Theoretical studies on the interaction between the nitrile-based inhibitors and the catalytic triad of Cathepsin K. Issue 3 (17th February 2018)

• Record Type: Journal Article
• Authors: Pitchumani Violet Mary, C.; Shankar, R.; Vijayakumar, S.
• Is Part Of: Journal of biomolecular structure & dynamics. Volume 36:Issue 3(2018)
• Page Start: 634
• Page End: 655
• Publication Date: 2018-02-17
• Subjects: Cathepsin K -- DFT -- MD simulation -- osteoporosis -- odanacatib -- catalytic triad -- AMBER14 -- OPLS3 -- covalent docking; Biomolecules -- Periodicals; Molecular structure -- Periodicals; Molecular Biology -- Periodicals; Biomechanics -- Periodicals; 572
• DOI: 10.1080/07391102.2017.1289863
• Languages: English
• ISSNs: 0739-1102

Abstract

Abstract : Computational studies on the interaction of novel inhibitor compounds with the Cathepsin K protease have been performed to study the inhibition properties of the inhibitor compounds. The quantum chemical calculations have been performed to analyze the molecular geometries, structural stability, reactivity, nature of interaction, and the charge transfer properties using B3LYP level of theory by implementing 6-311g(d, p) basis set. The calculated C–S and N–H…N bond lengths of the inhibitor-triad complexes are found to agree well with the previous literature results. The chemical reactivity of the inhibitors and catalytic triad are analyzed through frontier molecular orbital analysis and found that the inhibitors are subjected to nucleophilic attack by the catalytic triad. The nature of inhibition of the inhibitor compounds is examined using the quantum theory of Atoms in Molecules analysis and found to be partially covalent. The NBO stabilization energy for the Cys – inhibitor are found to be most stable than the other interactions. The molecular dynamic simulations were performed to study the influence of dynamic of the active site on the QM results. The many body decomposition interaction energy calculated for the final results of MD simulation reveals that the dynamic of the active site induces significant changes in the interaction energy and occupancy of H-bonds plays a major role in the stabilizing the active site inhibitor interactions. The present study reveals that the inhibitor compounds can inhibit the proteolytic activity of the proteases on binding with the catalytic active site.