Molecular dynamic simulation of complex NS2B-NS3 DENV2 protease with potential inhibitors of cyclic tripeptide

  • Usman S
  • Irwan K
  • Arli A
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The pathogenic dengue virus (DV) is a growing global threat for which there is no specific treatment\r<br />and prevention. Several vaccines have been developed against the disease, but they only prevent the\r<br />disease and reduce the risk of death. Consequently, the antiviral drug becomes the most powerful\r<br />treatment to solve this problem. The virus possesses a two component NS2B-NS3 protease that cleaves\r<br />viral precursor proteins, and therefore represents a target for the development of antiviral drugs. In\r<br />many researches, several models of peptides inhibitor were generated in complexes with the NS2B-NS3\r<br />DENV2 protease by performing molecular docking. The goal of this research was to study the\r<br />interaction of ligands as inhibitors for protein (enzyme) in solvent explicit condition by performing\r<br />molecular dynamics simulation at 300 and 312 K. The simulations were performed on four disulfide\r<br />cyclic tripeptide ligands (RGR, KRK, RRA and RKR) and two proline-proline based cyclic peptide\r<br />ligands (RKK and KKR) compared with linear peptide inhibitor Bz-Nle-K-R-R-H as standard ligand. The\r<br />results provide conformational changes of enzyme-inhibitor complex that is shown by root-meansquare\r<br />deviation (RMSD) values. These results show that dynamic behavior of the complex occurs in\r<br />the presence of solvent. The interaction between ligand and amino acid residue of enzyme changed\r<br />during simulation. By these parameters, RKR becomes the best ligand compared with others. The\r<br />ligand has hydrogen bond interaction with the residue of active side, and is stable during simulation at\r<br />both temperatures. In conclusion, RKR ligand is proposed as an antiviral drug by performing molecular\r<br />dynamics simulation




Usman, S. F. T., Irwan, K., & Arli, A. P. (2015). Molecular dynamic simulation of complex NS2B-NS3 DENV2 protease with potential inhibitors of cyclic tripeptide. African Journal of Biotechnology, 12(28), 4419ā€“4431.

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