A slow, tight binding inhibitor of InhA, the enoyl-acyl carrier protein reductase from Mycobacterium tuberculosis.
ABSTRACT InhA, the enoyl-ACP reductase in Mycobacterium tuberculosis is an attractive target for the development of novel drugs against tuberculosis, a disease that kills more than two million people each year. InhA is the target of the current first line drug isoniazid for the treatment of tuberculosis infections. Compounds that directly target InhA and do not require activation by the mycobacterial catalase-peroxidase KatG are promising candidates for treating infections caused by isoniazid-resistant strains. Previously we reported the synthesis of several diphenyl ethers with nanomolar affinity for InhA. However, these compounds are rapid reversible inhibitors of the enzyme, and based on the knowledge that long drug target residence times are an important factor for in vivo drug activity, we set out to generate a slow onset inhibitor of InhA using structure-based drug design. 2-(o-Tolyloxy)-5-hexylphenol (PT70) is a slow, tight binding inhibitor of InhA with a K(1) value of 22 pm. PT70 binds preferentially to the InhA x NAD(+) complex and has a residence time of 24 min on the target, which is 14,000 times longer than that of the rapid reversible inhibitor from which it is derived. The 1.8 A crystal structure of the ternary complex between InhA, NAD(+), and PT70 reveals the molecular details of enzyme-inhibitor recognition and supports the hypothesis that slow onset inhibition is coupled to ordering of an active site loop, which leads to the closure of the substrate-binding pocket.
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ABSTRACT: Molecular docking simulations are commonly used to identify and optimize drug candidates by examining the interactions between the target protein and small chemical ligands. This procedure is computationally expensive, especially when the receptor is treated as an ensemble of molecular dynamic conformations, namely the Fully-Flexible Receptor (FFR) model. An FFR model can vary from thousands to millions of conformations. Handling molecular docking experiments on FFR models with flexible ligands still constitutes a big challenge, since it may take hours, days, or even months to be completely executed for a single ligand. Moreover, thousands of molecular docking results are quite hard to be analyzed by a domain expert, who typically explores results starting with FEB and RMSD values. This paper addresses the high computational demand to exhaustively execute molecular docking simulations on FFR models, as well as the problem of accurately selecting a small set of representative docking results to be analyzed by a domain expert. Our approach is twofold: (1) we make use of the wFReDoW environment to decrease the dimension of the FFR model during docking experiments, trying to maintain the quality in the resulting reduced models, and (2) we perform careful analyses on docking results to select a set of representative candidate poses. Our simulation results show that the proposed method is able to achieve a trade-off between accuracy and computational cost. This is evidenced from the accuracy in wFReDoW results, which contain 96% of the snapshots within the set of the 100 best FEB values when only 67% of snapshots from the FFR model were docked.Expert Systems with Applications 06/2014; 41(16):7608-7620. · 1.97 Impact Factor
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ABSTRACT: New triclosan (TRC) analogues were evaluated for their activity against the enoyl–acyl carrier protein reductase InhA in Mycobacterium tuberculosis (Mtb). TRC is a well-known inhibitor of InhA, and specific modifications to its positions 5 and 4′ afforded 27 derivatives; of these compounds, seven derivatives showed improved potency over that of TRC. These analogues were active against both drug-susceptible and drug-resistant Mtb strains. The most active compound in this series, 4-(n-butyl)-1,2,3-triazolyl TRC derivative 3, had an MIC value of 0.6 μg mL−1 (1.5 μM) against wild-type Mtb. At a concentration equal to its MIC, this compound inhibited purified InhA by 98 %, and showed an IC50 value of 90 nM. Compound 3 and the 5-methylisoxazole-modified TRC 14 were able to inhibit the biosynthesis of mycolic acids. Furthermore, mc24914, an Mtb strain overexpressing inhA, was found to be less susceptible to compounds 3 and 14, supporting the notion that InhA is the likely molecular target of the TRC derivatives presented herein.ChemMedChem 08/2014; 9(11). · 3.05 Impact Factor
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ABSTRACT: Diphenyl ether derivatives are good candidates for anti-tuberculosis agents that display a promising potency for inhibition of InhA, an essential enoyl-acyl carrier protein (ACP) reductase involved in fatty acid biosynthesis pathways in Mycobacterium tuberculosis. In this work, key structural features for the inhibition were identified by 3D-QSAR CoMSIA models, constructed based on available experimental binding properties of diphenyl ether inhibitors, and a set of four representative compounds was subjected to MD simulations of inhibitor-InhA complexes for the calculation of binding free energies. The results show that bulky groups are required for the R1 substituent on the phenyl A ring of the inhibitors to favor a hydrophobic pocket formed by residues Phe149, Met155, Pro156, Ala157, Tyr158, Pro193, Met199, Val203, Leu207, Ile215, and Leu218. Small substituents with a hydrophilic property are required at the R3 and R4 positions of the inhibitor phenyl B rings to form hydrogen bonds with the backbones of Gly96 and Met98, respectively. For the R2 substituent, small substituents with simultaneous hydrophilic or hydrophobic properties are required to favor the interaction with the pyrophosphate moiety of NAD(+) and the methyl side chain of Ala198, respectively. The reported data provide structural guidance for the design of new and potent diphenyl ether-based inhibitors with high inhibitory activities against M. tuberculosis InhA.Journal of Molecular Modeling 07/2014; 20(7):2319. · 1.87 Impact Factor