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Unravelling lead antiviral phytochemicals for the inhibition of SARS-CoV-2 Mpro enzyme through in silico approach.
Gurung, Arun Bahadur; Ali, Mohammad Ajmal; Lee, Joongku; Farah, Mohammad Abul; Al-Anazi, Khalid Mashay.
  • Gurung AB; Department of Basic Sciences and Social Sciences, North-Eastern Hill University, Shillong 793022, Meghalaya, India. Electronic address: arunbgurung@gmail.com.
  • Ali MA; Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia.
  • Lee J; Department of Environment and Forest Resources, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea.
  • Farah MA; Genetics Laboratory, Department of Zoology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia.
  • Al-Anazi KM; Genetics Laboratory, Department of Zoology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia.
Life Sci ; 255: 117831, 2020 Aug 15.
Article in English | MEDLINE | ID: covidwho-365098
Semantic information from SemMedBD (by NLM)
1. Phytochemicals INHIBITS 3C-like proteas
Subject
Phytochemicals
Predicate
INHIBITS
Object
3C-like proteas
2. Peptide Hydrolases INTERACTS_WITH Drug
Subject
Peptide Hydrolases
Predicate
INTERACTS_WITH
Object
Drug
3. Peptide Hydrolases PART_OF Homo sapiens
Subject
Peptide Hydrolases
Predicate
PART_OF
Object
Homo sapiens
4. Small Molecule AFFECTS Virus Replication
Subject
Small Molecule
Predicate
AFFECTS
Object
Virus Replication
5. Peptide Hydrolases INTERACTS_WITH Pharmaceutical Preparations
Subject
Peptide Hydrolases
Predicate
INTERACTS_WITH
Object
Pharmaceutical Preparations
6. 3C-like proteas INTERACTS_WITH C0013227
Subject
3C-like proteas
Predicate
INTERACTS_WITH
Object
C0013227
7. Phytochemicals INHIBITS 3C-like protease, SARS coronavirus|SARS
Subject
Phytochemicals
Predicate
INHIBITS
Object
3C-like protease, SARS coronavirus|SARS
8. Peptide Hydrolases INTERACTS_WITH Drugs, Essential
Subject
Peptide Hydrolases
Predicate
INTERACTS_WITH
Object
Drugs, Essential
9. Peptide Hydrolases PART_OF Homo sapiens
Subject
Peptide Hydrolases
Predicate
PART_OF
Object
Homo sapiens
10. Small Molecule AFFECTS Virus Replication
Subject
Small Molecule
Predicate
AFFECTS
Object
Virus Replication
11. Peptide Hydrolases INTERACTS_WITH Pharmaceutical Preparations
Subject
Peptide Hydrolases
Predicate
INTERACTS_WITH
Object
Pharmaceutical Preparations
12. 3C-like protease, SARS coronavirus INTERACTS_WITH Pharmaceutical Preparations
Subject
3C-like protease, SARS coronavirus
Predicate
INTERACTS_WITH
Object
Pharmaceutical Preparations
13. 3C-like protease, SARS coronavirus|SARS INTERACTS_WITH Pharmaceutical Preparations
Subject
3C-like protease, SARS coronavirus|SARS
Predicate
INTERACTS_WITH
Object
Pharmaceutical Preparations
ABSTRACT
A new SARS coronavirus (SARS-CoV-2) belonging to the genus Betacoronavirus has caused a pandemic known as COVID-19. Among coronaviruses, the main protease (Mpro) is an essential drug target which, along with papain-like proteases catalyzes the processing of polyproteins translated from viral RNA and recognizes specific cleavage sites. There are no human proteases with similar cleavage specificity and therefore, inhibitors are highly likely to be nontoxic. Therefore, targeting the SARS-CoV-2 Mpro enzyme with small molecules can block viral replication. The present study is aimed at the identification of promising lead molecules for SARS-CoV-2 Mpro enzyme through virtual screening of antiviral compounds from plants. The binding affinity of selected small drug-like molecules to SARS-CoV-2 Mpro, SARS-CoV Mpro and MERS-CoV Mpro were studied using molecular docking. Bonducellpin D was identified as the best lead molecule which shows higher binding affinity (-9.28 kcal/mol) as compared to the control (-8.24 kcal/mol). The molecular binding was stabilized through four hydrogen bonds with Glu166 and Thr190 as well as hydrophobic interactions via eight residues. The SARS-CoV-2 Mpro shows identities of 96.08% and 50.65% to that of SARS-CoV Mpro and MERS-CoV Mpro respectively at the sequence level. At the structural level, the root mean square deviation (RMSD) between SARS-CoV-2 Mpro and SARS-CoV Mpro was found to be 0.517 Å and 0.817 Å between SARS-CoV-2 Mpro and MERS-CoV Mpro. Bonducellpin D exhibited broad-spectrum inhibition potential against SARS-CoV Mpro and MERS-CoV Mpro and therefore is a promising drug candidate, which needs further validations through in vitro and in vivo studies.
Subject(s)
Keywords

Full text: Available Collection: International databases Database: MEDLINE Main subject: Antiviral Agents / Pneumonia, Viral / Plant Extracts / Viral Nonstructural Proteins / Coronavirus Infections / Betacoronavirus Type of study: Observational study / Prognostic study Topics: Traditional medicine Limits: Humans Language: English Journal: Life Sci Year: 2020 Document Type: Article

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Antiviral Agents / Pneumonia, Viral / Plant Extracts / Viral Nonstructural Proteins / Coronavirus Infections / Betacoronavirus Type of study: Observational study / Prognostic study Topics: Traditional medicine Limits: Humans Language: English Journal: Life Sci Year: 2020 Document Type: Article