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Int. J. Mol. Sci. 2017, 18(7), 1377; doi:10.3390/ijms18071377

Ligand Shaping in Induced Fit Docking of MraY Inhibitors. Polynomial Discriminant and Laplacian Operator as Biological Activity Descriptors

Department of Chemistry, Faculty of Chemistry and Chemical Engineering, Babes-Bolyai University, 400028 Cluj, Romania
Laboratory of Computational and Structural Physical-Chemistry for Nanosciences and QSAR, Department of Biology-Chemistry, West University of Timisoara, Pestalozzi Str. 16, 300115 Timisoara, Romania
Laboratory of Renewable Energies-Photovoltaics, R&D National Institute for Electrochemistry and Condensed Matter, Dr. A. Paunescu Podeanu Str. No. 144, 300569 Timisoara, Romania
Author to whom correspondence should be addressed.
Received: 7 April 2017 / Revised: 13 June 2017 / Accepted: 17 June 2017 / Published: 27 June 2017
(This article belongs to the Section Molecular Recognition)
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Docking—i.e., interaction of a small molecule (ligand) with a proteic structure (receptor)—represents the ground of drug action mechanism of the vast majority of bioactive chemicals. Ligand and receptor accommodate their geometry and energy, within this interaction, in the benefit of receptor–ligand complex. In an induced fit docking, the structure of ligand is most susceptible to changes in topology and energy, comparative to the receptor. These changes can be described by manifold hypersurfaces, in terms of polynomial discriminant and Laplacian operator. Such topological surfaces were represented for each MraY (phospho-MurNAc-pentapeptide translocase) inhibitor, studied before and after docking with MraY. Binding affinities of all ligands were calculated by this procedure. For each ligand, Laplacian and polynomial discriminant were correlated with the ligand minimum inhibitory concentration (MIC) retrieved from literature. It was observed that MIC is correlated with Laplacian and polynomial discriminant. View Full-Text
Keywords: antibiotics; docking; Quantitative Structure Activity Relationship (QSAR); MraY; manifold antibiotics; docking; Quantitative Structure Activity Relationship (QSAR); MraY; manifold

This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Lungu, C.N.; Diudea, M.V.; Putz, M.V. Ligand Shaping in Induced Fit Docking of MraY Inhibitors. Polynomial Discriminant and Laplacian Operator as Biological Activity Descriptors. Int. J. Mol. Sci. 2017, 18, 1377.

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