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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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Hassan AMS, Elfiky AA, Elgohary AM. Triple in silico targeting of IMPDH enzyme and RNA-dependent RNA polymerase of both SARS-CoV-2 and Rhizopus oryzae. Future Microbiol 2024; 19:9-19. [PMID: 38294272 DOI: 10.2217/fmb-2023-0103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 08/23/2023] [Indexed: 02/01/2024] Open
Abstract
Aim: Mucormycosis has been associated with SARS-CoV-2 infections during the last year. The aim of this study was to triple-hit viral and fungal RNA-dependent RNA polymerases (RdRps) and human inosine monophosphate dehydrogenase (IMPDH). Materials & methods: Molecular docking and molecular dynamics simulation were used to test nucleotide inhibitors (NIs) against the RdRps of SARS-CoV-2 and Rhizopus oryzae RdRp. These same inhibitors targeted IMPDH. Results: Four NIs revealed a comparable binding affinity to the two drugs, remdesivir and sofosbuvir. Binding energies were calculated using the most abundant conformations of the RdRps after 100-ns molecular dynamics simulation. Conclusion: We suggest the triple-inhibition potential of four NIs against pathogenic RdRps and IMPDH, which is worth experimental validation.
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Affiliation(s)
| | - Abdo A Elfiky
- Biophysics Department, Faculty of Sciences, Cairo University, Giza, Dokki, 12613, Egypt
| | - Alaa M Elgohary
- Biophysics Department, Faculty of Sciences, Cairo University, Giza, Dokki, 12613, Egypt
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3
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Villemagne B, Faion L, Tangara S, Willand N. Recent advances in Fragment-based strategies against tuberculosis. Eur J Med Chem 2023; 258:115569. [PMID: 37423127 DOI: 10.1016/j.ejmech.2023.115569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 06/05/2023] [Accepted: 06/12/2023] [Indexed: 07/11/2023]
Abstract
Tuberculosis remains one of the world's leading infectious disease killers, causing more than 1.5 million of deaths each year. It is therefore a priority to discover and develop new classes of anti-tuberculosis drugs to design new treatments in order to fight the increasing burden of resistant-tuberculosis. Fragment-based drug discovery (FBDD) relies on the identification of small molecule hits, further improved to high-affinity ligands through three main approaches: fragment growing, merging and linking. The aim of this review is to highlight the recent progresses made in fragment-based approaches for the discovery and development of Mycobacterium tuberculosis inhibitors in a wide range of pathways. Hit discovery, hit-to-lead optimization, SAR and binding mode when available are discussed.
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Affiliation(s)
- Baptiste Villemagne
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France.
| | - Léo Faion
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Salia Tangara
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Nicolas Willand
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
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4
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Jia HW, Yang HL, Xiong ZL, Deng MH, Wang T, Liu Y, Cheng M. Design, synthesis and antitumor activity evaluation of novel indole acrylamide derivatives as IMPDH inhibitors. Bioorg Chem 2022; 129:106213. [DOI: 10.1016/j.bioorg.2022.106213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/13/2022] [Accepted: 10/15/2022] [Indexed: 11/02/2022]
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5
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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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6
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Sham Y. Meet the Editorial Board Member. Mini Rev Med Chem 2022. [DOI: 10.2174/138955752217220729104538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Yuk Sham
- Department of Integrative Biology and Physiology, Medical School University of Minnesota Minneapolis, MN, USA
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7
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Liu C, Shao M, Osire T, Xu Z, Rao Z. Identification of bottlenecks in 4-androstene-3,17-dione/1,4-androstadiene-3,17-dione synthesis by Mycobacterium neoaurum JC-12 through comparative proteomics. J Biosci Bioeng 2020; 131:264-270. [PMID: 33308966 DOI: 10.1016/j.jbiosc.2020.10.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 10/13/2020] [Accepted: 10/20/2020] [Indexed: 11/28/2022]
Abstract
Intermediates such as 4-androstene-3,17-dione (AD) and 1,4-androstadiene-3,17-dione (ADD) have extensive clinical applications in the production of steroid pharmaceuticals. The present study explores the effect of two factors in the production of these intermediates in Mycobacterium neoaurum JC-12: the precursor, phytosterol and a molecule that increases AD/ADD solubility, hydroxypropyl-β-cyclodextrin (HP-β-CD). Differentially expressed proteins were separated and identified using 2D gel electrophoresis (2-DE) and matrix assisted laser desorption/ionization time-of-flight/time-of-flight tandem mass spectrometry (MALDI-TOF/TOF-MS/MS). In total, 31 proteins were identified, and improved expression levels of ten proteins involved in metabolism was induced by phytosterol and/or HP-β-CD, which strengthened the stress resistance of the strain. In the presence of phytosterol and/or HP-β-CD, five proteins involved in the synthesis of AD/ADD, acetyl-CoA acetyltransferase (AAT), alcohol dehydrogenase (ADH), enoyl-CoA hydratase (EH) and short-chain dehydrogenase 1 and 2, increased their expression levels. Reverse transcription-quantitative PCR (RT-qPCR) was used to verify the 2-DE results and the transcriptional level of these five proteins. This analysis identified AAT, ADH, EH, and electron transfer flavoprotein subunit α/β as the possible bottlenecks for AD/ADD synthesis in M. neoaurum JC-12, which therefore are suggested as targets for strain modification.
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Affiliation(s)
- Chao Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Minglong Shao
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Tolbert Osire
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Zhenghong Xu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Zhiming Rao
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China.
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8
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Omolabi KF, Agoni C, Olotu FA, Soliman MES. Molecular Basis of P131 Cryptosporidial-IMPDH Selectivity-A Structural, Dynamical and Mechanistic Stance. Cell Biochem Biophys 2020; 79:11-24. [PMID: 33058015 DOI: 10.1007/s12013-020-00950-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/03/2020] [Indexed: 01/10/2023]
Abstract
Cryptosporidiosis accounts for a surge in infant (<5 years) mortality and morbidity. To date, several drug discovery efforts have been put in place to develop effective therapeutic options against the causative parasite. Based on a recent report, P131 spares inosine monophosphate dehydrogenase (IMPDH) in a eukaryotic model (mouse IMPDH (mIMPDH)) while binding selectively to the NAD+ site in Cryptosporidium parvum (CpIMPDH). However, no structural detail exists on the underlining mechanisms of P131-CpIMPDH selective targeting till date. To this effect, we investigate the selective inhibitory dynamics of P131 in CpIMPDH relative to mIMPDH via molecular biocomputation methods. Pairwise sequence alignment revealed prominent variations at the NAD+ binding regions of both proteins that accounted for disparate P131 binding activities. The influence of these variations was further revealed by the MM/PBSA energy estimations coupled with per-residue energy decomposition which monitored the systematic binding of the compound. Furthermore, relative high-affinity interactions occurred at the CpIMPDH NAD+ site which were majorly mediated by SER22, VAL24, PRO26, SER354, GLY357, and TYR358 located on chain D. These residues are unique to the parasite IMPDH form and not in the eukaryotic protein, highlighting variations that account for preferential P131 binding. Molecular insights provided herein corroborate previous experimental reports and further underpin the basis of CpIMPDH inhibitor selectivity. Findings from this study could present attractive prospects toward the design of novel anticryptosporidials with improved selectivity and binding affinity against parasitic targets.
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Affiliation(s)
- Kehinde F Omolabi
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Clement Agoni
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Fisayo A Olotu
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Mahmoud E S Soliman
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa.
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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: 0.3] [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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10
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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: 2.0] [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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11
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Immunosuppressive properties of amino acid and peptide derivatives of mycophenolic acid. Eur J Med Chem 2020; 189:112091. [PMID: 32007665 DOI: 10.1016/j.ejmech.2020.112091] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/20/2020] [Accepted: 01/21/2020] [Indexed: 11/23/2022]
Abstract
Mycophenolic acid (MPA) was coupled with amino acids and biologically active peptides including derivatives of tuftsin to modify its immunosuppressive properties. Both amino acid unit in the case of simple MPA amides and modifications within peptide moiety of MPA - tuftsin conjugates influenced the observed activity. Antiproliferative potential of the obtained conjugates was investigated in vitro and MPA amides with threonine methyl ester and conjugate of MPA with retro-tuftisin occurred to be more selective against PBMC in comparison to parent MPA. Both amino acid and peptide derivatives of MPA acted as inosine-5'-monophosphate dehydrogenaze (IMPDH) inhibitors.
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12
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Depaix A, Kowalska J. NAD Analogs in Aid of Chemical Biology and Medicinal Chemistry. Molecules 2019; 24:molecules24224187. [PMID: 31752261 PMCID: PMC6891637 DOI: 10.3390/molecules24224187] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/06/2019] [Accepted: 11/12/2019] [Indexed: 12/21/2022] Open
Abstract
Nicotinamide adenine dinucleotide (NAD) serves as an essential redox co-factor and mediator of multiple biological processes. Besides its well-established role in electron transfer reactions, NAD serves as a substrate for other biotransformations, which, at the molecular level, can be classified as protein post-translational modifications (protein deacylation, mono-, and polyADP-ribosylation) and formation of signaling molecules (e.g., cyclic ADP ribose). These biochemical reactions control many crucial biological processes, such as cellular signaling and recognition, DNA repair and epigenetic modifications, stress response, immune response, aging and senescence, and many others. However, the links between the biological effects and underlying molecular processes are often poorly understood. Moreover, NAD has recently been found to tag the 5′-ends of some cellular RNAs, but the function of these NAD-capped RNAs remains largely unrevealed. Synthetic NAD analogs are invaluable molecular tools to detect, monitor, structurally investigate, and modulate activity of NAD-related enzymes and biological processes in order to aid their deeper understanding. Here, we review the recent advances in the design and development of NAD analogs as probes for various cellular NAD-related enzymes, enzymatic inhibitors with anticancer or antimicrobial therapeutic potential, and other NAD-related chemical biology tools. We focus on research papers published within the last 10 years.
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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: 3.4] [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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14
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Novel adenosine-derived inhibitors of Cryptosporidium parvum inosine 5'-monophosphate dehydrogenase. J Antibiot (Tokyo) 2019; 72:934-942. [PMID: 31296916 DOI: 10.1038/s41429-019-0199-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 05/22/2019] [Accepted: 05/27/2019] [Indexed: 11/08/2022]
Abstract
We have found cyclophane-type adenosine derivatives having p-quinone amide moieties (1 and 2) as weak inhibitors of Cryptosporidium parvum inosine 5'-monophosphate dehydrogenase (CpIMPDH) from the Hokkaido University Chemical Library via the luciferase-based high-throughput screening. To obtain more potent inhibitors, we synthesized four new derivatives free from cyclophane rings (3-6). The N-H derivatives 3 and 5 showed more potent activities (24.4 and 11.1 μM, respectively) in the presence of dithiothreitol (DTT), whereas the N-methyl derivative 4 indicated more potent activity (2.1 μM) without DTT. Conformational analysis of compounds 3 and 4 suggested that N-H amide 3 binds to IMP-binding site in the DTT mediated manner.
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15
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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: 3.4] [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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Topchiy MA, Ageshina AA, Gribanov PS, Masoud SM, Akmalov TR, Nefedov SE, Osipov SN, Nechaev MS, Asachenko AF. Azide-Alkyne Cycloaddition (CuAAC) in Alkane Solvents Catalyzed by Fluorinated NHC Copper(I) Complex. European J Org Chem 2018. [DOI: 10.1002/ejoc.201801538] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Maxim A. Topchiy
- A. V. Topchiev Institute of Petrochemical Synthesis; Russian Academy of Sciences; Leninsky Prospect 29 119991 Moscow Russian Federation
| | - Alexandra A. Ageshina
- A. V. Topchiev Institute of Petrochemical Synthesis; Russian Academy of Sciences; Leninsky Prospect 29 119991 Moscow Russian Federation
| | - Pavel S. Gribanov
- A. V. Topchiev Institute of Petrochemical Synthesis; Russian Academy of Sciences; Leninsky Prospect 29 119991 Moscow Russian Federation
| | - Salekh M. Masoud
- A.N. Nesmeyanov Institute of Organoelement Compounds; Russian Academy of Sciences; Vavilov str. 28 119991 Moscow Russian Federation
| | - Timur R. Akmalov
- A.N. Nesmeyanov Institute of Organoelement Compounds; Russian Academy of Sciences; Vavilov str. 28 119991 Moscow Russian Federation
| | - Sergey E. Nefedov
- N.S. Kurnakov Institute of General and Inorganic Chemistry; Russian Academy of Sciences; Leninsky pr. 31 119991 Moscow Russian Federation
| | - Sergey N. Osipov
- A.N. Nesmeyanov Institute of Organoelement Compounds; Russian Academy of Sciences; Vavilov str. 28 119991 Moscow Russian Federation
| | - Mikhail S. Nechaev
- A. V. Topchiev Institute of Petrochemical Synthesis; Russian Academy of Sciences; Leninsky Prospect 29 119991 Moscow Russian Federation
| | - Andrey F. Asachenko
- A. V. Topchiev Institute of Petrochemical Synthesis; Russian Academy of Sciences; Leninsky Prospect 29 119991 Moscow Russian Federation
- A.N. Nesmeyanov Institute of Organoelement Compounds; Russian Academy of Sciences; Vavilov str. 28 119991 Moscow Russian Federation
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17
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Mironiuk-Puchalska E, Buchowicz W, Grześkowiak P, Wińska P, Wielechowska M, Karatsai O, Rędowicz MJ, Bretner M, Koszytkowska-Stawińska M. Potential bioisosteres of β-uracilalanines derived from 1H-1,2,3-triazole-C-carboxylic acids. Bioorg Chem 2018; 83:500-510. [PMID: 30453142 DOI: 10.1016/j.bioorg.2018.10.061] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 10/16/2018] [Accepted: 10/29/2018] [Indexed: 11/19/2022]
Abstract
The 1H-1,2,3-triazole-originated derivatives of willardiine were obtained by: (i) construction of the 1H-1,2,3-triazole ring in 1,3-dipolar cycloaddition of the uracil-derived azides and the carboxylate-bearing alkynes or α-acylphosphorus ylide, or (ii) N-alkylation of the uracil derivative with the 1H-1,2,3-triazole-4-carboxylate-derived mesylate. The latter method offered: (i) reproducible results, (ii) a significant reduction of amounts of auxiliary materials, (iii) reduction in wastes and (iv) reduction in a number of manual operations required for obtaining the reaction product. Compound 6a exhibited significant binding affinity to hHS1S2I ligand-binding domain of GluR2 receptor (EC50 = 2.90 µM) and decreased viability of human astrocytoma MOG-G-CCM cells in higher extent than known AMPA antagonist GYKI 52466.
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Affiliation(s)
- Ewa Mironiuk-Puchalska
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
| | - Włodzimierz Buchowicz
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
| | - Piotr Grześkowiak
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
| | - Patrycja Wińska
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
| | - Monika Wielechowska
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
| | - Olena Karatsai
- Laboratory of Molecular Basis of Cell Motility, Nencki Institute of Experimental Biology, 3 Pasteur St., 02-093 Warsaw, Poland
| | - Maria Jolanta Rędowicz
- Laboratory of Molecular Basis of Cell Motility, Nencki Institute of Experimental Biology, 3 Pasteur St., 02-093 Warsaw, Poland
| | - Maria Bretner
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
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18
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Kummari LK, Butler MS, Furlong E, Blundell R, Nouwens A, Silva AB, Kappler U, Fraser JA, Kobe B, Cooper MA, Robertson AAB. Antifungal benzo[b]thiophene 1,1-dioxide IMPDH inhibitors exhibit pan-assay interference (PAINS) profiles. Bioorg Med Chem 2018; 26:5408-5419. [PMID: 30322754 DOI: 10.1016/j.bmc.2018.09.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 08/21/2018] [Accepted: 09/03/2018] [Indexed: 12/14/2022]
Abstract
Fungi cause serious life-threatening infections in immunocompromised individuals and current treatments are now complicated by toxicity issues and the emergence of drug resistant strains. Consequently, there is a need for development of new antifungal drugs. Inosine monophosphate dehydrogenase (IMPDH), a key component of the de novo purine biosynthetic pathway, is essential for growth and virulence of fungi and is a potential drug target. In this study, a high-throughput screen of 114,000 drug-like compounds against Cryptococcus neoformans IMPDH was performed. We identified three 3-((5-substituted)-1,3,4-oxadiazol-2-yl)thio benzo[b]thiophene 1,1-dioxides that inhibited Cryptococcus IMPDH and also possessed whole cell antifungal activity. Analogs were synthesized to explore the SAR of these hits. Modification of the fifth substituent on the 1,3,4-oxadiazole ring yielded compounds with nanomolar in vitro activity, but with associated cytotoxicity. In contrast, two analogs generated by substituting the 1,3,4-oxadiazole ring with imidazole and 1,2,4-triazole gave reduced IMPDH inhibition in vitro, but were not cytotoxic. During enzyme kinetic studies in the presence of DTT, nucleophilic attack of a free thiol occurred with the benzo[b]thiophene 1,1-dioxide. Two representative compounds with substitution at the 5 position of the 1,3,4-oxadiazole ring, showed mixed inhibition in the absence of DTT. Incubation of these compounds with Cryptococcus IMPDH followed by mass spectrometry analysis showed non-specific and covalent binding with IMPDH at multiple cysteine residues. These results support recent reports that the benzo[b]thiophene 1,1-dioxides moiety as PAINS (pan-assay interference compounds) contributor.
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Affiliation(s)
- Lalith K Kummari
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia; Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Mark S Butler
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Emily Furlong
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Ross Blundell
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Amanda Nouwens
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Alberto B Silva
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia; AC Immune SA, EPFL Innovation Park, CH-1015 Lausanne, Switzerland
| | - Ulrike Kappler
- Centre for Metals in Biology, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - James A Fraser
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Bostjan Kobe
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Matthew A Cooper
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Avril A B Robertson
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia; Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.
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19
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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: 5.2] [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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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: 3.8] [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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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: 41] [Impact Index Per Article: 6.8] [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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22
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Fan YL, Jin XH, Huang ZP, Yu HF, Zeng ZG, Gao T, Feng LS. Recent advances of imidazole-containing derivatives as anti-tubercular agents. Eur J Med Chem 2018; 150:347-365. [PMID: 29544148 DOI: 10.1016/j.ejmech.2018.03.016] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 03/02/2018] [Accepted: 03/04/2018] [Indexed: 12/20/2022]
Abstract
Tuberculosis still remains one of the most common, communicable, and leading deadliest diseases known to mankind throughout the world. Drug-resistance in Mycobacterium tuberculosis which threatens to worsen the global tuberculosis epidemic has caused great concern in recent years. To overcome the resistance, the development of new drugs with novel mechanisms of actions is of great importance. Imidazole-containing derivatives endow with various biological properties, and some of them demonstrated excellent anti-tubercular activity. As the most emblematic example, 4-nitroimidazole delamanid has already received approval for treatment of multidrug-resistant tuberculosis infected patients. Thus, imidazole-containing derivatives have caused great interests in discovery of new anti-tubercular agents. Numerous of imidazole-containing derivatives were synthesized and screened for their in vitro and in vivo anti-mycobacterial activities against both drug-sensitive and drug-resistant Mycobacterium tuberculosis pathogens. This review aims to outline the recent advances of imidazole-containing derivatives as anti-tubercular agents, and summarize the structure-activity relationship of these derivatives. The enriched structure-activity relationship may pave the way for the further rational development of imidazole-containing derivatives as anti-tubercular agents.
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Affiliation(s)
- Yi-Lei Fan
- Key Laboratory of Drug Prevention and Control Technology of Zhejiang Province, Zhejiang Police College, Hangzhou, PR China
| | - Xiao-Hong Jin
- School of Nuclear Technology and Chemistry & Biology, Hubei University of Science and Technology, Xianning 437100, PR China
| | - Zhong-Ping Huang
- College of Chemical Engineering, Zhejiang University of Technology, Hangzhou, PR China.
| | - Hai-Feng Yu
- School of Nuclear Technology and Chemistry & Biology, Hubei University of Science and Technology, Xianning 437100, PR China
| | - Zhi-Gang Zeng
- School of Nuclear Technology and Chemistry & Biology, Hubei University of Science and Technology, Xianning 437100, PR China
| | - Tao Gao
- School of Nuclear Technology and Chemistry & Biology, Hubei University of Science and Technology, Xianning 437100, PR China.
| | - Lian-Shun Feng
- Synthetic and Functional Biomolecules Center, Peking University, Beijing, PR China
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23
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Shinde V, Mahulikar P, Mhaske PC, Nawale L, Sarkar D. Synthesis and biological evaluation of new 2-aryl-4-((4-aryl-1H-1,2,3-triazol-1-yl)methyl)thiazole derivatives. RESEARCH ON CHEMICAL INTERMEDIATES 2017. [DOI: 10.1007/s11164-017-3164-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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24
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Bonandi E, Christodoulou MS, Fumagalli G, Perdicchia D, Rastelli G, Passarella D. The 1,2,3-triazole ring as a bioisostere in medicinal chemistry. Drug Discov Today 2017; 22:1572-1581. [PMID: 28676407 DOI: 10.1016/j.drudis.2017.05.014] [Citation(s) in RCA: 401] [Impact Index Per Article: 57.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 05/16/2017] [Accepted: 05/25/2017] [Indexed: 10/25/2022]
Abstract
1,2,3-Triazole is a well-known scaffold that has a widespread occurrence in different compounds characterized by several bioactivities, such as antimicrobial, antiviral, and antitumor effects. Moreover, the structural features of 1,2,3-triazole enable it to mimic different functional groups, justifying its wide use as a bioisostere for the synthesis of new active molecules. Here, we provide an overview of the 1,2,3-triazole ring as a bioisostere for the design of drug analogs, highlighting relevant recent examples.
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Affiliation(s)
- Elisa Bonandi
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi 19, 20133 Milano, Italy
| | - Michael S Christodoulou
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi 19, 20133 Milano, Italy; Dipartimento di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Gaia Fumagalli
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi 19, 20133 Milano, Italy
| | - Dario Perdicchia
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi 19, 20133 Milano, Italy
| | - Giulio Rastelli
- Dipartimento di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Daniele Passarella
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi 19, 20133 Milano, Italy.
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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: 69] [Impact Index Per Article: 9.9] [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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Wang QQ, Wang ZX, Xu YS, Zhang XY, Fan XS. Bu4NI-Catalyzed andtBuOOH-Oxidized Esterification of Aldehydes with Alkyl Halides in Water. ASIAN J ORG CHEM 2016. [DOI: 10.1002/ajoc.201600342] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Qian-Qian Wang
- School of Chemistry and Chemical Engineering; Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals; Key Laboratory of Green Chemical Media and Reactions; Ministry of Education; Henan Normal University; 46 Jianshe Road, Xinxiang Henan 453007 P. R. China
- School of Pharmacy; Xinxiang Medical University, Xinxiang; Henan 453003 P. R. China
| | - Zhang-Xin Wang
- School of Chemistry and Chemical Engineering; Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals; Key Laboratory of Green Chemical Media and Reactions; Ministry of Education; Henan Normal University; 46 Jianshe Road, Xinxiang Henan 453007 P. R. China
| | - Yuan-Shuang Xu
- School of Chemistry and Chemical Engineering; Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals; Key Laboratory of Green Chemical Media and Reactions; Ministry of Education; Henan Normal University; 46 Jianshe Road, Xinxiang Henan 453007 P. R. China
| | - Xin-Ying Zhang
- School of Chemistry and Chemical Engineering; Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals; Key Laboratory of Green Chemical Media and Reactions; Ministry of Education; Henan Normal University; 46 Jianshe Road, Xinxiang Henan 453007 P. R. China
| | - Xue-Sen Fan
- School of Chemistry and Chemical Engineering; Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals; Key Laboratory of Green Chemical Media and Reactions; Ministry of Education; Henan Normal University; 46 Jianshe Road, Xinxiang Henan 453007 P. R. China
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27
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Inosine 5'-monophosphate dehydrogenase inhibitors as antimicrobial agents: recent progress and future perspectives. Future Med Chem 2016; 7:1415-29. [PMID: 26230881 DOI: 10.4155/fmc.15.72] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [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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28
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Simple and efficient synthesis of $$5'$$ 5 ′ -aryl- $$5'$$ 5 ′ -deoxyguanosine analogs by azide-alkyne click reaction and their antileishmanial activities. Mol Divers 2016; 20:507-19. [DOI: 10.1007/s11030-015-9652-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 12/28/2015] [Indexed: 01/06/2023]
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29
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Montgomery A, Szabo R, Skropeta D, Yu H. Computational characterisation of the interactions between human ST6Gal I and transition-state analogue inhibitors: insights for inhibitor design. J Mol Recognit 2015; 29:210-22. [PMID: 26669681 DOI: 10.1002/jmr.2520] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 10/21/2015] [Accepted: 10/22/2015] [Indexed: 11/06/2022]
Abstract
Human β-galactoside α-2,6-sialyltransferase I (hST6Gal I) catalyses the synthesis of sialylated glycoconjugates involved in cell-cell interactions. Overexpression of hST6Gal I is observed in many different types of cancers, where it promotes metastasis through altered cell surface sialylation. A wide range of sialyltransferase (ST) inhibitors have been developed based on the natural donor, cytidine 5'-monophosphate N-acetylneuraminic acid (CMP-Neu5Ac). Of these, analogues that are structurally similar to the transition state exhibit the highest inhibitory activity. In order to design inhibitors that are readily accessible synthetically and with favourable pharmacokinetic properties, an investigation of the replacement of the charged phosphodiester-linker, present in many ST inhibitors, with a potential neutral isostere such as a carbamate or a 1,2,3-triazole has been undertaken. To investigate this, molecular docking and molecular dynamics simulations were performed. These simulations provided an insight into the binding mode of previously reported phosphodiester-linked ST inhibitors and demonstrated that targeting the proposed sialyl acceptor site is a viable option for producing selective inhibitors. The potential for a carbamate- or triazole-linker as an isosteric replacement for the phosphodiester in transition-state analogue ST inhibitors was established using molecular docking. Molecular dynamics simulations of carbamate- and phosphodiester-linked compounds revealed that both classes exhibit consistent interactions with hST6Gal I. Overall, the results obtained from this study provide a rationale for synthetic and biological evaluation of triazole- and carbamate-linked transition-state analogue ST inhibitors as potential new antimetastatic agents.
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Affiliation(s)
- Andrew Montgomery
- School of Chemistry, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW, 2522, Australia
| | - Rémi Szabo
- School of Chemistry, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW, 2522, Australia
| | - Danielle Skropeta
- School of Chemistry, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW, 2522, Australia.,Centre for Medical and Molecular Bioscience, University of Wollongong, Wollongong, NSW, 2522, Australia
| | - Haibo Yu
- School of Chemistry, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW, 2522, Australia.,Centre for Medical and Molecular Bioscience, University of Wollongong, Wollongong, NSW, 2522, Australia
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30
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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: 3.6] [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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31
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Cummings AJ, Ravalico F, McColgan-Bannon KIS, Eguaogie O, Elliott PA, Shannon MR, Bermejo IA, Dwyer A, Maginty AB, Mack J, Vyle JS. Nucleoside azide-alkyne cycloaddition reactions under solvothermal conditions or using copper vials in a ball mill. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2015; 34:361-70. [PMID: 25874944 DOI: 10.1080/15257770.2014.1001855] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Novel nucleoside analogues containing photoswitchable moieties were prepared using 'click' cycloaddition reactions between 5'-azido-5'-deoxythymidine and mono- or bis-N-propargylamide-substituted azobenzenes. In solution, high to quantitative yields were achieved using 5 mol% Cu(I) in the presence of a stabilizing ligand. 'Click' reactions using the monopropargylamides were also effected in the absence of added cuprous salts by the application of liquid assisted grinding (LAG) in metallic copper reaction vials. Specifically, high speed vibration ball milling (HSVBM) using a 3/32″ (2.38 mm) diameter copper ball (62 mg) at 60 Hz overnight in the presence of ethyl acetate lead to complete consumption of the 5'-azido nucleoside with clean conversion to the corresponding 1,3-triazole.
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Affiliation(s)
- Andrew J Cummings
- a School of Chemistry and Chemical Engineering , Queen's University Belfast , Belfast , UK
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32
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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: 17] [Impact Index Per Article: 1.9] [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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33
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Makowska-Grzyska M, Kim Y, Maltseva N, Osipiuk J, Gu M, Zhang M, Mandapati K, Gollapalli DR, Gorla SK, Hedstrom L, Joachimiak A. A novel cofactor-binding mode in bacterial IMP dehydrogenases explains inhibitor selectivity. J Biol Chem 2015; 290:5893-911. [PMID: 25572472 PMCID: PMC4342496 DOI: 10.1074/jbc.m114.619767] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The steadily rising frequency of emerging diseases and antibiotic resistance creates an urgent need for new drugs and targets. Inosine 5'-monophosphate dehydrogenase (IMP dehydrogenase or IMPDH) is a promising target for the development of new antimicrobial agents. IMPDH catalyzes the oxidation of IMP to XMP with the concomitant reduction of NAD(+), which is the pivotal step in the biosynthesis of guanine nucleotides. Potent inhibitors of bacterial IMPDHs have been identified that bind in a structurally distinct pocket that is absent in eukaryotic IMPDHs. The physiological role of this pocket was not understood. Here, we report the structures of complexes with different classes of inhibitors of Bacillus anthracis, Campylobacter jejuni, and Clostridium perfringens IMPDHs. These structures in combination with inhibition studies provide important insights into the interactions that modulate selectivity and potency. We also present two structures of the Vibrio cholerae IMPDH in complex with IMP/NAD(+) and XMP/NAD(+). In both structures, the cofactor assumes a dramatically different conformation than reported previously for eukaryotic IMPDHs and other dehydrogenases, with the major change observed for the position of the NAD(+) adenosine moiety. More importantly, this new NAD(+)-binding site involves the same pocket that is utilized by the inhibitors. Thus, the bacterial IMPDH-specific NAD(+)-binding mode helps to rationalize the conformation adopted by several classes of prokaryotic IMPDH inhibitors. These findings offer a potential strategy for further ligand optimization.
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Affiliation(s)
- Magdalena Makowska-Grzyska
- From the Center for Structural Genomics of Infectious Diseases, Computational Institute, University of Chicago, Chicago, Illinois 60637
| | - Youngchang Kim
- From the Center for Structural Genomics of Infectious Diseases, the Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, Illinois 60439, and Computational Institute, University of Chicago, Chicago, Illinois 60637
| | - Natalia Maltseva
- From the Center for Structural Genomics of Infectious Diseases, Computational Institute, University of Chicago, Chicago, Illinois 60637
| | - Jerzy Osipiuk
- From the Center for Structural Genomics of Infectious Diseases, the Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, Illinois 60439, and Computational Institute, University of Chicago, Chicago, Illinois 60637
| | - Minyi Gu
- From the Center for Structural Genomics of Infectious Diseases, Computational Institute, University of Chicago, Chicago, Illinois 60637
| | | | | | | | | | - Lizbeth Hedstrom
- the Departments of Biology and Chemistry, Brandeis University, Waltham, Massachusetts 024549110
| | - Andrzej Joachimiak
- From the Center for Structural Genomics of Infectious Diseases, the Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, Illinois 60439, and Computational Institute, University of Chicago, Chicago, Illinois 60637,
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34
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Cholewiński G, Iwaszkiewicz-Grześ D, Prejs M, Głowacka A, Dzierzbicka K. Synthesis of the inosine 5′-monophosphate dehydrogenase (IMPDH) inhibitors. J Enzyme Inhib Med Chem 2014; 30:550-63. [DOI: 10.3109/14756366.2014.951349] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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35
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Mandapati K, Gorla SK, House AL, McKenney ES, Zhang M, Rao SN, Gollapalli DR, Mann BJ, Goldberg JB, Cuny GD, Glomski IJ, Hedstrom L. Repurposing cryptosporidium inosine 5'-monophosphate dehydrogenase inhibitors as potential antibacterial agents. ACS Med Chem Lett 2014; 5:846-50. [PMID: 25147601 DOI: 10.1021/ml500203p] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 06/10/2014] [Indexed: 11/29/2022] Open
Abstract
Inosine 5'-monophosphate dehydrogenase (IMPDH) catalyzes the pivotal step in guanine nucleotide biosynthesis. IMPDH is a target for immunosuppressive, antiviral, and anticancer drugs, but, as of yet, has not been exploited for antimicrobial therapy. We have previously reported potent inhibitors of IMPDH from the protozoan parasite Cryptosporidium parvum (CpIMPDH). Many pathogenic bacteria, including Bacillus anthracis, Staphylococcus aureus, and Listeria monocytogenes, contain IMPDHs that should also be inhibited by these compounds. Herein, we present the structure-activity relationships for the inhibition of B. anthracis IMPDH (BaIMPDH) and antibacterial activity of 140 compounds from five structurally distinct compound series. Many potent inhibitors of BaIMPDH were identified (78% with IC50 ≤ 1 μM). Four compounds had minimum inhibitory concentrations (MIC) of less than 2 μM against B. anthracis Sterne 770. These compounds also displayed antibacterial activity against S. aureus and L. monocytogenes.
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Affiliation(s)
| | | | - Amanda L. House
- Department of Microbiology, Immunology,
and Cancer Biology, University of Virginia, Charlottesville, Virginia 22908, United States
| | - Elizabeth S. McKenney
- Department of Microbiology, Immunology,
and Cancer Biology, University of Virginia, Charlottesville, Virginia 22908, United States
| | | | | | | | - Barbara J. Mann
- Department of Microbiology, Immunology,
and Cancer Biology, University of Virginia, Charlottesville, Virginia 22908, United States
- Department of Medicine, Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia 22908, United States
| | - Joanna B. Goldberg
- Department of Microbiology, Immunology,
and Cancer Biology, University of Virginia, Charlottesville, Virginia 22908, United States
| | - Gregory D. Cuny
- Department of Pharmacological and Pharmaceutical Sciences, College
of Pharmacy, University of Houston, 549A Science and Research Building
2, Houston, Texas 77204, United States
| | - Ian J. Glomski
- Department of Microbiology, Immunology,
and Cancer Biology, University of Virginia, Charlottesville, Virginia 22908, United States
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36
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Swarbrick JM, Graeff R, Garnham C, Thomas MP, Galione A, Potter BVL. 'Click cyclic ADP-ribose': a neutral second messenger mimic. Chem Commun (Camb) 2014; 50:2458-61. [PMID: 24452494 PMCID: PMC4047616 DOI: 10.1039/c3cc49249d] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 01/08/2014] [Indexed: 11/21/2022]
Abstract
Analogues of the potent Ca(2+) releasing second messenger cyclic ADP-ribose (cADPR) with a 1,2,3-triazole pyrophosphate bioisostere were synthesised by click-mediated macrocyclisation. The ability to activate Ca(2+) release was surprisingly retained, and hydrolysis of cADPR by CD38 could also be inhibited, illustrating the potential of this approach to design drug-like signalling pathway modulators.
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Affiliation(s)
- Joanna M. Swarbrick
- Wolfson Laboratory of Medicinal Chemistry , Dept. of Pharmacy and Pharmacology , University of Bath , Bath , BA2 7AY , UK . ; Fax: +44-(0)1225-386114 ; Tel: +44-(0)1225-386639
| | - Richard Graeff
- Department of Physiology , University of Hong Kong , Hong Kong , China
| | - Clive Garnham
- Department of Pharmacology , University of Oxford , Mansfield Road , Oxford OX1 3QT , UK
| | - Mark P. Thomas
- Wolfson Laboratory of Medicinal Chemistry , Dept. of Pharmacy and Pharmacology , University of Bath , Bath , BA2 7AY , UK . ; Fax: +44-(0)1225-386114 ; Tel: +44-(0)1225-386639
| | - Antony Galione
- Department of Pharmacology , University of Oxford , Mansfield Road , Oxford OX1 3QT , UK
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37
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Singh G, Singh J, Mangat SS, Arora A. Synthetic approach towards ‘click’ modified chalcone based organotriethoxysilanes; UV-Vis study. RSC Adv 2014. [DOI: 10.1039/c4ra08724k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The efficient linkage of a conjugate chalcone to n-propyltriethoxysilanes via a 1,2,3-triazole is reported. The synthesis involves a Claisen–Schmidt condensation followed by a copper(i) catalyzed azide–alkyne cycloaddition (CuAAC) reaction.
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Affiliation(s)
- Gurjaspreet Singh
- Department of Chemistry and Centre of Advanced Studies
- Panjab University
- Chandigarh, India
| | - Jandeep Singh
- Department of Chemistry and Centre of Advanced Studies
- Panjab University
- Chandigarh, India
| | | | - Aanchal Arora
- Department of Chemistry and Centre of Advanced Studies
- Panjab University
- Chandigarh, India
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38
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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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39
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de Carvalho da Silva F, Cardoso MFDC, Ferreira PG, Ferreira VF. Biological Properties of 1H-1,2,3- and 2H-1,2,3-Triazoles. TOPICS IN HETEROCYCLIC CHEMISTRY 2014. [DOI: 10.1007/7081_2014_124] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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40
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Banerjee DR, Dutta D, Saha B, Bhattacharyya S, Senapati K, Das AK, Basak A. Design, synthesis and characterization of novel inhibitors against mycobacterial β-ketoacyl CoA reductase FabG4. Org Biomol Chem 2014; 12:73-85. [DOI: 10.1039/c3ob41676c] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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41
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Felczak K, Vince R, Pankiewicz KW. NAD-based inhibitors with anticancer potential. Bioorg Med Chem Lett 2013; 24:332-6. [PMID: 24269162 DOI: 10.1016/j.bmcl.2013.11.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 11/01/2013] [Accepted: 11/05/2013] [Indexed: 11/27/2022]
Abstract
Three classes of novel inhibitors of inosine monophosphate dehydrogenase have been prepared and their anti-proliferative properties were evaluated against several cancer cell lines. (1) Mycophenolic adenine dinucleotide analogues (8-13) containing a substituent at the C2 of adenine ring were found to be potent inhibitors of IMPDH (Ki's in range of 0.6-82nM) and sub-μM inhibitors of leukemic K562 cell proliferation. (2) Mycophenolic adenosine (d and l) esters (20 and 21) showed a potent inhibition of IMPDH2 (Ki=102 and Ki=231nM, respectively) and inhibition of K562 cell growth (IC50=0.5 and IC50=1.6μM). These compounds serve both as inhibitors of the enzyme and as a depot form of mycophenolic acid. The corresponding amide analogue 22, also a potent inhibitor of IMPDH (Ki=84nM), did not inhibit cancer cell proliferation. (3) Mycophenolic-(l)- and (d)-valine adenine di-amide derivatives 25 (Ki=9nM) and 28 (Ki=3nM) were found to be very potent enzymatically, but did not inhibit proliferation of cancer cells.
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Affiliation(s)
- Krzysztof Felczak
- Center for Drug Design, University of Minnesota, 516 Delaware Street S.E., Minneapolis, MN 55455, USA
| | - Robert Vince
- Center for Drug Design, University of Minnesota, 516 Delaware Street S.E., Minneapolis, MN 55455, USA
| | - Krzysztof W Pankiewicz
- Center for Drug Design, University of Minnesota, 516 Delaware Street S.E., Minneapolis, MN 55455, USA.
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42
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Giangreco I, Packer MJ. Pharmacophore binding motifs for nicotinamide adenine dinucleotide analogues across multiple protein families: a detailed contact-based analysis of the interaction between proteins and NAD(P) cofactors. J Med Chem 2013; 56:6175-89. [PMID: 23889609 DOI: 10.1021/jm400644z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
We have analyzed the protein-binding pharmacophore of NAD and its close analogues in all protein-ligand structures available in the RCSB database as of February 2012; this analysis has then been used to assess the novelty of structures emerging after that date. We show that proteins have evolved diverse pharmacophore motifs for binding the adenine moiety, fewer, but still diverse, motifs for nicotinamide, and a very limited set of motifs for binding the pyrophosphate linker. Our exhaustive analysis includes a pharmacophore contact analysis for over 1900 protein-ligand structures containing NAD analogues; we have benchmarked this set of contacts against nearly 27 000 protein-ligand structures to demonstrate that the diversity of interactions seen with NAD is very similar to that seen for all other ligands. Hence, variation in binding motifs for NAD is not distinct from that observed for other ligands and they show significant variation across protein families.
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Affiliation(s)
- Ilenia Giangreco
- AstraZeneca, Mereside, Alderley Park, Macclesfield SK10 4TG, UK.
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43
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Synthesis and evaluation of α-ketotriazoles and α,β-diketotriazoles as inhibitors of Mycobacterium tuberculosis. Eur J Med Chem 2013; 69:167-73. [PMID: 24016834 DOI: 10.1016/j.ejmech.2013.06.042] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 06/14/2013] [Accepted: 06/18/2013] [Indexed: 12/23/2022]
Abstract
Two series of α-ketotriazole and α,β-diketotriazole derivatives were synthesized and evaluated for antitubercular and cytotoxic activities. Among them, two α,β-diketotriazole compounds, 6b and 9b, exhibited good activities (minimum inhibitory concentration = 7.6 μM and 6.9 μM, respectively) on Mycobacterium tuberculosis and multi-drug resistant M. tuberculosis strains and presented no cytotoxicity (IC₅₀ > 50 μM) on colorectal cancer HCT116 and normal fibroblast GM637H cell lines. These two compounds represent promising leads for further optimization.
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44
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Thirumurugan P, Matosiuk D, Jozwiak K. Click Chemistry for Drug Development and Diverse Chemical–Biology Applications. Chem Rev 2013; 113:4905-79. [DOI: 10.1021/cr200409f] [Citation(s) in RCA: 1309] [Impact Index Per Article: 119.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Prakasam Thirumurugan
- Laboratory
of Medical Chemistry and Neuroengineering, Department of Chemistry, and ‡Department of
Synthesis and Chemical Technology of Pharmaceutical Substances, Medical University of Lublin, Lublin
20093, Poland
| | - Dariusz Matosiuk
- Laboratory
of Medical Chemistry and Neuroengineering, Department of Chemistry, and ‡Department of
Synthesis and Chemical Technology of Pharmaceutical Substances, Medical University of Lublin, Lublin
20093, Poland
| | - Krzysztof Jozwiak
- Laboratory
of Medical Chemistry and Neuroengineering, Department of Chemistry, and ‡Department of
Synthesis and Chemical Technology of Pharmaceutical Substances, Medical University of Lublin, Lublin
20093, Poland
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45
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Design and synthesis of 1H-1,2,3-triazoles derived from econazole as antitubercular agents. Bioorg Med Chem Lett 2012; 22:6844-7. [DOI: 10.1016/j.bmcl.2012.09.041] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Revised: 08/30/2012] [Accepted: 09/14/2012] [Indexed: 11/20/2022]
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46
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Singh R, Vince R. 2-Azabicyclo[2.2.1]hept-5-en-3-one: Chemical Profile of a Versatile Synthetic Building Block and its Impact on the Development of Therapeutics. Chem Rev 2012; 112:4642-86. [DOI: 10.1021/cr2004822] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Rohit Singh
- Center for Drug Design, Academic Health Center, University of Minnesota, 516 Delaware Street Southeast,
Minneapolis, MN 55455, United States
| | - Robert Vince
- Center for Drug Design, Academic Health Center, University of Minnesota, 516 Delaware Street Southeast,
Minneapolis, MN 55455, United States
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47
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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: 1.8] [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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48
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Soares da Costa TP, Tieu W, Yap MY, Pendini NR, Polyak SW, Sejer Pedersen D, Morona R, Turnidge JD, Wallace JC, Wilce MCJ, Booker GW, Abell AD. Selective inhibition of biotin protein ligase from Staphylococcus aureus. J Biol Chem 2012; 287:17823-17832. [PMID: 22437830 DOI: 10.1074/jbc.m112.356576] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
There is a well documented need to replenish the antibiotic pipeline with new agents to combat the rise of drug resistant bacteria. One strategy to combat resistance is to discover new chemical classes immune to current resistance mechanisms that inhibit essential metabolic enzymes. Many of the obvious drug targets that have no homologous isozyme in the human host have now been investigated. Bacterial drug targets that have a closely related human homologue represent a new frontier in antibiotic discovery. However, to avoid potential toxicity to the host, these inhibitors must have very high selectivity for the bacterial enzyme over the human homolog. We have demonstrated that the essential enzyme biotin protein ligase (BPL) from the clinically important pathogen Staphylococcus aureus could be selectively inhibited. Linking biotin to adenosine via a 1,2,3 triazole yielded the first BPL inhibitor selective for S. aureus BPL over the human equivalent. The synthesis of new biotin 1,2,3-triazole analogues using click chemistry yielded our most potent structure (K(i) 90 nM) with a >1100-fold selectivity for the S. aureus BPL over the human homologue. X-ray crystallography confirmed the mechanism of inhibitor binding. Importantly, the inhibitor showed cytotoxicity against S. aureus but not cultured mammalian cells. The biotin 1,2,3-triazole provides a novel pharmacophore for future medicinal chemistry programs to develop this new antibiotic class.
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Affiliation(s)
- Tatiana P Soares da Costa
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - William Tieu
- School of Chemistry and Physics, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Min Y Yap
- School of Biomedical Science, Monash University, Victoria 3800, Australia
| | - Nicole R Pendini
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia; School of Biomedical Science, Monash University, Victoria 3800, Australia
| | - Steven W Polyak
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia.
| | - Daniel Sejer Pedersen
- School of Chemistry and Physics, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Renato Morona
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - John D Turnidge
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia; SA Pathology at Women's and Children's Hospital, South Australia 5006, Australia
| | - John C Wallace
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Matthew C J Wilce
- School of Biomedical Science, Monash University, Victoria 3800, Australia
| | - Grant W Booker
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Andrew D Abell
- School of Chemistry and Physics, University of Adelaide, Adelaide, South Australia 5005, Australia
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49
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Franco TMA, Rostirolla DC, Ducati RG, Lorenzini DM, Basso LA, Santos DS. Biochemical characterization of recombinant guaA-encoded guanosine monophosphate synthetase (EC 6.3.5.2) from Mycobacterium tuberculosis H37Rv strain. Arch Biochem Biophys 2011; 517:1-11. [PMID: 22119138 DOI: 10.1016/j.abb.2011.11.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Revised: 11/08/2011] [Accepted: 11/09/2011] [Indexed: 12/29/2022]
Abstract
Administration of the current tuberculosis (TB) vaccine to newborns is not a reliable route for preventing TB in adults. The conversion of XMP to GMP is catalyzed by guaA-encoded GMP synthetase (GMPS), and deletions in the Shiguella flexneri guaBA operon led to an attenuated auxotrophic strain. Here we present the cloning, expression, and purification of recombinant guaA-encoded GMPS from Mycobacterium tuberculosis (MtGMPS). Mass spectrometry data, oligomeric state determination, steady-state kinetics, isothermal titration calorimetry (ITC), and multiple sequence alignment are also presented. The homodimeric MtGMPS catalyzes the conversion of XMP, MgATP, and glutamine into GMP, ADP, PP(i), and glutamate. XMP, NH(4)(+), and Mg(2+) displayed positive homotropic cooperativity, whereas ATP and glutamine displayed hyperbolic saturation curves. The activity of ATP pyrophosphatase domain is independent of glutamine amidotransferase domain, whereas the latter cannot catalyze hydrolysis of glutamine to NH(3) and glutamate in the absence of substrates. ITC data suggest random order of binding of substrates, and PP(i) is the last product released. Sequence comparison analysis showed conservation of both Cys-His-Glu catalytic triad of N-terminal Class I amidotransferase and of amino acid residues of the P-loop of the N-type ATP pyrophosphatase family.
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Affiliation(s)
- Tathyana Mar A Franco
- Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
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50
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Hedstrom L, Liechti G, Goldberg JB, Gollapalli DR. The antibiotic potential of prokaryotic IMP dehydrogenase inhibitors. Curr Med Chem 2011; 18:1909-18. [PMID: 21517780 DOI: 10.2174/092986711795590129] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2011] [Accepted: 04/04/2011] [Indexed: 12/30/2022]
Abstract
Inosine 5'-monophosphate dehydrogenase (IMPDH) catalyzes the first committed step of guanosine 5'-monophosphate (GMP) biosynthesis, and thus regulates the guanine nucleotide pool, which in turn governs proliferation. Human IMPDHs are validated targets for immunosuppressive, antiviral and anticancer drugs, but as yet microbial IMPDHs have not been exploited in antimicrobial chemotherapy. Selective inhibitors of IMPDH from Cryptosporidium parvum have recently been discovered that display anti-parasitic activity in cell culture models of infection. X-ray crystal structure and mutagenesis experiments identified the structural features that determine inhibitor susceptibility. These features are found in IMPDHs from a wide variety of pathogenic bacteria, including select agents and multiply drug resistant strains. A second generation inhibitor displays antibacterial activity against Helicobacter pylori, demonstrating the antibiotic potential of IMPDH inhibitors.
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Affiliation(s)
- L Hedstrom
- Brandeis University, Departments of Biology, Waltham, MA 02454-9110, USA.
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