Structural basis of SARS-CoV-2 3CL and anti-COVID-19 drug discovery from medicinal plants
Authors: Ling-Ling Chen
Mubarak A Alamri
Safar M Alqahtani
Muhammad Tahir Ul Qamar
Journal: Journal of Pharmaceutical Analysis (2020)
Discipline: PHARMACOLOGY & TOXICOLOGY
Keywords: COVID-19; Coronavirus; Molecular docking; Molecular dynamics simulation; Natural products
Affiliations: Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, 11323, Alkarj, Saudi Arabia., College of Life Science and Technology, Guangxi University, Nanning, 530004, PR China., Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, PR China.

Abstract:  The recent pandemic of coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 has raised global health concerns. The viral 3-chymotrypsin-like cysteine protease (3CLpro) enzyme controls coronavirus replication and is essential for its life cycle. 3CLpro is a proven drug discovery target in the case of severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV). Recent studies revealed that the genome sequence of SARS-CoV-2 is very similar to that of SARS-CoV. Therefore, herein, we analysed the 3CLpro sequence, constructed its 3D homology model, and screened it against a medicinal plant library containing 32,297 potential anti-viral phytochemicals/traditional Chinese medicinal compounds. Our analyses revealed that the top nine hits might serve as potential anti- SARS-CoV-2 lead molecules for further optimisation and drug development process to combat COVID-19. 

Retracted: No

PubPeer comments:
 This paper was previously published as a preprint [1] that was withdrawn. The only information that can be gleaned is  This preprint has been withdrawn. Can the authors kindly offer the explanation for withdrawal and why the preprint cannot be found. [1] https: www.preprints.org manuscript 202002.0193 v1 , 
 Supplementary file 4 of this paper leads to an error. Is this an html page or an Excel (xls) file? The authors claim the following: u201cA comprehensive medicinal plant library containing 32,297 potential anti-viral phytochemicals and traditional Chinese medicinal compounds was generated from our previously collected data and studies [13,[21], [22], [23]],u201d However, none of the supplementary files contain the list of these u201c32,297 potential anti-viral phytochemicals and traditional Chinese medicinal compoundsu201d. Most importantly, there is no data for the u201cdocking score, binding affinity and interacting residuesu201d of these 32,297 compounds, Instead, the authors seem to have only selected 12 compounds in Table 2. From these 12, the authors conclude, in the abstract: u201cOur analyses revealed that the top nine hits might serve as potential anti- SARS-CoV-2 lead molecules for further optimisation and drug development process to combat COVID-19u201d. It is important to see the docking and other biomolecular data for the remaining 32,285 compounds, to be able to compare with other molecular docking studies conducted by other authors using plant-derived compounds. ,