Identification of allosteric regulation sites of Kaposis sarcoma virus DNA polymerase to discover its specific inhibitors via analysis of correlated intramolecular motions

Abstract

Human herpesvirus 8 (HHV8) also known as Kaposi sarcoma herpesvirus (KSHV) is a DNA virus associated with several dangerous diseases (Castleman disease, inflammatory cytokine syndrome, Kaposi sarcoma itself, etc). The exceptional importance of DNA-dependent DNA polymerases (DNA pols) in double-strand DNA viruses' lifecycle makes them attractive targets for specific low-weight molecular inhibitors, which can be used as antiviral drugs. Among the drug discovery strategies, the search/design of allosteric inhibitors of target enzymes seems to be the most promising. As a rule, allosteric regulatory sites have individual amino acid compositions, and the selectivity of the appropriate allosteric inhibitors is much higher compared to competitive inhibitors, especially in the case of nucleotide-binding enzymes. The general structural regularities of the location of allosteric regulation sites on the protein surface remain unclear. However, it is quite natural to assume some interdependence between behavior of amino acids in active and allosteric binding site that can be revealed by correlation analysis of intramolecular motions. Thus, the aim of this work was identification of site(-s) of allosteric regulation of KSHV DNA pol for the next rational design / search for compounds - potential drugs against KSHV dependent diseases. According to the aim the following tasks are set: to calculate the molecular dynamics of KSHV DNA polymerase as well as HIV reverse transcriptase for which allosteric regulation sites are known; to evaluate a correlation between motions in active and allosteric site of HIV reverse transcriptase and on the basis of these data to determine a localization of such site(-s) on the surface of KSHV DNA polymerase; to carry out a molecular docking of several compounds with known antipolymerase activity into the identified site of allosteric regulation and estimate the appropriate binding energies. As a primary result, the correlation between the motions of amino acid residues in the active and allosteric site of HIV reverse transcriptase was revealed. The corresponding correlation coefficients are in the range of 0.55–0.62. Thus, the initial hypothesis about interdependence of the behavior of the active site and the site of allosteric regulation was confirmed. In the KSHV DNA pol was revealed a region in the range from 420 to 460 amino acid residue which motions correlate with the motions of the active site of this enzyme. The correlation coefficients are in the range of 0.52–0.57. Analysis of the molecular surface of the KSHV DNA pol revealed a site able to bind small organic compounds, which seems to be allosteric regulation site of KSHV DNA pol. As a result of molecular docking, two compounds with binding energies of -22.41 and -20.65 kJ/mol respectively were identified as potential non-competitive inhibitors of KSVH DNA pol. The identified compounds can be structural prototypes for the development of new drugs against KSHV caused pathologies. The proposed approach to the identification of allosteric regulatory sites by analysis of intramolecular correlated motions can be used for rational design/search of high selective inhibitors with a non-competitive mechanism of action for a wide range of enzymes.