Unveiling the Possible Oryzalin-Binding Site in the α-Tubulin of Toxoplasma gondii

Abstract

Dinitroaniline derivatives have been widely used as herbicidal agents to control weeds and grass. Previous studies demonstrated that these compounds also exhibit good antiparasitic activity against some protozoan parasites. Oryzalin (ORY), a representative dinitroaniline derivative, exerts its antiprotozoal activity against Toxoplasma gondii by inhibiting the microtubule polymerization process. Moreover, the identification of ORY-resistant T. gondii lines obtained by chemical mutagenesis confirmed that this compound binds selectively to α-tubulin. Based on experimental information reported so far and a multiple sequence analysis carried out in this work, we propose that the pironetin (PIR) site is the potential ORY-binding site. Therefore, we employed state-of-the-art computational approaches to characterize the interaction profile of ORY at the proposed site in the α-tubulin of T. gondii . An exhaustive search for other possible binding sites was performed using the Wrap “N” Shake method, which showed that ORY exhibits highest stability and affinity for the PIR site. Moreover, our molecular dynamics simulations revealed that the dipropylamine substituent of ORY interacts with a hydrophobic pocket, while the sulfonamide group formed hydrogen bonds with water molecules at the site entrance. Overall, our results suggest that ORY binds to the PIR site on the α-tubulin of the protozoan parasite T. gondii . This information will be very useful for designing less toxic and more potent antiprotozoal agents.

Differences in amino acid composition of carrot α-tubulin potentially confer the resistance to dinitroaniline herbicides

“…It should be noted that there are several hypotheses of the protein-ligand interaction between α-tubulin and dinitroaniline compounds [7,13,14,18,[19][20][21][22]. In our study, we adhered to recent hypothesis proposed by Aguayo-Ortiz et al (2022) using the model of α-tubulin from T. gondii [18]. In our opinion, this hypothesis is not only the most structurally substantiated, but also overlaps with the majority of known mutations, associated with dinitroaniline resistance.…”

“…In the present study, we aimed to analyze amino acid composition of the target site in carrot α-tubulin isotypes, and to reveal whatever this native resistance is caused by amino acid substitution(s) in the site. It should be noted that there are several hypotheses of the protein-ligand interaction between α-tubulin and dinitroaniline compounds [7,13,14,18,[19][20][21][22]. In our study, we adhered to recent hypothesis proposed by Aguayo-Ortiz et al (2022) using the model of α-tubulin from T. gondii [18].…”

“…In our opinion, this hypothesis is not only the most structurally substantiated, but also overlaps with the majority of known mutations, associated with dinitroaniline resistance. [8,20] Since this hypothesis is based on the ligandinduced mechanism of site formation, our study involved the analysis of the target binding site in open and closed conformations [18].…”

Comparison of Receptor–Ligand Restraint Schemes for Alchemical Absolute Binding Free Energy Calculations

“…The performance of the Boresch restraints with the force constants fit to simulation were compared to those with all force constants set to the common defaults of 10 or 20 kcal mol −1 Å −2 [rad −2 ], denoted by -10 and -20 (Table 1). 37,80,81 No significant differences in ΔG Bound o were found compared to when the force constants were fit to simulation, which was unsurprising given that the theoretical independence of the binding free energy with respect to the strength of restraints has been previously confirmed. 17,69 If there were any improvements in precision or increases in the rate of convergence with the force constants fit to simulation, these were not observed above the noise generated by other sources of error.…”

Construction of Histone–Protein Complex Structures by Peptide Growing

“…Fragment-based docking is a popular and widely used approach in drug design [ 48 , 49 , 50 , 51 , 52 ], and is based on the linking of docked fragments into the whole bound ligand structure. The number of fragment-based docking methods applied for peptide ligands is still limited.…”