Point Mutation I261M Affects the Dynamics of BVDV and its Interaction with Benzimidazole Antiviral 227G

Abstract

Bovine viral diarrhea virus (BVDV) is a Pestivirus of the Flaviviridae family and represents a major viral pathogen in cattle and other ruminants. Infection with BVDV can result in a wide assortment of disease manifestations including resorption, mummification, or abortion of the dead fetus. Recently the point mutation I261M on the thumb domain was shown to confer resistance to BDVD against 227G and other benzimidazole compounds. Here we investigated the role of this mutation by using a multidisciplinary protocol, not involving free energy calculations on structures of the mutated complex which are taken a priori similar to those of the wild one. Namely, we firstly performed MD simulations on the wild and mutated BVDV RdRp proteins in aqueous solution. Then, we selected representative equilibrium conformations by performing a cluster analysis, and ran docking calculations of 277G on representative of the 5 most populated clusters of each protein. Finally, we performed MD simulation on selected complexes as to assess structural and dynamical differences between wild and mutated 227G-protein adducts.Interestingly, the mutation affects the structure and the dynamics of the protein, particularly in the region of binding of the ligand, and this results in a different binding site of 227G with respect to the wild protein. Moreover, while 227G closes the entrance to the RNA strand in the case of the wild protein, a gate and a channel leading to the catalytic site are still present in the mutated complex. These results could offer a possible molecular explanation of the resistance mechanism by mutation I261M.