Virtual screening, ADME/T, and binding free energy analysis of anti-viral, anti-protease, and anti-infectious compounds against NSP10/NSP16 methyltransferase and main protease of SARS CoV-2

Abstract

Recently, a pathogen has been identified as a novel coronavirus (SARS-CoV-2) and found to trigger novel pneumonia (COVID-19) in human beings and some other mammals. The uncontrolled release of cytokines is seen from the primary stages of symptoms to last acute respiratory distress syndrome (ARDS). Thus, it is necessary to find out safe and effective drugs against this deadly coronavirus as soon as possible. Here, we downloaded the three-dimensional model of NSP10/NSP16 methyltransferase (PDB-ID: 6w6l) and main protease (PDB-ID: 6lu7) of COVID-19. Using these molecular models, we performed virtual screening with our anti-viral, inti-infectious, and anti-protease compounds, which are attractive therapeutics to prevent infection of the COVID-19. We found that top screened compound binds with protein molecules with good dock score with the help of hydrophobic interactions and hydrogen bonding. We observed that protease complexed with Cyclocytidine hydrochloride (anti-viral and anti-cancer), Trifluridine (anti-viral), Adonitol, and Meropenem (anti-bacterial), and Penciclovir (anti-viral) bound with a good docking score ranging from −6.8 to −5.1 (Kcal/mol). Further, NSP10/NSP16 methyltransferase complexed with Telbivudine, Oxytetracycline dihydrate (anti-viral), Methylgallate (anti-malarial), 2-deoxyglucose and Daphnetin (anti-cancer) from the docking score of −7.0 to −5.7 (Kcal/mol). In conclusion, the selected compounds may be used as a novel therapeutic agent to combat this deadly pandemic disease, SARS-CoV-2 infection, but needs further experimental research.

Highlights

• NSP10/NSP16 methyltransferase and main protease complex of SARS CoV-2 bind with selected drugs.

• NSP10/NSP16 methyltransferase and protease interacted with drugs by hydrophobic interactions.

• Compounds show good DG binging free energy with protein complexes.

• Ligands were found to follow the Lipinski rule of five.

Keywords:

• SARS CoV-2
• COVID-19
• NSP10/NSP16 methyltransferase
• protease complex
• anti-viral/anti-infectious/anti-protease drugs

Acknowledgments

The authors acknowledge the Indian Institute of Information technology and Aligarh Muslim University for providing infrastructure facilities.

Disclosure statement

The authors declare no conflict of interest.

Additional information

Funding

SK acknowledges DST-SERB, India, for providing financial assistance as a Junior Research Fellowship. HRS is thankful to the UGC [Grant no. F.30-377/2017(BSR)] and DST-SERB [Grant no. EMR/20l7/001758], New Delhi, for providing financial help.