Towards the identification of the binding site of benzimidazoles to β-tubulin of Trichinella spiralis: insights from computational and experimental data

Abstract

Benzimidazole-2-carbamate derivatives (BzC) are among the most important broad-spectrum anthelmintic drugs for the treatment of nematode infections. BzC selectively bind to the β-tubulin monomer and inhibit microtubule polymerization. However, the crystallographic structure of the nematode tubulin and the mechanism of action are still unknown. Moreover, the relation between the mechanism of action and the binding site of BzC has not yet been explained accurately. By using the amino acid sequence of Trichinella spiralis β-tubulin as a basis and by applying homology modeling techniques, we were able to build a 3D structure of this protein. In order to identify a binding site for BzC, molecular docking and molecular dynamics calculations were carried out with this model. The results were in good agreement with the most common amino acid mutations associated with drug resistance (F167Y, E198A and F200Y) and with the experimental results of competitive inhibition of colchicine binding to tubulin. Besides, Glu198, Thr165, Cys239 and Gln134 were identified as important amino acids in the binding process since they directly interact with BzC in the formation of hydrogen bonds. The results presented in this paper are a step further towards the understanding, at the molecular level, of the mode of action of anthelmintic drugs. These results constitute valuable information for the design or improvement of more potent and selective molecules.