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      Mycobacterium tuberculosis IMPDH in Complexes with Substrates, Products and Antitubercular Compounds

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          Abstract

          Tuberculosis (TB) remains a worldwide problem and the need for new drugs is increasingly more urgent with the emergence of multidrug- and extensively-drug resistant TB. Inosine 5’-monophosphate dehydrogenase 2 (IMPDH2) from Mycobacterium tuberculosis ( Mtb) is an attractive drug target. The enzyme catalyzes the conversion of inosine 5’-monophosphate into xanthosine 5’-monophosphate with the concomitant reduction of NAD + to NADH. This reaction controls flux into the guanine nucleotide pool. We report seventeen selective IMPDH inhibitors with antitubercular activity. The crystal structures of a deletion mutant of MtbIMPDH2 in the apo form and in complex with the product XMP and substrate NAD + are determined. We also report the structures of complexes with IMP and three structurally distinct inhibitors, including two with antitubercular activity. These structures will greatly facilitate the development of MtbIMPDH2-targeted antibiotics.

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          Most cited references42

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          Genes required for mycobacterial growth defined by high density mutagenesis.

          Despite over a century of research, tuberculosis remains a leading cause of infectious death worldwide. Faced with increasing rates of drug resistance, the identification of genes that are required for the growth of this organism should provide new targets for the design of antimycobacterial agents. Here, we describe the use of transposon site hybridization (TraSH) to comprehensively identify the genes required by the causative agent, Mycobacterium tuberculosis, for optimal growth. These genes include those that can be assigned to essential pathways as well as many of unknown function. The genes important for the growth of M. tuberculosis are largely conserved in the degenerate genome of the leprosy bacillus, Mycobacterium leprae, indicating that non-essential functions have been selectively lost since this bacterium diverged from other mycobacteria. In contrast, a surprisingly high proportion of these genes lack identifiable orthologues in other bacteria, suggesting that the minimal gene set required for survival varies greatly between organisms with different evolutionary histories.
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            Dynamic persistence of antibiotic-stressed mycobacteria.

            Exposure of an isogenic bacterial population to a cidal antibiotic typically fails to eliminate a small fraction of refractory cells. Historically, fractional killing has been attributed to infrequently dividing or nondividing "persisters." Using microfluidic cultures and time-lapse microscopy, we found that Mycobacterium smegmatis persists by dividing in the presence of the drug isoniazid (INH). Although persistence in these studies was characterized by stable numbers of cells, this apparent stability was actually a dynamic state of balanced division and death. Single cells expressed catalase-peroxidase (KatG), which activates INH, in stochastic pulses that were negatively correlated with cell survival. These behaviors may reflect epigenetic effects, because KatG pulsing and death were correlated between sibling cells. Selection of lineages characterized by infrequent KatG pulsing could allow nonresponsive adaptation during prolonged drug exposure.
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              IMP dehydrogenase: structure, mechanism, and inhibition.

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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                6 October 2015
                2015
                : 10
                : 10
                : e0138976
                Affiliations
                [1 ]Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, IL, United States of America
                [2 ]Structural Biology Center, Biosciences, Argonne National Laboratory, 9700 S Cass Ave. Argonne, IL, United States of America
                [3 ]Department of Biology, Brandeis University, 415 South St. Waltham, MA, United States of America
                [4 ]Tuberculosis Research Section, National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States of America
                [5 ]Center for Drug Design, Academic Health Center, University of Minnesota, 516 Delaware St. SE, Minneapolis, MN, United States of America
                [6 ]Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, 549A Science and Research Building 2, Houston, TX, United States of America
                [7 ]Department of Chemistry, Brandeis University, 415 South St. Waltham, MA, United States of America
                University of Padova, Medical School, ITALY
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Performed the experiments: MMG SKG YW KM MZ NM GM HB MG. Analyzed the data: MMG SKG YK CA GC LH AJ. Wrote the paper: MMG YK LH AJ.

                Article
                PONE-D-15-30921
                10.1371/journal.pone.0138976
                4594927
                26440283
                034abab2-e217-446b-aa57-1aaa92b52bfb

                This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication

                History
                : 14 July 2015
                : 7 September 2015
                Page count
                Figures: 5, Tables: 4, Pages: 21
                Funding
                This work was supported by the National Institute of Health (NIH) and the National Institute of Allergy and Infectious Diseases (NIAID) [contracts HHSN272200700058C and HHSN272201200026C to the Center of Structural Genomics of Infectious Diseases], grant AI093459 (to LH) and the Intramural Research Program of NIAID (HB). The use of Structural Biology Center beamlines was supported by the U.S. Department of Energy, Office of Biological and Environmental Research [contract DE-AC02-06CH11357]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Custom metadata
                All relevant data are within the paper and its Supporting Information files. Coordinates and Structure factors are available in the Protein Data Bank (accession numbers 4ZQR, 4ZQP, 4ZQN, 4ZQO, 4ZQM).

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