1
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Zhou Y, Aliagas I, Wang S, Li CS, Liu Z, Bowman CM, Burdick DJ, Clark KR, Dening TJ, Flygare J, Ganti A, Girgis HS, Hanan EJ, Harris SF, Hu C, Kapadia SB, Koehler MFT, Lai T, Liang J, Liu X, Ma F, Mao J, Nicolai J, Sims J, Unhayaker S, Wai J, Wang X, Wu P, Xu Y, Yen CW, Zhang R, Elfert TF, Tan MW, Kofoed EM, Crawford TD. Discovery of potent dihydro-oxazinoquinolinone inhibitors of GuaB for the treatment of tuberculosis. Bioorg Med Chem Lett 2025; 117:130026. [PMID: 39536836 DOI: 10.1016/j.bmcl.2024.130026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2024] [Revised: 11/07/2024] [Accepted: 11/08/2024] [Indexed: 11/16/2024]
Abstract
Tuberculosis is the leading cause of death from an infectious disease, and is caused by Mycobacterium tuberculosis (M.tb). More than 1 billion people worldwide are thought to harbor an M.tb infection. The multidrug therapy that represents the current standard of care requires a minimum of four months of dosing and drug resistant Mycobacterium tuberculosis treatment regimens are significantly longer. Inosine-5'-monophosphate dehydrogenase (GuaB) is the enzyme that performs the rate-limiting step in de novo guanine nucleotide biosynthesis that is critical for growth and viability of bacteria including M.tb. The development of a novel antibiotic that inhibits GuaB could combine with existing therapies in novel ways and thereby contribute to effective therapeutic regimens for the treatment of tuberculosis. Here we describe the discovery of structurally distinct small molecule GuaB inhibitors that are potent against M.tb H37Ra and H37Rv strains and have desirable safety and ADME profiles.
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Affiliation(s)
- Yuebiao Zhou
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, United States.
| | - Ignacio Aliagas
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Shumei Wang
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Chun Sing Li
- Wuxi Apptec Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, PR China
| | - Zhiguo Liu
- Wuxi Apptec Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, PR China
| | | | - Daniel J Burdick
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Kevin R Clark
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Tahnee J Dening
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - John Flygare
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Anjani Ganti
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Hany S Girgis
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Emily J Hanan
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Seth F Harris
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Chloe Hu
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | | | | | - Tommy Lai
- Wuxi Apptec Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, PR China
| | - Jun Liang
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Xingrong Liu
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Fang Ma
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Jialin Mao
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Jeremy Nicolai
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Jessica Sims
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Savita Unhayaker
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - John Wai
- Wuxi Apptec Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, PR China
| | - Xiaojing Wang
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Ping Wu
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Yiming Xu
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Chun-Wan Yen
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Renwei Zhang
- Wuxi Apptec Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, PR China
| | - Torben F Elfert
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Man-Wah Tan
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Eric M Kofoed
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Terry D Crawford
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, United States.
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2
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Bulvas O, Knejzlík Z, Sýs J, Filimoněnko A, Čížková M, Clarová K, Rejman D, Kouba T, Pichová I. Deciphering the allosteric regulation of mycobacterial inosine-5'-monophosphate dehydrogenase. Nat Commun 2024; 15:6673. [PMID: 39107302 PMCID: PMC11303537 DOI: 10.1038/s41467-024-50933-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 07/24/2024] [Indexed: 08/10/2024] Open
Abstract
Allosteric regulation of inosine 5'-monophosphate dehydrogenase (IMPDH), an essential enzyme of purine metabolism, contributes to the homeostasis of adenine and guanine nucleotides. However, the precise molecular mechanism of IMPDH regulation in bacteria remains unclear. Using biochemical and cryo-EM approaches, we reveal the intricate molecular mechanism of the IMPDH allosteric regulation in mycobacteria. The enzyme is inhibited by both GTP and (p)ppGpp, which bind to the regulatory CBS domains and, via interactions with basic residues in hinge regions, lock the catalytic core domains in a compressed conformation. This results in occlusion of inosine monophosphate (IMP) substrate binding to the active site and, ultimately, inhibition of the enzyme. The GTP and (p)ppGpp allosteric effectors bind to their dedicated sites but stabilize the compressed octamer by a common mechanism. Inhibition is relieved by the competitive displacement of GTP or (p)ppGpp by ATP allowing IMP-induced enzyme expansion. The structural knowledge and mechanistic understanding presented here open up new possibilities for the development of allosteric inhibitors with antibacterial potential.
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Affiliation(s)
- Ondřej Bulvas
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Zdeněk Knejzlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jakub Sýs
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Anatolij Filimoněnko
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Monika Čížková
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Kamila Clarová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Dominik Rejman
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Tomáš Kouba
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.
| | - Iva Pichová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.
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3
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Ayoub N, Gedeon A, Munier-Lehmann H. A journey into the regulatory secrets of the de novo purine nucleotide biosynthesis. Front Pharmacol 2024; 15:1329011. [PMID: 38444943 PMCID: PMC10912719 DOI: 10.3389/fphar.2024.1329011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 02/01/2024] [Indexed: 03/07/2024] Open
Abstract
De novo purine nucleotide biosynthesis (DNPNB) consists of sequential reactions that are majorly conserved in living organisms. Several regulation events take place to maintain physiological concentrations of adenylate and guanylate nucleotides in cells and to fine-tune the production of purine nucleotides in response to changing cellular demands. Recent years have seen a renewed interest in the DNPNB enzymes, with some being highlighted as promising targets for therapeutic molecules. Herein, a review of two newly revealed modes of regulation of the DNPNB pathway has been carried out: i) the unprecedent allosteric regulation of one of the limiting enzymes of the pathway named inosine 5'-monophosphate dehydrogenase (IMPDH), and ii) the supramolecular assembly of DNPNB enzymes. Moreover, recent advances that revealed the therapeutic potential of DNPNB enzymes in bacteria could open the road for the pharmacological development of novel antibiotics.
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Affiliation(s)
- Nour Ayoub
- Institut Pasteur, Université Paris Cité, INSERM UMRS-1124, Paris, France
| | - Antoine Gedeon
- Sorbonne Université, École Normale Supérieure, Université PSL, CNRS UMR7203, Laboratoire des Biomolécules, LBM, Paris, France
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4
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Hernández-Gómez A, Irisarri I, Fernández-Justel D, Peláez R, Jiménez A, Revuelta JL, Balsera M, Buey RM. GuaB3, an overlooked enzyme in cyanobacteria's toolbox that sheds light on IMP dehydrogenase evolution. Structure 2023; 31:1526-1534.e4. [PMID: 37875114 DOI: 10.1016/j.str.2023.09.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/05/2023] [Accepted: 09/28/2023] [Indexed: 10/26/2023]
Abstract
IMP dehydrogenase and GMP reductase are enzymes from the same protein family with analogous structures and catalytic mechanisms that have gained attention because of their essential roles in nucleotide metabolism and as potential drug targets. This study focusses on GuaB3, a less-explored enzyme within this family. Phylogenetic analysis uncovers GuaB3's independent evolution from other members of the family and it predominantly occurs in Cyanobacteria. Within this group, GuaB3 functions as a unique IMP dehydrogenase, while its counterpart in Actinobacteria has a yet unknown function. Synechocystis sp. PCC6803 GuaB3 structures demonstrate differences in the active site compared to canonical IMP dehydrogenases, despite shared catalytic mechanisms. These findings highlight the essential role of GuaB3 in Cyanobacteria, provide insights into the diversity and evolution of the IMP dehydrogenase protein family, and reveal a distinctive characteristic in nucleotide metabolism, potentially aiding in combating harmful cyanobacterial blooms-a growing concern for humans and wildlife.
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Affiliation(s)
- Alejandro Hernández-Gómez
- Metabolic Engineering Group, Dpto. Microbiología y Genética, Universidad de Salamanca, Edificio Departamental, Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | - Iker Irisarri
- Section Phylogenomics, Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Museum of Nature Hamburg, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
| | - David Fernández-Justel
- Metabolic Engineering Group, Dpto. Microbiología y Genética, Universidad de Salamanca, Edificio Departamental, Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | - Rafael Peláez
- Laboratorio de Química Orgánica y Farmacéutica, Dpto. Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | - Alberto Jiménez
- Metabolic Engineering Group, Dpto. Microbiología y Genética, Universidad de Salamanca, Edificio Departamental, Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | - José Luis Revuelta
- Metabolic Engineering Group, Dpto. Microbiología y Genética, Universidad de Salamanca, Edificio Departamental, Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | - Mónica Balsera
- Department Abiotic Stress, Instituto de Recursos Naturales y Agrobiología (IRNASA-CSIC), Cordel de Merinas 40-52, 37008 Salamanca, Spain
| | - Rubén M Buey
- Metabolic Engineering Group, Dpto. Microbiología y Genética, Universidad de Salamanca, Edificio Departamental, Campus Miguel de Unamuno, 37007 Salamanca, Spain.
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5
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Togre NS, Vargas AM, Bhargavi G, Mallakuntla MK, Tiwari S. Fragment-Based Drug Discovery against Mycobacteria: The Success and Challenges. Int J Mol Sci 2022; 23:10669. [PMID: 36142582 PMCID: PMC9500838 DOI: 10.3390/ijms231810669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/10/2022] [Accepted: 09/10/2022] [Indexed: 11/29/2022] Open
Abstract
The emergence of drug-resistant mycobacteria, including Mycobacterium tuberculosis (Mtb) and non-tuberculous mycobacteria (NTM), poses an increasing global threat that urgently demands the development of new potent anti-mycobacterial drugs. One of the approaches toward the identification of new drugs is fragment-based drug discovery (FBDD), which is the most ingenious among other drug discovery models, such as structure-based drug design (SBDD) and high-throughput screening. Specialized techniques, such as X-ray crystallography, nuclear magnetic resonance spectroscopy, and many others, are part of the drug discovery approach to combat the Mtb and NTM global menaces. Moreover, the primary drawbacks of traditional methods, such as the limited measurement of biomolecular toxicity and uncertain bioavailability evaluation, are successfully overcome by the FBDD approach. The current review focuses on the recognition of fragment-based drug discovery as a popular approach using virtual, computational, and biophysical methods to identify potent fragment molecules. FBDD focuses on designing optimal inhibitors against potential therapeutic targets of NTM and Mtb (PurC, ArgB, MmpL3, and TrmD). Additionally, we have elaborated on the challenges associated with the FBDD approach in the identification and development of novel compounds. Insights into the applications and overcoming the challenges of FBDD approaches will aid in the identification of potential therapeutic compounds to treat drug-sensitive and drug-resistant NTMs and Mtb infections.
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Affiliation(s)
| | | | | | | | - Sangeeta Tiwari
- Department of Biological Sciences & Border Biomedical Research Centre, University of Texas at El Paso, El Paso, TX 79968, USA
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6
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Knejzlík Z, Doležal M, Herkommerová K, Clarova K, Klíma M, Dedola M, Zborníková E, Rejman D, Pichová I. The mycobacterial guaB1 gene encodes a guanosine 5'-monophosphate reductase with a cystathionine-β-synthase domain. FEBS J 2022; 289:5571-5598. [PMID: 35338694 PMCID: PMC9790621 DOI: 10.1111/febs.16448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 02/11/2022] [Accepted: 03/24/2022] [Indexed: 12/30/2022]
Abstract
Mycobacteria express enzymes from both the de novo and purine-salvage pathways. However, the regulation of these processes and the roles of individual metabolic enzymes have not been sufficiently detailed. Both Mycobacterium tuberculosis (Mtb) and Mycobacterium smegmatis (Msm) possess three guaB genes, but information is only available on guaB2, which encodes an essential inosine 5'-monophosphate dehydrogenase (IMPDH) involved in de novo purine biosynthesis. This study shows that guaB1, annotated in databases as a putative IMPDH, encodes a guanosine 5'-monophosphate reductase (GMPR), which recycles guanosine monophosphate to inosine monophosphate within the purine-salvage pathway and contains a cystathionine-β-synthase domain (CBS), which is essential for enzyme activity. GMPR activity is allosterically regulated by the ATP/GTP ratio in a pH-dependent manner. Bioinformatic analysis has indicated the presence of GMPRs containing CBS domains across the entire Actinobacteria phylum.
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Affiliation(s)
- Zdeněk Knejzlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesPragueCzech Republic
| | - Michal Doležal
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesPragueCzech Republic
| | - Klára Herkommerová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesPragueCzech Republic
| | - Kamila Clarova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesPragueCzech Republic
| | - Martin Klíma
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesPragueCzech Republic
| | - Matteo Dedola
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesPragueCzech Republic
| | - Eva Zborníková
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesPragueCzech Republic
| | - Dominik Rejman
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesPragueCzech Republic
| | - Iva Pichová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesPragueCzech Republic
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7
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Perveen S, Sharma R. Screening approaches and therapeutic targets: The two driving wheels of tuberculosis drug discovery. Biochem Pharmacol 2022; 197:114906. [PMID: 34990594 DOI: 10.1016/j.bcp.2021.114906] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 12/28/2021] [Accepted: 12/28/2021] [Indexed: 12/21/2022]
Abstract
Tuberculosis (TB) is an infectious disease, infecting a quarter of world's population. Drug resistant TB further exacerbates the grim scenario of the drying TB drug discovery pipeline. The limited arsenal to fight TB presses the need for thorough efforts for identifying promising hits to combat the disease. The review highlights the efforts in the field of tuberculosis drug discovery, with an emphasis on massive drug screening campaigns for identifying novel hits against Mtb in both industry and academia. As an intracellular pathogen, mycobacteria reside in a complicated intracellular environment with multiple factors at play. Here, we outline various strategies employed in an effort to mimic the intracellular milieu for bringing the screening models closer to the actual settings. The review also focuses on the novel targets and pathways that could aid in target-based drug discovery in TB. The recent high throughput screening efforts resulting in the identification of potent hits against Mtb has been summarized in this article. There is a pressing need for effective screening strategies and approaches employing innovative tools and recent technologies; including nanotechnology, gene-editing tools such as CRISPR-cas system, host-directed bacterial killing and high content screening to augment the TB drug discovery pipeline with safer and shorter drug regimens.
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Affiliation(s)
- Summaya Perveen
- Infectious Diseases Division, CSIR- Indian Institute of Integrative Medicine, Jammu 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Rashmi Sharma
- Infectious Diseases Division, CSIR- Indian Institute of Integrative Medicine, Jammu 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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8
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Modi G, Marqus GM, Vippila MR, Gollapalli DR, Kim Y, Manna AC, Chacko S, Maltseva N, Wang X, Cullinane RT, Zhang Y, Kotler JLM, Kuzmic P, Zhang M, Lawson AP, Joachimiak A, Cheung A, Snider BB, Rothstein DM, Cuny GD, Hedstrom L. The Enzymatic Activity of Inosine 5'-Monophosphate Dehydrogenase May Not Be a Vulnerable Target for Staphylococcus aureus Infections. ACS Infect Dis 2021; 7:3062-3076. [PMID: 34590817 DOI: 10.1021/acsinfecdis.1c00342] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Many bacterial pathogens, including Staphylococcus aureus, require inosine 5'-monophosphate dehydrogenase (IMPDH) for infection, making this enzyme a promising new target for antibiotics. Although potent selective inhibitors of bacterial IMPDHs have been reported, relatively few have displayed antibacterial activity. Here we use structure-informed design to obtain inhibitors of S. aureus IMPDH (SaIMPDH) that have potent antibacterial activity (minimal inhibitory concentrations less than 2 μM) and low cytotoxicity in mammalian cells. The physicochemical properties of the most active compounds were within typical Lipinski/Veber space, suggesting that polarity is not a general requirement for achieving antibacterial activity. Five compounds failed to display activity in mouse models of septicemia and abscess infection. Inhibitor-resistant S. aureus strains readily emerged in vitro. Resistance resulted from substitutions in the cofactor/inhibitor binding site of SaIMPDH, confirming on-target antibacterial activity. These mutations decreased the binding of all inhibitors tested, but also decreased catalytic activity. Nonetheless, the resistant strains had comparable virulence to wild-type bacteria. Surprisingly, strains expressing catalytically inactive SaIMPDH displayed only a mild virulence defect. Collectively these observations question the vulnerability of the enzymatic activity of SaIMPDH as a target for the treatment of S. aureus infections, suggesting other functions of this protein may be responsible for its role in infection.
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Affiliation(s)
- Gyan Modi
- Department of Biology, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Gary M. Marqus
- Graduate Program in Chemistry, Brandeis University, Waltham Massachusetts 02453, United States
| | - Mohana Rao Vippila
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Health Building 2, 4849 Calhoun Rd., Houston, Texas 77204, United States
| | | | - Youngchang Kim
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois 60667, United States
- The Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Adhar C. Manna
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755, United States
| | - Shibin Chacko
- Department of Biology, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Natalia Maltseva
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois 60667, United States
- The Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Xingyou Wang
- Graduate Program in Chemistry, Brandeis University, Waltham Massachusetts 02453, United States
| | - Ryan T. Cullinane
- Department of Biochemistry, Brandeis University, Massachusetts 02453, United States
| | - Yubo Zhang
- Department of Biochemistry, Brandeis University, Massachusetts 02453, United States
| | - Judy L. M. Kotler
- Graduate Program in Biochemistry and Biophysics, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Petr Kuzmic
- BioKin Ltd., Watertown, Massachusetts 02472, United States
| | - Minjia Zhang
- Department of Biology, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Ann P. Lawson
- Department of Biology, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois 60667, United States
- The Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60367, United States
| | - Ambrose Cheung
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755, United States
| | - Barry B. Snider
- Department of Chemistry, Brandeis University, Waltham, Massachusetts 02453, United States
| | - David M. Rothstein
- David Rothstein Consulting, LLC, Lexington, Massachusetts 02421, United States
| | - Gregory D. Cuny
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Health Building 2, 4849 Calhoun Rd., Houston, Texas 77204, United States
| | - Lizbeth Hedstrom
- Department of Biology, Brandeis University, Waltham, Massachusetts 02453, United States
- Department of Chemistry, Brandeis University, Waltham, Massachusetts 02453, United States
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9
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Zhang Y, Zhang H, Chen Y, Qiao L, Han Y, Lin Y, Si S, Jiang JD. Screening and Identification of a Novel Anti-tuberculosis Compound That Targets Deoxyuridine 5'-Triphosphate Nucleotidohydrolase. Front Microbiol 2021; 12:757914. [PMID: 34707597 PMCID: PMC8544286 DOI: 10.3389/fmicb.2021.757914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 09/10/2021] [Indexed: 01/08/2023] Open
Abstract
Tuberculosis (TB) is still a threat to humans worldwide. The rise of drug-resistant TB strains has escalated the need for developing effective anti-TB agents. Deoxyuridine 5′-triphosphate nucleotidohydrolase (dUTPase) is essential for thymidylate biosynthesis to maintain the DNA integrity. In Mycobacterium tuberculosis, dUTPase provides the sole source for thymidylate biosynthesis, which also has the specific five-residue loop and the binding pockets absent in human dUTPase. Therefore, dUTPase has been regarded as a promising anti-TB drug target. Herein, we used a luminescence-based dUTPase assay to search for the inhibitors target M. tuberculosis dUTPase (Mt-dUTPase) and identified compound F0414 as a potent Mt-dUTPase inhibitor with an IC50 of 0.80 ± 0.09 μM. F0414 exhibited anti-TB activity with low cytotoxicity. Molecular docking model and site-directed mutation experiments revealed that P79 was the key residue in the interaction of Mt-dUTPase and F0414. Moreover, F0414 was shown to have stronger binding with Mt-dUTPase than with Mt-P79A-dUTPase by surface plasmon resonance (SPR) detection. Interestingly, F0414 exhibited insensitivity and weak directly binding on human dUTPase compared with that on Mt-dUTPase. All the results highlight that F0414 is the first compound reported to have anti-TB activity by inhibiting Mt-dUTPase, which indicates the potential application in anti-TB therapy.
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Affiliation(s)
- Yu Zhang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hongjuan Zhang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ying Chen
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Luyao Qiao
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yanxing Han
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuan Lin
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shuyi Si
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jian-Dong Jiang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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10
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Targeting NAD-dependent dehydrogenases in drug discovery against infectious diseases and cancer. Biochem Soc Trans 2021; 48:693-707. [PMID: 32311017 DOI: 10.1042/bst20191261] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 03/10/2020] [Accepted: 03/16/2020] [Indexed: 12/24/2022]
Abstract
Dehydrogenases are oxidoreductase enzymes that play a variety of fundamental functions in the living organisms and have primary roles in pathogen survival and infection processes as well as in cancer development. We review here a sub-set of NAD-dependent dehydrogenases involved in human diseases and the recent advancements in drug development targeting pathogen-associated NAD-dependent dehydrogenases. We focus also on the molecular aspects of the inhibition process listing the structures of the most relevant molecules targeting this enzyme family. Our aim is to review the most impacting findings regarding the discovery of novel inhibitory compounds targeting the selected NAD-dependent dehydrogenases involved in cancer and infectious diseases.
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11
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Cheng K, He M, Shu Q, Wu M, Chen C, Xue Y. Analysis of the Risk Factors for Nosocomial Bacterial Infection in Patients with COVID-19 in a Tertiary Hospital. Risk Manag Healthc Policy 2020; 13:2593-2599. [PMID: 33223859 PMCID: PMC7671853 DOI: 10.2147/rmhp.s277963] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 10/23/2020] [Indexed: 12/14/2022] Open
Abstract
Background Infection surveillance and risk factor analysis are among the most important prerequisites for the prevention and treatment of nosocomial bacteria infections, which are the demands for both infected and non-infected patients. Purpose To explore the risk factors for nosocomial bacterial infection of patients with COVID-19, and further to provide a theoretical basis for scientific prevention and control of nosocomial bacterial infection. Methods Between 10 January 2020 and 9 March 2020, we collected data of 212 patients with COVID-19 and then explored the influence of age, gender, length of stay, use of ventilator, urinary catheterization, central venous catheterization, white blood cell (WBC) count and procalcitonin on the nosocomial bacterial infection of patients with COVID-19 by a retrospective study. Results There were 212 confirmed cases of COVID-19, of which 31 cases had nosocomial bacterial infections, with an incidence of 14.62%. The most common types of nosocomial bacterial infections were lower respiratory tract (12 cases, 38.71%), which was the most frequent site, followed by urinary tract (10 cases, 32.26%), blood stream (7 cases, 22.58%), upper respiratory tract (1 case, 3.23%) and gastrointestinal tract infection (1 case, 3.23%). The incidence of nosocomial bacterial infection was significantly correlated with age, arteriovenous catheterization, urinary catheterization, WBC count and procalcitonin. Moreover, multivariate analysis confirmed that WBC (OR 8.38, 95% CI 1.07 to 65.55), procalcitonin (OR 4.92, 95% CI 1.39 to 17.33) and urinary catheterization (OR 25.38, 95% CI 5.09 to 126.53) were independent risk factors for the nosocomial bacterial infection of patients with COVID-19. Conclusion Understanding the risk factors for nosocomial bacterial infection of patients with COVID-19 and strengthening the monitoring of various susceptible factors are helpful to control the occurrence of nosocomial bacterial infection in the COVID-19 isolation wards.
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Affiliation(s)
- Keping Cheng
- Department of Infection Management, Zhongda Hospital Affiliated to Southeast University, Nanjing 210009, People's Republic of China
| | - Miao He
- Department of Public Health, Huangshi Central Hospital, Huangshi 435000, People's Republic of China
| | - Qin Shu
- Department of Infection Prevention and Control, Huangshi Traditional Chinese Medicine Hospital, Huangshi 435004, People's Republic of China
| | - Ming Wu
- Department of Infection Prevention and Control, Huangshi Traditional Chinese Medicine Hospital, Huangshi 435004, People's Republic of China
| | - Cuifang Chen
- Department of Public Health, Huangshi Central Hospital, Huangshi 435000, People's Republic of China
| | - Yulei Xue
- Department of Infectious Diseases, Jiangsu Provincial Hospital of Traditional Chinese Medicine, Nanjing 210029, People's Republic of China
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12
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Nan J, Zhang S, Zhan P, Jiang L. Evaluation of Bronopol and Disulfiram as Potential Candidatus Liberibacter asiaticus Inosine 5'-Monophosphate Dehydrogenase Inhibitors by Using Molecular Docking and Enzyme Kinetic. Molecules 2020; 25:E2313. [PMID: 32423116 PMCID: PMC7287799 DOI: 10.3390/molecules25102313] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 04/30/2020] [Accepted: 05/11/2020] [Indexed: 12/12/2022] Open
Abstract
Citrus huanglongbing (HLB) is a destructive disease that causes significant damage to many citrus producing areas worldwide. To date, no strategy against this disease has been established. Inosine 5'-monophosphate dehydrogenase (IMPDH) plays crucial roles in the de novo synthesis of guanine nucleotides. This enzyme is used as a potential target to treat bacterial infection. In this study, the crystal structure of a deletion mutant of CLas IMPDHΔ98-201 in the apo form was determined. Eight known bioactive compounds were used as ligands for molecular docking. The results showed that bronopol and disulfiram bound to CLas IMPDHΔ98-201 with high affinity. These compounds were tested for their inhibition against CLas IMPDHΔ98-201 activity. Bronopol and disulfiram showed high inhibition at nanomolar concentrations, and bronopol was found to be the most potent molecule (Ki = 234 nM). The Ki value of disulfiram was 616 nM. These results suggest that bronopol and disulfiram can be considered potential candidate agents for the development of CLas inhibitors.
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Affiliation(s)
- Jing Nan
- College of Horticulture and Forestry, Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; (J.N.); (P.Z.)
| | - Shaoran Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Ping Zhan
- College of Horticulture and Forestry, Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; (J.N.); (P.Z.)
| | - Ling Jiang
- College of Horticulture and Forestry, Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; (J.N.); (P.Z.)
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13
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Miggiano R, Morrone C, Rossi F, Rizzi M. Targeting Genome Integrity in Mycobacterium Tuberculosis: From Nucleotide Synthesis to DNA Replication and Repair. Molecules 2020; 25:E1205. [PMID: 32156001 PMCID: PMC7179400 DOI: 10.3390/molecules25051205] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/04/2020] [Accepted: 03/05/2020] [Indexed: 12/12/2022] Open
Abstract
Mycobacterium tuberculosis (MTB) is the causative agent of tuberculosis (TB), an ancient disease which still today causes 1.4 million deaths worldwide per year. Long-term, multi-agent anti-tubercular regimens can lead to the anticipated non-compliance of the patient and increased drug toxicity, which in turn can contribute to the emergence of drug-resistant MTB strains that are not susceptible to first- and second-line available drugs. Hence, there is an urgent need for innovative antitubercular drugs and vaccines. A number of biochemical processes are required to maintain the correct homeostasis of DNA metabolism in all organisms. Here we focused on reviewing our current knowledge and understanding of biochemical and structural aspects of relevance for drug discovery, for some such processes in MTB, and particularly DNA synthesis, synthesis of its nucleotide precursors, and processes that guarantee DNA integrity and genome stability. Overall, the area of drug discovery in DNA metabolism appears very much alive, rich of investigations and promising with respect to new antitubercular drug candidates. However, the complexity of molecular events that occur in DNA metabolic processes requires an accurate characterization of mechanistic details in order to avoid major flaws, and therefore the failure, of drug discovery approaches targeting genome integrity.
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Affiliation(s)
- Riccardo Miggiano
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Via Bovio 6, 28100 Novara, Italy; (C.M.); (F.R.)
| | | | | | - Menico Rizzi
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Via Bovio 6, 28100 Novara, Italy; (C.M.); (F.R.)
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14
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Hypoxanthine-Guanine Phosphoribosyltransferase Is Dispensable for Mycobacterium smegmatis Viability. J Bacteriol 2020; 202:JB.00710-19. [PMID: 31818925 DOI: 10.1128/jb.00710-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 12/05/2019] [Indexed: 12/19/2022] Open
Abstract
Purine metabolism plays a ubiquitous role in the physiology of Mycobacterium tuberculosis and other mycobacteria. The purine salvage enzyme hypoxanthine-guanine phosphoribosyltransferase (HGPRT) is essential for M. tuberculosis growth in vitro; however, its precise role in M. tuberculosis physiology is unclear. Membrane-permeable prodrugs of specifically designed HGPRT inhibitors arrest the growth of M. tuberculosis and represent potential new antituberculosis compounds. Here, we investigated the purine salvage pathway in the model organism Mycobacterium smegmatis Using genomic deletion analysis, we confirmed that HGPRT is the only guanine and hypoxanthine salvage enzyme in M. smegmatis but is not required for in vitro growth of this mycobacterium or survival under long-term stationary-phase conditions. We also found that prodrugs of M. tuberculosis HGPRT inhibitors displayed an unexpected antimicrobial activity against M. smegmatis that is independent of HGPRT. Our data point to a different mode of mechanism of action for these inhibitors than was originally proposed.IMPORTANCE Purine bases, released by the hydrolytic and phosphorolytic degradation of nucleic acids and nucleotides, can be salvaged and recycled. The hypoxanthine-guanine phosphoribosyltransferase (HGPRT), which catalyzes the formation of guanosine-5'-monophosphate from guanine and inosine-5'-monophosphate from hypoxanthine, represents a potential target for specific inhibitor development. Deletion of the HGPRT gene (Δhgprt) in the model organism Mycobacterium smegmatis confirmed that this enzyme is not essential for M. smegmatis growth. Prodrugs of acyclic nucleoside phosphonates (ANPs), originally designed against HGPRT from Mycobacterium tuberculosis, displayed anti-M. smegmatis activities comparable to those obtained for M. tuberculosis but also inhibited the Δhgprt M. smegmatis strain. These results confirmed that ANPs act in M. smegmatis by a mechanism independent of HGPRT.
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15
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Juvale K, Shaik A, Kirubakaran S. Inhibitors of inosine 5'-monophosphate dehydrogenase as emerging new generation antimicrobial agents. MEDCHEMCOMM 2019; 10:1290-1301. [PMID: 31534651 PMCID: PMC6727467 DOI: 10.1039/c9md00179d] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 05/01/2019] [Indexed: 12/15/2022]
Abstract
Inosine 5'-monophosphate dehydrogenase (IMPDH) is a vital enzyme involved in the de novo synthesis of guanine nucleotides. IMPDH catalyzes a crucial step of converting IMP into XMP that is further converted into GMP. Microbial infections rely on the rapid proliferation of bacteria, and this requires the rate-limiting enzyme IMPDH to expand the guanine nucleotide pool and hence, IMPDH has recently received lots of attention as a potential target for treating infections. Owing to the structural and kinetic differences in the host IMPDH and bacterial IMPDH, a selective targeting is possible and is a crucial feature in the development of new potent and selective inhibitors of bacterial IMPDH. Earlier screening of small molecules revealed a structural requirement for the bacterial/protozoal IMPDH. Early optimization of benzimidazole and benzoxazole scaffolds led to the discovery of new potent and selective inhibitors of pathogenic IMPDH. Further research is vastly focused on the development of highly potent and selective inhibitors of various bacterial IMPDHs. Such studies reveal the importance of this excellent target for treating infectious diseases. The current review focuses on the recent developments in the discovery and development of selective inhibitors of bacterial/protozoal IMPDH with emphasis on the inhibition mechanism and structure-activity relationship.
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Affiliation(s)
- Kapil Juvale
- Shobhaben Pratapbhai Patel School of Pharmacy & Technology Management , SVKM's NMIMS , V.L. Mehta Road, Vile Parle (W) , Mumbai , 400056 India
| | - Althaf Shaik
- Chemistry , Indian Institute of Technology Gandhinagar , Palaj Village , Gandhinagar , 382355 India .
| | - Sivapriya Kirubakaran
- Chemistry , Indian Institute of Technology Gandhinagar , Palaj Village , Gandhinagar , 382355 India .
- Bio-engineering , Indian Institute of Technology Gandhinagar , Palaj Village , Gandhinagar , 382355 India
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16
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Yang X, Yuan T, Ma R, Chacko KI, Smith M, Deikus G, Sebra R, Kasarskis A, van Bakel H, Franzblau SG, Sampson NS. Mce3R Stress-Resistance Pathway Is Vulnerable to Small-Molecule Targeting That Improves Tuberculosis Drug Activities. ACS Infect Dis 2019; 5:1239-1251. [PMID: 31012313 PMCID: PMC6630528 DOI: 10.1021/acsinfecdis.9b00099] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
![]()
One-third of the world’s population
carries Mycobacterium tuberculosis (Mtb), the infectious agent that causes tuberculosis (TB), and every
17 s someone dies of TB. After infection, Mtb can
live dormant for decades in a granuloma structure arising from the
host immune response, and cholesterol is important for this persistence
of Mtb. Current treatments require long-duration
drug regimens with many associated toxicities, which are compounded
by the high doses required. We phenotypically screened 35 6-azasteroid
analogues against Mtb and found that, at low micromolar
concentrations, a subset of the analogues sensitized Mtb to multiple TB drugs. Two analogues were selected for further study
to characterize the bactericidal activity of bedaquiline and isoniazid
under normoxic and low-oxygen conditions. These two 6-azasteroids
showed strong synergy with bedaquiline (fractional inhibitory concentration
index = 0.21, bedaquiline minimal inhibitory concentration = 16 nM
at 1 μM 6-azasteroid). The rate at which spontaneous resistance
to one of the 6-azasteroids arose in the presence of bedaquiline was
approximately 10–9, and the 6-azasteroid-resistant
mutants retained their isoniazid and bedaquiline sensitivity. Genes
in the cholesterol-regulated Mce3R regulon were required for 6-azasteroid
activity, whereas genes in the cholesterol catabolism pathway were
not. Expression of a subset of Mce3R genes was down-regulated upon
6-azasteroid treatment. The Mce3R regulon is implicated in stress
resistance and is absent in saprophytic mycobacteria. This regulon
encodes a cholesterol-regulated stress-resistance pathway that we
conclude is important for pathogenesis and contributes to drug tolerance,
and this pathway is vulnerable to small-molecule targeting in live
mycobacteria.
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Affiliation(s)
- Xinxin Yang
- Department of Chemistry, Stony Brook University, 100 John S. Toll Drive, Stony Brook, New York 11794-3400, United States
| | - Tianao Yuan
- Department of Chemistry, Stony Brook University, 100 John S. Toll Drive, Stony Brook, New York 11794-3400, United States
| | - Rui Ma
- Institute for Tuberculosis Research, University of Illinois at Chicago, 833 South Wood Street, 425 PHARM, Chicago, Illinois 60612-7231, United States
| | - Kieran I. Chacko
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York City, New York 10029, United States
| | - Melissa Smith
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York City, New York 10029, United States
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York City, New York, 10029-6574, United States
| | - Gintaras Deikus
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York City, New York 10029, United States
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York City, New York, 10029-6574, United States
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York City, New York 10029, United States
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York City, New York, 10029-6574, United States
| | - Andrew Kasarskis
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York City, New York 10029, United States
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York City, New York, 10029-6574, United States
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York City, New York 10029, United States
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York City, New York, 10029-6574, United States
| | - Scott G. Franzblau
- Institute for Tuberculosis Research, University of Illinois at Chicago, 833 South Wood Street, 425 PHARM, Chicago, Illinois 60612-7231, United States
| | - Nicole S. Sampson
- Department of Chemistry, Stony Brook University, 100 John S. Toll Drive, Stony Brook, New York 11794-3400, United States
- Institute of Chemical Biology and Drug Discovery, Stony Brook University, 100 John S. Toll Drive, Stony Brook, New York 11794-3400, United States
- Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, 10 Marais Street, Stellenbosch 7600, South Africa
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17
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Synthesis and Structure-Activity relationship of 1-(5-isoquinolinesulfonyl)piperazine analogues as inhibitors of Mycobacterium tuberculosis IMPDH. Eur J Med Chem 2019; 174:309-329. [PMID: 31055147 PMCID: PMC6990405 DOI: 10.1016/j.ejmech.2019.04.027] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 04/11/2019] [Accepted: 04/11/2019] [Indexed: 02/06/2023]
Abstract
Tuberculosis (TB) is a major infectious disease associated increasingly with drug resistance. Thus, new anti-tubercular agents with novel mechanisms of action are urgently required for the treatment of drug-resistant TB. In prior work, we identified compound 1 (cyclohexyl(4-(isoquinolin-5-ylsulfonyl)piperazin-1-yl)methanone) and showed that its anti-tubercular activity is attributable to inhibition of inosine-5′-monophosphate dehydrogenase (IMPDH) in Mycobacterium tuberculosis. In the present study, we explored the structure–activity relationship around compound 1 by synthesizing and evaluating the inhibitory activity of analogues against M. tuberculosis IMPDH in biochemical and whole-cell assays. X-ray crystallography was performed to elucidate the mode of binding of selected analogues to IMPDH. We establish the importance of the cyclohexyl, piperazine and isoquinoline rings for activity, and report the identification of an analogue with IMPDH-selective activity against a mutant of M. tuberculosis that is highly resistant to compound 1. We also show that the nitrogen in urea analogues is required for anti-tubercular activity and identify benzylurea derivatives as promising inhibitors that warrant further investigation. Forty-eight analogues of 1-(5-isoquinolinesulfonyl)piperazine were synthesized. Biochemical, whole-cell, and X-ray studies were performed to elucidate the IMPDH inhibition. Piperazine and isoquinoline rings were essential for target-selective whole-cell activity. Compound 47 showed improved IC50 against the MtbIMPDH and maintained on-target whole-cell activity. Compound 21 showed activity against IMPDH in both wild type M. tuberculosis and a resistant mutant of compound 1.
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18
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Veale CGL. Unpacking the Pathogen Box-An Open Source Tool for Fighting Neglected Tropical Disease. ChemMedChem 2019; 14:386-453. [PMID: 30614200 DOI: 10.1002/cmdc.201800755] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Indexed: 12/13/2022]
Abstract
The Pathogen Box is a 400-strong collection of drug-like compounds, selected for their potential against several of the world's most important neglected tropical diseases, including trypanosomiasis, leishmaniasis, cryptosporidiosis, toxoplasmosis, filariasis, schistosomiasis, dengue virus and trichuriasis, in addition to malaria and tuberculosis. This library represents an ensemble of numerous successful drug discovery programmes from around the globe, aimed at providing a powerful resource to stimulate open source drug discovery for diseases threatening the most vulnerable communities in the world. This review seeks to provide an in-depth analysis of the literature pertaining to the compounds in the Pathogen Box, including structure-activity relationship highlights, mechanisms of action, related compounds with reported activity against different diseases, and, where appropriate, discussion on the known and putative targets of compounds, thereby providing context and increasing the accessibility of the Pathogen Box to the drug discovery community.
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Affiliation(s)
- Clinton G L Veale
- School of Chemistry and Physics, Pietermaritzburg Campus, University of KwaZulu-Natal, Private Bag X01, Scottsville, 3209, South Africa
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19
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Transcriptome analysis of extended-spectrum β-lactamase-producing Escherichia coli and methicillin-resistant Staphylococcus aureus exposed to cefotaxime. Sci Rep 2018; 8:16076. [PMID: 30375423 PMCID: PMC6207760 DOI: 10.1038/s41598-018-34191-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 10/11/2018] [Indexed: 12/25/2022] Open
Abstract
Previous studies on bacterial response to antibiotics mainly focused on susceptible strains. Here we characterized the transcriptional responses of distinct cephalosporin-resistant bacteria of public health relevance to cefotaxime (CTX), a cephalosporin widely used in clinical practice. Adaptation to therapeutic concentrations of CTX (30 µg/ml) was investigated by RNA sequencing in mid-exponential phase cultures of a methicillin-resistant Staphylococcus aureus (MRSA) and two genetically diverse E. coli producing CTX-M-15 or CMY-2 β-lactamase following genome sequencing and annotation for each strain. MRSA showed the most notable adaptive changes in the transcriptome after exposure to CTX, mainly associated with cell envelope functions. This reprogramming coincided with a transient reduction in cell growth, which also occurred in the CMY-2-producing E. coli but not in the CTX-M-15-producing strain. Re-establishment of growth in the CMY-2 producer proceeded without any notable adaptive transcriptional response, while limited reprogramming of gene transcription was observed in the CTX-M-15 producer. Our data show that the transcriptional response of CTX-resistant bacteria to CTX depends on the bacterial species, level of resistance and resistance determinant involved. Gene products induced in the presence of CTX may play an essential role for bacterial survival during therapy and merit further investigation as possible targets for potentiating CTX.
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20
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Sahu NU, Singh V, Ferraris DM, Rizzi M, Kharkar PS. Hit discovery of Mycobacterium tuberculosis inosine 5'-monophosphate dehydrogenase, GuaB2, inhibitors. Bioorg Med Chem Lett 2018; 28:1714-1718. [PMID: 29699922 DOI: 10.1016/j.bmcl.2018.04.045] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 04/13/2018] [Accepted: 04/17/2018] [Indexed: 02/05/2023]
Abstract
Tuberculosis remains a global concern. There is an urgent need of newer antitubercular drugs due to the development of resistant forms of Mycobacterium tuberculosis (Mtb). Inosine 5'-monophosphate dehydrogenase (IMPDH), guaB2, of Mtb, required for guanine nucleotide biosynthesis, is an attractive target for drug development. In this study, we screened a focused library of 73 drug-like molecules with desirable calculated/predicted physicochemical properties, for growth inhibitory activity against drug-sensitive MtbH37Rv. The eight hits and mycophenolic acid, a prototype IMPDH inhibitor, were further evaluated for activity on purified Mtb-GuaB2 enzyme, target selectivity using a conditional knockdown mutant of guaB2 in Mtb, followed by cross-resistance to IMPDH inhibitor-resistant SRMV2.6 strain of Mtb, and activity on human IMPDH2 isoform. One of the hits, 13, a 5-amidophthalide derivative, has shown growth inhibitory potential and target specificity against the Mtb-GuaB2 enzyme. The hit, 13, is a promising molecule with potential for further development as an antitubercular agent.
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Affiliation(s)
- Niteshkumar U Sahu
- Department of Pharmaceutical Chemistry, SPP School of Pharmacy & Technology Management, SVKM's NMIMS, V.L. Mehta Road, Vile Parle (West), Mumbai 400 056, India
| | - Vinayak Singh
- Drug Discovery and Development Centre (H3D), University of Cape Town, Rondebosch 7701, Cape Town, South Africa; South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch 7701, South Africa
| | - Davide M Ferraris
- Dipartimento di Scienze del Farmaco, Università del Piemonte Orientale, Via Bovio 6, 28100 Novara, Italy
| | - Menico Rizzi
- Dipartimento di Scienze del Farmaco, Università del Piemonte Orientale, Via Bovio 6, 28100 Novara, Italy
| | - Prashant S Kharkar
- Department of Pharmaceutical Chemistry, SPP School of Pharmacy & Technology Management, SVKM's NMIMS, V.L. Mehta Road, Vile Parle (West), Mumbai 400 056, India.
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21
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Chacko S, Boshoff HIM, Singh V, Ferraris DM, Gollapalli DR, Zhang M, Lawson AP, Pepi MJ, Joachimiak A, Rizzi M, Mizrahi V, Cuny GD, Hedstrom L. Expanding Benzoxazole-Based Inosine 5'-Monophosphate Dehydrogenase (IMPDH) Inhibitor Structure-Activity As Potential Antituberculosis Agents. J Med Chem 2018; 61:4739-4756. [PMID: 29746130 DOI: 10.1021/acs.jmedchem.7b01839] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
New drugs and molecular targets are urgently needed to address the emergence and spread of drug-resistant tuberculosis. Mycobacterium tuberculosis ( Mtb) inosine 5'-monophosphate dehydrogenase 2 ( MtbIMPDH2) is a promising yet controversial potential target. The inhibition of MtbIMPDH2 blocks the biosynthesis of guanine nucleotides, but high concentrations of guanine can potentially rescue the bacteria. Herein we describe an expansion of the structure-activity relationship (SAR) for the benzoxazole series of MtbIMPDH2 inhibitors and demonstrate that minimum inhibitory concentrations (MIC) of ≤1 μM can be achieved. The antibacterial activity of the most promising compound, 17b (Q151), is derived from the inhibition of MtbIMPDH2 as demonstrated by conditional knockdown and resistant strains. Importantly, guanine does not change the MIC of 17b, alleviating the concern that guanine salvage can protect Mtb in vivo. These findings suggest that MtbIMPDH2 is a vulnerable target for tuberculosis.
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Affiliation(s)
| | - Helena I M Boshoff
- Tuberculosis Research Section , National Institute of Allergy and Infectious Diseases , Bethesda , Maryland 20892 , United States
| | - Vinayak Singh
- Department of Drug Discovery and Development & Institute of Infectious Disease and Molecular Medicine , H3D Drug Discovery and Development Centre, University of Cape Town , Rondebosch , Cape Town 7701 , South Africa
| | - Davide M Ferraris
- Dipartimento di Scienze del Farmaco , Universitá del Piemonte Orientale , Via Bovio 6 , 28100 Novara , Italy
| | | | | | | | | | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases and Department of Biochemistry and Molecular Biology , University of Chicago , Chicago , Illinois 60557 , United States.,Structural Biology Center, Biosciences , Argonne National Laboratory , 9700 S. Cass Avenue, Argonne , Illinois 60439 , United States
| | - Menico Rizzi
- Dipartimento di Scienze del Farmaco , Universitá del Piemonte Orientale , Via Bovio 6 , 28100 Novara , Italy
| | - Valerie Mizrahi
- MRC/NHLS/UCT Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence for Biomedical TB Research, Institute of Infectious Disease and Molecular Medicine & Department of Pathology , University of Cape Town , Anzio Road , Observatory 7925 , South Africa
| | - Gregory D Cuny
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy , University of Houston , Health Building 2, 4849 Calhoun Road , Houston , Texas 77204 , United States
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22
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Trapero A, Pacitto A, Singh V, Sabbah M, Coyne AG, Mizrahi V, Blundell TL, Ascher DB, Abell C. Fragment-Based Approach to Targeting Inosine-5'-monophosphate Dehydrogenase (IMPDH) from Mycobacterium tuberculosis. J Med Chem 2018; 61:2806-2822. [PMID: 29547284 PMCID: PMC5900554 DOI: 10.1021/acs.jmedchem.7b01622] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
![]()
Tuberculosis (TB)
remains a major cause of mortality worldwide,
and improved treatments are needed to combat emergence of drug resistance.
Inosine 5′-monophosphate dehydrogenase (IMPDH), a crucial enzyme
required for de novo synthesis of guanine nucleotides,
is an attractive TB drug target. Herein, we describe the identification
of potent IMPDH inhibitors using fragment-based screening and structure-based
design techniques. Screening of a fragment library for Mycobacterium
thermoresistible (Mth) IMPDH ΔCBS
inhibitors identified a low affinity phenylimidazole derivative. X-ray
crystallography of the Mth IMPDH ΔCBS–IMP–inhibitor
complex revealed that two molecules of the fragment were bound in
the NAD binding pocket of IMPDH. Linking the two molecules of the
fragment afforded compounds with more than 1000-fold improvement in
IMPDH affinity over the initial fragment hit.
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Affiliation(s)
- Ana Trapero
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Angela Pacitto
- Department of Biochemistry , University of Cambridge , 80 Tennis Court Road , Cambridge CB2 1GA , United Kingdom
| | - Vinayak Singh
- MRC/NHLS/UCT Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence for Biomedical TB Research, Institute of Infectious Disease and Molecular Medicine and Division of Medical Microbiology, Faculty of Health Sciences , University of Cape Town , Rondebosch 7701 , Cape Town , South Africa
| | - Mohamad Sabbah
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Anthony G Coyne
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Valerie Mizrahi
- MRC/NHLS/UCT Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence for Biomedical TB Research, Institute of Infectious Disease and Molecular Medicine and Division of Medical Microbiology, Faculty of Health Sciences , University of Cape Town , Rondebosch 7701 , Cape Town , South Africa
| | - Tom L Blundell
- Department of Biochemistry , University of Cambridge , 80 Tennis Court Road , Cambridge CB2 1GA , United Kingdom
| | - David B Ascher
- Department of Biochemistry , University of Cambridge , 80 Tennis Court Road , Cambridge CB2 1GA , United Kingdom.,Department of Biochemistry and Molecular Biology, Bio21 Institute , University of Melbourne , 30 Flemington Road , Parkville , Victoria 3052 , Australia
| | - Chris Abell
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
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23
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Ferraris DM, Miggiano R, Rossi F, Rizzi M. Mycobacterium tuberculosis Molecular Determinants of Infection, Survival Strategies, and Vulnerable Targets. Pathogens 2018; 7:E17. [PMID: 29389854 PMCID: PMC5874743 DOI: 10.3390/pathogens7010017] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 01/26/2018] [Accepted: 01/28/2018] [Indexed: 12/13/2022] Open
Abstract
Mycobacterium tuberculosis is the causative agent of tuberculosis, an ancient disease which, still today, represents a major threat for the world population. Despite the advances in medicine and the development of effective antitubercular drugs, the cure of tuberculosis involves prolonged therapies which complicate the compliance and monitoring of drug administration and treatment. Moreover, the only available antitubercular vaccine fails to provide an effective shield against adult lung tuberculosis, which is the most prevalent form. Hence, there is a pressing need for effective antitubercular drugs and vaccines. This review highlights recent advances in the study of selected M. tuberculosis key molecular determinants of infection and vulnerable targets whose structures could be exploited for the development of new antitubercular agents.
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Affiliation(s)
- Davide M Ferraris
- Department of Pharmaceutical Sciences, Università del Piemonte Orientale "A. Avogadro", Largo Donegani 2, 28100 Novara, Italy.
| | - Riccardo Miggiano
- Department of Pharmaceutical Sciences, Università del Piemonte Orientale "A. Avogadro", Largo Donegani 2, 28100 Novara, Italy.
| | - Franca Rossi
- Department of Pharmaceutical Sciences, Università del Piemonte Orientale "A. Avogadro", Largo Donegani 2, 28100 Novara, Italy.
| | - Menico Rizzi
- Department of Pharmaceutical Sciences, Università del Piemonte Orientale "A. Avogadro", Largo Donegani 2, 28100 Novara, Italy.
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24
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Singh V, Donini S, Pacitto A, Sala C, Hartkoorn RC, Dhar N, Keri G, Ascher DB, Mondésert G, Vocat A, Lupien A, Sommer R, Vermet H, Lagrange S, Buechler J, Warner D, McKinney JD, Pato J, Cole ST, Blundell TL, Rizzi M, Mizrahi V. The Inosine Monophosphate Dehydrogenase, GuaB2, Is a Vulnerable New Bactericidal Drug Target for Tuberculosis. ACS Infect Dis 2017; 3:5-17. [PMID: 27726334 PMCID: PMC5241705 DOI: 10.1021/acsinfecdis.6b00102] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Indexed: 12/14/2022]
Abstract
VCC234718, a molecule with growth inhibitory activity against Mycobacterium tuberculosis (Mtb), was identified by phenotypic screening of a 15344-compound library. Sequencing of a VCC234718-resistant mutant identified a Y487C substitution in the inosine monophosphate dehydrogenase, GuaB2, which was subsequently validated to be the primary molecular target of VCC234718 in Mtb. VCC234718 inhibits Mtb GuaB2 with a Ki of 100 nM and is uncompetitive with respect to IMP and NAD+. This compound binds at the NAD+ site, after IMP has bound, and makes direct interactions with IMP; therefore, the inhibitor is by definition uncompetitive. VCC234718 forms strong pi interactions with the Y487 residue side chain from the adjacent protomer in the tetramer, explaining the resistance-conferring mutation. In addition to sensitizing Mtb to VCC234718, depletion of GuaB2 was bactericidal in Mtb in vitro and in macrophages. When supplied at a high concentration (≥125 μM), guanine alleviated the toxicity of VCC234718 treatment or GuaB2 depletion via purine salvage. However, transcriptional silencing of guaB2 prevented Mtb from establishing an infection in mice, confirming that Mtb has limited access to guanine in this animal model. Together, these data provide compelling validation of GuaB2 as a new tuberculosis drug target.
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Affiliation(s)
- Vinayak Singh
- MRC/NHLS/UCT Molecular Mycobacteriology
Research Unit & DST/NRF Centre of Excellence for Biomedical TB
Research, Institute of Infectious Disease and Molecular Medicine &
Department of Pathology, University of Cape
Town, Anzio Road, Observatory 7925, South Africa
| | - Stefano Donini
- Dipartimento di Scienze del Farmaco, University of Piemonte Orientale, Via Bovio 6, 28100 Novara, Italy
| | - Angela Pacitto
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Claudia Sala
- Ecole Polytechnique Fédérale de Lausanne, Global Health Institute, Station 19, 1015 Lausanne, Switzerland
| | - Ruben C. Hartkoorn
- Ecole Polytechnique Fédérale de Lausanne, Global Health Institute, Station 19, 1015 Lausanne, Switzerland
| | - Neeraj Dhar
- Ecole Polytechnique Fédérale de Lausanne, Global Health Institute, Station 19, 1015 Lausanne, Switzerland
| | - Gyorgy Keri
- Vichem
Chemie, Herman Ottó
út 15, Budapest, 1022 Hungary
| | - David B. Ascher
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Guillaume Mondésert
- Sanofi-Aventis Research
& Development, Infectious Diseases Unit,
Biology Group, Campus Mérieux, 1541 avenue Marcel Mérieux, 69280 Marcy L’Etoile, France
| | - Anthony Vocat
- Ecole Polytechnique Fédérale de Lausanne, Global Health Institute, Station 19, 1015 Lausanne, Switzerland
| | - Andréanne Lupien
- Ecole Polytechnique Fédérale de Lausanne, Global Health Institute, Station 19, 1015 Lausanne, Switzerland
| | - Raphael Sommer
- Ecole Polytechnique Fédérale de Lausanne, Global Health Institute, Station 19, 1015 Lausanne, Switzerland
| | - Hélène Vermet
- Sanofi-Aventis Research
& Development, Infectious Diseases Unit,
Biology Group, Campus Mérieux, 1541 avenue Marcel Mérieux, 69280 Marcy L’Etoile, France
| | - Sophie Lagrange
- Sanofi-Aventis Research
& Development, Infectious Diseases Unit,
Biology Group, Campus Mérieux, 1541 avenue Marcel Mérieux, 69280 Marcy L’Etoile, France
| | - Joe Buechler
- Alere (San Diego), Summer Ridge Road, San Diego, California 92121, United States
| | - Digby
F. Warner
- MRC/NHLS/UCT Molecular Mycobacteriology
Research Unit & DST/NRF Centre of Excellence for Biomedical TB
Research, Institute of Infectious Disease and Molecular Medicine &
Department of Pathology, University of Cape
Town, Anzio Road, Observatory 7925, South Africa
| | - John D. McKinney
- Ecole Polytechnique Fédérale de Lausanne, Global Health Institute, Station 19, 1015 Lausanne, Switzerland
| | - Janos Pato
- Vichem
Chemie, Herman Ottó
út 15, Budapest, 1022 Hungary
| | - Stewart T. Cole
- Ecole Polytechnique Fédérale de Lausanne, Global Health Institute, Station 19, 1015 Lausanne, Switzerland
| | - Tom L. Blundell
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Menico Rizzi
- Dipartimento di Scienze del Farmaco, University of Piemonte Orientale, Via Bovio 6, 28100 Novara, Italy
| | - Valerie Mizrahi
- MRC/NHLS/UCT Molecular Mycobacteriology
Research Unit & DST/NRF Centre of Excellence for Biomedical TB
Research, Institute of Infectious Disease and Molecular Medicine &
Department of Pathology, University of Cape
Town, Anzio Road, Observatory 7925, South Africa
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25
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Park Y, Pacitto A, Bayliss T, Cleghorn LAT, Wang Z, Hartman T, Arora K, Ioerger TR, Sacchettini J, Rizzi M, Donini S, Blundell TL, Ascher DB, Rhee K, Breda A, Zhou N, Dartois V, Jonnala SR, Via LE, Mizrahi V, Epemolu O, Stojanovski L, Simeons F, Osuna-Cabello M, Ellis L, MacKenzie CJ, Smith ARC, Davis SH, Murugesan D, Buchanan KI, Turner PA, Huggett M, Zuccotto F, Rebollo-Lopez MJ, Lafuente-Monasterio MJ, Sanz O, Diaz GS, Lelièvre J, Ballell L, Selenski C, Axtman M, Ghidelli-Disse S, Pflaumer H, Bösche M, Drewes G, Freiberg GM, Kurnick MD, Srikumaran M, Kempf DJ, Green SR, Ray PC, Read K, Wyatt P, Barry CE, Boshoff HI. Essential but Not Vulnerable: Indazole Sulfonamides Targeting Inosine Monophosphate Dehydrogenase as Potential Leads against Mycobacterium tuberculosis. ACS Infect Dis 2017; 3:18-33. [PMID: 27704782 DOI: 10.1021/acsinfecdis.6b00103] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A potent, noncytotoxic indazole sulfonamide was identified by high-throughput screening of >100,000 synthetic compounds for activity against Mycobacterium tuberculosis (Mtb). This noncytotoxic compound did not directly inhibit cell wall biogenesis but triggered a slow lysis of Mtb cells as measured by release of intracellular green fluorescent protein (GFP). Isolation of resistant mutants followed by whole-genome sequencing showed an unusual gene amplification of a 40 gene region spanning from Rv3371 to Rv3411c and in one case a potential promoter mutation upstream of guaB2 (Rv3411c) encoding inosine monophosphate dehydrogenase (IMPDH). Subsequent biochemical validation confirmed direct inhibition of IMPDH by an uncompetitive mode of inhibition, and growth inhibition could be rescued by supplementation with guanine, a bypass mechanism for the IMPDH pathway. Beads containing immobilized indazole sulfonamides specifically interacted with IMPDH in cell lysates. X-ray crystallography of the IMPDH-IMP-inhibitor complex revealed that the primary interactions of these compounds with IMPDH were direct pi-pi interactions with the IMP substrate. Advanced lead compounds in this series with acceptable pharmacokinetic properties failed to show efficacy in acute or chronic murine models of tuberculosis (TB). Time-kill experiments in vitro suggest that sustained exposure to drug concentrations above the minimum inhibitory concentration (MIC) for 24 h were required for a cidal effect, levels that have been difficult to achieve in vivo. Direct measurement of guanine levels in resected lung tissue from tuberculosis-infected animals and patients revealed 0.5-2 mM concentrations in caseum and normal lung tissue. The high lesional levels of guanine and the slow lytic, growth-rate-dependent effect of IMPDH inhibition pose challenges to developing drugs against this target for use in treating TB.
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Affiliation(s)
- Yumi Park
- Tuberculosis
Research Section, Laboratory of Clinical Infectious Diseases, National
Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland 20892-3206, United States
| | - Angela Pacitto
- Department
of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Tracy Bayliss
- Drug
Discovery Unit, College of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Laura A. T. Cleghorn
- Drug
Discovery Unit, College of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Zhe Wang
- Division
of Infectious Diseases, Department of Medicine, Weill Cornell Medical College, New York, New York 10065, United States
| | - Travis Hartman
- Division
of Infectious Diseases, Department of Medicine, Weill Cornell Medical College, New York, New York 10065, United States
| | - Kriti Arora
- Tuberculosis
Research Section, Laboratory of Clinical Infectious Diseases, National
Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland 20892-3206, United States
| | - Thomas R. Ioerger
- Department of Computer Science and Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Jim Sacchettini
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Menico Rizzi
- Dipartimento
di Scienze del Farmaco, University of Piemonte Orientale, Via Bovio
6, 28100 Novara, Italy
| | - Stefano Donini
- Dipartimento
di Scienze del Farmaco, University of Piemonte Orientale, Via Bovio
6, 28100 Novara, Italy
| | - Tom L. Blundell
- Department
of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - David B. Ascher
- Department
of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Kyu Rhee
- Division
of Infectious Diseases, Department of Medicine, Weill Cornell Medical College, New York, New York 10065, United States
| | - Ardala Breda
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Nian Zhou
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Veronique Dartois
- Public
Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey 07103, United States
| | - Surendranadha Reddy Jonnala
- Tuberculosis
Research Section, Laboratory of Clinical Infectious Diseases, National
Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland 20892-3206, United States
| | - Laura E. Via
- Tuberculosis
Research Section, Laboratory of Clinical Infectious Diseases, National
Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland 20892-3206, United States
- MRC/NHLS/UCT
Molecular Mycobacteriology Research Unit, Institute of Infectious
Disease and Molecular Medicine, University of Cape Town, Rondebosch 7700, South Africa
| | - Valerie Mizrahi
- MRC/NHLS/UCT
Molecular Mycobacteriology Research Unit, Institute of Infectious
Disease and Molecular Medicine, University of Cape Town, Rondebosch 7700, South Africa
| | - Ola Epemolu
- Drug
Discovery Unit, College of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Laste Stojanovski
- Drug
Discovery Unit, College of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Fred Simeons
- Drug
Discovery Unit, College of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Maria Osuna-Cabello
- Drug
Discovery Unit, College of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Lucy Ellis
- Drug
Discovery Unit, College of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Claire J. MacKenzie
- Drug
Discovery Unit, College of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Alasdair R. C. Smith
- Drug
Discovery Unit, College of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Susan H. Davis
- Drug
Discovery Unit, College of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Dinakaran Murugesan
- Drug
Discovery Unit, College of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Kirsteen I. Buchanan
- Drug
Discovery Unit, College of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Penelope A. Turner
- Drug
Discovery Unit, College of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Margaret Huggett
- Drug
Discovery Unit, College of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Fabio Zuccotto
- Drug
Discovery Unit, College of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Maria Jose Rebollo-Lopez
- Diseases
of the Developing World, GlaxoSmithKline, Calle Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | | | - Olalla Sanz
- Diseases
of the Developing World, GlaxoSmithKline, Calle Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Gracia Santos Diaz
- Diseases
of the Developing World, GlaxoSmithKline, Calle Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Joël Lelièvre
- Diseases
of the Developing World, GlaxoSmithKline, Calle Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Lluis Ballell
- Diseases
of the Developing World, GlaxoSmithKline, Calle Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Carolyn Selenski
- GlaxoSmithKline, 5 Crescent Drive, Philadelphia, Pennsylvania 19112, United States
| | - Matthew Axtman
- GlaxoSmithKline, 5 Crescent Drive, Philadelphia, Pennsylvania 19112, United States
| | - Sonja Ghidelli-Disse
- Cellzome
GmbH, Molecular Discovery Research, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Hannah Pflaumer
- Cellzome
GmbH, Molecular Discovery Research, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Markus Bösche
- Cellzome
GmbH, Molecular Discovery Research, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Gerard Drewes
- Cellzome
GmbH, Molecular Discovery Research, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Gail M. Freiberg
- AbbVie Molecular Characterization, 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Matthew D. Kurnick
- AbbVie Molecular Characterization, 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Myron Srikumaran
- AbbVie Molecular Characterization, 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Dale J. Kempf
- AbbVie Molecular Characterization, 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Simon R. Green
- Drug
Discovery Unit, College of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Peter C. Ray
- Drug
Discovery Unit, College of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Kevin Read
- Drug
Discovery Unit, College of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Paul Wyatt
- Drug
Discovery Unit, College of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Clifton E. Barry
- Tuberculosis
Research Section, Laboratory of Clinical Infectious Diseases, National
Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland 20892-3206, United States
- MRC/NHLS/UCT
Molecular Mycobacteriology Research Unit, Institute of Infectious
Disease and Molecular Medicine, University of Cape Town, Rondebosch 7700, South Africa
| | - Helena I. Boshoff
- Tuberculosis
Research Section, Laboratory of Clinical Infectious Diseases, National
Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland 20892-3206, United States
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26
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Cox JAG, Mugumbate G, Del Peral LVG, Jankute M, Abrahams KA, Jervis P, Jackenkroll S, Perez A, Alemparte C, Esquivias J, Lelièvre J, Ramon F, Barros D, Ballell L, Besra GS. Novel inhibitors of Mycobacterium tuberculosis GuaB2 identified by a target based high-throughput phenotypic screen. Sci Rep 2016; 6:38986. [PMID: 27982051 PMCID: PMC5159837 DOI: 10.1038/srep38986] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 11/16/2016] [Indexed: 12/16/2022] Open
Abstract
High-throughput phenotypic screens have re-emerged as screening tools in antibiotic discovery. The advent of such technologies has rapidly accelerated the identification of 'hit' compounds. A pre-requisite to medicinal chemistry optimisation programmes required to improve the drug-like properties of a 'hit' molecule is identification of its mode of action. Herein, we have combined phenotypic screening with a biased target-specific screen. The inosine monophosphate dehydrogenase (IMPDH) protein GuaB2 has been identified as a drugable target in Mycobacterium tuberculosis, however previously identified compounds lack the desired characteristics necessary for further development into lead-like molecules. This study has identified 7 new chemical series from a high-throughput resistance-based phenotypic screen using Mycobacterium bovis BCG over-expressing GuaB2. Hit compounds were identified in a single shot high-throughput screen, validated by dose response and subjected to further biochemical analysis. The compounds were also assessed using molecular docking experiments, providing a platform for their further optimisation using medicinal chemistry. This work demonstrates the versatility and potential of GuaB2 as an anti-tubercular drug target.
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Affiliation(s)
- Jonathan A. G. Cox
- Life and Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Grace Mugumbate
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom, CB10 1SD
| | - Laura Vela-Glez Del Peral
- Molecular Discovery Research, GlaxoSmithKline, Santiago Grisolia 4, 28760 Tres Cantos, Madrid, Spain
| | - Monika Jankute
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | | | - Peter Jervis
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Stefan Jackenkroll
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Arancha Perez
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Carlos Alemparte
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Jorge Esquivias
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Joël Lelièvre
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Fernando Ramon
- Molecular Discovery Research, GlaxoSmithKline, Santiago Grisolia 4, 28760 Tres Cantos, Madrid, Spain
| | - David Barros
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Lluis Ballell
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Gurdyal S. Besra
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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27
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Venkatesan A, Palaniyandi K, Sharma D, Bisht D, Narayanan S. Functional Characterization of PknI-Rv2159c Interaction in Redox Homeostasis of Mycobacterium tuberculosis. Front Microbiol 2016; 7:1654. [PMID: 27818650 PMCID: PMC5073100 DOI: 10.3389/fmicb.2016.01654] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 10/04/2016] [Indexed: 01/02/2023] Open
Abstract
Mycobacterium tuberculosis adapts to stress conditions by responding to the signals from its external environment. M. tuberculosis genome encodes 11 eukaryotic like serine/threonine protein kinases (STPK) and their importance in regulating the physiology and virulence of the bacteria are being explored. Previous study from our lab identified the M. tuberculosis STPK, PknI interacts with two peroxidase proteins such as Rv2159c and Rv0148. In this study, we have characterized the biological function behind the PknI-Rv2159c interaction in M. tuberculosis. Point mutation of Ala-Gly-Trp motif identified that only Ala49 and Gly50 amino acids of Rv2159c are responsible for interaction and there is no phosphorylation involved in the PknI-Rv2159c interaction. Rv2159c is a member from the carboxymuconolactone decarboxylase family with peroxidase activity. Enzymatic assays with catalytic site point mutants showed that Cys84 of Rv2159c was responsible for its alkylhydroperoxidase activity. Interestingly, interaction with PknI increased its peroxidase activity by several folds. Gene knockdown of Rv2159c in M. tuberculosis showed increased sensitivity to peroxides such as cumene hydroperoxide and hydrogen peroxide. Proteomic analysis of differentially expressing Rv2159c strains by 2D gel electrophoresis and mass spectrometry revealed the differential abundance of 21 proteins. The total absence of oxidoreductase, GuaB1 suggests the essential role of Rv2159c in redox maintenance. Our findings provide new insights on signaling mechanisms of PknI in maintaining the redox homeostasis during oxidative stresses.
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Affiliation(s)
- Arunkumar Venkatesan
- Department of Immunology, National Institute for Research in TuberculosisChennai, India
| | - Kannan Palaniyandi
- Department of Immunology, National Institute for Research in TuberculosisChennai, India
| | - Divakar Sharma
- Department of Biochemistry, National JALMA Institute for Leprosy and other Mycobacterial DiseasesAgra, India
| | - Deepa Bisht
- Department of Biochemistry, National JALMA Institute for Leprosy and other Mycobacterial DiseasesAgra, India
| | - Sujatha Narayanan
- Department of Immunology, National Institute for Research in TuberculosisChennai, India
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28
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Abstract
The development and application of a highly versatile suite of tools for mycobacterial genetics, coupled with widespread use of "omics" approaches to elucidate the structure, function, and regulation of mycobacterial proteins, has led to spectacular advances in our understanding of the metabolism and physiology of mycobacteria. In this article, we provide an update on nucleotide metabolism and DNA replication in mycobacteria, highlighting key findings from the past 10 to 15 years. In the first section, we focus on nucleotide metabolism, ranging from the biosynthesis, salvage, and interconversion of purine and pyrimidine ribonucleotides to the formation of deoxyribonucleotides. The second part of the article is devoted to DNA replication, with a focus on replication initiation and elongation, as well as DNA unwinding. We provide an overview of replication fidelity and mutation rates in mycobacteria and summarize evidence suggesting that DNA replication occurs during states of low metabolic activity, and conclude by suggesting directions for future research to address key outstanding questions. Although this article focuses primarily on observations from Mycobacterium tuberculosis, it is interspersed, where appropriate, with insights from, and comparisons with, other mycobacterial species as well as better characterized bacterial models such as Escherichia coli. Finally, a common theme underlying almost all studies of mycobacterial metabolism is the potential to identify and validate functions or pathways that can be exploited for tuberculosis drug discovery. In this context, we have specifically highlighted those processes in mycobacterial DNA replication that might satisfy this critical requirement.
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Makowska-Grzyska M, Kim Y, Gorla SK, Wei Y, Mandapati K, Zhang M, Maltseva N, Modi G, Boshoff HI, Gu M, Aldrich C, Cuny GD, Hedstrom L, Joachimiak A. Mycobacterium tuberculosis IMPDH in Complexes with Substrates, Products and Antitubercular Compounds. PLoS One 2015; 10:e0138976. [PMID: 26440283 PMCID: PMC4594927 DOI: 10.1371/journal.pone.0138976] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 09/07/2015] [Indexed: 11/30/2022] Open
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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Affiliation(s)
- Magdalena Makowska-Grzyska
- Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, IL, United States of America
| | - Youngchang Kim
- Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, IL, United States of America
- Structural Biology Center, Biosciences, Argonne National Laboratory, 9700 S Cass Ave. Argonne, IL, United States of America
| | - Suresh Kumar Gorla
- Department of Biology, Brandeis University, 415 South St. Waltham, MA, United States of America
| | - Yang Wei
- Department of Biology, Brandeis University, 415 South St. Waltham, MA, United States of America
| | - Kavitha Mandapati
- Department of Biology, Brandeis University, 415 South St. Waltham, MA, United States of America
| | - Minjia Zhang
- Department of Biology, Brandeis University, 415 South St. Waltham, MA, United States of America
| | - Natalia Maltseva
- Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, IL, United States of America
| | - Gyan Modi
- Department of Biology, Brandeis University, 415 South St. Waltham, MA, United States of America
| | - Helena I. Boshoff
- Tuberculosis Research Section, National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States of America
| | - Minyi Gu
- Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, IL, United States of America
| | - Courtney Aldrich
- Center for Drug Design, Academic Health Center, University of Minnesota, 516 Delaware St. SE, Minneapolis, MN, United States of America
| | - Gregory D. Cuny
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, 549A Science and Research Building 2, Houston, TX, United States of America
- Department of Chemistry, Brandeis University, 415 South St. Waltham, MA, United States of America
| | - Lizbeth Hedstrom
- Department of Biology, Brandeis University, 415 South St. Waltham, MA, United States of America
- Department of Chemistry, Brandeis University, 415 South St. Waltham, MA, United States of America
- * E-mail: (LH); (AJ)
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, IL, United States of America
- Structural Biology Center, Biosciences, Argonne National Laboratory, 9700 S Cass Ave. Argonne, IL, United States of America
- * E-mail: (LH); (AJ)
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30
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Punina NV, Makridakis NM, Remnev MA, Topunov AF. Whole-genome sequencing targets drug-resistant bacterial infections. Hum Genomics 2015; 9:19. [PMID: 26243131 PMCID: PMC4525730 DOI: 10.1186/s40246-015-0037-z] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 07/03/2015] [Indexed: 01/07/2023] Open
Abstract
During the past two decades, the technological progress of whole-genome sequencing (WGS) had changed the fields of Environmental Microbiology and Biotechnology, and, currently, is changing the underlying principles, approaches, and fundamentals of Public Health, Epidemiology, Health Economics, and national productivity. Today’s WGS technologies are able to compete with conventional techniques in cost, speed, accuracy, and resolution for day-to-day control of infectious diseases and outbreaks in clinical laboratories and in long-term epidemiological investigations. WGS gives rise to an exciting future direction for personalized Genomic Epidemiology. One of the most vital and growing public health problems is the emerging and re-emerging of multidrug-resistant (MDR) bacterial infections in the communities and healthcare settings, reinforced by a decline in antimicrobial drug discovery. In recent years, retrospective analysis provided by WGS has had a great impact on the identification and tracking of MDR microorganisms in hospitals and communities. The obtained genomic data are also important for developing novel easy-to-use diagnostic assays for clinics, as well as for antibiotic and therapeutic development at both the personal and population levels. At present, this technology has been successfully applied as an addendum to the real-time diagnostic methods currently used in clinical laboratories. However, the significance of WGS for public health may increase if: (a) unified and user-friendly bioinformatics toolsets for easy data interpretation and management are established, and (b) standards for data validation and verification are developed. Herein, we review the current and future impact of this technology on diagnosis, prevention, treatment, and control of MDR infectious bacteria in clinics and on the global scale.
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Affiliation(s)
- N V Punina
- Bach Institute of Biochemistry, Russian Academy of Science, Moscow, 119071, Russia.
| | - N M Makridakis
- Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA
| | - M A Remnev
- The Federal State Unitary Enterprise All-Russia Research Institute of Automatics, Moscow, 127055, Russia
| | - A F Topunov
- Bach Institute of Biochemistry, Russian Academy of Science, Moscow, 119071, Russia
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31
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Alexandre T, Rayna B, Munier-Lehmann H. Two classes of bacterial IMPDHs according to their quaternary structures and catalytic properties. PLoS One 2015; 10:e0116578. [PMID: 25706619 PMCID: PMC4338043 DOI: 10.1371/journal.pone.0116578] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 12/10/2014] [Indexed: 11/19/2022] Open
Abstract
Inosine-5'-monophosphate dehydrogenase (IMPDH) occupies a key position in purine nucleotide metabolism. In this study, we have performed the biochemical and physico-chemical characterization of eight bacterial IMPDHs, among which six were totally unexplored. This study led to a classification of bacterial IMPDHs according to the regulation of their catalytic properties and their quaternary structures. Class I IMPDHs are cooperative enzymes for IMP, which are activated by MgATP and are octameric in all tested conditions. On the other hand, class II IMPDHs behave as Michaelis-Menten enzymes for both substrates and are tetramers in their apo state or in the presence of IMP, which are shifted to octamers in the presence of NAD or MgATP. Our work provides new insights into the IMPDH functional regulation and a model for the quaternary structure modulation is proposed.
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Affiliation(s)
- Thomas Alexandre
- Institut Pasteur, Unité de Chimie et Biocatalyse, Département de Biologie Structurale et Chimie, 28 rue du Dr Roux, F-75015, Paris, France
- Centre Nationale de la Recherche Scientifique, Unité Mixte de Recherche 3523, F-75015, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, F-75205, Paris, France
| | - Bertrand Rayna
- Institut Pasteur, Proteopole, Plateforme de biophysique des macromolecules et de leurs interactions, 25 rue du Dr Roux, F-75015, Paris, France
- Centre Nationale de la Recherche Scientifique, Unité Mixte de Recherche 3528, F-75015, Paris, France
| | - Hélène Munier-Lehmann
- Institut Pasteur, Unité de Chimie et Biocatalyse, Département de Biologie Structurale et Chimie, 28 rue du Dr Roux, F-75015, Paris, France
- Centre Nationale de la Recherche Scientifique, Unité Mixte de Recherche 3523, F-75015, Paris, France
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32
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Abstract
Very few chemically novel agents have been approved for antibacterial chemotherapies during the last 50 yr. Yet new antibacterial drugs are needed to reduce the impact on global health of an increasing number of drug-resistant infections, including highly drug-resistant forms of tuberculosis. This review discusses how genetic approaches can be used to study the mechanism of action of whole-cell screening hits and facilitate target-driven strategies for antimicrobial drug development.
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Affiliation(s)
- Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065
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33
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Shah CP, Kharkar PS. Inosine 5'-monophosphate dehydrogenase inhibitors as antimicrobial agents: recent progress and future perspectives. Future Med Chem 2015; 7:1415-1429. [PMID: 26230881 DOI: 10.4155/fmc.15.72] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Inosine 5'-monophosphate dehydrogenase (IMPDH), a crucial enzyme required for de novo synthesis of guanine nucleotides, is an important target for cancer, bacterial, parasitic and viral infections and autoimmune disorders. Several classes of IMPDH inhibitors are known in the literature. The current review succinctly summarizes the progress made in the design and development of IMPDH inhibitors as antimicrobial agents in last five years or so. The focus is on the inhibitor and enzyme structural features responsible for imparting selectivity for the microbial over the host enzyme. Future perspectives clearly outline the inhibitor design opportunities available in this area to address the present challenges of drug resistance and re-emergence of newer and deadly strains of microbes, posing a serious threat to public.
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Affiliation(s)
- Chetan P Shah
- Department of Pharmaceutical Chemistry, SPP School of Pharmacy & Technology Management, SVKM's NMIMS, VL Mehta Road, Vile Parle (West), Mumbai 400 056, India
| | - Prashant S Kharkar
- Department of Pharmaceutical Chemistry, SPP School of Pharmacy & Technology Management, SVKM's NMIMS, VL Mehta Road, Vile Parle (West), Mumbai 400 056, India
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34
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Rostirolla DC, Milech de Assunção T, Bizarro CV, Basso LA, Santos DS. Biochemical characterization of Mycobacterium tuberculosis IMP dehydrogenase: kinetic mechanism, metal activation and evidence of a cooperative system. RSC Adv 2014. [DOI: 10.1039/c4ra02142h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Proposed kinetic mechanism forMtIMPDH in the presence of K+.
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Affiliation(s)
- Diana Carolina Rostirolla
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF)
- Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB)
- Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS)
- Porto Alegre, Brazil
- Programa de Pós-Graduação em Medicina e Ciências da Saúde
| | | | - Cristiano Valim Bizarro
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF)
- Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB)
- Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS)
- Porto Alegre, Brazil
| | - Luiz Augusto Basso
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF)
- Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB)
- Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS)
- Porto Alegre, Brazil
- Programa de Pós-Graduação em Medicina e Ciências da Saúde
| | - Diogenes Santiago Santos
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF)
- Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB)
- Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS)
- Porto Alegre, Brazil
- Programa de Pós-Graduação em Medicina e Ciências da Saúde
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35
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Meriga B, Mopuri R, MuraliKrishna T. Insecticidal, antimicrobial and antioxidant activities of bulb extracts of Allium sativum. ASIAN PAC J TROP MED 2012; 5:391-395. [PMID: 22546657 DOI: 10.1016/s1995-7645(12)60065-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2011] [Revised: 01/15/2012] [Accepted: 03/15/2012] [Indexed: 11/20/2022] Open
Abstract
OBJECTIVE To evaluate the insecticidal, antimicrobial and antioxidant activities of bulb extracts of Allium sativum (A. sativum). METHODS Dried bulbs of A. sativum were extracted with different solvents and evaluated for insecticidal, antimicrobial and antioxidant activities. METHODS Aqueous and methanol extracts showed highest insecticidal activity (mortality rate of 81% and 64% respectively) against the larvae of Spodoptera litura (S. litura) at a concentration of 1 000 ppm. With regard to antimicrobial activity, aqueous extract exhibited antibacterial activity against gram positive (Bacillus subtilis, Staphylococcus aureu,) and gram negative (Escherichia coli and Klebsiella pneumonia) strains and antifungal activity against Candida albicans. While methanol extract showed antimicrobial activity against all the tested micro organisms except two (Staphylococcus aureus and Candida albicans), the extracts of hexane, chloroform and ethyl acetate did not show any anti microbial activity. Minimum inhibitory concentration of aqueous and methanol extracts against tested bacterial and fungal strains was 100-150 μg/mL. Antioxidant activity of the bulb extracts was evaluated in terms of inhibition of free radicals by 2, 2'-diphenly-1-picrylhydrazyl. Aqueous and methanol extracts exhibited strong antioxidant activity (80%-90% of the standard). CONCLUSIONS Antioxidant and antimicrobial activity of A. sativum against the tested organisms therefore, provides scientific basis for its utilization in traditional and folk medicine. Also, our results demonstrated the insecticidal efficacy of A. sativum against S. litura, a polyphagous insect.
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Affiliation(s)
- Balaji Meriga
- Department of Biochemistry, Sri Venkateswara University, Tirupati, India.
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Usha V, Hobrath JV, Gurcha SS, Reynolds RC, Besra GS. Identification of novel Mt-Guab2 inhibitor series active against M. tuberculosis. PLoS One 2012; 7:e33886. [PMID: 22479467 PMCID: PMC3315515 DOI: 10.1371/journal.pone.0033886] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Accepted: 02/23/2012] [Indexed: 12/17/2022] Open
Abstract
Tuberculosis (TB) remains a leading cause of mortality worldwide. With the emergence of multidrug resistant TB, extensively drug resistant TB and HIV-associated TB it is imperative that new drug targets be identified. The potential of Mycobacterium tuberculosis inosine monophosphate dehydrogenase (IMPDH) as a novel drug target was explored in the present study. IMPDH exclusively catalyzes the conversion of inosine monophosphate (IMP) to xanthosine monophosphate (XMP) in the presence of the cofactor nicotinamide adenine dinucleotide (NAD+). Although the enzyme is a dehydrogenase, the enzyme does not catalyze the reverse reaction i.e. the conversion of XMP to IMP. Unlike other bacteria, M. tuberculosis harbors three IMPDH-like genes, designated as Mt-guaB1, Mt-guaB2 and Mt-guaB3 respectively. Of the three putative IMPDH's, we previously confirmed that Mt-GuaB2 was the only functional ortholog by characterizing the enzyme kinetically. Using an in silico approach based on designed scaffolds, a series of novel classes of inhibitors was identified. The inhibitors possess good activity against M. tuberculosis with MIC values in the range of 0.4 to 11.4 µg mL−1. Among the identified ligands, two inhibitors have nanomolar Kis against the Mt-GuaB2 enzyme.
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Affiliation(s)
- Veeraraghavan Usha
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Judith V. Hobrath
- Drug Discovery Division, Southern Research Institute, Birmingham, Alabama, United States of America
| | - Sudagar S. Gurcha
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Robert C. Reynolds
- Drug Discovery Division, Southern Research Institute, Birmingham, Alabama, United States of America
| | - Gurdyal S. Besra
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
- * E-mail:
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37
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Sharma U. Current possibilities and unresolved issues of drug target validation inMycobacterium tuberculosis. Expert Opin Drug Discov 2011; 6:1171-86. [DOI: 10.1517/17460441.2011.626763] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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38
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The structure-activity relationship of urea derivatives as anti-tuberculosis agents. Bioorg Med Chem 2011; 19:5585-95. [PMID: 21840723 DOI: 10.1016/j.bmc.2011.07.034] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2011] [Revised: 07/12/2011] [Accepted: 07/19/2011] [Indexed: 11/21/2022]
Abstract
The treatment of tuberculosis is becoming more difficult due to the ever increasing prevalence of drug resistance. Thus, it is imperative that novel anti-tuberculosis agents, with unique mechanisms of action, be discovered and developed. The direct anti-tubercular testing of a small compound library led to discovery of adamantyl urea hit compound 1. In this study, the hit was followed up through the synthesis of an optimization library. This library was generated by systematically replacing each section of the molecule with a similar moiety until a clear structure-activity relationship was obtained with respect to anti-tubercular activity. The best compounds in this series contained a 1-adamantyl-3-phenyl urea core and had potent activity against Mycobacterium tuberculosis plus an acceptable therapeutic index. It was noted that the compounds identified and the pharmacophore developed is consistent with inhibitors of epoxide hydrolase family of enzymes. Consequently, the compounds were tested for inhibition of representative epoxide hydrolases: M. tuberculosis EphB and EphE; and human soluble epoxide hydrolase. Many of the optimized inhibitors showed both potent EphB and EphE inhibition suggesting the antitubercular activity is through inhibition of multiple epoxide hydrolase enzymes. The inhibitors also showed potent inhibition of humans soluble epoxide hydrolase, but limited cytotoxicity suggesting that future studies must be towards increasing the selectivity of epoxide hydrolase inhibition towards the M. tuberculosis enzymes.
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