1
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Mori M, Cocorullo M, Tresoldi A, Cazzaniga G, Gelain A, Stelitano G, Chiarelli LR, Tomaiuolo M, Delre P, Mangiatordi GF, Garofalo M, Cassetta A, Covaceuszach S, Villa S, Meneghetti F. Structural basis for specific inhibition of salicylate synthase from Mycobacterium abscessus. Eur J Med Chem 2024; 265:116073. [PMID: 38169270 DOI: 10.1016/j.ejmech.2023.116073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/15/2023] [Accepted: 12/17/2023] [Indexed: 01/05/2024]
Abstract
Blocking iron uptake and metabolism has been emerging as a promising therapeutic strategy for the development of novel antimicrobial compounds. Like all mycobacteria, M. abscessus (Mab) has evolved several countermeasures to scavenge iron from host carrier proteins, including the production of siderophores, which play a crucial role in these processes. In this study, we solved, for the first time, the crystal structure of Mab-SaS, the first enzyme involved in the biosynthesis of siderophores. Moreover, we screened a small, focused library and identified a compound exhibiting a potent inhibitory effect against Mab-SaS (IC50 ≈ 2 μM). Its binding mode was investigated by means of Induced Fit Docking simulations, performed on the crystal structure presented herein. Furthermore, cytotoxicity data and pharmacokinetic predictions revealed the safety and drug-likeness of this class of compounds. Finally, the crystallographic data were used to optimize the model for future virtual screening campaigns. Taken together, the findings of our study pave the way for the identification of potent Mab-SaS inhibitors, based on both established and unexplored chemotypes.
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Affiliation(s)
- Matteo Mori
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133, Milano, Italy
| | - Mario Cocorullo
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Via A. Ferrata 9, 27100, Pavia, Italy
| | - Andrea Tresoldi
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133, Milano, Italy
| | - Giulia Cazzaniga
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133, Milano, Italy
| | - Arianna Gelain
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133, Milano, Italy
| | - Giovanni Stelitano
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Via A. Ferrata 9, 27100, Pavia, Italy
| | - Laurent R Chiarelli
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Via A. Ferrata 9, 27100, Pavia, Italy
| | - Martina Tomaiuolo
- Institute of Crystallography, National Research Council, Trieste Outstation, Area Science Park - Basovizza, S.S.14 - Km. 163.5, 34149, Trieste, Italy
| | - Pietro Delre
- Institute of Crystallography, National Research Council, Via G. Amendola 122/o, 70126, Bari, Italy
| | - Giuseppe F Mangiatordi
- Institute of Crystallography, National Research Council, Via G. Amendola 122/o, 70126, Bari, Italy
| | - Mariangela Garofalo
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via F. Marzolo 5, 35131, Padova, Italy
| | - Alberto Cassetta
- Institute of Crystallography, National Research Council, Trieste Outstation, Area Science Park - Basovizza, S.S.14 - Km. 163.5, 34149, Trieste, Italy
| | - Sonia Covaceuszach
- Institute of Crystallography, National Research Council, Trieste Outstation, Area Science Park - Basovizza, S.S.14 - Km. 163.5, 34149, Trieste, Italy.
| | - Stefania Villa
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133, Milano, Italy.
| | - Fiorella Meneghetti
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133, Milano, Italy
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2
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Mori M, Stelitano G, Gelain A, Pini E, Chiarelli LR, Sammartino JC, Poli G, Tuccinardi T, Beretta G, Porta A, Bellinzoni M, Villa S, Meneghetti F. Shedding X-ray Light on the Role of Magnesium in the Activity of Mycobacterium tuberculosis Salicylate Synthase (MbtI) for Drug Design. J Med Chem 2020; 63:7066-7080. [PMID: 32530281 PMCID: PMC8008425 DOI: 10.1021/acs.jmedchem.0c00373] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
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The
Mg2+-dependent Mycobacterium tuberculosis salicylate synthase (MbtI) is a key enzyme involved in the biosynthesis
of siderophores. Because iron is essential for the survival and pathogenicity
of the microorganism, this protein constitutes an attractive target
for antitubercular therapy, also considering the absence of homologous
enzymes in mammals. An extension of the structure–activity
relationships of our furan-based candidates allowed us to disclose
the most potent competitive inhibitor known to date (10, Ki = 4 μM), which also proved
effective on mycobacterial cultures. By structural studies, we characterized
its unexpected Mg2+-independent binding mode. We also investigated
the role of the Mg2+ cofactor in catalysis, analyzing the
first crystal structure of the MbtI–Mg2+–salicylate
ternary complex. Overall, these results pave the way for the development
of novel antituberculars through the rational design of improved MbtI
inhibitors.
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Affiliation(s)
- Matteo Mori
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, via L. Mangiagalli 25, 20133 Milano,Italy
| | - Giovanni Stelitano
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università degli Studi di Pavia, via A. Ferrata 9, 27100 Pavia, Italy
| | - Arianna Gelain
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, via L. Mangiagalli 25, 20133 Milano,Italy
| | - Elena Pini
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, via L. Mangiagalli 25, 20133 Milano,Italy
| | - Laurent R Chiarelli
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università degli Studi di Pavia, via A. Ferrata 9, 27100 Pavia, Italy
| | - José C Sammartino
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università degli Studi di Pavia, via A. Ferrata 9, 27100 Pavia, Italy
| | - Giulio Poli
- Dipartimento di Farmacia, Università di Pisa, via Bonanno Pisano 6, 56126 Pisa, Italy
| | - Tiziano Tuccinardi
- Dipartimento di Farmacia, Università di Pisa, via Bonanno Pisano 6, 56126 Pisa, Italy.,Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Giangiacomo Beretta
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, via G. Celoria 2, 20133 Milano, Italy
| | - Alessio Porta
- Dipartimento di Chimica, Università degli Studi di Pavia, via T. Taramelli 12, 27100 Pavia, Italy
| | - Marco Bellinzoni
- Unité de Microbiologie Structurale, Institut Pasteur, CNRS, Université de Paris, F-75015 Paris, France
| | - Stefania Villa
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, via L. Mangiagalli 25, 20133 Milano,Italy
| | - Fiorella Meneghetti
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, via L. Mangiagalli 25, 20133 Milano,Italy
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3
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Genotypic differences between strains of the opportunistic pathogen Corynebacterium bovis isolated from humans, cows, and rodents. PLoS One 2018; 13:e0209231. [PMID: 30586440 PMCID: PMC6306256 DOI: 10.1371/journal.pone.0209231] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 11/30/2018] [Indexed: 01/21/2023] Open
Abstract
Corynebacterium bovis is an opportunistic bacterial pathogen shown to cause eye and prosthetic joint infections as well as abscesses in humans, mastitis in dairy cattle, and skin disease in laboratory mice and rats. Little is known about the genetic characteristics and genomic diversity of C. bovis because only a single draft genome is available for the species. The overall aim of this study was to sequence and compare the genome of C. bovis isolates obtained from different species, locations, and time points. Whole-genome sequencing was conducted on 20 C. bovis isolates (six human, four bovine, nine mouse and one rat) using the Illumina MiSeq platform and submitted to various comparative analysis tools. Sequencing generated high-quality contigs (over 2.53 Mbp) that were comparable to the only reported assembly using C. bovis DSM 20582T (97.8 ± 0.36% completeness). The number of protein-coding DNA sequences (2,174 ± 12.4) was similar among all isolates. A Corynebacterium genus neighbor-joining tree was created, which revealed Corynebacterium falsenii as the nearest neighbor to C. bovis (95.87% similarity), although the reciprocal comparison shows Corynebacterium jeikeium as closest neighbor to C. falsenii. Interestingly, the average nucleotide identity demonstrated that the C. bovis isolates clustered by host, with human and bovine isolates clustering together, and the mouse and rat isolates forming a separate group. The average number of genomic islands and putative virulence factors were significantly higher (p<0.001) in the mouse and rat isolates as compared to human/bovine isolates. Corynebacterium bovis’ pan-genome contained a total of 3,067 genes of which 1,354 represented core genes. The known core genes of all isolates were primarily related to ‘‘metabolism” and ‘‘information storage/processing.” However, most genes were classified as ‘‘function unknown” or “unclassified”. Surprisingly, no intact prophages were found in any isolate; however, almost all isolates had at least one complete CRISPR-Cas system.
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4
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Pini E, Poli G, Tuccinardi T, Chiarelli LR, Mori M, Gelain A, Costantino L, Villa S, Meneghetti F, Barlocco D. New Chromane-Based Derivatives as Inhibitors of Mycobacterium tuberculosis Salicylate Synthase (MbtI): Preliminary Biological Evaluation and Molecular Modeling Studies. Molecules 2018; 23:molecules23071506. [PMID: 29933627 PMCID: PMC6099841 DOI: 10.3390/molecules23071506] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 06/15/2018] [Accepted: 06/19/2018] [Indexed: 12/12/2022] Open
Abstract
Tuberculosis is the leading cause of death from a single infectious agent worldwide; therefore, the need for new antitubercular drugs is desperate. The recently validated target salicylate synthase MbtI is the first enzyme involved in the biosynthesis of mycobactins, compounds able to chelate iron, an essential cofactor for the survival of Mycobacterium tuberculosis in the host. Here, we report on the synthesis and biological evaluation of chromane-based compounds as new potential inhibitors of MbtI. Our approach successfully allowed the identification of a novel lead compound (1), endowed with a promising activity against this enzyme (IC50 = 55 μM). Molecular modeling studies were performed in order to evaluate the binding mode of 1 and rationalize the preliminary structure-activity relationships, thus providing crucial information to carry out further optimization studies.
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Affiliation(s)
- Elena Pini
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milano, Italy.
| | - Giulio Poli
- Dipartimento di Farmacia, Università di Pisa, via Bonanno 6, 56126 Pisa, Italy.
| | - Tiziano Tuccinardi
- Dipartimento di Farmacia, Università di Pisa, via Bonanno 6, 56126 Pisa, Italy.
| | - Laurent Roberto Chiarelli
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università degli Studi di Pavia, via Ferrata 9, 27100 Pavia, Italy.
| | - Matteo Mori
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milano, Italy.
| | - Arianna Gelain
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milano, Italy.
| | - Luca Costantino
- Dipartimento Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, via Campi 103, 41121 Modena, Italy.
| | - Stefania Villa
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milano, Italy.
| | - Fiorella Meneghetti
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milano, Italy.
| | - Daniela Barlocco
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milano, Italy.
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5
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Chiarelli LR, Mori M, Barlocco D, Beretta G, Gelain A, Pini E, Porcino M, Mori G, Stelitano G, Costantino L, Lapillo M, Bonanni D, Poli G, Tuccinardi T, Villa S, Meneghetti F. Discovery and development of novel salicylate synthase (MbtI) furanic inhibitors as antitubercular agents. Eur J Med Chem 2018; 155:754-763. [PMID: 29940465 DOI: 10.1016/j.ejmech.2018.06.033] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 06/05/2018] [Accepted: 06/13/2018] [Indexed: 01/10/2023]
Abstract
We report on the virtual screening, synthesis, and biological evaluation of new furan derivatives targeting Mycobacterium tuberculosis salicylate synthase (MbtI). A receptor-based virtual screening procedure was applied to screen the Enamine database, identifying two compounds, I and III, endowed with a good enzyme inhibitory activity. Considering the most active compound I as starting point for the development of novel MbtI inhibitors, we obtained new derivatives based on the furan scaffold. Among the SAR performed on this class, compound 1a emerged as the most potent MbtI inhibitor reported to date (Ki = 5.3 μM). Moreover, compound 1a showed a promising antimycobacterial activity (MIC99 = 156 μM), which is conceivably related to mycobactin biosynthesis inhibition.
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Affiliation(s)
- Laurent R Chiarelli
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università degli Studi di Pavia, via Ferrata 9, 27100, Pavia, Italy
| | - Matteo Mori
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133, Milano, Italy
| | - Daniela Barlocco
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133, Milano, Italy
| | - Giangiacomo Beretta
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Via Celoria 2, 20133, Milano, Italy
| | - Arianna Gelain
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133, Milano, Italy
| | - Elena Pini
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133, Milano, Italy
| | - Marianna Porcino
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133, Milano, Italy
| | - Giorgia Mori
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università degli Studi di Pavia, via Ferrata 9, 27100, Pavia, Italy
| | - Giovanni Stelitano
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università degli Studi di Pavia, via Ferrata 9, 27100, Pavia, Italy
| | - Luca Costantino
- Dipartimento Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, via Campi 103, 41121, Modena, Italy
| | - Margherita Lapillo
- Dipartimento di Farmacia, Università di Pisa, via Bonanno 6, 56126, Pisa, Italy
| | - Davide Bonanni
- Dipartimento di Farmacia, Università di Pisa, via Bonanno 6, 56126, Pisa, Italy
| | - Giulio Poli
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro 2, 53100, Siena, Italy
| | - Tiziano Tuccinardi
- Dipartimento di Farmacia, Università di Pisa, via Bonanno 6, 56126, Pisa, Italy.
| | - Stefania Villa
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133, Milano, Italy.
| | - Fiorella Meneghetti
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133, Milano, Italy
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6
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Yokoo S, Inoue S, Suzuki N, Amakawa N, Matsui H, Nakagami H, Takahashi A, Arai R, Katou S. Comparative analysis of plant isochorismate synthases reveals structural mechanisms underlying their distinct biochemical properties. Biosci Rep 2018; 38:BSR20171457. [PMID: 29436485 PMCID: PMC5843753 DOI: 10.1042/bsr20171457] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 01/30/2018] [Accepted: 02/04/2018] [Indexed: 12/27/2022] Open
Abstract
Isochorismate synthase (ICS) converts chorismate into isochorismate, a precursor of primary and secondary metabolites including salicylic acid (SA). SA plays important roles in responses to stress conditions in plants. Many studies have suggested that the function of plant ICSs is regulated at the transcriptional level. In Arabidopsis thaliana, the expression of AtICS1 is induced by stress conditions in parallel with SA synthesis, and AtICS1 is required for SA synthesis. In contrast, the expression of NtICS is not induced when SA synthesis is activated in tobacco, and it is unlikely to be involved in SA synthesis. Studies on the biochemical properties of plant ICSs are limited, compared with those on transcriptional regulation. We analyzed the biochemical properties of four plant ICSs: AtICS1, NtICS, NbICS from Nicotiana benthamiana, and OsICS from rice. Multiple sequence alignment analysis revealed that their primary structures were well conserved, and predicted key residues for ICS activity were almost completely conserved. However, AtICS1 showed much higher activity than the other ICSs when expressed in Escherichia coli and N. benthamiana leaves. Moreover, the levels of AtICS1 protein expression in N. benthamiana leaves were higher than the other ICSs. Construction and analysis of chimeras between AtICS1 and OsICS revealed that the putative chloroplast transit peptides (TPs) significantly affected the levels of protein accumulation in N. benthamiana leaves. Chimeric and point-mutation analyses revealed that Thr531, Ser537, and Ile550 of AtICS1 are essential for its high activity. These distinct biochemical properties of plant ICSs may suggest different roles in their respective plant species.
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Affiliation(s)
- Shohei Yokoo
- Faculty of Agriculture, Shinshu University, Minamiminowa 8304, Nagano 399-4598, Japan
| | - Seiya Inoue
- Faculty of Agriculture, Shinshu University, Minamiminowa 8304, Nagano 399-4598, Japan
| | - Nana Suzuki
- Faculty of Agriculture, Shinshu University, Minamiminowa 8304, Nagano 399-4598, Japan
| | - Naho Amakawa
- Faculty of Agriculture, Shinshu University, Minamiminowa 8304, Nagano 399-4598, Japan
| | - Hidenori Matsui
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Okayama 700-8530, Japan
- Plant Proteomics Research Unit, RIKEN CSRS, Yokohama, Kanagawa 230-0045, Japan
| | - Hirofumi Nakagami
- Plant Proteomics Research Unit, RIKEN CSRS, Yokohama, Kanagawa 230-0045, Japan
- Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
| | - Akira Takahashi
- Division of Plant and Microbial Sciences, Institute of Agrobiological Sciences, NARO, Tsukuba, Ibaraki 305-8602, Japan
| | - Ryoichi Arai
- Research Center for Fungal and Microbial Dynamism, Shinshu University, Minamiminowa 8304, Nagano 399-4598, Japan
- Faculty of Textile Science and Technology, Shinshu University, Ueda, Nagano 386-8567, Japan
| | - Shinpei Katou
- Faculty of Agriculture, Shinshu University, Minamiminowa 8304, Nagano 399-4598, Japan
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7
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Shelton CL, Lamb AL. Unraveling the Structure and Mechanism of the MST(ery) Enzymes. Trends Biochem Sci 2018; 43:342-357. [PMID: 29573882 DOI: 10.1016/j.tibs.2018.02.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 02/23/2018] [Accepted: 02/27/2018] [Indexed: 01/06/2023]
Abstract
The menaquinone, siderophore, and tryptophan (MST) enzymes transform chorismate to generate precursor molecules for the biosynthetic pathways defined in their name. Kinetic data, both steady-state and transient-state, and X-ray crystal structures indicate that these enzymes are highly conserved both in mechanism and in structure. Because these enzymes are found in pathogens but not in humans, there is considerable interest in these enzymes as drug design targets. While great progress has been made in defining enzyme structure and mechanism, inhibitor design has lagged behind. This review provides a detailed description of the evidence that begins to unravel the mystery of how the MST enzymes work, and how that information has been used in inhibitor design.
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Affiliation(s)
- Catherine L Shelton
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA
| | - Audrey L Lamb
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA.
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8
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Nonribosomal peptides for iron acquisition: pyochelin biosynthesis as a case study. Curr Opin Struct Biol 2018; 53:1-11. [PMID: 29455106 DOI: 10.1016/j.sbi.2018.01.015] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 01/25/2018] [Accepted: 01/29/2018] [Indexed: 01/03/2023]
Abstract
Microbes synthesize small, iron-chelating molecules known as siderophores to acquire iron from the environment. One way siderophores are generated is by nonribosomal peptide synthetases (NRPSs). The bioactive peptides generated by NRPS enzymes have unique chemical features, which are incorporated by accessory and tailoring domains or proteins. The first part of this review summarizes recent progress in NRPS structural biology. The second part uses the biosynthesis of pyochelin, a siderophore from Pseudomonas aeruginosa, as a case study to examine enzymatic methods for generating the observed diversity in NRPS-derived natural products.
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9
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Meneely KM, Sundlov JA, Gulick AM, Moran GR, Lamb AL. An Open and Shut Case: The Interaction of Magnesium with MST Enzymes. J Am Chem Soc 2016; 138:9277-93. [PMID: 27373320 PMCID: PMC5029964 DOI: 10.1021/jacs.6b05134] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
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The shikimate pathway of bacteria,
fungi, and plants generates
chorismate, which is drawn into biosynthetic pathways that form aromatic
amino acids and other important metabolites, including folates, menaquinone,
and siderophores. Many of the pathways initiated at this branch point
transform chorismate using an MST enzyme. The MST enzymes (menaquinone, siderophore, and tryptophan biosynthetic enzymes) are structurally homologous and magnesium-dependent,
and all perform similar chemical permutations to chorismate by nucleophilic
addition (hydroxyl or amine) at the 2-position of the ring, inducing
displacement of the 4-hydroxyl. The isomerase enzymes release isochorismate
or aminodeoxychorismate as the product, while the synthase enzymes
also have lyase activity that displaces pyruvate to form either salicylate
or anthranilate. This has led to the hypothesis that the isomerase
and lyase activities performed by the MST enzymes are functionally
conserved. Here we have developed tailored pre-steady-state approaches
to establish the kinetic mechanisms of the isochorismate and salicylate
synthase enzymes of siderophore biosynthesis. Our data are centered
on the role of magnesium ions, which inhibit the isochorismate synthase
enzymes but not the salicylate synthase enzymes. Prior structural
data have suggested that binding of the metal ion occludes access
or egress of substrates. Our kinetic data indicate that for the production
of isochorismate, a high magnesium ion concentration suppresses the
rate of release of product, accounting for the observed inhibition
and establishing the basis of the ordered-addition kinetic mechanism.
Moreover, we show that isochorismate is channeled through the synthase
reaction as an intermediate that is retained in the active site by
the magnesium ion. Indeed, the lyase-active enzyme has 3 orders of
magnitude higher affinity for the isochorismate complex relative to
the chorismate complex. Apparent negative-feedback inhibition by ferrous
ions is documented at nanomolar concentrations, which is a potentially
physiologically relevant mode of regulation for siderophore biosynthesis
in vivo.
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Affiliation(s)
- Kathleen M Meneely
- Department of Molecular Biosciences, University of Kansas , Lawrence, Kansas 66045, United States
| | - Jesse A Sundlov
- Hauptman-Woodward Medical Research Institute , 700 Ellicott Street, Buffalo, New York 14203, United States
| | - Andrew M Gulick
- Hauptman-Woodward Medical Research Institute , 700 Ellicott Street, Buffalo, New York 14203, United States
| | - Graham R Moran
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee , Milwaukee, Wisconsin 53201, United States
| | - Audrey L Lamb
- Department of Molecular Biosciences, University of Kansas , Lawrence, Kansas 66045, United States
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10
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Plach MG, Löffler P, Merkl R, Sterner R. Conversion of anthranilate synthase into isochorismate synthase: implications for the evolution of chorismate-utilizing enzymes. Angew Chem Int Ed Engl 2016; 54:11270-4. [PMID: 26352034 DOI: 10.1002/anie.201505063] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 06/23/2015] [Indexed: 02/06/2023]
Abstract
Chorismate-utilizing enzymes play a vital role in the biosynthesis of metabolites in plants as well as free-living and infectious microorganisms. Among these enzymes are the homologous primary metabolic anthranilate synthase (AS) and secondary metabolic isochorismate synthase (ICS). Both catalyze mechanistically related reactions by using ammonia and water as nucleophiles, respectively. We report that the nucleophile specificity of AS can be extended from ammonia to water by just two amino acid exchanges in a channel leading to the active site. The observed ICS/AS bifunctionality demonstrates that a secondary metabolic enzyme can readily evolve from a primary metabolic enzyme without requiring an initial gene duplication event. In a general sense, these findings add to our understanding how nature has used the structurally predetermined features of enzyme superfamilies to evolve new reactions.
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Affiliation(s)
- Maximilian G Plach
- Institut für Biophysik und physikalische Biochemie, Universität Regensburg, 93040 Regensburg (Germany)
| | - Patrick Löffler
- Institut für Biophysik und physikalische Biochemie, Universität Regensburg, 93040 Regensburg (Germany)
| | - Rainer Merkl
- Institut für Biophysik und physikalische Biochemie, Universität Regensburg, 93040 Regensburg (Germany)
| | - Reinhard Sterner
- Institut für Biophysik und physikalische Biochemie, Universität Regensburg, 93040 Regensburg (Germany).
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11
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Bashiri G, Johnston JM, Evans GL, Bulloch EMM, Goldstone DC, Jirgis ENM, Kleinboelting S, Castell A, Ramsay RJ, Manos-Turvey A, Payne RJ, Lott JS, Baker EN. Structure and inhibition of subunit I of the anthranilate synthase complex of Mycobacterium tuberculosis and expression of the active complex. ACTA ACUST UNITED AC 2015; 71:2297-308. [DOI: 10.1107/s1399004715017216] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 09/14/2015] [Indexed: 01/16/2023]
Abstract
The tryptophan-biosynthesis pathway is essential for Mycobacterium tuberculosis (Mtb) to cause disease, but not all of the enzymes that catalyse this pathway in this organism have been identified. The structure and function of the enzyme complex that catalyses the first committed step in the pathway, the anthranilate synthase (AS) complex, have been analysed. It is shown that the open reading frames Rv1609 (trpE) and Rv0013 (trpG) encode the chorismate-utilizing (AS-I) and glutamine amidotransferase (AS-II) subunits of the AS complex, respectively. Biochemical assays show that when these subunits are co-expressed a bifunctional AS complex is obtained. Crystallization trials on Mtb-AS unexpectedly gave crystals containing only AS-I, presumably owing to its selective crystallization from solutions containing a mixture of the AS complex and free AS-I. The three-dimensional structure reveals that Mtb-AS-I dimerizes via an interface that has not previously been seen in AS complexes. As is the case in other bacteria, it is demonstrated that Mtb-AS shows cooperative allosteric inhibition by tryptophan, which can be rationalized based on interactions at this interface. Comparative inhibition studies on Mtb-AS-I and related enzymes highlight the potential for single inhibitory compounds to target multiple chorismate-utilizing enzymes for TB drug discovery.
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12
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Plach MG, Löffler P, Merkl R, Sterner R. Umwandlung einer Anthranilatsynthase in eine Isochorismatsynthase: Implikationen für die Evolution von Chorismat-umsetzenden Enzymen. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201505063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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13
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Total Biosynthesis and Diverse Applications of the Nonribosomal Peptide-Polyketide Siderophore Yersiniabactin. Appl Environ Microbiol 2015; 81:5290-8. [PMID: 26025901 DOI: 10.1128/aem.01373-15] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 05/15/2015] [Indexed: 02/02/2023] Open
Abstract
Yersiniabactin (Ybt) is a mixed nonribosomal peptide-polyketide natural product natively produced by the pathogen Yersinia pestis. The compound enables iron scavenging capabilities upon host infection and is biosynthesized by a nonribosomal peptide synthetase featuring a polyketide synthase module. This pathway has been engineered for expression and biosynthesis using Escherichia coli as a heterologous host. In the current work, the biosynthetic process for Ybt formation was improved through the incorporation of a dedicated step to eliminate the need for exogenous salicylate provision. When this improvement was made, the compound was tested in parallel applications that highlight the metal-chelating nature of the compound. In the first application, Ybt was assessed as a rust remover, demonstrating a capacity of ∼40% compared to a commercial removal agent and ∼20% relative to total removal capacity. The second application tested Ybt in removing copper from a variety of nonbiological and biological solution mixtures. Success across a variety of media indicates potential utility in diverse scenarios that include environmental and biomedical settings.
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14
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Lamb AL. Breaking a pathogen's iron will: Inhibiting siderophore production as an antimicrobial strategy. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1054-70. [PMID: 25970810 DOI: 10.1016/j.bbapap.2015.05.001] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Revised: 04/29/2015] [Accepted: 05/06/2015] [Indexed: 12/24/2022]
Abstract
The rise of antibiotic resistance is a growing public health crisis. Novel antimicrobials are sought, preferably developing nontraditional chemical scaffolds that do not inhibit standard targets such as cell wall synthesis or the ribosome. Iron scavenging has been proposed as a viable target, because bacterial and fungal pathogens must overcome the nutritional immunity of the host to be virulent. This review highlights the recent work toward exploiting the biosynthetic enzymes of siderophore production for the design of next generation antimicrobials.
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Affiliation(s)
- Audrey L Lamb
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA.
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15
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Culbertson JE, Chung DH, Ziebart KT, Espiritu E, Toney MD. Conversion of aminodeoxychorismate synthase into anthranilate synthase with Janus mutations: mechanism of pyruvate elimination catalyzed by chorismate enzymes. Biochemistry 2015; 54:2372-84. [PMID: 25710100 DOI: 10.1021/acs.biochem.5b00013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The central importance of chorismate enzymes in bacteria, fungi, parasites, and plants combined with their absence in mammals makes them attractive targets for antimicrobials and herbicides. Two of these enzymes, anthranilate synthase (AS) and aminodeoxychorismate synthase (ADCS), are structurally and mechanistically similar. The first catalytic step, amination at C2, is common between them, but AS additionally catalyzes pyruvate elimination, aromatizing the aminated intermediate to anthranilate. Despite prior attempts, the conversion of a pyruvate elimination-deficient enzyme into an elimination-proficient one has not been reported. Janus, a bioinformatics method for predicting mutations required to functionally interconvert homologous enzymes, was employed to predict mutations to convert ADCS into AS. A genetic selection on a library of Janus-predicted mutations was performed. Complementation of an AS-deficient strain of Escherichia coli grown on minimal medium led to several ADCS mutants that allow growth in 6 days compared to 2 days for wild-type AS. The purified mutant enzymes catalyze the conversion of chorismate to anthranilate at rates that are ∼50% of the rate of wild-type ADCS-catalyzed conversion of chorismate to aminodeoxychorismate. The residues mutated do not contact the substrate. Molecular dynamics studies suggest that pyruvate elimination is controlled by the conformation of the C2-aminated intermediate. Enzymes that catalyze elimination favor the equatorial conformation, which presents the C2-H to a conserved active site lysine (Lys424) for deprotonation and maximizes stereoelectronic activation. Acid/base catalysis of pyruvate elimination was confirmed in AS and salicylate synthase by showing incorporation of a solvent-derived proton into the pyruvate methyl group and by solvent kinetic isotope effects on pyruvate elimination catalyzed by AS.
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Affiliation(s)
- Justin E Culbertson
- †Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - Dong hee Chung
- †Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - Kristin T Ziebart
- ‡Department of Chemistry, Oregon State University, Corvallis, Oregon 97331-4003, United States
| | - Eduardo Espiritu
- §Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Michael D Toney
- †Department of Chemistry, University of California, Davis, Davis, California 95616, United States
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16
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Xie F, Dai S, Shen J, Ren B, Huang P, Wang Q, Liu X, Zhang B, Dai H, Zhang L. A new salicylate synthase AmS is identified for siderophores biosynthesis in Amycolatopsis methanolica 239(T). Appl Microbiol Biotechnol 2015; 99:5895-905. [PMID: 25586582 DOI: 10.1007/s00253-014-6370-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 12/17/2014] [Accepted: 12/26/2014] [Indexed: 12/14/2022]
Abstract
Siderophores are important for the growth of bacteria or the applications in treatment of iron overload-associated diseases due to the iron-chelating property. Salicylate synthase played a key role in the biosynthesis of some NRPS-derived siderophores by the providing of an iron coordination moiety as the initial building block. A new salicylate synthase, namely AmS, was identified in the biosynthesis pathway of siderophore amychelin in Amycolatopsis methanolica 239(T), since it shunt chorismate, an integrant precursor, from primary to secondary metabolite flow. The amino acid sequence alignment and phylogenetic analysis showed that AmS grouped into a new cluster. In vitro assays of AmS revealed its wide temperature tolerance ranged from 0 to 40 °C and narrow pH tolerant ranged from 7.0 to 9.0. AmS was resistant to organic solvents and non-ionic detergents. Moreover, AmS converted chorismate to salicylate with K m of 129.05 μM, k cat of 2.20 min(-1) at optimal conditions, indicating its low substrate specificity and comparable velocity to reported counterparts (Irp9 and MbtI). These properties of AmS may improve the iron-seizing ability of A. methanolica to compete with its neighbors growing in natural environments. Most importantly, serine and cysteine residues were found to be important for the catalytic activity of AmS. This study presented AmS as a new cluster of salicylate synthase and the reaction mechanism and potential applications of salicylate synthase were highlighted as well.
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Affiliation(s)
- Feng Xie
- School of Life Sciences, University of Science and Technology of China, No. 443 HuangShan Road, Hefei, 230061, China
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17
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Meneely KM, Luo Q, Lamb AL. Redesign of MST enzymes to target lyase activity instead promotes mutase and dehydratase activities. Arch Biochem Biophys 2013; 539:70-80. [PMID: 24055536 DOI: 10.1016/j.abb.2013.09.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 09/10/2013] [Accepted: 09/11/2013] [Indexed: 11/20/2022]
Abstract
The isochorismate and salicylate synthases are members of the MST family of enzymes. The isochorismate synthases establish an equilibrium for the conversion chorismate to isochorismate and the reverse reaction. The salicylate synthases convert chorismate to salicylate with an isochorismate intermediate; therefore, the salicylate synthases perform isochorismate synthase and isochorismate-pyruvate lyase activities sequentially. While the active site residues are highly conserved, there are two sites that show trends for lyase-activity and lyase-deficiency. Using steady state kinetics and HPLC progress curves, we tested the "interchange" hypothesis that interconversion of the amino acids at these sites would promote lyase activity in the isochorismate synthases and remove lyase activity from the salicylate synthases. An alternative, "permute" hypothesis, that chorismate-utilizing enzymes are designed to permute the substrate into a variety of products and tampering with the active site may lead to identification of adventitious activities, is tested by more sensitive NMR time course experiments. The latter hypothesis held true. The variant enzymes predominantly catalyzed chorismate mutase-prephenate dehydratase activities, sequentially generating prephenate and phenylpyruvate, augmenting previously debated (mutase) or undocumented (dehydratase) adventitious activities.
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Affiliation(s)
- Kathleen M Meneely
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, United States
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18
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Domagalski MJ, Tkaczuk KL, Chruszcz M, Skarina T, Onopriyenko O, Cymborowski M, Grabowski M, Savchenko A, Minor W. Structure of isochorismate synthase DhbC from Bacillus anthracis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:956-61. [PMID: 23989140 PMCID: PMC3758140 DOI: 10.1107/s1744309113021246] [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: 03/20/2013] [Accepted: 07/30/2013] [Indexed: 06/02/2023]
Abstract
The isochorismate synthase DhbC from Bacillus anthracis is essential for the biosynthesis of the siderophore bacillibactin by this pathogenic bacterium. The structure of the selenomethionine-substituted protein was determined to 2.4 Å resolution using single-wavelength anomalous diffraction. B. anthracis DhbC bears the strongest resemblance to the Escherichia coli isochorismate synthase EntC, which is involved in the biosynthesis of another siderophore, namely enterobactin. Both proteins adopt the characteristic fold of other chorismate-utilizing enzymes, which are involved in the biosynthesis of various products, including siderophores, menaquinone and tryptophan. The conservation of the active-site residues, as well as their spatial arrangement, suggests that these enzymes share a common Mg(2+)-dependent catalytic mechanism.
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Affiliation(s)
- M. J. Domagalski
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Jordan Hall, Charlottesville, VA 22908, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), USA
| | - K. L. Tkaczuk
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Jordan Hall, Charlottesville, VA 22908, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), USA
| | - M. Chruszcz
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Jordan Hall, Charlottesville, VA 22908, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), USA
| | - T. Skarina
- Center for Structural Genomics of Infectious Diseases (CSGID), USA
- Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, ON M5G 1L6, Canada
| | - O. Onopriyenko
- Center for Structural Genomics of Infectious Diseases (CSGID), USA
- Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, ON M5G 1L6, Canada
| | - M. Cymborowski
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Jordan Hall, Charlottesville, VA 22908, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), USA
| | - M. Grabowski
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Jordan Hall, Charlottesville, VA 22908, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), USA
| | - A. Savchenko
- Center for Structural Genomics of Infectious Diseases (CSGID), USA
- Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, ON M5G 1L6, Canada
| | - W. Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Jordan Hall, Charlottesville, VA 22908, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), USA
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19
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Meneely KM, Luo Q, Dhar P, Lamb AL. Lysine221 is the general base residue of the isochorismate synthase from Pseudomonas aeruginosa (PchA) in a reaction that is diffusion limited. Arch Biochem Biophys 2013; 538:49-56. [PMID: 23942051 DOI: 10.1016/j.abb.2013.07.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Revised: 07/25/2013] [Accepted: 07/28/2013] [Indexed: 01/30/2023]
Abstract
The isochorismate synthase from Pseudomonas aeruginosa (PchA) catalyzes the conversion of chorismate to isochorismate, which is subsequently converted by a second enzyme (PchB) to salicylate for incorporation into the salicylate-capped siderophore pyochelin. PchA is a member of the MST family of enzymes, which includes the structurally homologous isochorismate synthases from Escherichia coli (EntC and MenF) and salicylate synthases from Yersinia enterocolitica (Irp9) and Mycobacterium tuberculosis (MbtI). The latter enzymes generate isochorismate as an intermediate before generating salicylate and pyruvate. General acid-general base catalysis has been proposed for isochorismate synthesis in all five enzymes, but the residues required for the isomerization are a matter of debate, with both lysine221 and glutamate313 proposed as the general base (PchA numbering). This work includes a classical characterization of PchA with steady state kinetic analysis, solvent kinetic isotope effect analysis and by measuring the effect of viscosogens on catalysis. The results suggest that isochorismate production from chorismate by the MST enzymes is the result of general acid-general base catalysis with a lysine as the base and a glutamic acid as the acid, in reverse protonation states. Chemistry is determined to not be rate limiting, favoring the hypothesis of a conformational or binding step as the slow step.
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Affiliation(s)
- Kathleen M Meneely
- Molecular Biosciences, University of Kansas, Lawrence, KS 66045, United States
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20
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Culbertson JE, Toney MD. Expression and characterization of PhzE from P. aeruginosa PAO1: aminodeoxyisochorismate synthase involved in pyocyanin and phenazine-1-carboxylate production. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1834:240-6. [PMID: 23099261 DOI: 10.1016/j.bbapap.2012.10.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Revised: 10/04/2012] [Accepted: 10/15/2012] [Indexed: 12/21/2022]
Abstract
PhzE from Pseudomonas aeruginosa catalyzes the first step in the biosynthesis of phenazine-1-carboxylic acid, pyocyanin, and other phenazines, which are virulence factors for Pseudomonas species. The reaction catalyzed converts chorismate into aminodeoxyisochorismate using ammonia supplied by a glutamine amidotransferase domain. It has structural and sequence homology to other chorismate-utilizing enzymes such as anthranilate synthase, isochorismate synthase, aminodeoxychorismate synthase, and salicylate synthase. Like these enzymes, it is Mg(2+) dependent and catalyzes a similar S(N)2" nucleophilic substitution reaction. PhzE catalyzes the addition of ammonia to C2 of chorismate, as does anthranilate synthase, yet unlike anthranilate synthase it does not catalyze elimination of pyruvate from enzyme-bound aminodeoxyisochorismate. Herein, the cloning of the phzE gene, high level expression of active enzyme in E. coli, purification, and kinetic characterization of the enzyme is presented, including temperature and pH dependence. Steady-state kinetics give K(chorismate)=20±4μM, K(Mg)(2+)=294±22μM, K(L-gln)=11±1mM, and k(cat)=2.2±0.2s(-1) for a random kinetic mechanism. PhzE can use NH(4)(+) as an alternative nucleophile, while Co(2+) and Mn(2+) are alternative divalent metals.
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Affiliation(s)
- Justin E Culbertson
- Department of Chemistry, University of California, Davis, Davis, CA 95616, USA
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21
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Chi G, Manos-Turvey A, O’Connor PD, Johnston JM, Evans GL, Baker EN, Payne RJ, Lott JS, Bulloch EMM. Implications of Binding Mode and Active Site Flexibility for Inhibitor Potency against the Salicylate Synthase from Mycobacterium tuberculosis. Biochemistry 2012; 51:4868-79. [DOI: 10.1021/bi3002067] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Gamma Chi
- School of Biological Sciences
and Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3 Symonds Street, Private
Bag 92019, Auckland 1142, New Zealand
| | | | - Patrick D. O’Connor
- Auckland Cancer Society Research
Centre, Faculty of Medical and Health Sciences, The University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Jodie M. Johnston
- School of Biological Sciences
and Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3 Symonds Street, Private
Bag 92019, Auckland 1142, New Zealand
| | - Genevieve L. Evans
- School of Biological Sciences
and Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3 Symonds Street, Private
Bag 92019, Auckland 1142, New Zealand
| | - Edward N. Baker
- School of Biological Sciences
and Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3 Symonds Street, Private
Bag 92019, Auckland 1142, New Zealand
| | - Richard J. Payne
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | - J. Shaun Lott
- School of Biological Sciences
and Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3 Symonds Street, Private
Bag 92019, Auckland 1142, New Zealand
| | - Esther M. M. Bulloch
- School of Biological Sciences
and Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3 Symonds Street, Private
Bag 92019, Auckland 1142, New Zealand
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22
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Ferrer S, Martí S, Moliner V, Tuñón I, Bertrán J. Understanding the different activities of highly promiscuous MbtI by computational methods. Phys Chem Chem Phys 2012; 14:3482-9. [DOI: 10.1039/c2cp23149b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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23
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Abstract
One of the fundamental questions of enzymology is how catalytic power is derived. This review focuses on recent developments in the structure--function relationships of chorismate-utilizing enzymes involved in siderophore biosynthesis to provide insight into the biocatalysis of pericyclic reactions. Specifically, salicylate synthesis by the two-enzyme pathway in Pseudomonas aeruginosa is examined. The isochorismate-pyruvate lyase is discussed in the context of its homologues, the chorismate mutases, and the isochorismate synthase is compared to its homologues in the MST family (menaquinone, siderophore, or tryptophan biosynthesis) of enzymes. The tentative conclusion is that the activities observed cannot be reconciled by inspection of the active site participants alone. Instead, individual activities must arise from unique dynamic properties of each enzyme that are tuned to promote specific chemistries.
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Affiliation(s)
- Audrey L Lamb
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, United States.
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24
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Seipke RF, Song L, Bicz J, Laskaris P, Yaxley AM, Challis GL, Loria R. The plant pathogen Streptomyces scabies 87-22 has a functional pyochelin biosynthetic pathway that is regulated by TetR- and AfsR-family proteins. MICROBIOLOGY-SGM 2011; 157:2681-2693. [PMID: 21757492 DOI: 10.1099/mic.0.047977-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Siderophores are high-affinity iron-chelating compounds produced by bacteria for iron uptake that can act as important virulence determinants for both plant and animal pathogens. Genome sequencing of the plant pathogen Streptomyces scabies 87-22 revealed the presence of a putative pyochelin biosynthetic gene cluster (PBGC). Liquid chromatography (LC)-MS analyses of culture supernatants of S. scabies mutants, in which expression of the cluster is upregulated and which lack a key biosynthetic gene from the cluster, indicated that pyochelin is a product of the PBGC. LC-MS comparisons with authentic standards on a homochiral stationary phase confirmed that pyochelin and not enantio-pyochelin (ent-pyochelin) is produced by S. scabies. Transcription of the S. scabies PBGC occurs via ~19 kb and ~3 kb operons and transcription of the ~19 kb operon is regulated by TetR- and AfsR-family proteins encoded by the cluster. This is the first report, to our knowledge, of pyochelin production by a Gram-positive bacterium; interestingly regulation of pyochelin production is distinct from characterized PBGCs in Gram-negative bacteria. Though pyochelin-mediated iron acquisition by Pseudomonas aeruginosa is important for virulence, in planta bioassays failed to demonstrate that pyochelin production by S. scabies is required for development of disease symptoms on excised potato tuber tissue or radish seedlings.
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Affiliation(s)
- Ryan F Seipke
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
| | - Lijiang Song
- Department of Chemistry, University of Warwick, Coventry, UK
| | - Joanna Bicz
- Department of Chemistry, University of Warwick, Coventry, UK
| | - Paris Laskaris
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
| | - Alice M Yaxley
- Department of Biological Sciences, University of Warwick, Coventry, UK
| | | | - Rosemary Loria
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
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25
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Li QA, Mavrodi DV, Thomashow LS, Roessle M, Blankenfeldt W. Ligand binding induces an ammonia channel in 2-amino-2-desoxyisochorismate (ADIC) synthase PhzE. J Biol Chem 2011; 286:18213-21. [PMID: 21454481 DOI: 10.1074/jbc.m110.183418] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
PhzE utilizes chorismate and glutamine to synthesize 2-amino-2-desoxyisochorismate (ADIC) in the first step of phenazine biosynthesis. The PhzE monomer contains both a chorismate-converting menaquinone, siderophore, tryptophan biosynthesis (MST) and a type 1 glutamine amidotransferase (GATase1) domain connected by a 45-residue linker. We present here the crystal structure of PhzE from Burkholderia lata 383 in a ligand-free open and ligand-bound closed conformation at 2.9 and 2.1 Å resolution, respectively. PhzE arranges in an intertwined dimer such that the GATase1 domain of one chain provides NH(3) to the MST domain of the other. This quaternary structure was confirmed by small angle x-ray scattering. Binding of chorismic acid, which was found converted to benzoate and pyruvate in the MST active centers of the closed form, leads to structural rearrangements that establish an ammonia transport channel approximately 25 Å in length within each of the two MST/GATase1 functional units of the dimer. The assignment of PhzE as an ADIC synthase was confirmed by mass spectrometric analysis of the product, which was also visualized at 1.9 Å resolution by trapping in crystals of an inactive mutant of PhzD, an isochorismatase that catalyzes the subsequent step in phenazine biosynthesis. Unlike in some of the related anthranilate synthases, no allosteric inhibition was observed in PhzE. This can be attributed to a tryptophan residue of the protein blocking the potential regulatory site. Additional electron density in the GATase1 active center was identified as zinc, and it was demonstrated that Zn(2+), Mn(2+), and Ni(2+) reduce the activity of PhzE.
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Affiliation(s)
- Qi-Ang Li
- Department of Physical Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
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26
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Dempsey DA, Vlot AC, Wildermuth MC, Klessig DF. Salicylic Acid biosynthesis and metabolism. THE ARABIDOPSIS BOOK 2011; 9:e0156. [PMID: 22303280 PMCID: PMC3268552 DOI: 10.1199/tab.0156] [Citation(s) in RCA: 401] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Salicylic acid (SA) has been shown to regulate various aspects of growth and development; it also serves as a critical signal for activating disease resistance in Arabidopsis thaliana and other plant species. This review surveys the mechanisms involved in the biosynthesis and metabolism of this critical plant hormone. While a complete biosynthetic route has yet to be established, stressed Arabidopsis appear to synthesize SA primarily via an isochorismate-utilizing pathway in the chloroplast. A distinct pathway utilizing phenylalanine as the substrate also may contribute to SA accumulation, although to a much lesser extent. Once synthesized, free SA levels can be regulated by a variety of chemical modifications. Many of these modifications inactivate SA; however, some confer novel properties that may aid in long distance SA transport or the activation of stress responses complementary to those induced by free SA. In addition, a number of factors that directly or indirectly regulate the expression of SA biosynthetic genes or that influence the rate of SA catabolism have been identified. An integrated model, encompassing current knowledge of SA metabolism in Arabidopsis, as well as the influence other plant hormones exert on SA metabolism, is presented.
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Affiliation(s)
| | | | - Mary C. Wildermuth
- Department of Plant and Microbial Biology, 221 Koshland Hall, University of California, Berkeley, California 94720-3102
- Address correspondence to and
| | - Daniel F. Klessig
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853
- Address correspondence to and
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27
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Youard ZA, Wenner N, Reimmann C. Iron acquisition with the natural siderophore enantiomers pyochelin and enantio-pyochelin in Pseudomonas species. Biometals 2010; 24:513-22. [PMID: 21188474 DOI: 10.1007/s10534-010-9399-9] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Accepted: 12/13/2010] [Indexed: 11/24/2022]
Abstract
The bacterial siderophore pyochelin is composed of salicylate and two cysteine-derived heterocycles, the second of which is modified by reduction and N-methylation during biosynthesis. In Pseudomonas aeruginosa, the first cysteine residue is converted to its D-isoform during thiazoline ring formation, whereas the second cysteine remains in its L-configuration. Stereochemistry is opposite in the Pseudomonas fluorescens siderophore enantio-pyochelin, in which the first ring originates from L-cysteine and the second ring from D-cysteine. Both siderophores promote growth of the producer organism during iron limitation and induce the expression of their biosynthesis genes by activating the transcriptional AraC-type regulator PchR. However, neither siderophore is functional as an iron carrier or as a transcriptional inducer in the other species, demonstrating that both processes are highly stereospecific. Stereospecificity of pyochelin/enantio-pyochelin-mediated iron uptake is ensured at two levels: (i) by the outer membrane siderophore receptors and (ii) by the cytosolic PchR regulators.
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Affiliation(s)
- Zeb A Youard
- Département de Microbiologie Fondamentale, Université de Lausanne, Bâtiment Biophore, Lausanne, Switzerland
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28
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Manos-Turvey A, Bulloch EMM, Rutledge PJ, Baker EN, Lott JS, Payne RJ. Inhibition studies of Mycobacterium tuberculosis salicylate synthase (MbtI). ChemMedChem 2010; 5:1067-79. [PMID: 20512795 DOI: 10.1002/cmdc.201000137] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Mycobacterium tuberculosis salicylate synthase (MbtI), a member of the chorismate-utilizing enzyme family, catalyses the first committed step in the biosynthesis of the siderophore mycobactin T. This complex secondary metabolite is essential for both virulence and survival of M. tuberculosis, the etiological agent of tuberculosis (TB). It is therefore anticipated that inhibitors of this enzyme may serve as TB therapies with a novel mode of action. Herein we describe the first inhibition study of M. tuberculosis MbtI using a library of functionalized benzoate-based inhibitors designed to mimic the substrate (chorismate) and intermediate (isochorismate) of the MbtI-catalyzed reaction. The most potent inhibitors prepared were those designed to mimic the enzyme intermediate, isochorismate. These compounds, based on a 2,3-dihydroxybenzoate scaffold, proved to be low-micromolar inhibitors of MbtI. The most potent inhibitors in this series possessed hydrophobic enol ether side chains at C3 in place of the enol-pyruvyl side chain found in chorismate and isochorismate.
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29
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Ziebart KT, Toney MD. Nucleophile Specificity in Anthranilate Synthase, Aminodeoxychorismate Synthase, Isochorismate Synthase, and Salicylate Synthase. Biochemistry 2010; 49:2851-9. [DOI: 10.1021/bi100021x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kristin T. Ziebart
- Department of Chemistry, University of California, Davis, California 95616
| | - Michael D. Toney
- Department of Chemistry, University of California, Davis, California 95616
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30
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Crystal Structure of Escherichia coli Enterobactin-specific Isochorismate Synthase (EntC) Bound to its Reaction Product Isochorismate: Implications for the Enzyme Mechanism and Differential Activity of Chorismate-utilizing Enzymes. J Mol Biol 2010; 397:290-300. [DOI: 10.1016/j.jmb.2010.01.019] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Revised: 01/07/2010] [Accepted: 01/07/2010] [Indexed: 11/17/2022]
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31
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Theoretical QM/MM studies of enzymatic pericyclic reactions. Interdiscip Sci 2010; 2:115-31. [DOI: 10.1007/s12539-010-0095-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2009] [Revised: 12/07/2009] [Accepted: 12/09/2009] [Indexed: 11/25/2022]
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32
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Martí S, Andrés J, Moliner V, Silla E, Tuñón I, Bertrán J. Mechanism and plasticity of isochorismate pyruvate lyase: a computational study. J Am Chem Soc 2010; 131:16156-61. [PMID: 19835359 DOI: 10.1021/ja905271g] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The isochorismate pyruvate lyase (IPL) from Pseudomonas aeruginosa, designated as PchB, catalyzes the transformation of isochorismate into pyruvate and salicylate, but it also catalyzes the rearrangement of chorismate into prephenate, suggesting that both reactions may proceed by a pericyclic mechanism. In this work, molecular dynamics simulations employing hybrid quantum mechanics/molecular mechanics methods have been carried out to get a detailed knowledge of the reaction mechanism of PchB. The results provide a theoretical rate constant enhancement by comparison with the reaction in solution, in agreement with the experimental data, and confirm the pericyclic nature of the reaction mechanism. The robustness of this promiscuous enzyme has been checked by considering the impact of Ala37Ile mutation, previously proposed by us to improve the secondary chorismate mutase (CM) activity. The effect of this mutation, which was shown to increase the rate constant for the CM activity by a factor of 10(3), also increases the IPL catalytic efficiency, although only by a factor of 6.
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Affiliation(s)
- Sergio Martí
- Departament de Quimica Fisica i Analitica, Universitat Jaume I, 12071 Castellon, Spain
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33
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Cisar JS, Tan DS. Small molecule inhibition of microbial natural product biosynthesis-an emerging antibiotic strategy. Chem Soc Rev 2008; 37:1320-9. [PMID: 18568158 DOI: 10.1039/b702780j] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
A variety of natural products modulate critical biological processes in the microorganisms that produce them. Thus, inhibition of the corresponding natural product biosynthesis pathways represents a promising avenue to develop novel antibiotics. In this tutorial review, we describe several recent examples of designed small molecule inhibitors of microbial natural product biosynthesis and their use in evaluating this emerging antibiotic strategy.
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Affiliation(s)
- Justin S Cisar
- Tri-Institutional Training Program in Chemical Biology, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, Box 422, New York, NY 10065, USA
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34
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Abstract
High-affinity iron acquisition is mediated by siderophore-dependent pathways in the majority of pathogenic and nonpathogenic bacteria and fungi. Considerable progress has been made in characterizing and understanding mechanisms of siderophore synthesis, secretion, iron scavenging, and siderophore-delivered iron uptake and its release. The regulation of siderophore pathways reveals multilayer networks at the transcriptional and posttranscriptional levels. Due to the key role of many siderophores during virulence, coevolution led to sophisticated strategies of siderophore neutralization by mammals and (re)utilization by bacterial pathogens. Surprisingly, hosts also developed essential siderophore-based iron delivery and cell conversion pathways, which are of interest for diagnostic and therapeutic studies. In the last decades, natural and synthetic compounds have gained attention as potential therapeutics for iron-dependent treatment of infections and further diseases. Promising results for pathogen inhibition were obtained with various siderophore-antibiotic conjugates acting as "Trojan horse" toxins and siderophore pathway inhibitors. In this article, general aspects of siderophore-mediated iron acquisition, recent findings regarding iron-related pathogen-host interactions, and current strategies for iron-dependent pathogen control will be reviewed. Further concepts including the inhibition of novel siderophore pathway targets are discussed.
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Affiliation(s)
- Marcus Miethke
- Philipps Universität Marburg, FB Chemie Biochemie, Hans Meerwein Strasse, D-35032 Marburg, Germany
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35
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Kerbarh O, Ciulli A, Chirgadze DY, Blundell TL, Abell C. Nucleophile Selectivity of Chorismate-Utilizing Enzymes. Chembiochem 2007; 8:622-4. [PMID: 17335098 DOI: 10.1002/cbic.200700019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Olivier Kerbarh
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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36
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Kolappan S, Zwahlen J, Zhou R, Truglio JJ, Tonge PJ, Kisker C. Lysine 190 is the catalytic base in MenF, the menaquinone-specific isochorismate synthase from Escherichia coli: implications for an enzyme family. Biochemistry 2007; 46:946-53. [PMID: 17240978 DOI: 10.1021/bi0608515] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Menaquinone biosynthesis is initiated by the conversion of chorismate to isochorismate, a reaction that is catalyzed by the menaquinone-specific isochorismate synthase, MenF. The catalytic mechanism of MenF has been probed using a combination of structural and biochemical studies, including the 2.5 A structure of the enzyme, and Lys190 has been identified as the base that activates water for nucleophilic attack at the chorismate C2 carbon. MenF is a member of a larger family of Mg2+ dependent chorismate binding enzymes catalyzing distinct chorismate transformations. The studies reported here extend the mechanism recently proposed for this enzyme family by He et al.: He, Z., Stigers Lavoie, K. D., Bartlett, P. A., and Toney, M. D. (2004) J. Am. Chem. Soc. 126, 2378-85.
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Affiliation(s)
- Subramaniapillai Kolappan
- Department of Pharmacological Sciences and Center for Structural Biology, Stony Brook University, Stony Brook, New York 11794-5115, USA
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37
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Strawn MA, Marr SK, Inoue K, Inada N, Zubieta C, Wildermuth MC. Arabidopsis Isochorismate Synthase Functional in Pathogen-induced Salicylate Biosynthesis Exhibits Properties Consistent with a Role in Diverse Stress Responses. J Biol Chem 2007; 282:5919-33. [PMID: 17190832 DOI: 10.1074/jbc.m605193200] [Citation(s) in RCA: 181] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Salicylic acid (SA) is a phytohormone best known for its role in plant defense. It is synthesized in response to diverse pathogens and responsible for the large scale transcriptional induction of defense-related genes and the establishment of systemic acquired resistance. Surprisingly, given its importance in plant defense, an understanding of the underlying enzymology is lacking. In Arabidopsis thaliana, the pathogen-induced accumulation of SA requires isochorismate synthase (AtICS1). Here, we show that AtICS1 is a plastid-localized, stromal protein using chloroplast import assays and immunolocalization. AtICS1 acts as a monofunctional isochorismate synthase (ICS), catalyzing the conversion of chorismate to isochorismate (IC) in a reaction that operates near equilibrium (K(eq) = 0.89). It does not convert chorismate directly to SA (via an IC intermediate) as does Yersinia enterocolitica Irp9. Using an irreversible coupled spectrophotometric assay, we found that AtICS1 exhibits an apparent K(m) of 41.5 mum and k(cat) = 38.7 min(-1) for chorismate. This affinity for chorismate would allow it to successfully compete with other pathogen-induced, chorismate-utilizing enzymes. Furthermore, the biochemical properties of AtICS1 indicate its activity is not regulated by light-dependent changes in stromal pH, Mg(2+), or redox and that it is remarkably active at 4 degrees C consistent with a role for SA in cold-tolerant growth. Finally, our analyses support plastidic synthesis of stress-induced SA with the requirement for one or more additional enzymes responsible for the conversion of IC to SA, because non-enzymatic conversion of IC to SA under physiological conditions was negligible.
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Affiliation(s)
- Marcus A Strawn
- Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, California 94720-3102, USA
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38
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Scott DE, Ciulli A, Abell C. Coenzyme biosynthesis: enzyme mechanism, structure and inhibition. Nat Prod Rep 2007; 24:1009-26. [PMID: 17898895 DOI: 10.1039/b703108b] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This review highlights five key reactions in vitamin biosynthesis and in particular focuses on their mechanisms and inhibition and insights from structural studies. Each of the enzymes has the potential to be a target for novel antimicrobial agents.
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Affiliation(s)
- Duncan E Scott
- University Chemical Laboratory, Lensfield Road, Cambridge, CB2 1EW, UK
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39
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Harrison AJ, Yu M, Gårdenborg T, Middleditch M, Ramsay RJ, Baker EN, Lott JS. The structure of MbtI from Mycobacterium tuberculosis, the first enzyme in the biosynthesis of the siderophore mycobactin, reveals it to be a salicylate synthase. J Bacteriol 2006; 188:6081-91. [PMID: 16923875 PMCID: PMC1595383 DOI: 10.1128/jb.00338-06] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2006] [Accepted: 06/21/2006] [Indexed: 11/20/2022] Open
Abstract
The ability to acquire iron from the extracellular environment is a key determinant of pathogenicity in mycobacteria. Mycobacterium tuberculosis acquires iron exclusively via the siderophore mycobactin T, the biosynthesis of which depends on the production of salicylate from chorismate. Salicylate production in other bacteria is either a two-step process involving an isochorismate synthase (chorismate isomerase) and a pyruvate lyase, as observed for Pseudomonas aeruginosa, or a single-step conversion catalyzed by a salicylate synthase, as with Yersinia enterocolitica. Here we present the structure of the enzyme MbtI (Rv2386c) from M. tuberculosis, solved by multiwavelength anomalous diffraction at a resolution of 1.8 A, and biochemical evidence that it is the salicylate synthase necessary for mycobactin biosynthesis. The enzyme is critically dependent on Mg2+ for activity and produces salicylate via an isochorismate intermediate. MbtI is structurally similar to salicylate synthase (Irp9) from Y. enterocolitica and the large subunit of anthranilate synthase (TrpE) and shares the overall architecture of other chorismate-utilizing enzymes, such as the related aminodeoxychorismate synthase PabB. Like Irp9, but unlike TrpE or PabB, MbtI is neither regulated by nor structurally stabilized by bound tryptophan. The structure of MbtI is the starting point for the design of inhibitors of siderophore biosynthesis, which may make useful lead compounds for the production of new antituberculosis drugs, given the strong dependence of pathogenesis on iron acquisition in M. tuberculosis.
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Affiliation(s)
- Anthony J Harrison
- Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
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40
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Zaitseva J, Lu J, Olechoski KL, Lamb AL. Two crystal structures of the isochorismate pyruvate lyase from Pseudomonas aeruginosa. J Biol Chem 2006; 281:33441-9. [PMID: 16914555 DOI: 10.1074/jbc.m605470200] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Enzymatic systems that exploit pericyclic reaction mechanisms are rare. A recent addition to this class is the enzyme PchB, an 11.4-kDa isochorismate pyruvate lyase from Pseudomonas aeruginosa. The apo and pyruvate-bound structures of PchB reveal that the enzyme is a structural homologue of chorismate mutases in the AroQalpha class despite low sequence identity (20%). The enzyme is an intertwined dimer of three helices with connecting loops, and amino acids from each monomer participate in each of two active sites. The apo structure (2.35 A resolution) has one dimer per asymmetric unit with nitrate bound in an open active site. The loop between the first and second helices is disordered, providing a gateway for substrate entry and product exit. The pyruvate-bound structure (1.95 A resolution) has two dimers per asymmetric unit. One has two open active sites like the apo structure, and the other has two closed active sites with the loop between the first and second helices ordered for catalysis. Determining the structure of PchB is part of a larger effort to elucidate protein structures involved in siderophore biosynthesis, as these enzymes are crucial for bacterial iron uptake and virulence and have been identified as antimicrobial drug targets.
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Affiliation(s)
- Jelena Zaitseva
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
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