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Article

Structure-Based Identification of Natural Products as SARS-CoV-2 Mpro Antagonist from Echinacea angustifolia Using Computational Approaches

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Department of Biotechnology, Institute of Biotechnology, College of Life and Applied Sciences, Yeungnam University, 280 Daehak-Ro, Gyeongsan, Gyeongbuk 38541, Korea
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Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, 21589 Jeddah, Saudi Arabia
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Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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Biochemistry Department, Faculty of Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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Department of Biosciences, Integral University, Lucknow 226026, India
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Computational Chemistry and Drug Discovery Division, Quanta Calculus Pvt. Ltd., Kushinagar 274203, India
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Department of Applied Sciences, Indian Institute of Information Technology Allahabad, Allahabad 211015, Uttar Pradesh, India
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Department of Physics, Deen Dayal Upadhyay Gorakhpur University, Gorakhpur 273009, India
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Enzymoics, 7 Peterlee Place, Novel Global Community Educational Foundation, Hebersham, NSW 2770, Australia
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Centre for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida 201308, India
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Authors to whom correspondence should be addressed.
Academic Editors: Kenneth Lundstrom and Alaa A. A. Aljabali
Viruses 2021, 13(2), 305; https://doi.org/10.3390/v13020305
Received: 12 January 2021 / Revised: 5 February 2021 / Accepted: 10 February 2021 / Published: 15 February 2021
(This article belongs to the Special Issue Vaccines and Therapeutics against Coronaviruses)
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. View Full-Text
Keywords: SARS-CoV-2; COVID-19; natural products; Echinacea-angustifolia; molecular dynamics simulation; Quercetagetin 7-glucoside SARS-CoV-2; COVID-19; natural products; Echinacea-angustifolia; molecular dynamics simulation; Quercetagetin 7-glucoside
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MDPI and ACS Style

Bharadwaj, S.; El-Kafrawy, S.A.; Alandijany, T.A.; Bajrai, L.H.; Shah, A.A.; Dubey, A.; Sahoo, A.K.; Yadava, U.; Kamal, M.A.; Azhar, E.I.; Kang, S.G.; Dwivedi, V.D. Structure-Based Identification of Natural Products as SARS-CoV-2 Mpro Antagonist from Echinacea angustifolia Using Computational Approaches. Viruses 2021, 13, 305. https://doi.org/10.3390/v13020305

AMA Style

Bharadwaj S, El-Kafrawy SA, Alandijany TA, Bajrai LH, Shah AA, Dubey A, Sahoo AK, Yadava U, Kamal MA, Azhar EI, Kang SG, Dwivedi VD. Structure-Based Identification of Natural Products as SARS-CoV-2 Mpro Antagonist from Echinacea angustifolia Using Computational Approaches. Viruses. 2021; 13(2):305. https://doi.org/10.3390/v13020305

Chicago/Turabian Style

Bharadwaj, Shiv, Sherif A. El-Kafrawy, Thamir A. Alandijany, Leena H. Bajrai, Altaf A. Shah, Amit Dubey, Amaresh K. Sahoo, Umesh Yadava, Mohammad A. Kamal, Esam I. Azhar, Sang G. Kang, and Vivek D. Dwivedi 2021. "Structure-Based Identification of Natural Products as SARS-CoV-2 Mpro Antagonist from Echinacea angustifolia Using Computational Approaches" Viruses 13, no. 2: 305. https://doi.org/10.3390/v13020305

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