Structure-Based Optimization of Quinazolines as Cruzain and TbrCATL Inhibitors

Abstract

The cysteine proteases, cruzain and TbrCATL (rhodesain), are therapeutic targets for Chagas disease and Human African Trypanosomiasis, respectively. Among the known inhibitors for these proteases, we have described N 4-benzyl-N 2-phenylquinazoline-2,4-diamine (compound 7 in the original publication, 1a in this study), as a competitive cruzain inhibitor (K i = 1.4 μM). Here, we describe the synthesis and biological evaluation of 22 analogs of 1a, containing modifications in the quinazoline core, and in the substituents in positions 2 and 4 of this ring. The analogs demonstrate low micromolar inhibition of the target proteases and cidal activity against Trypanosoma cruzi with up to two log selectivity indices in counterscreens with myoblasts. Fourteen compounds were active against Trypanosoma brucei at low to mid micromolar concentrations. During the optimization of 1a, structure-based design and prediction of physicochemical properties were employed to maintain potency against the enzymes while removing colloidal aggregator characteristics observed for some molecules in this series.

Intramolecular Interactions Enhance the Potency of Gallinamide A Analogues against Trypanosoma cruzi

“…A 10 mM stock solution of Z-FR-AMC was prepared in dimethyl sulfoxide (DMSO). All assays were performed in black flat-bottom 96-well plates (Costar, catalog 3915), in 200 μL of 0.1 M sodium acetate, pH 5.5, supplemented with 1 mM DTT, 0.01% Triton X-100, 0.5 nM cruzain, and 2.5 μM Z-FR-AMC. , Prior to the addition of the substrate, the enzyme was incubated with the test compounds for 10 min. Following the substrate addition, the fluorescent signal was recorded.…”

Discovery of (5-(Benzylthio)-4-(3-(trifluoromethyl)phenyl)-4H-1,2,4-triazol-3-yl) Methanols as Potent Phytoene Desaturase Inhibitors through Virtual Screening and Structure Optimization

“…We speculated that it has an important role in enhancing the herbicidal activity, so we further introduced this pharmacophore into compounds T25 and T32 , namely compounds A and B (Figure ). To improve the hydrophilicity of the compounds, we performed molecular optimization to obtain a potent lead compound 1a with a novel triazole heterocyclic moiety through the replacement of a large hydrophobic group . Furthermore, the structural alignment of all seven commercialized PDS inhibitors revealed a common m -(trifluoro­methyl)­phenyl moiety, which might be important in binding to PDS protein .…”

“…Encouraged by discovering the 1,2,4-triazole ring as the potential pharmacophore, we further optimized the structures to improve the water solubility, bioactivity, and absorption conductivity in plants. As reported, the large hydrophobic group could be replaced with hydrophilic groups such as propanol or a morpholine ring to add to the hydrophilicity and bioactivity. Furthermore, the structural alignment of all seven commercialized PDS inhibitors revealed a common m -(trifluoro­methyl)­phenyl moiety, which might be involved in the binding to PDS protein .…”

Computational approaches towards the discovery and optimisation of cruzain inhibitors

“…Once hits are known, docking-based virtual screening can also aid in prioritising analogs for synthesis. Starting with a micromolar-range cruzain inhibitor (compound 1a , IC 50 of 7.5µM), Barbosa da Silva et al 8 screened 3,365 analogs and selected 22 for synthesis and biological assays, resulting in an optimised compound 1s with an IC 50 of 2.5 µM.…”

“…Pereira et al 9 have predicted binding modes of two competitive non-covalent cruzain inhibitors, and one of them was later optimised through a Structure-Based Drug Discovery (SBDD) approach. 8 More sophisticated pipelines have also been described toward ligand binding mode prediction. Martins et al 10 combined docking with molecular dynamics (MD) simulations and molecular mechanics-generalised Born/surface area (MM-GB/SA) calculations to compare possible binding modes of a quinoline derivative.…”