Abstract
Problem statement: Our researches have proposed two ligands of disulfide cyclic polypeptide, which are CDEEC and CDGSC as potential inhibitor of DENV RNA-dependent RNApolymerase by molecular docking. Approach: Methodological approach was conducted to determine the best ligand to act as inhibitor. Molecular docking simulation was conducted without a solvent in which enzyme was made rigid and ligand was left free to find the most suitable conformation. In actual cellular system there is a solvent which makes the enzyme to have a dynamic movement. Results: Therefore in this study, Molecular Dynamic (MD) simulation was performed to estimate more reliable condition of enzyme-ligand complex. In this study, molecular dynamics simulation was performed during 5 ns with two different temperatures, 300 and 312 K. At the end of MD simulation at 300 K, CDEEC bound to two RdRp important residues, Arg-729 and Arg-737 while CDGSC didn’t bind to any important residues. Conclusion: Simulation at 312 K also showed almost similar result. CDEEC was bound to two RdRP important residues, Arg-737 and Ser-710, whereas CDGSC didn’t bind to any important residues. Based on the result of these two simulations, CDEEC is proposed as a better inhibitor of RdRp dengue virus and feasible to be developed as anti-dengue drug.
Highlights
Docking techniques is designed to find the most suitable conformation of ligand and its receptor (AlonsoThe rapid developments in science have brought et al, 2006)
Fast and inexpensive docking progress, most research in the pharmaceutical industry protocols can be combined with accurate but more has started to identify suitable targets in the organism costly Molecular Dynamic (MD) techniques to predict more reliable proteinand to design drugs, which interact with the target ligand complexes
Based on docking result visualization, it is known the ioinization level of certain group would affect the that CDEEC peptide ligand was bound with RNA-dependent RNA polymerase (RdRp) crystalization process
Summary
Docking techniques is designed to find the most suitable conformation of ligand and its receptor (AlonsoThe rapid developments in science have brought et al, 2006). Analysis of docking result toward peptide-RdRp enzyme complex: The docking analysis was conducted by examining the conformation which has the lowest energy value from the most populated cluster. CDEEC peptide has hydrogen bond interaction change enzyme into ionized state level and exposing the with five other residues and they binded with Arg-729 position of hydrogen atom on the crystal.
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