Structure‐based approach to pharmacophore identification, in silico screening, and three‐dimensional quantitative structure–activity relationship studies for inhibitors of Trypanosoma cruzi dihydrofolate reductase function

Abstract

We have employed a structure-based three-dimensional quantitative structure-activity relationship (3D-QSAR) approach to predict the biochemical activity for inhibitors of T. cruzi dihydrofolate reductase-thymidylate synthase (DHFR-TS). Crystal structures of complexes of the enzyme with eight different inhibitors of the DHFR activity together with the structure in the substrate-free state (DHFR domain) were used to validate and refine docking poses of ligands that constitute likely active conformations. Structural information from these complexes formed the basis for the structure-based alignment used as input for the QSAR study. Contrary to indirect ligand-based approaches the strategy described here employs a direct receptor-based approach. The goal is to generate a library of selective lead inhibitors for further development as antiparasitic agents. 3D-QSAR models were obtained for T. cruzi DHFR-TS (30 inhibitors in learning set) and human DHFR (36 inhibitors in learning set) that show a very good agreement between experimental and predicted enzyme inhibition data. For crossvalidation of the QSAR model(s), we have used the 10% leave-one-out method. The derived 3D-QSAR models were tested against a few selected compounds (a small test set of six inhibitors for each enzyme) with known activity, which were not part of the learning set, and the quality of prediction of the initial 3D-QSAR models demonstrated that such studies are feasible. Further refinement of the models through integration of additional activity data and optimization of reliable docking poses is expected to lead to an improved predictive ability.

Synthesis and characterization of potent inhibitors of Trypanosoma cruzi dihydrofolate reductase

“…7 We also identified a number of highly active inhibitors of TcDHFR from libraries of antifolate compounds and developed a three-dimensional model for quantitative structureactivity (3D-QSAR) analysis of inhibitors of TcDHFR activity. 8 Based on earlier results of Davoll et al 9 and our data we have recently synthesized six compounds that contain the 2,4-diaminoquinazoline scaffold similar to TMQ but the methyl group at the C5-position in the quinazoline ring is absent (Fig. 1).…”

“…deviations of 1.17 and 1.53 Å between the X-ray pose and docking pose for TMQ and 6b, respectively. 8 The calculated total estimated ligand-receptor interaction energy and the hydrogen bonding pattern are essentially the same for both poses of each molecule (see Table 3). Hydrogen bonds are observed between ring N-atoms and amino groups in the 2,4-diaminoquinazoline ring and the backbone O atoms of residues Val26, Val27, and Ile154 as well as the side chain O atoms of Asp48 in the TcDHFR active site.…”

Pharmacophore Modeling and Molecular Dynamics Simulation to Find the Potent Leads for Aurora Kinase B

“…The molecules with their good conformation (lowest energy) are used to generate the hypothesis. 36,37 The best conformation models were used not only for hypothesis generation but also to find how well the molecules fit in the generated hypothesis. Test set was used to validate the generated hypotheses which consist of 19 molecules (10 selective Aurora-B and 9 selective Aurora-A inhibitors).…”

Crystallization and preliminary crystallographic studies of dihydrofolate reductase-thymidylate synthase fromTrypanosoma cruzi, the Chagas disease pathogen

“…1) at 2.4, 3.0 and 3.3 Å resolution in space groups C222 1 , I4 1 22 and P4 3 2 1 2, respectively (Senkovich et al, 2009;Schormann et al, 2008). The quinazoline analogue TMQ and the aminopterin analogue MTX have similar structures to that of the physiological substrate DHF.…”

“…Inhibition of DHFR or TS prevents DNA biosynthesis, leading to cell death. However, trypanosomatid protozoans such as T. cruzi can salvage pteridine and biopterin, which are then reduced by pteridine reductase 1 (PTR1; Bello et al, 1994;Schormann et al, 2001Schormann et al, , 2008. PTR2 of T. cruzi, which has a similar primary sequence to PTR1, can only reduce dihydrobiopterin and dihydrofolate (Robello et al, 1997;Senkovich et al, 2003).…”