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Computational study of the IRES subdomain IIa structural plasticity and the ligand binding affinity

The internal ribosome entry site (IRES) of the hepatitis C virus (HCV) drives noncanonical initiation of protein synthesis necessary for viral replication. In order to fulfill its role in HCV translation its domain II should adopt an L-shaped conformation. We performed detailed molecular dynamics (MD) simulations for the ligand free RNA and its (native and mutated) complexes with the potential HCV inhibitors, with and without the presence of magnesium ions. We have shown that upon ligand removal conformation of the IIa subdomain changed from extended into the L-shaped one during several tens of ns MD simulation. Differently, binding of the benzimidazole translation inhibitors locked IIa in the extended conformation. We also performed MD study for the IIa in complex with newly discovered translation inhibitor diaminopiperidine (DAP) for which is experimentally suggested that locks the IIa RNA switch in the bent conformation and inhibits IRES function perhaps by preventing ribosome releas1. The starting points for our calculations were the three-dimensional structures of the IRES subdomain IIa determined by X-ray diffraction (34 nucleotides) (PDB ID code 3TZR)2 and by NMR spectroscopy (38 nucleotides) (PDB ID code 2KTZ)3. In both of them the subdomain IIa is complexed with a benzimidazole translation inhibitor 2. Since there are no crystallographically determined structure of the complexes with ligand 1, analog 3 and inhibitor DAP, we constructed them and performed molecular modeling calculations. Besides MD, we determined changes in the inhibitor structure and electronic charge distribution at the presence of magnesium cations and RNA using QM/MM approach.

HCV inhibitor; IRES subdomain IIa; molecular modelling; MD simulations; QM/MM method

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