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Structure-Based Identification of Natural Products as SARS-CoV-2 Mpro Antagonist from Echinacea angustifolia Using Computational Approaches.
Bharadwaj, Shiv; El-Kafrawy, Sherif Aly; Alandijany, Thamir A; Bajrai, Leena Hussein; Shah, Altaf Ahmad; Dubey, Amit; Sahoo, Amaresh Kumar; Yadava, Umesh; Kamal, Mohammad Amjad; Azhar, Esam Ibraheem; Kang, Sang Gu; Dwivedi, Vivek Dhar.
  • Bharadwaj S; Department of Biotechnology, Institute of Biotechnology, College of Life and Applied Sciences, Yeungnam University, 280 Daehak-Ro, Gyeongsan, Gyeongbuk 38541, Korea.
  • El-Kafrawy SA; Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, 21589 Jeddah, Saudi Arabia.
  • Alandijany TA; Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
  • Bajrai LH; Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, 21589 Jeddah, Saudi Arabia.
  • Shah AA; Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
  • Dubey A; Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, 21589 Jeddah, Saudi Arabia.
  • Sahoo AK; Biochemistry Department, Faculty of Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
  • Yadava U; Department of Biosciences, Integral University, Lucknow 226026, India.
  • Kamal MA; Computational Chemistry and Drug Discovery Division, Quanta Calculus Pvt. Ltd., Kushinagar 274203, India.
  • Azhar EI; Department of Applied Sciences, Indian Institute of Information Technology Allahabad, Allahabad 211015, Uttar Pradesh, India.
  • Kang SG; Department of Physics, Deen Dayal Upadhyay Gorakhpur University, Gorakhpur 273009, India.
  • Dwivedi VD; Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, 21589 Jeddah, Saudi Arabia.
Viruses ; 13(2)2021 02 15.
Article in English | MEDLINE | ID: covidwho-1122257
Semantic information from SemMedBD (by NLM)
1. Natural Products PREVENTS Respiratory Tract Infections
Subject
Natural Products
Predicate
PREVENTS
Object
Respiratory Tract Infections
2. Natural Products PREVENTS Upper Respiratory Infections
Subject
Natural Products
Predicate
PREVENTS
Object
Upper Respiratory Infections
3. Natural Products INTERACTS_WITH Peptide Hydrolases
Subject
Natural Products
Predicate
INTERACTS_WITH
Object
Peptide Hydrolases
4. Cichorium intybus LOCATION_OF inulin
Subject
Cichorium intybus
Predicate
LOCATION_OF
Object
inulin
5. dicaffeoylquinic acid COEXISTS_WITH Peptide Hydrolases
Subject
dicaffeoylquinic acid
Predicate
COEXISTS_WITH
Object
Peptide Hydrolases
6. Natural Products PART_OF Peptide Hydrolases
Subject
Natural Products
Predicate
PART_OF
Object
Peptide Hydrolases
7. Natural Products PREVENTS Respiratory Tract Infections
Subject
Natural Products
Predicate
PREVENTS
Object
Respiratory Tract Infections
8. Natural Products PREVENTS Upper Respiratory Infections
Subject
Natural Products
Predicate
PREVENTS
Object
Upper Respiratory Infections
9. Natural Products INTERACTS_WITH Peptide Hydrolases
Subject
Natural Products
Predicate
INTERACTS_WITH
Object
Peptide Hydrolases
10. Cichorium intybus LOCATION_OF inulin
Subject
Cichorium intybus
Predicate
LOCATION_OF
Object
inulin
11. dicaffeoylquinic acid COEXISTS_WITH Peptide Hydrolases
Subject
dicaffeoylquinic acid
Predicate
COEXISTS_WITH
Object
Peptide Hydrolases
12. Natural Products PART_OF Peptide Hydrolases
Subject
Natural Products
Predicate
PART_OF
Object
Peptide Hydrolases
ABSTRACT
Coronavirus disease-19 (COVID-19) pandemic, caused by the novel SARS-CoV-2 virus, continues to be a global threat. The number of cases and deaths will remain escalating due to the lack of effective therapeutic agents. Several studies have established the importance of the viral main protease (Mpro) in the replication of SARS-CoV-2 which makes it an attractive target for antiviral drug development, including pharmaceutical repurposing and other medicinal chemistry approaches. Identification of natural products with considerable inhibitory potential against SARS-CoV-2 could be beneficial as a rapid and potent alternative with drug-likeness by comparison to de novo antiviral drug discovery approaches. Thereof, we carried out the structure-based screening of natural products from Echinacea-angustifolia, commonly used to prevent cold and other microbial respiratory infections, targeting SARS-CoV-2 Mpro. Four natural products namely, Echinacoside, Quercetagetin 7-glucoside, Levan N, Inulin from chicory, and 1,3-Dicaffeoylquinic acid, revealed significant docking energy (>-10 kcal/mol) in the SARS-CoV-2 Mpro catalytic pocket via substantial intermolecular contacts formation against co-crystallized ligand (<-4 kcal/mol). Furthermore, the docked poses of SARS-CoV-2 Mpro with selected natural products showed conformational stability through molecular dynamics. Exploring the end-point net binding energy exhibited substantial contribution of Coulomb and van der Waals interactions to the stability of respective docked conformations. These results advocated the natural products from Echinacea angustifolia for further experimental studies with an elevated probability to discover the potent SARS-CoV-2 Mpro antagonist with higher affinity and drug-likeness.
Subject(s)
Keywords

Full text: Available Collection: International databases Database: MEDLINE Main subject: Antiviral Agents / Protease Inhibitors / Echinacea / Coronavirus 3C Proteases Language: English Year: 2021 Document Type: Article

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Antiviral Agents / Protease Inhibitors / Echinacea / Coronavirus 3C Proteases Language: English Year: 2021 Document Type: Article