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Prediction of Novel Inhibitors of the Main Protease (M-pro) of SARS-CoV-2 through Consensus Docking and Drug Reposition
Open AccessArticle

Investigation of Some Antiviral N-Heterocycles as COVID 19 Drug: Molecular Docking and DFT Calculations

1
Chemistry Department, College of Sciences, Yanbu, Taibah University, Yanbu 30799, Saudi Arabia
2
Chemistry Department, Faculty of Science, Alexandria University, Alexandria 21321, Egypt
3
Department of Chemistry, Faculty of Science, Cairo University, Cairo 12613, Egypt
4
Chemistry Department, College of Sciences, Al-Madina Al-Munawarah, Taibah University, Al-Madina 30002, Saudi Arabia
*
Authors to whom correspondence should be addressed.
Int. J. Mol. Sci. 2020, 21(11), 3922; https://doi.org/10.3390/ijms21113922
Received: 16 April 2020 / Revised: 29 April 2020 / Accepted: 30 April 2020 / Published: 30 May 2020
(This article belongs to the Special Issue New Avenues in Molecular Docking for Drug Design 2020)
The novel coronavirus, COVID-19, caused by SARS-CoV-2, is a global health pandemic that started in December 2019. The effective drug target among coronaviruses is the main protease Mpro, because of its essential role in processing the polyproteins that are translated from the viral RNA. In this study, the bioactivity of some selected heterocyclic drugs named Favipiravir (1), Amodiaquine (2), 2′-Fluoro-2′-deoxycytidine (3), and Ribavirin (4) was evaluated as inhibitors and nucleotide analogues for COVID-19 using computational modeling strategies. The density functional theory (DFT) calculations were performed to estimate the thermal parameters, dipole moment, polarizability, and molecular electrostatic potential of the present drugs; additionally, Mulliken atomic charges of the drugs as well as the chemical reactivity descriptors were investigated. The nominated drugs were docked on SARS-CoV-2 main protease (PDB: 6LU7) to evaluate the binding affinity of these drugs. Besides, the computations data of DFT the docking simulation studies was predicted that the Amodiaquine (2) has the least binding energy (−7.77 Kcal/mol) and might serve as a good inhibitor to SARS-CoV-2 comparable with the approved medicines, hydroxychloroquine, and remdesivir which have binding affinity −6.06 and −4.96 Kcal/mol, respectively. The high binding affinity of 2 was attributed to the presence of three hydrogen bonds along with different hydrophobic interactions between the drug and the critical amino acids residues of the receptor. Finally, the estimated molecular electrostatic potential results by DFT were used to illustrate the molecular docking findings. The DFT calculations showed that drug 2 has the highest of lying HOMO, electrophilicity index, basicity, and dipole moment. All these parameters could share with different extent to significantly affect the binding affinity of these drugs with the active protein sites. View Full-Text
Keywords: COVID 19; N-heterocycles; molecular docking; DFT calculations; hydroxychloroquine COVID 19; N-heterocycles; molecular docking; DFT calculations; hydroxychloroquine
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Hagar, M.; Ahmed, H.A.; Aljohani, G.; Alhaddad, O.A. Investigation of Some Antiviral N-Heterocycles as COVID 19 Drug: Molecular Docking and DFT Calculations. Int. J. Mol. Sci. 2020, 21, 3922.

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