In silico evaluation of the compounds of the ayurvedic drug, AYUSH-64, for the action against the SARS-CoV-2 main protease

Ram, Thrigulla Saketh; Munikumar, Manne; Raju, Vankudavath Naik; Devaraj, Parasannanavar; Boiroju, Naveen Kumar; Hemalatha, Rajkumar; Prasad, P.V.V.; Gundeti, Manohar; Sisodia, Brijesh S.; Pawar, Sharad; Prasad, G.P.; Chincholikar, Mukesh; Goel, Sumeet; Mangal, Anupam; Gaidhani, Sudesh; Srikanth, N.; Dhiman, K.S.

BACKGROUND: Outbreak of Corona Virus Disease in late 2019 (COVID-19) has become a pandemic global Public health emergency. Since there is no approved anti-viral drug or vaccine declared for the disease and investigating existing drugs against the COVID-19. OBJECTIVE: AYUSH-64 is an Ayurvedic formulation, developed and patented by Central Council of Research in Ayurvedic Sciences, India, has been in clinical use as anti-malarial, anti-inflammatory, anti-pyretic drug for few decades. Thus, the present study was undertaken to evaluate AYUSH-64 compounds available in this drug against Severe Acute Respiratory Syndrome-Corona Virus (SARS-CoV-2) Main Protease (M(pro); PDB ID: 6LU7) via in silico techniques. MATERIALS AND METHODS: Different molecular docking software’s of Discovery studio and Auto Dock Vina were used for drugs from selected AYUSH-64 compounds against SARS-CoV-2. We also conducted 100 ns period of molecular dynamics simulations with Desmond and further MM/GBSA for the best complex of AYUSH-64 with M(pro) of SARS-CoV-2. RESULTS: Among 36 compounds of four ingredients of AYUSH-64 screened, 35 observed to exhibits good binding energies than the published positive co-crystal compound of N3 pepetide. The best affinity and interactions of Akuammicine N-Oxide (from Alstonia scholaris) towards the M(pro) with binding energy (AutoDock Vina) of -8.4 kcal/mol and Discovery studio of Libdock score of 147.92 kcal/mol. Further, molecular dynamics simulations with MM-GBSA were also performed for M(pro)– Akuammicine N-Oxide docked complex to identify the stability, specific interaction between the enzyme and the ligand. Akuammicine N-Oxide is strongly formed h-bonds with crucial M(pro) residues, Cys145, and His164. CONCLUSION: The results provide lead that, the presence of M(pro)– Akuammicine N-Oxide with highest M(pro) binding energy along with other 34 chemical compounds having similar activity as part of AYUSH-64 make it a suitable candidate for repurposing to management of COVID-19 by further validating through experimental, clinical studies.