Conformational changes in 2-trans-enoyl-ACP (CoA) reductase (InhA) from M. tuberculosis induced by an inorganic complex: a molecular dynamics simulation study

Abstract

InhA, the NADH-dependent 2-trans-enoyl-ACP reductase enzyme from Mycobacterium tuberculosis (MTB), is involved in the biosynthesis of mycolic acids, the hallmark of mycobacterial cell wall. InhA has been shown to be the primary target of isoniazid (INH), one of the oldest synthetic antitubercular drugs. INH is a prodrug which is biologically activated by the MTB catalase-peroxidase KatG enzyme. The activation reaction promotes the formation of an isonicotinyl-NAD adduct which inhibits the InhA enzyme, resulting in reduction of mycolic acid biosynthesis. As a result of rational drug design efforts to design alternative drugs capable of inhibiting MTB's InhA, the inorganic complex pentacyano(isoniazid)ferrate(II) (PIF) was developed. PIF inhibited both wild-type and INH-resistant Ile21Val mutants of InhA and this inactivation did not require activation by KatG. Since no three-dimensional structure of the InhA-PIF complex is available to confirm the binding mode and to assess the molecular interactions with the protein active site residues, here we report the results of molecular dynamics simulations of PIF interaction with InhA. We found that PIF strongly interacts with InhA and that these interactions lead to macromolecular instabilities reflected in the long time necessary for simulation convergence. These instabilities were mainly due to perturbation of the substrate binding loop, particularly the partial denaturation of helices α6 and α7. We were also able to correlate the changes in the SASAs of Trp residues with the recent spectrofluorimetric investigation of the InhA-PIF complex and confirm their suggestion that the changes in fluorescence are due to InhA conformational changes upon PIF binding. The InhA-PIF association is very strong in the first 20.0 ns, but becomes very week at the end of the simulation, suggesting that the PIF binding mode we simulated may not reflect that of the actual InhA-PIF complex.

Biochemical and Cellular Analysis of Human Variants of the DYT1 Dystonia Protein, TorsinA/TOR1A

“…These include analysis of molecular complex formation and stability [Monecke et al, 2013; Norberto de Souza and Ornstein, 1999], predictions of enzyme-substrate activity [Chien et al, 2012], effects of mutations on drug resistance [Schroeder et al, 2005], and inhibitor binding [Costa et al, 2012]. …”

[Fe(CN)5(isoniazid)]3−: An iron isoniazid complex with redox behavior implicated in tuberculosis therapy

“…Additionally, molecular docking calculations have also suggested that IQG607 can bind directly and reversibly to InhA [53]. These data were the only mechanistic pieces of information regarding IQG607 action until now.…”

Two Birds with One Stone? Possible Dual-Targeting H1N1 Inhibitors from Traditional Chinese Medicine

“…In recent years, application of molecular dynamics to investigate internal motions and biological functions of biomacromolecules has opened new frontiers. Vast amounts of information on molecular recognition and binding [68][69][70][71], conformations or conformational changes [72][73][74][75], molecular mechanisms of bioactivity and stability [76][77][78][79], and drug discovery [80][81][82][83][84] have been found. To understand interaction of drugs with proteins or DNA, consideration should be given not only to the static structures but dynamical information obtained by simulation through a dynamic process.…”