Inverse Molecular Docking Study of NS3-Helicase and NS5-RNA Polymerase of Zika Virus as Possible Therapeutic Targets of Ligands Derived from Marcetia taxifolia and Its Implications to Dengue Virus

Abstract

Dengue and Zika are two mosquito-borne diseases of great impact on public health around the world in tropical and subtropical countries. DENV and ZIKV belong to the Flaviviridae family and the Flavivirus genus. Currently, there are no effective therapeutic agents to treat or prevent these pathologies. The main objective of this work was to evaluate potential inhibitors from active compounds obtained from Marcetia taxifolia by performing inverse molecular docking on ZIKV-NS3-helicase and ZIKV-NS5-RNA polymerase as targets. This computational strategy is based on renormalizing the binding scores of the compounds to these two proteins, allowing a direct comparison of the results across the proteins. The crystallographic structures of the ZIKV-NS3-helicase and ZIKV-NS5-RNA-polymerase proteins share a great similarity with DENV homologous proteins. The P-loop active site of the crystallographic structure of ZIKV-NS3-helicase presents a high percentage of homology with the four dengue serotypes. It was found that most ligands of the active compounds (5,3’-dihydroxy-3,6,7,8,4′-pentamethoxyflavone (5DP); 5-hydroxy-3,6,7,8,3′,4′-hexamethoxyflavone (5HH); myricetin-3-O-rhamnoside (M3OR)) from Marcetia taxifolia had a better affinity for ZIKV-NS3-helicase than for ZIKV-NS5-RNA polymerase, as indicated by the negative multiple active site correction (MASC) score, except for M3RG that showed a higher affinity for ZIKV-NS5-RNA polymerase. On the other hand, the AutoDock Vina scores showed that M3OR had the highest score value (−9.60 kcal/mol) and the highest normalized score (1.13) against ZIKV-NS3-helicase. These results in silico demonstrated that the nonstructural proteins NS3-helicase and NS5-RNA polymerase, which share similar molecular structures between the selected viruses, could become therapeutic targets for some bioactive compounds derived from Marcetia taxifolia.

Natural Products and Derivatives as Potential Zika virus Inhibitors: A Comprehensive Review

“…The bioactive metabolites 5,3′-dihydroxy-3,6,7,8,4′-pentamethoxyflavone, 5-hydroxy-3,6,7,8,3′,4′-hexamethoxyflavone, and myricetin-3- O -rhamnoside from Marcetia taxifolia showed better interactions with the ZIKV-NS3-helicase than ZIKV-NS5-RNA-polymerase [ 61 ]. Galloylquinic acid, isolated from Euphorbia hirta , along with bacopaside III and bacopaside A, obtained from Bacopa monnieri , were reported to interact with NS1, NS3 and the envelope protein domain III of ZIKV [ 62 ].…”

Complementary Dual Approach for In Silico Target Identification of Potential Pharmaceutical Compounds in Cystic Fibrosis

“…For example, a molecular shape-based method was employed to identify the cyclin dependent kinase (CDK2) as target of the phytochemical curcumin as possible explanation for its cancer-preventive properties [ 48 ]. Furthermore, inverse docking, i.e., a target-based approach, has been used to, amongst others, study different helicases in Zika viruses as targets of ligands from a flowering plant [ 49 ], investigate the effect of thyme derived thymol on fat deposition [ 50 ], and shed light on the antitumor targets of a library of natural bioactive compounds [ 51 ]. While most studies use either one or the other approach, we here use both a target- and ligand-based approach independently and combined to identify possible targets in the CFTR Lifecycle Map of the active compounds from CandActCFTR.…”