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Lux MC, Standke LC, Tan DS. Targeting adenylate-forming enzymes with designed sulfonyladenosine inhibitors. J Antibiot (Tokyo) 2019; 72:325-349. [PMID: 30982830 PMCID: PMC6594144 DOI: 10.1038/s41429-019-0171-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/19/2019] [Accepted: 02/26/2019] [Indexed: 02/07/2023]
Abstract
Adenylate-forming enzymes are a mechanistic superfamily that are involved in diverse biochemical pathways. They catalyze ATP-dependent activation of carboxylic acid substrates as reactive acyl adenylate (acyl-AMP) intermediates and subsequent coupling to various nucleophiles to generate ester, thioester, and amide products. Inspired by natural products, acyl sulfonyladenosines (acyl-AMS) that mimic the tightly bound acyl-AMP reaction intermediates have been developed as potent inhibitors of adenylate-forming enzymes. This simple yet powerful inhibitor design platform has provided a wide range of biological probes as well as several therapeutic lead compounds. Herein, we provide an overview of the nine structural classes of adenylate-forming enzymes and examples of acyl-AMS inhibitors that have been developed for each.
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Affiliation(s)
- Michaelyn C Lux
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Lisa C Standke
- Pharmacology Graduate Program, Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Derek S Tan
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA. .,Pharmacology Graduate Program, Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA. .,Chemical Biology Program, Sloan Kettering Institute, and Tri-Institutional Research Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.
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2
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Abstract
Natural products harbor unique and complex structures that provide valuable antibiotic scaffolds. With an increase in antibiotic resistance, natural products once again hold promise for new antimicrobial therapies, especially those with unique scaffolds that have been overlooked due to a lack of understanding of how they function. Dithiolopyrrolones (DTPs) are an underexplored class of disulfide-containing natural products, which exhibit potent antimicrobial activities against multidrug-resistant pathogens. DTPs were thought to target RNA polymerase, but conflicting observations leave the mechanisms elusive. Using a chemical genomics screen in Escherichia coli, we uncover a mode of action for DTPs-the disruption of metal homeostasis. We show that holomycin, a prototypical DTP, is reductively activated, and reduced holomycin chelates zinc with high affinity. Examination of reduced holomycin against zinc-dependent metalloenzymes revealed that it inhibits E. coli class II fructose bisphosphate aldolase, but not RNA polymerase. Reduced holomycin also strongly inhibits metallo-β-lactamases in vitro, major contributors to clinical carbapenem resistance, by removing active site zinc. These results indicate that holomycin is an intracellular metal-chelating antibiotic that inhibits a subset of metalloenzymes and that RNA polymerase is unlikely to be the primary target. Our work establishes a link between the chemical structures of DTPs and their antimicrobial action; the ene-dithiol group of DTPs enables high-affinity metal binding as a central mechanism to inhibit metabolic processes. Our study also validates the use of chemical genomics in characterizing modes of actions of antibiotics and emphasizes the potential of metal-chelating natural products in antimicrobial therapy.
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Balhara M, Chaudhary R, Ruhil S, Singh B, Dahiya N, Parmar VS, Jaiwal PK, Chhillar AK. Siderophores; iron scavengers: the novel & promising targets for pathogen specific antifungal therapy. Expert Opin Ther Targets 2016; 20:1477-1489. [PMID: 27797604 DOI: 10.1080/14728222.2016.1254196] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
INTRODUCTION The recent emergence of resistance, toxicity paradigm and limited efficacy of conventional antifungal drugs necessitate the identification of de novo targets in fungal metabolism. One of the most critical physiological processes during in vivo pathogenesis is maintenance of iron homeostasis. The most life threatening opportunistic human fungal pathogens like Aspergillus, Candida and Cryptococcus exploit the siderophore mediated iron uptake mechanism either for survival, virulence, propagation or resistance to oxidative stress envisaged in vivo during infection. Areas covered: In this review, we will highlight the metabolic pathways; specifically siderophore biosynthesis, uptake and utilisation, triggered in the fungal pathogens in iron starving conditions and the various putative targets viable in these pathways to be recruited as novel therapeutic antidotes either via biosynthetic enzymes catalytic site inhibitors or as drug conjugates through trojan horse approach and further role in the development of fungal specific reliable diagnostic markers. Expert opinion: Siderophores are the weapons released by a pathogen to conquer the battle for iron acquisition. Hence, the fungal siderophore biosynthetic pathways along with their uptake and utilisation mechanisms represent an ideal target for pathogen specific, host friendly therapeutic strategy which would block the proliferation of parasite without causing any harm to the mammalian host.
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Affiliation(s)
- Meenakshi Balhara
- a Centre for Biotechnology , Maharshi Dayanand University , Rohtak , Haryana , India
| | - Renu Chaudhary
- a Centre for Biotechnology , Maharshi Dayanand University , Rohtak , Haryana , India
| | - Sonam Ruhil
- a Centre for Biotechnology , Maharshi Dayanand University , Rohtak , Haryana , India
| | - Bharat Singh
- a Centre for Biotechnology , Maharshi Dayanand University , Rohtak , Haryana , India
| | - Nisha Dahiya
- b Division of Epidemiology and Communicable Diseases , Indian Council of Medical Research , Delhi , India
| | - Virinder S Parmar
- c Bioorganic Laboratory, Department of Chemistry , University of Delhi , Delhi , India
| | - Pawan K Jaiwal
- a Centre for Biotechnology , Maharshi Dayanand University , Rohtak , Haryana , India
| | - Anil K Chhillar
- a Centre for Biotechnology , Maharshi Dayanand University , Rohtak , Haryana , India
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Design, synthesis, and biological evaluation of α-hydroxyacyl-AMS inhibitors of amino acid adenylation enzymes. Bioorg Med Chem Lett 2016; 26:5340-5345. [PMID: 27692545 DOI: 10.1016/j.bmcl.2016.09.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 09/09/2016] [Indexed: 11/22/2022]
Abstract
Biosynthesis of bacterial natural-product virulence factors is emerging as a promising antibiotic target. Many such natural products are produced by nonribosomal peptide synthetases (NRPS) from amino acid precursors. To develop selective inhibitors of these pathways, we have previously described aminoacyl-AMS (sulfamoyladenosine) macrocycles that inhibit NRPS amino acid adenylation domains but not mechanistically-related aminoacyl-tRNA synthetases. To improve the cell permeability of these inhibitors, we explore herein replacement of the α-amino group with an α-hydroxy group. In both macrocycles and corresponding linear congeners, this leads to decreased biochemical inhibition of the cysteine adenylation domain of the Yersina pestis siderophore synthetase HMWP2, which we attribute to loss of an electrostatic interaction with a conserved active-site aspartate. However, inhibitory activity can be regained by installing a cognate β-thiol moiety in the linear series. This provides a path forward to develop selective, cell-penetrant inhibitors of the biosynthesis of virulence factors to probe their biological functions and potential as therapeutic targets.
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Ishikawa F, Kakeya H. A Competitive Enzyme-Linked Immunosorbent Assay System for Adenylation Domains in Nonribosomal Peptide Synthetases. Chembiochem 2016; 17:474-8. [PMID: 26748933 DOI: 10.1002/cbic.201500553] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Indexed: 12/16/2022]
Abstract
We describe a proof-of-concept study of a competitive enzyme-linked immunosorbent assay (ELISA) system for the adenylation (A) domains of nonribosomal peptide synthetases (NRPSs) with active-site-directed probes coupled to a 5'-O-N-(aminoacyl)sulfamoyladenosine scaffold. A biotin functionality immobilizes the probes onto a streptavidin-coated solid support. Dissociation constants were determined with a series of ligands, including enzyme substrates and a library of sulfamoyloxy-linked aminoacyl/aryl-AMP analogues. As it enables direct readout of protein-ligand interaction, the competitive ELISA technique provided information on comparative structure- activity relationships and insights into the enzyme active-site architecture of NRPS A-domains. These studies indicate that the ELISA technique can accelerate the discovery of small-molecule inhibitors of the A-domains with new scaffolds that perturb the production of NRPS-related virulence factors.
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Affiliation(s)
- Fumihiro Ishikawa
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto, 606-8501, Japan.
| | - Hideaki Kakeya
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto, 606-8501, Japan.
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6
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Konno S, Ishikawa F, Suzuki T, Dohmae N, Burkart MD, Kakeya H. Active site-directed proteomic probes for adenylation domains in nonribosomal peptide synthetases. Chem Commun (Camb) 2015; 51:2262-5. [PMID: 25563804 DOI: 10.1039/c4cc09412c] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We describe a general strategy for selective chemical labeling of individual adenylation (A) domains in nonribosomal peptide synthetases (NRPSs) using active site-directed proteomic probes coupled to the 5'-O-N-(aminoacyl)sulfamoyladenosine (AMS) scaffold with a clickable benzophenone functionality. These proteomic tools can greatly facilitate the molecular identification, functional characterization, and profiling of virtually any kind of A domains of NRPS enzymes in complex biological systems.
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Affiliation(s)
- Sho Konno
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan.
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7
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Ishikawa F, Konno S, Suzuki T, Dohmae N, Kakeya H. Profiling Nonribosomal Peptide Synthetase Activities Using Chemical Proteomic Probes for Adenylation Domains. ACS Chem Biol 2015; 10:1989-97. [PMID: 26038981 DOI: 10.1021/acschembio.5b00097] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Nonribosomal peptide synthetases (NRPSs) and polyketide synthases are large diverse families of biosynthetic enzymes that catalyze the synthesis of natural products that display biologically important activities. Genetic investigations have greatly contributed to our understanding of these biosynthetic enzymes; however, proteomic studies are limited. Here we describe the application of active site-directed proteomic probes for adenylation (A) domains to profile the activity of NRPSs directly in native proteomic environments. Derivatization of a 5'-O-N-(aminoacyl)sulfamoyladenosine appended clickable benzophenone functionality enabled activity-based protein profiling of the A-domains in NRPSs in proteomic extracts. These probes were used to identify natural product producing microorganisms, optimize culture conditions, and profile the activity dynamics of NRPSs. Our proteomic approach offers a simple and versatile method to monitor NRPS expression at the protein level and will facilitate the identification of orphan enzymatic pathways involved in secondary metabolite production.
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Affiliation(s)
- Fumihiro Ishikawa
- Department
of System Chemotherapy and Molecular Sciences, Division of Bioinformatics
and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Sho Konno
- Department
of System Chemotherapy and Molecular Sciences, Division of Bioinformatics
and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Takehiro Suzuki
- Biomolecular
Characterization Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Naoshi Dohmae
- Biomolecular
Characterization Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Hideaki Kakeya
- Department
of System Chemotherapy and Molecular Sciences, Division of Bioinformatics
and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
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8
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Acyl peptidic siderophores: structures, biosyntheses and post-assembly modifications. Biometals 2015; 28:445-59. [PMID: 25677460 DOI: 10.1007/s10534-015-9827-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 01/28/2015] [Indexed: 10/24/2022]
Abstract
Acyl peptidic siderophores are produced by a variety of bacteria and possess unique amphiphilic properties. Amphiphilic siderophores are generally produced in a suite where the iron(III)-binding headgroup remains constant while the fatty acid appendage varies by length and functionality. Acyl peptidic siderophores are commonly synthesized by non-ribosomal peptide synthetases; however, the method of peptide acylation during biosynthesis can vary between siderophores. Following biosynthesis, acyl siderophores can be further modified enzymatically to produce a more hydrophilic compound, which retains its ferric chelating abilities as demonstrated by pyoverdine from Pseudomonas aeruginosa and the marinobactins from certain Marinobacter species. Siderophore hydrophobicity can also be altered through photolysis of the ferric complex of certain β-hydroxyaspartic acid-containing acyl peptidic siderophores.
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9
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Quadri LEN. Biosynthesis of mycobacterial lipids by polyketide synthases and beyond. Crit Rev Biochem Mol Biol 2014; 49:179-211. [DOI: 10.3109/10409238.2014.896859] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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10
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Ahrendt T, Miltenberger M, Haneburger I, Kirchner F, Kronenwerth M, Brachmann AO, Hilbi H, Bode HB. Biosynthesis of the natural fluorophore legioliulin from legionella. Chembiochem 2013; 14:1415-8. [PMID: 23821465 DOI: 10.1002/cbic.201300373] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Indexed: 11/07/2022]
Abstract
Let it shine: The biosynthesis of the UV fluorophore legioliulin (1) from Legionella spp. was elucidated and the phenylalanine ammonium lyase LglD responsible for the formation of the starter unit cinnamic acid was biochemically characterized. Additionally, two novel derivatives differing in the starter unit have been identified by mutasynthesis experiments.
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Affiliation(s)
- Tilman Ahrendt
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
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11
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van der Westhuyzen R, Hammons JC, Meier JL, Dahesh S, Moolman WJA, Pelly SC, Nizet V, Burkart MD, Strauss E. The antibiotic CJ-15,801 is an antimetabolite that hijacks and then inhibits CoA biosynthesis. ACTA ACUST UNITED AC 2012; 19:559-71. [PMID: 22633408 DOI: 10.1016/j.chembiol.2012.03.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 03/13/2012] [Accepted: 03/27/2012] [Indexed: 01/21/2023]
Abstract
The natural product CJ-15,801 is an inhibitor of Staphylococcus aureus, but not other bacteria. Its close structural resemblance to pantothenic acid, the vitamin precursor of coenzyme A (CoA), and its Michael acceptor moiety suggest that it irreversibly inhibits an enzyme involved in CoA biosynthesis or utilization. However, its mode of action and the basis for its specificity have not been elucidated to date. We demonstrate that CJ-15,801 is transformed by the uniquely selective S. aureus pantothenate kinase, the first CoA biosynthetic enzyme, into a substrate for the next enzyme, phosphopantothenoylcysteine synthetase, which is inhibited through formation of a tight-binding structural mimic of its native reaction intermediate. These findings reveal CJ-15,801 as a vitamin biosynthetic pathway antimetabolite with a mechanism similar to that of the sulfonamide antibiotics and highlight CoA biosynthesis as a viable antimicrobial drug target.
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12
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O’Hanlon KA, Margison GP, Hatch A, Fitzpatrick DA, Owens RA, Doyle S, Jones GW. Molecular characterization of an adaptive response to alkylating agents in the opportunistic pathogen Aspergillus fumigatus. Nucleic Acids Res 2012; 40:7806-20. [PMID: 22669901 PMCID: PMC3439912 DOI: 10.1093/nar/gks522] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
An adaptive response to alkylating agents based upon the conformational change of a methylphosphotriester (MPT) DNA repair protein to a transcriptional activator has been demonstrated in a number of bacterial species, but this mechanism appears largely absent from eukaryotes. Here, we demonstrate that the human pathogen Aspergillus fumigatus elicits an adaptive response to sub-lethal doses of the mono-functional alkylating agent N-methyl-N'-nitro-N-nitrosoguanidine (MNNG). We have identified genes that encode MPT and O(6)-alkylguanine DNA alkyltransferase (AGT) DNA repair proteins; deletions of either of these genes abolish the adaptive response and sensitize the organism to MNNG. In vitro DNA repair assays confirm the ability of MPT and AGT to repair methylphosphotriester and O(6)-methylguanine lesions respectively. In eukaryotes, the MPT protein is confined to a select group of fungal species, some of which are major mammalian and plant pathogens. The evolutionary origin of the adaptive response is bacterial and rooted within the Firmicutes phylum. Inter-kingdom horizontal gene transfer between Firmicutes and Ascomycete ancestors introduced the adaptive response into the Fungal kingdom. Our data constitute the first detailed characterization of the molecular mechanism of the adaptive response in a lower eukaryote and has applications for development of novel fungal therapeutics targeting this DNA repair system.
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Affiliation(s)
- Karen A. O’Hanlon
- Biotechnology Laboratory, Department of Biology, National University of Ireland, Maynooth, County Kildare, Ireland, Cancer Research-UK Carcinogenesis Group, Paterson Institute for Cancer Research, University of Manchester, Manchester M20 4BX, UK, Genome Evolution Laboratory and Yeast Genetics Laboratory, Department of Biology, National University of Ireland Maynooth, Maynooth, County Kildare, Ireland
| | - Geoffrey P. Margison
- Biotechnology Laboratory, Department of Biology, National University of Ireland, Maynooth, County Kildare, Ireland, Cancer Research-UK Carcinogenesis Group, Paterson Institute for Cancer Research, University of Manchester, Manchester M20 4BX, UK, Genome Evolution Laboratory and Yeast Genetics Laboratory, Department of Biology, National University of Ireland Maynooth, Maynooth, County Kildare, Ireland
| | - Amy Hatch
- Biotechnology Laboratory, Department of Biology, National University of Ireland, Maynooth, County Kildare, Ireland, Cancer Research-UK Carcinogenesis Group, Paterson Institute for Cancer Research, University of Manchester, Manchester M20 4BX, UK, Genome Evolution Laboratory and Yeast Genetics Laboratory, Department of Biology, National University of Ireland Maynooth, Maynooth, County Kildare, Ireland
| | - David A. Fitzpatrick
- Biotechnology Laboratory, Department of Biology, National University of Ireland, Maynooth, County Kildare, Ireland, Cancer Research-UK Carcinogenesis Group, Paterson Institute for Cancer Research, University of Manchester, Manchester M20 4BX, UK, Genome Evolution Laboratory and Yeast Genetics Laboratory, Department of Biology, National University of Ireland Maynooth, Maynooth, County Kildare, Ireland
| | - Rebecca A. Owens
- Biotechnology Laboratory, Department of Biology, National University of Ireland, Maynooth, County Kildare, Ireland, Cancer Research-UK Carcinogenesis Group, Paterson Institute for Cancer Research, University of Manchester, Manchester M20 4BX, UK, Genome Evolution Laboratory and Yeast Genetics Laboratory, Department of Biology, National University of Ireland Maynooth, Maynooth, County Kildare, Ireland
| | - Sean Doyle
- Biotechnology Laboratory, Department of Biology, National University of Ireland, Maynooth, County Kildare, Ireland, Cancer Research-UK Carcinogenesis Group, Paterson Institute for Cancer Research, University of Manchester, Manchester M20 4BX, UK, Genome Evolution Laboratory and Yeast Genetics Laboratory, Department of Biology, National University of Ireland Maynooth, Maynooth, County Kildare, Ireland
| | - Gary W. Jones
- Biotechnology Laboratory, Department of Biology, National University of Ireland, Maynooth, County Kildare, Ireland, Cancer Research-UK Carcinogenesis Group, Paterson Institute for Cancer Research, University of Manchester, Manchester M20 4BX, UK, Genome Evolution Laboratory and Yeast Genetics Laboratory, Department of Biology, National University of Ireland Maynooth, Maynooth, County Kildare, Ireland
- *To whom correspondence should be addressed. Tel: +353 1 708 3839; Fax: +353 1 708 3845;
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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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14
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Lu X, Zhou R, Sharma I, Li X, Kumar G, Swaminathan S, Tonge PJ, Tan DS. Stable analogues of OSB-AMP: potent inhibitors of MenE, the o-succinylbenzoate-CoA synthetase from bacterial menaquinone biosynthesis. Chembiochem 2011; 13:129-36. [PMID: 22109989 DOI: 10.1002/cbic.201100585] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Indexed: 12/15/2022]
Abstract
MenE, the o-succinylbenzoate (OSB)-CoA synthetase from bacterial menaquinone biosynthesis, is a promising new antibacterial target. Sulfonyladenosine analogues of the cognate reaction intermediate, OSB-AMP, have been developed as inhibitors of the MenE enzymes from Mycobacterium tuberculosis (mtMenE), Staphylococcus aureus (saMenE) and Escherichia coli (ecMenE). Both a free carboxylate and a ketone moiety on the OSB side chain are required for potent inhibitory activity. OSB-AMS (4) is a competitive inhibitor of mtMenE with respect to ATP (K(i) =5.4±0.1 nM) and a noncompetitive inhibitor with respect to OSB (K(i) =11.2±0.9 nM). These data are consistent with a Bi Uni Uni Bi Ping-Pong kinetic mechanism for these enzymes. In addition, OSB-AMS inhibits saMenE with K(i)(app) =22±8 nM and ecMenE with K(i)(OSB) =128±5 nM. Putative active-site residues, Arg222, which may interact with the OSB aromatic carboxylate, and Ser302, which may bind the OSB ketone oxygen, have been identified through computational docking of OSB-AMP with the unliganded crystal structure of saMenE. A pH-dependent interconversion of the free keto acid and lactol forms of the inhibitors is also described, along with implications for inhibitor design.
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Affiliation(s)
- Xuequan Lu
- Molecular Pharmacology and Chemistry Program and Tri-Institutional Research Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
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16
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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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17
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18
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Payne RJ, Bulloch EMM, Kerbarh O, Abell C. Inhibition of chorismate-utilising enzymes by 2-amino-4-carboxypyridine and 4-carboxypyridone and 5-carboxypyridone analogues. Org Biomol Chem 2010; 8:3534-42. [PMID: 20532401 DOI: 10.1039/c004062b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Several 2-amino-4-carboxypyridine, 4- and 5-carboxypyridone-based compounds were prepared and tested against three members of the chorismate-utilising enzyme family, anthranilate synthase, isochorismate synthase and salicylate synthase. Most compounds exhibited low micromolar inhibition of these three enzymes. The most potent inhibitor was a 4-carboxypyridone analogue bearing a lactate side chain on the pyridyl nitrogen which exhibited inhibition constants of 5, 91 and 54 muM against anthranilate synthase, isochorismate synthase and salicylate synthase respectively.
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Affiliation(s)
- Richard J Payne
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UKCB2 1EW.
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Lu X, Olsen SK, Capili AD, Cisar JS, Lima CD, Tan DS. Designed semisynthetic protein inhibitors of Ub/Ubl E1 activating enzymes. J Am Chem Soc 2010; 132:1748-9. [PMID: 20099854 DOI: 10.1021/ja9088549] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Semisynthetic, mechanism-based protein inhibitors of ubiquitin (Ub) and ubiquitin-like modifier (Ubl) activating enzymes (E1s) have been developed to target E1-catalyzed adenylation and thioesterification of the Ub/Ubl C-terminus during the processes of protein SUMOylation and ubiquitination. The inhibitors were generated by intein-mediated expressed protein ligation using a truncated Ub/Ubl protein (SUMO residues 1-94; Ub residues 1-71) with a C-terminal thioester and synthetic tripeptides having a C-terminal adenosine analogue and an N-terminal cysteine residue. SUMO-AMSN (4a) and Ub-AMSN (4b) contain a sulfamide group as a nonhydrolyzable mimic of the phosphate group in the cognate Ub/Ubl-AMP adenylate intermediate in the first half-reaction, and these constructs selectively inhibit SUMO E1 and Ub E1, respectively, in a dose-dependent manner. SUMO-AVSN (5a) and Ub-AVSN (5b) contain an electrophilic vinyl sulfonamide designed to trap the incoming E1 cysteine nucleophile (Uba2 Cys173 in SUMO E1; Uba1 Cys593 in Ub E1) in the second half-reaction, and these constructs selectively, covalently, and stably cross-link to SUMO E1 and Ub E1, respectively, in a cysteine nucleophile-dependent manner. These inhibitors are powerful tools to probe outstanding mechanistic questions in E1 function and can also be used to study the biological functions of E1 enzymes.
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Affiliation(s)
- Xuequan Lu
- Molecular Pharmacology and Chemistry Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, Box 422, New York, New York 10065, USA
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20
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Meier JL, Niessen S, Hoover HS, Foley TL, Cravatt BF, Burkart MD. An orthogonal active site identification system (OASIS) for proteomic profiling of natural product biosynthesis. ACS Chem Biol 2009; 4:948-57. [PMID: 19785476 DOI: 10.1021/cb9002128] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
A significant gap exists between genetics-based investigations of polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) biosynthetic pathways and our understanding of their regulation, interaction, and activity in living systems. To help bridge this gap, here we present an orthogonal active site identification system (OASIS) for the proteomic identification and analysis of PKS/NRPS biosynthetic enzymes. OASIS probes target conserved features of PKS/NRPS active sites to provide activity-based enrichment of modular synthases, followed by analysis through multidimensional protein identification technology (MudPIT) LC-MS/MS analysis. When applied to the model bacterium Bacillus subtilis, this functional proteomics method detects and quantifies all four modular synthases in the organism. Furthermore, tandem application of multiple OASIS probes enhances identification of specific PKS/NRPS modules from complex proteomic mixtures. By expanding the dynamic range of proteomic analysis for PKS/NRPS enzymes, OASIS offers a valuable tool for strain comparison, culture condition optimization, and enzyme discovery.
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Affiliation(s)
- Jordan L. Meier
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92037-0358
| | - Sherry Niessen
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Center for Physiological Proteomics, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Heather S. Hoover
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Center for Physiological Proteomics, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Timothy L. Foley
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92037-0358
| | - Benjamin F. Cravatt
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Center for Physiological Proteomics, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92037-0358
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Meier JL, Burkart MD. The chemical biology of modular biosynthetic enzymes. Chem Soc Rev 2009; 38:2012-45. [DOI: 10.1039/b805115c] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Lu X, Zhang H, Tonge PJ, Tan DS. Mechanism-based inhibitors of MenE, an acyl-CoA synthetase involved in bacterial menaquinone biosynthesis. Bioorg Med Chem Lett 2008; 18:5963-6. [PMID: 18762421 PMCID: PMC2628629 DOI: 10.1016/j.bmcl.2008.07.130] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2008] [Revised: 07/28/2008] [Accepted: 07/29/2008] [Indexed: 11/22/2022]
Abstract
Menaquinone (vitamin K(2)) is an essential component of the electron transfer chain in many pathogens, including Mycobacterium tuberculosis and Staphylococcus aureus, and menaquinone biosynthesis is a potential target for antibiotic drug discovery. We report herein a series of mechanism-based inhibitors of MenE, an acyl-CoA synthetase that catalyzes adenylation and thioesterification of o-succinylbenzoic acid (OSB) during menaquinone biosynthesis. The most potent compound inhibits MenE with an IC(50) value of 5.7microM.
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Affiliation(s)
- Xuequan Lu
- Molecular Pharmacology & Chemistry Program and Tri-Institutional Research Program, Memorial Sloan–Kettering Cancer Center, New York, NY 10065, USA
| | - Huaning Zhang
- Institute of Chemical Biology & Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, NY 11794, USA
| | - Peter J. Tonge
- Institute of Chemical Biology & Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, NY 11794, USA
| | - Derek S. Tan
- Molecular Pharmacology & Chemistry Program and Tri-Institutional Research Program, Memorial Sloan–Kettering Cancer Center, New York, NY 10065, USA
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