In silico drug discovery of major metabolites from spices as SARS-CoV-2 main protease inhibitors
- Publication type:
- Journal article
- Metadata:
-
- Autoren
- Mahmoud AA Ibrahim
- Alaa HM Abdelrahman
- Taha A Hussien
- Esraa AA Badr
- Tarik A Mohamed
- Hesham R El-Seedi
- Paul W Pare
- Thomas Efferth
- Mohamed-Elamir F Hegazy
- Autoren-URL
- https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=fis-test-1&SrcAuth=WosAPI&KeyUT=WOS:000582723600036&DestLinkType=FullRecord&DestApp=WOS_CPL
- DOI
- 10.1016/j.compbiomed.2020.104046
- eISSN
- 1879-0534
- Externe Identifier
- Clarivate Analytics Document Solution ID: OH6RT
- PubMed Identifier: 33065388
- ISSN
- 0010-4825
- Zeitschrift
- COMPUTERS IN BIOLOGY AND MEDICINE
- Schlüsselwörter
- Spices
- Secondary metabolites
- SARS-CoV-2 main protease
- Molecular dynamics
- Molecular docking
- Artikelnummer
- ARTN 104046
- Datum der Veröffentlichung
- 2020
- Status
- Published
- Titel
- <i>In silico</i> drug discovery of major metabolites from spices as SARS-CoV-2 main protease inhibitors
- Sub types
- Article
- Ausgabe der Zeitschrift
- 126
Data source: Web of Science (Lite)
- Other metadata sources:
-
- Autoren
- Mahmoud AA Ibrahim
- Alaa HM Abdelrahman
- Taha A Hussien
- Esraa AA Badr
- Tarik A Mohamed
- Hesham R El-Seedi
- Paul W Pare
- Thomas Efferth
- Mohamed-Elamir F Hegazy
- DOI
- 10.1016/j.compbiomed.2020.104046
- ISSN
- 0010-4825
- Zeitschrift
- Computers in Biology and Medicine
- Sprache
- en
- Artikelnummer
- 104046
- Paginierung
- 104046 - 104046
- Datum der Veröffentlichung
- 2020
- Status
- Published
- Herausgeber
- Elsevier BV
- Herausgeber URL
- http://dx.doi.org/10.1016/j.compbiomed.2020.104046
- Datum der Datenerfassung
- 2021
- Titel
- In silico drug discovery of major metabolites from spices as SARS-CoV-2 main protease inhibitors
- Ausgabe der Zeitschrift
- 126
Data source: Crossref
- Abstract
- Coronavirus Disease 2019 (COVID-19) is an infectious illness caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), originally identified in Wuhan, China (December 2019) and has since expanded into a pandemic. Here, we investigate metabolites present in several common spices as possible inhibitors of COVID-19. Specifically, 32 compounds isolated from 14 cooking seasonings were examined as inhibitors for SARS-CoV-2 main protease (M<sup>pro</sup>), which is required for viral multiplication. Using a drug discovery approach to identify possible antiviral leads, in silico molecular docking studies were performed. Docking calculations revealed a high potency of salvianolic acid A and curcumin as M<sup>pro</sup> inhibitors with binding energies of -9.7 and -9.2 kcal/mol, respectively. Binding mode analysis demonstrated the ability of salvianolic acid A and curcumin to form nine and six hydrogen bonds, respectively with amino acids proximal to M<sup>pro</sup>'s active site. Stabilities and binding affinities of the two identified natural spices were calculated over 40 ns molecular dynamics simulations and compared to an antiviral protease inhibitor (lopinavir). Molecular mechanics-generalized Born surface area energy calculations revealed greater salvianolic acid A affinity for the enzyme over curcumin and lopinavir with energies of -44.8, -34.2 and -34.8 kcal/mol, respectively. Using a STRING database, protein-protein interactions were identified for salvianolic acid A included the biochemical signaling genes ACE, MAPK14 and ESR1; and for curcumin, EGFR and TNF. This study establishes salvianolic acid A as an in silico natural product inhibitor against the SARS-CoV-2 main protease and provides a promising inhibitor lead for in vitro enzyme testing.
- Addresses
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, 61519, Egypt. Electronic address: m.ibrahim@compchem.net.
- Autoren
- Mahmoud AA Ibrahim
- Alaa HM Abdelrahman
- Taha A Hussien
- Esraa AA Badr
- Tarik A Mohamed
- Hesham R El-Seedi
- Paul W Pare
- Thomas Efferth
- Mohamed-Elamir F Hegazy
- DOI
- 10.1016/j.compbiomed.2020.104046
- eISSN
- 1879-0534
- Externe Identifier
- PubMed Identifier: 33065388
- PubMed Central ID: PMC7543985
- Funding acknowledgements
- Vetenskapsrådet: 2016–05885
- Alexander von Humboldt-Stiftung:
- Science and Technology Development Fund:
- Vetenskapsrådet: 2015–05468
- Open access
- true
- ISSN
- 0010-4825
- Zeitschrift
- Computers in biology and medicine
- Schlüsselwörter
- Humans
- Pneumonia, Viral
- Coronavirus Infections
- Caffeic Acids
- Lactates
- Curcumin
- Cysteine Endopeptidases
- Viral Nonstructural Proteins
- Protease Inhibitors
- Thermodynamics
- Drug Discovery
- Molecular Dynamics Simulation
- Pandemics
- Molecular Docking Simulation
- Betacoronavirus
- COVID-19
- SARS-CoV-2
- Coronavirus 3C Proteases
- Sprache
- eng
- Medium
- Print-Electronic
- Online publication date
- 2020
- Open access status
- Open Access
- Paginierung
- 104046
- Datum der Veröffentlichung
- 2020
- Status
- Published
- Datum der Datenerfassung
- 2020
- Titel
- In silico drug discovery of major metabolites from spices as SARS-CoV-2 main protease inhibitors.
- Sub types
- research-article
- Journal Article
- Ausgabe der Zeitschrift
- 126
Files
https://europepmc.org/articles/PMC7543985?pdf=render
Data source: Europe PubMed Central
- Abstract
- Coronavirus Disease 2019 (COVID-19) is an infectious illness caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), originally identified in Wuhan, China (December 2019) and has since expanded into a pandemic. Here, we investigate metabolites present in several common spices as possible inhibitors of COVID-19. Specifically, 32 compounds isolated from 14 cooking seasonings were examined as inhibitors for SARS-CoV-2 main protease (Mpro), which is required for viral multiplication. Using a drug discovery approach to identify possible antiviral leads, in silico molecular docking studies were performed. Docking calculations revealed a high potency of salvianolic acid A and curcumin as Mpro inhibitors with binding energies of -9.7 and -9.2 kcal/mol, respectively. Binding mode analysis demonstrated the ability of salvianolic acid A and curcumin to form nine and six hydrogen bonds, respectively with amino acids proximal to Mpro's active site. Stabilities and binding affinities of the two identified natural spices were calculated over 40 ns molecular dynamics simulations and compared to an antiviral protease inhibitor (lopinavir). Molecular mechanics-generalized Born surface area energy calculations revealed greater salvianolic acid A affinity for the enzyme over curcumin and lopinavir with energies of -44.8, -34.2 and -34.8 kcal/mol, respectively. Using a STRING database, protein-protein interactions were identified for salvianolic acid A included the biochemical signaling genes ACE, MAPK14 and ESR1; and for curcumin, EGFR and TNF. This study establishes salvianolic acid A as an in silico natural product inhibitor against the SARS-CoV-2 main protease and provides a promising inhibitor lead for in vitro enzyme testing.
- Date of acceptance
- 2020
- Autoren
- Mahmoud AA Ibrahim
- Alaa HM Abdelrahman
- Taha A Hussien
- Esraa AA Badr
- Tarik A Mohamed
- Hesham R El-Seedi
- Paul W Pare
- Thomas Efferth
- Mohamed-Elamir F Hegazy
- Autoren-URL
- https://www.ncbi.nlm.nih.gov/pubmed/33065388
- DOI
- 10.1016/j.compbiomed.2020.104046
- eISSN
- 1879-0534
- Externe Identifier
- PubMed Central ID: PMC7543985
- Zeitschrift
- Comput Biol Med
- Schlüsselwörter
- Molecular docking
- Molecular dynamics
- SARS-CoV-2 main protease
- Secondary metabolites
- Spices
- Betacoronavirus
- COVID-19
- Caffeic Acids
- Coronavirus 3C Proteases
- Coronavirus Infections
- Curcumin
- Cysteine Endopeptidases
- Drug Discovery
- Humans
- Lactates
- Molecular Docking Simulation
- Molecular Dynamics Simulation
- Pandemics
- Pneumonia, Viral
- Protease Inhibitors
- SARS-CoV-2
- Thermodynamics
- Viral Nonstructural Proteins
- Sprache
- eng
- Country
- United States
- Paginierung
- 104046
- PII
- S0010-4825(20)30377-2
- Datum der Veröffentlichung
- 2020
- Status
- Published
- Datum, an dem der Datensatz öffentlich gemacht wurde
- 2020
- Titel
- In silico drug discovery of major metabolites from spices as SARS-CoV-2 main protease inhibitors.
- Sub types
- Journal Article
- Ausgabe der Zeitschrift
- 126
Data source: PubMed
- Autoren
- Mahmoud AA Ibrahim
- Alaa HM Abdelrahman
- Taha A Hussien
- Esraa AA Badr
- Tarik A Mohamed
- Hesham R El-Seedi
- Paul W Pare
- Thomas Efferth
- Mohamed-Elamir F Hegazy
- Zeitschrift
- Comput. Biol. Medicine
- Paginierung
- 104046 - 104046
- Datum der Veröffentlichung
- 2020
- Titel
- In silico drug discovery of major metabolites from spices as SARS-CoV-2 main protease inhibitors.
- Ausgabe der Zeitschrift
- 126
Data source: DBLP
- Beziehungen:
- Property of