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      Pharmacophore and Molecular Docking Guided 3D-QSAR Study of Bacterial Enoyl-ACP Reductase (FabI) Inhibitors

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          Abstract

          Enoyl acyl carrier protein (ACP) reductase (FabI) is a potential target for the development of antibacterial agents. Three-dimensional quantitative structure-activity relationships (3D-QSAR) for substituted formamides series of FabI inhibitors were investigated using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) techniques. Pharmacophore and molecular docking methods were used for construction of the molecular alignments. A training set of 36 compounds was performed to create the 3D-QSAR models and their external predictivity was proven using a test set of 11 compounds. Graphical interpretation of the results revealed important structural features of the formamides related to the active site of FabI. The results may be exploited for further optimization of the design of new potent FabI inhibitors.

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          Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins.

          Richard D. Cramer, David E Patterson, Jeffrey Bunce (1988)
          Article 0 comments Cited 365 times – based on 0 reviews     Review now
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            Molecular similarity indices in a comparative analysis (CoMSIA) of drug molecules to correlate and predict their biological activity.

            Gerhard Klebe, Ute Abraham, Thomas Mietzner (1994)
            An alternative approach is reported to compute property fields based on similarity indices of drug molecules that have been brought into a common alignment. The fields of different physicochemical properties use a Gaussian-type distance dependence, and no singularities occur at the atomic positions. Accordingly, no arbitrary definitions of cutoff limits and deficiencies due to different slopes of the fields are encountered. The fields are evaluated by a PLS analysis similar to the CoMFA formalism. Two data sets of steroids binding to the corticosteroid-binding-globulin and thermolysin inhibitors were analyzed in terms of the conventional CoMFA method (Lennard-Jones and Coulomb potential fields) and the new comparative molecular similarity indices analysis (CoMSIA). Models of comparative statistical significance were obtained. Field contribution maps were produced for the different models. Due to cutoff settings in the CoMFA fields and the steepness of the potentials close to the molecular surface, the CoMFA maps are often rather fragmentary and not contiguously connected. This makes their interpretation difficult. The maps obtained by the new CoMSIA approach are superior and easier to interpret. Whereas the CoMFA maps denote regions apart from the molecules where interactions with a putative environment are to be expected, the CoMSIA maps highlight those regions within the area occupied by the ligand skeletons that require a particular physicochemical property important for activity. This is a more significant guide to trace the features that really matter especially with respect to the design of novel compounds.
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              Epidemiology of drug resistance: implications for a post-antimicrobial era.

              M. Cohen (1992)
              In the last several years, the frequency and spectrum of antimicrobial-resistant infections have increased in both the hospital and the community. Certain infections that are essentially untreatable have begun to occur as epidemics both in the developing world and in institutional settings in the United States. The increasing frequency of drug resistance has been attributed to combinations of microbial characteristics, selective pressures of antimicrobial use, and societal and technologic changes that enhance the transmission of drug-resistant organisms. Antimicrobial resistance is resulting in increased morbidity, mortality, and health-care costs. Prevention and control of these infections will require new antimicrobial agents, prudent use of existing agents, new vaccines, and enhanced public health efforts to reduce transmission.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Int J Mol Sci
                Journal ID (iso-abbrev): Int J Mol Sci
                Journal ID (publisher-id): ijms
                Title: International Journal of Molecular Sciences
                Publisher: Molecular Diversity Preservation International (MDPI)
                ISSN (Electronic): 1422-0067
                Publication date Collection: 2012
                Publication date (Electronic): 20 March 2012
                Volume: 13
                Issue: 6
                Pages: 6620-6638
                Affiliations
                [1 ]Key Laboratory of Regenerative Biology and Institute of Chemical Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190, Kaiyuan Avenue, Science Park, Guangzhou 510530, China; E-Mails: lv_man@ 123456gibh.ac.cn (M.L.); ding_ke@ 123456gibh.ac.cn (K.D.)
                [2 ]Department of Medicinal Chemistry, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, China; E-Mails: huangkun0214888@ 123456yahoo.com.cn (K.H.); youqidong@ 123456gmail.com (Q.Y.)
                Author notes
                [* ]Author to whom correspondence should be addressed; E-Mail: lu_xiaoyun@ 123456gibh.ac.cn ; Tel.: +86-020-32015349; Fax: +86-020-32015229.
                Article
                Publisher ID: ijms-13-06620
                DOI: 10.3390/ijms13066620
                PMC ID: 3397485
                PubMed ID: 22837653
                SO-VID: c49f12f6-e7e4-4f32-806d-87a8e76391dc
                Copyright © © 2012 by the authors; licensee Molecular Diversity Preservation International, Basel, Switzerland.
                License:

                This article is an open-access article distributed under the terms and conditions of the Creative Commons Attribution license ( http://creativecommons.org/licenses/by/3.0/).

                History
                Date received : 20 May 2012
                Date revision received : 07 May 2012
                Date accepted : 14 May 2012
                Categories
                Subject: Article

                ScienceOpen disciplines: Molecular biology
                Keywords: comfa,molecular docking,3d-qsar,fabi inhibitors,pharmacophore,comsia
                Data availability:
                ScienceOpen disciplines: Molecular biology
                Keywords: comfa, molecular docking, 3d-qsar, fabi inhibitors, pharmacophore, comsia

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