Drug resistance mechanism of ns3/4a protease and identification of potent compounds inhibiting reverse transcriptase of hepatitis virus

Abstract

Viral Hepatitis has become a public health concern which caused 1.34 million deaths in 2015 and 95% of sickness and untimely deaths come from chronic hepatitis B and C virus infections. The epidemic of viral hepatitis B and C affects around 325 million people worldwide and is 10 times more than the global HIV epidemic. Hepatitis C virus (HCV), which is the main cause of hepatitis C, has a high mutation rate due to the lack of proofreading activity of the RNA polymerase enzyme. One of an attractive target for anti-HCV drug design and development is the NS3/4A serine protease. Whereas hepatitis B virus (HBV) infection can result in both acute and chronic diseases in the human liver. Current therapeutic drugs for HBV treatment are the nucleos(t)ide analogues (NAs) acting as competitive inhibitor against HBV reverse transcriptase (RT). In the present study, all-atom molecular dynamics (MD) simulations were performed to investigate the influence of the single point mutations (R155K and D168A) in the HCV genotype 1 NS3/4A protease on the structural dynamics, molecular interactions and susceptibility of asunaprevir (ASV). Principal component analysis (PCA) indicated that these two mutations caused a loss of the hydrogen bond network of residues R123--R155--D168. In addition, the free energy calculations based on different semiempirical QM/MM-GBSA methods revealed that the binding affinity of ASV with the two mutant forms was significantly decreased in the order of wild-type < R155K < D168A. In the case of HBV, MD simulations were performed on the HBV-RT in complex with anti-HIV drugs (stavudine, didanosine and zidovudine) and anti-HBV drug (lamivudine) to determine the ligand-protein interactions and binding efficiency towards the HBV-RT. The predicted binding free energies showed that stavudine had the binding affinity against HBV-RT similar to zidovudine and relatively better than the substrate and lamivudine. Afterward, the conformations of anti-HIV drugs in bound state with HBV-RT were investigated with their unbound form to elucidate the most stable conformation of anti-HIV drugs using replica exchange molecular dynamic. The results suggested that the conformations of all anti-HIV drugs in bound form were the most stable conformation. Moreover, the exploration of new potent drugs against HBV-RT, which were screened from the three-dimensional pharmacophore modeling was evaluated their anti-HBV activity. Based on pharmacophore-based screening and similarity search for 50% of nucleoside-based scaffold, the three commercial drugs, including floxuridine, trifluridine and sofosbuvir were selected. The in vitro study showed that floxuridine possibly reduced the HBV DNA but still had toxicity with hepatocytes. This research provided the useful structural information regarding the atomistic understanding of acquired drug resistance and a rational guidance for antiviral drug design and development.