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Online Journal of Bioinformatics©
Volume 22 (1): 24-31, 2021.
In silico docking 1,8 cineole in eucalyptus oil to 2019-N-CoV spike S1 protein and drug pharmacodynamics.
Arun Dev Sharma and Inderjeet Kaur.
Department of Biotechnology, Lyallpur Khalsa College, Jalandhar, India
Sharma AD, Kaur I., In silico docking 1,8 cineole in eucalyptus oil to 2019-N-CoV Spike S1 protein and drug pharmacodynamics, Onl J Bioinform, 22 (1): 24-32, 2021. Spike (S) proteins on coronaviruses are required for replication and are thus considered a drug target. We describe an In silico molecular docking model for Eucalyptol 1,8 cineole oil binding to spiked protein on SARS-CoV-2 by PATCHDOCK. Docking scores were used to calculate optimal binding and residues at active site for ligand binding. We generated 20 docking poses by score and area with highest values representing maximum binding. Eucalyptol docked in pocket host cell receptor (S1 unit) and fused with cellular membrane (S2) subunit. Binding in S2-protein pocket was mediated by hydrophobic interactions via ALA998 and ALA1002 with B and C chains at atomic distances of 3.18, 3.19, 3.24 and 3.42 angstrom. Comparing side chain ligand contact plots ligands suggested that eucalyptol caused conformational rearrangement of SARS-CoV-2 S-proteins that could inhibit the virus. We assessed eucalyptol protein interactions pharmacodynamics and toxicity by ADMET. Results showed that eucalyptol ligands did not violate Lipinski’s rule of 5 with surface polarity <90°A and log Po/w lipophilicity octanol-water partition 2.67 with high lipophilicity and no affinity for P-glycoprotein efflux transporter with high gastrointestinal absorption. Our results suggest that Eucalyptol may inhibit SARS-Cov-2- S-protein but further in vitro and in vivo research are required to validate our findings.
Keywords: COVID19; Docking; Eucalyptol; Herbal Drug