</name>
<name sortKey="Liu, Hung Te" sort="Liu, Hung Te" uniqKey="Liu H" first="Hung Te" last="Liu">Hung Te Liu</name>
<name sortKey="Shu, Li Hsin" sort="Shu, Li Hsin" uniqKey="Shu L" first="Li-Hsin" last="Shu">Li-Hsin Shu</name>
<name sortKey="Wu, Ching Yuan" sort="Wu, Ching Yuan" uniqKey="Wu C" first="Ching-Yuan" last="Wu">Ching-Yuan Wu</name>
<name sortKey="Yang, Yao Hsu" sort="Yang, Yao Hsu" uniqKey="Yang Y" first="Yao-Hsu" last="Yang">Yao-Hsu Yang</name>
</country>
</tree>
</affiliations>
</record>

Pour manipuler ce document sous Unix (Dilib)

EXPLOR_STEP=$WICRI_ROOT/Wicri/Sante/explor/CovidV2/Data/Main/Exploration

HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000232 | SxmlIndent | more

HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 000232 | SxmlIndent | more

Pour mettre un lien sur cette page dans le réseau Wicri

{{Explor lien
   |wiki=    Wicri/Sante
   |area=    CovidV2
   |flux=    Main
   |étape=   Exploration
   |type=    RBID
   |clé=     pubmed:32167173
   |texte=   The potential chemical structure of anti-SARS-CoV-2 RNA-dependent RNA polymerase.
}}

Pour générer des pages wiki

HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i   -Sk "pubmed:32167173" \
       | HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd   \
       | NlmPubMed2Wicri -a CovidV2

This area was generated with Dilib version V0.6.33.
Data generation: Sat Mar 28 17:51:24 2020. Site generation: Sun Jan 31 15:35:48 2021

Serveur d'exploration Covid (26 mars)

The potential chemical structure of anti-SARS-CoV-2 RNA-dependent RNA polymerase.

The potential chemical structure of anti-SARS-CoV-2 RNA-dependent RNA polymerase.

Source :

Abstract

Links toward previous steps (curation, corpus...)

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri

Pour générer des pages wiki

	Serveur d'exploration Covid (26 mars)
	Attention, ce site est en cours de développement ! Attention, site généré par des moyens informatiques à partir de corpus bruts. Les informations ne sont donc pas validées.