title: Blind Dockings of Benzothiazoles to Multiple Receptor Conformations of Triosephosphate Isomerase from Trypanosoma cruzi and Human.
abstract: We aim to uncover the binding modes of benzothiazoles, which have been reported as specific inhibitors of triosephosphate isomerase from the parasite Trypanosoma cruzi (TcTIM), by performing blind dockings on both TcTIM and human TIM (hTIM). Detailed analysis of binding sites and specific interactions are carried out based on ensemble dockings to multiple receptor conformers obtained from molecular dynamics simulations. In TcTIM dimer dockings, the inhibitors preferentially bind to the tunnel-shaped cavity formed at the interface of the subunits, whereas non-inhibitors mostly choose other sites. In contrast, TcTIM monomer binding interface and hTIM dimer interface do not present a specific binding site for the inhibitors. These findings point to the importance of the tunnel and of the dimeric form for inhibition of TcTIM. Specific interactions of the inhibitors and their sulfonate-free derivatives with the receptor residues indicate the significance of sulfonate group for binding affinity and positioning on the TcTIM dimer interface. One of the inhibitors also binds to the active site, which may explain its relatively higher inhibition effect on hTIM.
authors.affiliation: Department of Chemical Engineering and Polymer Research Center, Bogazici University, Bebek, 34342, Istanbul, Turkey.
authors.forename: Zeynep
authors.initials: Z
authors.lastname: Kurkcuoglu
authors.affiliation: Program of Computational Science and Engineering and Polymer Research Center, Bogazici University, Bebek, 34342, Istanbul, Turkey.
authors.forename: Gulgun
authors.initials: G
authors.lastname: Ural
authors.affiliation: Department of Information Technologies, Kadir Has University, Cibali, 34083, Istanbul, Turkey. demet.akten@khas.edu.tr.
authors.forename: E
authors.initials: E
authors.lastname: Demet Akten
authors.affiliation: Department of Chemical Engineering and Polymer Research Center, Bogazici University, Bebek, 34342, Istanbul, Turkey. doruker@boun.edu.tr.|Program of Computational Science and Engineering and Polymer Research Center, Bogazici University, Bebek, 34342, Istanbul, Turkey. doruker@boun.edu.tr.
authors.forename: Pemra
authors.initials: P
authors.lastname: Doruker
keywords: Benzothiazole; Blind docking; Molecular dynamics; Triosephosphate isomerase; Trypanosoma cruzi