Homology Modeling of DNA polymerases of Herpesviridae family and structure-based virtual screening for inhibitor identification.

Human herpes viruses are responsible for the several transmitted infections in human. It is known that the DNA polymerase enzyme is one of the putative targets for herpes. Therefore, it is of interest to model all known DNA polymerases of Herpesviridae family. Here, all the DNA polymerases of Herpesviridae without any crystal structure were modeled using HHV-1 DNA polymerase as a template. Modeled structures were screened by ramachandran plot and Descrete Optimization of Protein Energy (DOPE) score. To find out multi-target inhibitor for Herpesviridae, 21 natural antiviral compounds were selected from literature and screened using Lipinski’s rule of five. Binding pose of acyclovir with HHV-1 DNA polymerase was taken for the comparative docking study. Comparative binding analysis was done after settling of 120 and eight partial mono flexible protein-ligand docking sets for natural compounds and acyclovir, respectively. From the study it is found that alliin and gallic acid exhibit good binding affinity than acyclovir and other natural compounds. So, here we purpose that these two compounds can be potential candidates to inhibit Herpesviridae family.