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

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...

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Published in:	Journal of molecular modeling Vol. 18; no. 5; pp. 1779 - 1790
Main Authors:	da Costa, André L. P., Pauli, Ivani, Dorn, Márcio, Schroeder, Evelyn K., Zhan, Chang-Guo, Norberto de Souza, Osmar
Format:	Journal Article
Language:	English
Published:	Berlin/Heidelberg Springer-Verlag 01-05-2012
Subjects:	Antitubercular Agents - chemistry Bacterial Proteins - chemistry Bacterial Proteins - metabolism Catalase - chemistry Catalase - metabolism Catalytic Domain Characterization and Evaluation of Materials Chemistry Chemistry and Materials Science Computer Appl. in Life Sciences Computer Applications in Chemistry Drug Design Ferrous Compounds - chemistry Isoniazid - analogs & derivatives Isoniazid - chemistry Kinetics Molecular Dynamics Simulation Molecular Medicine Mycobacterium tuberculosis - chemistry Original Paper Oxidoreductases - chemistry Protein Binding Protein Conformation Theoretical and Computational Chemistry FAS-II pathway Molecular dynamics simulations Pentacyano(isoniazid)ferrate(II) InhA Conformational changes
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Summary:	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. Figure Conformational changes in 2- trans -enoyl-ACP (CoA) reductase (InhA) from M. tuberculosis induced by an inorganic complex
ISSN:	1610-2940 0948-5023
DOI:	10.1007/s00894-011-1200-7