Alternative Medicine against Herpes Simplex Virus Type- 1(HSV-1) via molecular docking

Thymidine kinase enzyme of HSV-1 was selected to identify putative functional sites and alternative drug molecules through molecular docking .The functional sites were predicted by PINTS, Q-Site finder and PROFUNC servers. A total of 62 antiviral plant metabolites and 13 drug molecules were docked against both the chains of Thymidine kinase enzyme using Patchdock tool. The plant metabolite Geraniin has produced higher score (5680 (chain A), 6562(chain B)) than the commercially known anti-herpes compound Acyclovir (3504 (chain A), 3264 (chain B)). In addition, Gemdockv2.0 also produced the lower best fitness values for Geraniin (-130.123226 (chain A), -132.309075 (chain B)) as compared to Acyclovir (-102.182402 (chain A), -84.599474 (chain B)). Furthermore, docking through Autodock4 by considering the predicted site as a grid centre also produced lowest docking energy of -13.40 Kcal/mol (chain A), 15.17Kcal/mol (chain B) for Geraniin compound in comparison to Acyclovir -7.48Kcal/mol (chain A), 7.96Kcal/mol (chain B). Geraniin firmly binds at the cavity of the enzyme 3F0T (A and B chains) at these surrounding residues: H58 G59 M60 G61 K62 T63 T64 T66 Q67 L69 V70 A71 G73 E83 W88 R89 M85 E95 I97 Y101 K219 D162 R220 R222 P223 E225. Moreover, this compound makes appropriate hydrogen bonds with RA89, QA67, KA219 residues from chain A and EB83, KB62, RB163, EB225, KB219 residues of chain B. We conclude that the natural plant metabolite Geraniin can serve as an effective antiviral drug against thymidine kinase enzyme of HSV-1.