Abstract
The outbreak of novel coronavirus (SARS-CoV-2) found in Wuhan China is rapidly spreading to all nations of the world. Currently, there are no approved drugs for the treatment of the novel coronaviral disease. Meanwhile, repositioning of some antibiotics, antiviral and antimalaria drugs have been employed. In this study, we used azithromycin as a model drug to virtual screen the ZINC database and the molecules obtained were docked against SARS-CoV-2 protein with PDB code: 5r7y. The best five ligands with high affinity for the target protein was compared with the reference molecule (Azithromycin). The docking score for the predicted ligands with high affinity for the target protein include ZINC10635972 (-6.3 kcal/mol), ZINC02651653 (-6.2 kcal/mol), ZINC09728215 (-6.2 kcal/mol), ZINC15003138 (-6.1 kcal/mol), ZINC89836288 (-6.1 kcal/mol) and azithromycin (+28.2 kcal/mol). The lead molecule (ZINC10635972) was observed to interacted with LUE 141, ASN 142, SER 144, SER 46, GLY 189, GLU 166, MET 165, HIS163, MET 49, HIS 164, PHE 140, GLY 143,THR 25, CYS 145, HIS 41, CYS 44 and THR 45. Meanwhile, hydrogen bond was predominant in the ZINC10635972-5r7y interaction. The lead molecule demonstrated good pharmacokinetics properties, drug-like characteristic and moderate chemical reactivity index. Besides, ZINC10635972 was noticed to fit the class 5 toxicity index. Hence, ZINC10635972 is a promising compound that should be further examined as drug candidates before clinical evaluation.
Highlights
The outbreak of novel coronavirus is rapidly spreading with an extremely high degree of virulence
We explored the pharmacophoric features of azithromycin for the virtual-screening of the ZINC database for a molecule with inhibitory activity against SARS-CoV-2 via molecular docking approach
(http://zincpharmer.csb.pitt.edu/pharmer.html) was employed for pharmacophore-based virtual screening to obtain drug-like compounds having similar pharmacophoric feature with azithromycin on the ZINC database to identify possible 5r7y inhibitors with a robust capacity to stop the spread of COVID-19, the screening was performed [8,9,10]
Summary
The outbreak of novel coronavirus is rapidly spreading with an extremely high degree of virulence. The World Health Organization (WHO) has declared that the coronavirus disease is a pandemic
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