Preprint Article Version 3 Preserved in Portico This version is not peer-reviewed

Potential of Plant Bioactive Compounds as SARS-CoV-2 Main Protease (Mpro) and Spike (S) Glycoprotein Inhibitors: A Molecular Docking Study

Version 1 : Received: 6 April 2020 / Approved: 7 April 2020 / Online: 7 April 2020 (12:08:57 CEST)
Version 2 : Received: 8 April 2020 / Approved: 9 April 2020 / Online: 9 April 2020 (12:39:54 CEST)
Version 3 : Received: 30 June 2020 / Approved: 1 July 2020 / Online: 1 July 2020 (08:37:49 CEST)

How to cite: Tallei, T.E.; Tumilaar, S.G.; Niode, N.J.; Fatimawali, F.; Kepel, B.J.; Idroes, R.; Effendi, Y. Potential of Plant Bioactive Compounds as SARS-CoV-2 Main Protease (Mpro) and Spike (S) Glycoprotein Inhibitors: A Molecular Docking Study. Preprints 2020, 2020040102 (doi: 10.20944/preprints202004.0102.v3). Tallei, T.E.; Tumilaar, S.G.; Niode, N.J.; Fatimawali, F.; Kepel, B.J.; Idroes, R.; Effendi, Y. Potential of Plant Bioactive Compounds as SARS-CoV-2 Main Protease (Mpro) and Spike (S) Glycoprotein Inhibitors: A Molecular Docking Study. Preprints 2020, 2020040102 (doi: 10.20944/preprints202004.0102.v3).

Abstract

Since the outbreak of the COVID-19 (Coronavirus Disease 19) pandemic, researchers have been trying to investigate several active compounds found in plants that have the potential to inhibit the proliferation of SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2). The present study aimed to evaluate bioactive compounds found in plants by using a molecular docking approach to inhibit the Main Protease (Mpro) and Spike (S) glycoprotein of SARS-CoV-2. The evaluation was performed on the docking scores calculated using AutoDock Vina as a docking engine. A rule of five (RO5) was calculated to determine whether a compound meets the criteria as an active drug orally in humans. The determination of the docking score was done by selecting the best conformation of the protein-ligand complex that had the highest affinity (most negative Gibbs' free energy of binding / ΔG). As a comparison, nelfinavir (an antiretroviral drug), chloroquine and hydroxychloroquine sulfate (anti-malarial drugs recommended by the FDA as emergency drugs) were used. The results showed that hesperidin, nabiximols, pectolinarin, epigallocatechin gallate, and rhoifolin had better poses than nelfinavir, chloroquine, and hydroxychloroquine sulfate as spike glycoprotein inhibitors. Hesperidin, rhoifolin, pectolinarin, and nabiximols had about the same pose as nelfinavir, but were better than chloroquine and hydroxychloroquine sulfate as Mpro inhibitors. These plant compounds have the potential to be developed as specific therapeutic agents against COVID-19. Several natural compounds of plants evaluated in this study showed better binding free energy compared to nelfinavir, chloroquine, and hydroxychloroquine sulfate which so far are recommended in the treatment of COVID-19. As judged by the RO5 and previous study by others, the compounds kaempferol, herbacetin, eugenol, and 6-shogaol have good oral bioavailability, so they are also seen as promising candidates for the development lead compounds to treat infections caused by SARS-CoV-2.

Subject Areas

Medicinal plants; Mpro; 3CLpro; spike (S) glycoprotein; COVID-19; SARS-CoV-2

Comments (1)

Comment 1
Received: 1 July 2020
Commenter: Trina Tallei
Commenter's Conflict of Interests: Author
Comment: Dear Editor,
Herewith please find our revised manuscript. The revised manuscript is an improvement from the previous version 2 manuscript.

Best Regards
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