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Jaroensuk J, Chuaboon L, Kesornpun C, Chaiyen P. Enzymes in riboflavin biosynthesis: Potential antibiotic drug targets. Arch Biochem Biophys 2023; 748:109762. [PMID: 37739114 DOI: 10.1016/j.abb.2023.109762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 09/13/2023] [Accepted: 09/19/2023] [Indexed: 09/24/2023]
Abstract
The rapid resistance of pathogens to antibiotics has emerged as a major threat to global health. Identification of new antibiotic targets is thus needed for developing alternative drugs. Genes encoding enzymes involved in the biosynthesis of riboflavin and flavin cofactors (FMN/FAD) are attractive targets because these enzymatic reactions are necessary for most bacteria to synthesize flavin cofactors for use in their central metabolic reactions. Moreover, humans lack most of these enzymes because we uptake riboflavin from our diet. This review discusses the current knowledge of enzymes involved in bacterial biosynthesis of riboflavin and other flavin cofactors, as well as the functions of the FMN riboswitch. Here, we highlight recent progress in the structural and mechanistic characterization, and inhibition of GTP cyclohydrolase II (GCH II), lumazine synthase (LS), riboflavin synthase (RFS), FAD synthetase (FADS), and FMN riboswitch, which have been identified as plausible antibiotic targets. As the structures and functions of these enzymes and regulatory systems are not completely understood, they are attractive as subjects for future in-depth biochemical and biophysical analysis.
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Affiliation(s)
- Juthamas Jaroensuk
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Wangchan, Rayong, 21210, Thailand
| | - Litavadee Chuaboon
- School of Pharmacy and Biomass and Oil Palm Center of Excellence, Walailak University, Nakhon Si Thammarat, 80160, Thailand
| | - Chatchai Kesornpun
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Wangchan, Rayong, 21210, Thailand
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Wangchan, Rayong, 21210, Thailand.
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2
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Islam Z, Kumar P. Inhibitors of riboflavin biosynthetic pathway enzymes as potential antibacterial drugs. Front Mol Biosci 2023; 10:1228763. [PMID: 37496776 PMCID: PMC10366380 DOI: 10.3389/fmolb.2023.1228763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 07/03/2023] [Indexed: 07/28/2023] Open
Abstract
Multiple drug resistance is the main obstacle in the treatment of bacterial diseases. Resistance against antibiotics demands the exploration of new antimicrobial drug targets. A variety of in silico and genetic approaches show that the enzymes of the riboflavin biosynthetic pathway are crucial for the survival of bacteria. This pathway is absent in humans thus enzymes of the riboflavin biosynthetic pathway are emerging drug targets for resistant pathogenic bacterial strains. Exploring the structural details, their mechanism of action, intermediate elucidation, and interaction analysis would help in designing suitable inhibitors of these enzymes. The riboflavin biosynthetic pathway consists of seven distinct enzymes, namely, 3,4-dihydroxy-2-butanone 4-phosphate synthase, GTP cyclohydrolase II, pyrimidine deaminase/reductase, phosphatase, lumazine synthase, and riboflavin synthase. The present review summarizes the research work that has been carried out on these enzymes in terms of their structures, active site architectures, and molecular mechanism of catalysis. This review also walks through small molecule inhibitors that have been developed against several of these enzymes.
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Affiliation(s)
- Zeyaul Islam
- Qatar Biomedical Research Institute (QBRI), Qatar Foundation, Hamad Bin Khalifa University, Doha, Qatar
| | - Pankaj Kumar
- Department of Biochemistry, Jamia Hamdard, New Delhi, India
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3
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A research on structural vibrational, surface characterization of 2-methyl-3-{5-methyl-[1,2,4]triazolo[1,5-a]pyrimidin-7-yl}-4H-pyrido[1,2-a]pyrimidin-4-one hydrate: SCXRD, FT-IR, MEP, Hirshfeld and molecular docking studies. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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4
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Zangouei M, Esmaeili AA. One-pot, catalyst-free synthesis of novel spiro[indole-3,4′-pyrano[2′,3′:4,5]pyrimido [2,1-b][1,3]benzothiazole] derivatives. JOURNAL OF CHEMICAL RESEARCH 2020. [DOI: 10.1177/1747519820916926] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The present report describes one-pot three-component condensation of isatins, malononitrile, and 2-hydroxy-4 H-pyrimido[2,1- b][1,3]benzothiazol-4-one in water–ethanol mixture at reflux to develop an efficient one-pot protocol for the synthesis of novel spiro[indole-3,4′-pyrano[2′,3′:4,5]pyrimido[2,1- b][1,3]benzothiazole] derivatives. The significant features of this protocol are short reaction times, avoidance of toxic catalysts, and provision of excellent yields, no column chromatographic purification, and use of ethanol-water as an environmentally benign solvent. The molecular structure of 4a has been supported by single-crystal X-ray diffraction.
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Affiliation(s)
- Mahdieh Zangouei
- Department of Chemistry, Faculty of Sciences, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Abbas Ali Esmaeili
- Department of Chemistry, Faculty of Sciences, Ferdowsi University of Mashhad, Mashhad, Iran
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5
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Serer MI, Carrica MDC, Trappe J, López Romero S, Bonomi HR, Klinke S, Cerutti ML, Goldbaum FA. A high-throughput screening for inhibitors of riboflavin synthase identifies novel antimicrobial compounds to treat brucellosis. FEBS J 2019; 286:2522-2535. [PMID: 30927485 DOI: 10.1111/febs.14829] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/26/2019] [Accepted: 03/29/2019] [Indexed: 10/27/2022]
Abstract
Brucella spp. are pathogenic intracellular Gram-negative bacteria adapted to life within cells of several mammals, including humans. These bacteria are the causative agent of brucellosis, one of the zoonotic infections with the highest incidence in the world and for which a human vaccine is still unavailable. Current therapeutic treatments against brucellosis are based on the combination of two or more antibiotics for prolonged periods, which may lead to antibiotic resistance in the population. Riboflavin (vitamin B2) is biosynthesized by microorganisms and plants but mammals, including humans, must obtain it from dietary sources. Owing to the absence of the riboflavin biosynthetic enzymes in animals, this pathway is nowadays regarded as a rich resource of targets for the development of new antimicrobial agents. In this work, we describe a high-throughput screening approach to identify inhibitors of the enzymatic activity of riboflavin synthase, the last enzyme in this pathway. We also provide evidence for their subsequent validation as potential drug candidates in an in vitro brucellosis infection model. From an initial set of 44 000 highly diverse low molecular weight compounds with drug-like properties, we were able to identify ten molecules with 50% inhibitory concentrations in the low micromolar range. Further Brucella culture and intramacrophagic replication experiments showed that the most effective bactericidal compounds share a 2-Phenylamidazo[2,1-b][1,3]benzothiazole chemical scaffold. Altogether, these findings set up the basis for the subsequent lead optimization process and represent a promising advancement in the pursuit of novel and effective antimicrobial compounds against brucellosis.
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Affiliation(s)
- María Inés Serer
- Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina
| | | | - Jörg Trappe
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | | | - Sebastián Klinke
- Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina.,Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Buenos Aires, Argentina
| | - María Laura Cerutti
- Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina.,Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Buenos Aires, Argentina
| | - Fernando Alberto Goldbaum
- Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina.,Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Buenos Aires, Argentina
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6
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Kundu B, Sarkar D, Ray N, Talukdar A. Understanding the riboflavin biosynthesis pathway for the development of antimicrobial agents. Med Res Rev 2019; 39:1338-1371. [PMID: 30927319 DOI: 10.1002/med.21576] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 02/14/2019] [Accepted: 03/08/2019] [Indexed: 12/13/2022]
Abstract
Life on earth depends on the biosynthesis of riboflavin, which plays a vital role in biological electron transport processes. Higher mammals obtain riboflavin from dietary sources; however, various microorganisms, including Gram-negative pathogenic bacteria and yeast, lack an efficient riboflavin-uptake system and are dependent on endogenous riboflavin biosynthesis. Consequently, the inhibition of enzymes in the riboflavin biosynthesis pathway would allow selective toxicity to a pathogen and not the host. Thus, the riboflavin biosynthesis pathway is an attractive target for designing novel antimicrobial drugs, which are urgently needed to address the issue of multidrug resistance seen in various pathogens. The enzymes involved in riboflavin biosynthesis are lumazine synthase (LS) and riboflavin synthase (RS). Understanding the details of the mechanisms of the enzyme-catalyzed reactions and the structural changes that occur in the enzyme active sites during catalysis can facilitate the design and synthesis of suitable analogs that can specifically inhibit the relevant enzymes and stop the generation of riboflavin in pathogenic bacteria. The present review is the first compilation of the work that has been carried out over the last 25 years focusing on the design of inhibitors of the biosynthesis of riboflavin based on an understanding of the mechanisms of LS and RS. This review aimed to address the fundamental advances in our understanding of riboflavin biosynthesis as applied to the rational design of a novel class of inhibitors. These advances have been aided by X-ray structures of ligand-enzyme complexes, rotational-echo, double-resonance nuclear magnetic resonance spectroscopy, high-throughput screening, virtual screenings, and various mechanistic probes.
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Affiliation(s)
- Biswajit Kundu
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Dipayan Sarkar
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research, Kolkata, India
| | - Namrata Ray
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, Kolkata, India.,Department of Chemistry, Adamas University, Kolkata, India
| | - Arindam Talukdar
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research, Kolkata, India
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Wei Y, Kumar P, Wahome N, Mantis NJ, Middaugh CR. Biomedical Applications of Lumazine Synthase. J Pharm Sci 2018; 107:2283-2296. [DOI: 10.1016/j.xphs.2018.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 05/02/2018] [Accepted: 05/02/2018] [Indexed: 10/16/2022]
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8
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Wei Y, Wahome N, Kumar P, Whitaker N, Picking WL, Middaugh CR. Effect of Phosphate Ion on the Structure of Lumazine Synthase, an Antigen Presentation System From Bacillus anthracis. J Pharm Sci 2017; 107:814-823. [PMID: 29045884 DOI: 10.1016/j.xphs.2017.10.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 10/06/2017] [Accepted: 10/09/2017] [Indexed: 12/20/2022]
Abstract
Lumazine synthase (LS) is an oligomeric enzyme involved in the biosynthesis of riboflavin in microorganisms, fungi, and plants. LS has become of significant interest to biomedical science because of its critical biological role and attractive structural properties for antigen presentation in vaccines. LS derived from Bacillus anthracis (BaLS) consists of 60 identical subunits forming an icosahedron. Its crystal structure has been solved, but its dynamic conformational properties have not yet been studied. We investigated the conformation of BaLS in response to different stress conditions (e.g., chemical denaturants, pH, and temperature) using a variety of biophysical techniques. The physical basis for these thermal transitions was studied, indicating that a molten globular state was present during chemical unfolding by guanidine HCl. In addition, BaLS showed 2 distinct thermal transitions in phosphate-containing buffers. The first transition was due to the dissociation of phosphate ions from BaLS and the second one came from the dissociation and conformational alteration of its icosahedral structure. A small conformational alteration was induced by the binding/dissociation of phosphate ions to BaLS. This work provides a closer view of the conformational behavior of BaLS and provides important information for the formulation of vaccines which use this protein.
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Affiliation(s)
- Yangjie Wei
- Macromolecule and Vaccine Stabilization Center, Department of Pharmaceutical Chemistry, University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047; Department of Pharmaceutical Chemistry, University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047
| | - Newton Wahome
- Macromolecule and Vaccine Stabilization Center, Department of Pharmaceutical Chemistry, University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047; Department of Pharmaceutical Chemistry, University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047
| | - Prashant Kumar
- Macromolecule and Vaccine Stabilization Center, Department of Pharmaceutical Chemistry, University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047; Department of Pharmaceutical Chemistry, University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047
| | - Neal Whitaker
- Macromolecule and Vaccine Stabilization Center, Department of Pharmaceutical Chemistry, University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047; Department of Pharmaceutical Chemistry, University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047
| | - Wendy L Picking
- Department of Pharmaceutical Chemistry, University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047
| | - C Russell Middaugh
- Macromolecule and Vaccine Stabilization Center, Department of Pharmaceutical Chemistry, University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047; Department of Pharmaceutical Chemistry, University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047.
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9
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One-pot three component isocyanide-based reaction: Synthesis of novel tetracyclic fused furo[2′,3′:4,5]pyrimido[2,1- b ][1,3]benzothiazole. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.03.082] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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10
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Shinde VV, Jeong YT. Organic-base-catalyzed diversity-oriented synthesis of novel pyrimido[1,2-b]indazole-3-carbonitrile. Tetrahedron 2016. [DOI: 10.1016/j.tet.2016.06.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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11
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Chandrashaker V, Ptaszek M, Taniguchi M, Lindsey JS. Synthesis of diverse acyclic precursors to pyrroles for studies of prebiotic routes to tetrapyrrole macrocycles. NEW J CHEM 2016. [DOI: 10.1039/c6nj02048h] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Some 50 ketones, β-diketones, β-ketoesters and α-aminoketones have been prepared for studies of the formation of trisubstituted pyrroles equipped for self-condensation leading to tetrapyrrole macrocycles.
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Affiliation(s)
| | - Marcin Ptaszek
- Department of Chemistry
- North Carolina State University
- Raleigh
- USA
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12
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Hemdan MM, Abd El-Mawgoude HK. Uses of 1-(3-Cyano-4,5,6,7-tetrahydrobenzo[ b]-thiophen-2-yl)-3-dodecanoylthiourea as a Building Block in the Synthesis of Fused Pyrimidine and Thiazine Systems. Chem Pharm Bull (Tokyo) 2015; 63:450-6. [DOI: 10.1248/cpb.c15-00047] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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13
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Haase I, Gräwert T, Illarionov B, Bacher A, Fischer M. Recent advances in riboflavin biosynthesis. Methods Mol Biol 2014; 1146:15-40. [PMID: 24764086 DOI: 10.1007/978-1-4939-0452-5_2] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Riboflavin is biosynthesized from GTP and ribulose 5-phosphate. Whereas the early reactions conducing to 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione 5'-phosphate show significant taxonomic variation, the subsequent reaction steps are universal in all taxonomic kingdoms. With the exception of a hitherto elusive phosphatase, all enzymes of the pathway have been characterized in some detail at the structural and mechanistic level. Some of the pathway enzymes (GTP cycloyhdrolase II, 3,4-dihydroxy-2-butanone 4-phosphate synthase, riboflavin synthase) have exceptionally complex reaction mechanisms. The commercial production of the vitamin is now entirely based on highly productive fermentation processes. Due to their absence in animals, the pathway enzymes are potential targets for the development of novel anti-infective drugs.
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Affiliation(s)
- Ilka Haase
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146, Hamburg, Germany
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14
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Aly AA, Ishak EA, Ramadan M, Germoush MO, El-Emary TI, Al-Muaikel NS. Recent Report on Thieno[2,3-d]pyrimidines. Their Preparation Including Microwave and Their Utilities in Fused Heterocycles Synthesis. J Heterocycl Chem 2013. [DOI: 10.1002/jhet.1118] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
| | | | - Mohamed Ramadan
- Department of Organic Chemistry, Faculty of Pharmacy; Al-Azhar University; Assuit; Egypt
| | - Mousa O. Germoush
- Biology Department, College of Science; Al-Jouf University; Sakaka; Kingdom of Saudi Arabia
| | - Talaat I. El-Emary
- Department of Chemistry, Faculty of Science; Assiut University; Assiut; Egypt
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15
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Thermally-induced ring contraction as a novel and straightforward route for the synthesis of 2-furyl acetonitrile derivatives. Tetrahedron Lett 2013. [DOI: 10.1016/j.tetlet.2013.03.033] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Ladenstein R, Fischer M, Bacher A. The lumazine synthase/riboflavin synthase complex: shapes and functions of a highly variable enzyme system. FEBS J 2013; 280:2537-63. [PMID: 23551830 DOI: 10.1111/febs.12255] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 03/01/2013] [Accepted: 03/04/2013] [Indexed: 11/30/2022]
Abstract
The xylene ring of riboflavin (vitamin B2 ) is assembled from two molecules of 3,4-dihydroxy-2-butanone 4-phosphate by a mechanistically complex process that is jointly catalyzed by lumazine synthase and riboflavin synthase. In Bacillaceae, these enzymes form a structurally unique complex comprising an icosahedral shell of 60 lumazine synthase subunits and a core of three riboflavin synthase subunits, whereas many other bacteria have empty lumazine synthase capsids, fungi, Archaea and some eubacteria have pentameric lumazine synthases, and the riboflavin synthases of Archaea are paralogs of lumazine synthase. The structures of the molecular ensembles have been studied in considerable detail by X-ray crystallography, X-ray small-angle scattering and electron microscopy. However, certain mechanistic aspects remain unknown. Surprisingly, the quaternary structure of the icosahedral β subunit capsids undergoes drastic changes, resulting in formation of large, quasi-spherical capsids; this process is modulated by sequence mutations. The occurrence of large shells consisting of 180 or more lumazine synthase subunits has recently generated interest for protein engineering topics, particularly the construction of encapsulation systems.
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Affiliation(s)
- Rudolf Ladenstein
- Department of Bioscience and Nutrition, Karolinska Institutet NOVUM, SE-14183 Huddinge, Sweden.
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17
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Talukdar A, Zhao Y, Lv W, Bacher A, Illarionov B, Fischer M, Cushman M. O-Nucleoside, S-nucleoside, and N-nucleoside probes of lumazine synthase and riboflavin synthase. J Org Chem 2012; 77:6239-61. [PMID: 22780198 PMCID: PMC3444172 DOI: 10.1021/jo3010364] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Lumazine synthase catalyzes the penultimate step in the biosynthesis of riboflavin, while riboflavin synthase catalyzes the last step. O-Nucleoside, S-nucleoside, and N-nucleoside analogues of hypothetical lumazine biosynthetic intermediates have been synthesized in order to obtain structure and mechanism probes of these two enzymes, as well as inhibitors of potential value as antibiotics. Methods were devised for the selective cleavage of benzyl protecting groups in the presence of other easily reduced functionality by controlled hydrogenolysis over Lindlar catalyst. The deprotection reaction was performed in the presence of other reactive functionality including nitro groups, alkenes, and halogens. The target compounds were tested as inhibitors of lumazine synthase and riboflavin synthase obtained from a variety of microorganisms. In general, the S-nucleosides and N-nucleosides were more potent than the corresponding O-nucleosides as lumazine synthase and riboflavin synthase inhibitors, while the C-nucleosides were the least potent. A series of molecular dynamics simulations followed by free energy calculations using the Poisson-Boltzmann/surface area (MM-PBSA) method were carried out in order to rationalize the results of ligand binding to lumazine synthase, and the results provide insight into the dynamics of ligand binding as well as the molecular forces stabilizing the intermediates in the enzyme-catalyzed reaction.
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Affiliation(s)
- Arindam Talukdar
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, and The Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Yujie Zhao
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, and The Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Wei Lv
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, and The Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Adelbert Bacher
- Institute of Biochemistry and Food Chemistry, Food Chemistry Division, University of Hamburg, D-20146 Hamburg, Germany
| | - Boris Illarionov
- Institute of Biochemistry and Food Chemistry, Food Chemistry Division, University of Hamburg, D-20146 Hamburg, Germany
| | - Markus Fischer
- Institute of Biochemistry and Food Chemistry, Food Chemistry Division, University of Hamburg, D-20146 Hamburg, Germany
| | - Mark Cushman
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, and The Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana, 47907, USA
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Jiang X, Chu L, Qing FL. Copper-mediated oxidative cross-coupling reaction of terminal alkynes with α-silyldifluoromethylphosphonates: an efficient method for α,α-difluoropropargylphosphonates. Org Lett 2012; 14:2870-3. [PMID: 22587619 DOI: 10.1021/ol301113v] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A copper-mediated oxidative cross-coupling reaction of terminal alkynes with readily available α-silyldifluoromethylphosphonates under mild conditions has been developed. This method allows for an efficient synthesis of a series of synthetically useful α,α-difluoropropargylphosphonates with excellent functional group compatibility.
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Affiliation(s)
- Xueliang Jiang
- Key Laboratory of Organofluorine Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Lu, Shanghai 200032, China
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Zhang Y, Zhong H, Wang T, Geng D, Zhang M, Li K. Synthesis of novel 2, 5-dihydrofuran derivatives and evaluation of their anticancer activity. Eur J Med Chem 2012; 48:69-80. [DOI: 10.1016/j.ejmech.2011.11.036] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2011] [Revised: 11/19/2011] [Accepted: 11/23/2011] [Indexed: 10/14/2022]
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20
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Abstract
The biosynthesis of riboflavin requires 1 equivalent of GTP and 2 equivalents of ribulose phosphate. The first committed reactions of the convergent pathway are catalyzed by GTP hydrolase II and 3,4-dihydroxy-2-butanone 4-phosphate synthase. The initial reaction steps afford 5-amino-6-ribitylaminopyrimidine 5'-phosphate, which needs to be dephosphorylated by a hitherto elusive hydrolase. The dephosphorylated pyrimidine is condensed with the carbohydrate precursor, 3,4-dihydroxy-2-butanone 4-phosphate. The resulting 6,7-dimethyl-8-ribityllumazine affords riboflavin by a mechanistically unique dismutation, i.e., by formation of a pentacyclic dimer that is subsequently fragmented.
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Morgunova E, Illarionov B, Saller S, Popov A, Sambaiah T, Bacher A, Cushman M, Fischer M, Ladenstein R. Structural study and thermodynamic characterization of inhibitor binding to lumazine synthase from Bacillus anthracis. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:1001-11. [PMID: 20823551 PMCID: PMC2935281 DOI: 10.1107/s0907444910029690] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2010] [Accepted: 07/26/2010] [Indexed: 11/10/2022]
Abstract
The crystal structure of lumazine synthase from Bacillus anthracis was solved by molecular replacement and refined to R(cryst) = 23.7% (R(free) = 28.4%) at a resolution of 3.5 A. The structure reveals the icosahedral symmetry of the enzyme and specific features of the active site that are unique in comparison with previously determined orthologues. The application of isothermal titration calorimetry in combination with enzyme kinetics showed that three designed pyrimidine derivatives bind to lumazine synthase with micromolar dissociation constants and competitively inhibit the catalytic reaction. Structure-based modelling suggested the binding modes of the inhibitors in the active site and allowed an estimation of the possible contacts formed upon binding. The results provide a structural framework for the design of antibiotics active against B. anthracis.
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Affiliation(s)
- Ekaterina Morgunova
- Karolinska Institutet NOVUM, Center of Structural Biochemistry, Hälsovägen 7–9, 141 57 Huddinge, Sweden
| | - Boris Illarionov
- Institut für Lebensmittelchemie, Universität Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Sabine Saller
- Institut für Lebensmittelchemie, Universität Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Aleksander Popov
- European Synchrotron Radiation Facility, BP 220, F-38043 Grenoble CEDEX 09, France
| | - Thota Sambaiah
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, USA
| | - Adelbert Bacher
- Chemistry Department, Technical University of Munich, 85747 Garching, Germany
| | - Mark Cushman
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, USA
| | - Markus Fischer
- Institut für Lebensmittelchemie, Universität Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Rudolf Ladenstein
- Karolinska Institutet NOVUM, Center of Structural Biochemistry, Hälsovägen 7–9, 141 57 Huddinge, Sweden
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Talukdar A, Morgunova E, Duan J, Meining W, Foloppe N, Nilsson L, Bacher A, Illarionov B, Fischer M, Ladenstein R, Cushman M. Virtual screening, selection and development of a benzindolone structural scaffold for inhibition of lumazine synthase. Bioorg Med Chem 2010; 18:3518-34. [PMID: 20430628 PMCID: PMC2868945 DOI: 10.1016/j.bmc.2010.03.072] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2010] [Revised: 03/24/2010] [Accepted: 03/25/2010] [Indexed: 10/19/2022]
Abstract
Virtual screening of a library of commercially available compounds versus the structure of Mycobacterium tuberculosis lumazine synthase identified 2-(2-oxo-1,2-dihydrobenzo[cd]indole-6-sulfonamido)acetic acid (9) as a possible lead compound. Compound 9 proved to be an effective inhibitor of M. tuberculosis lumazine synthase with a K(i) of 70microM. Lead optimization through replacement of the carboxymethylsulfonamide sidechain with sulfonamides substituted with alkyl phosphates led to a four-carbon phosphate 38 that displayed a moderate increase in enzyme inhibitory activity (K(i) 38microM). Molecular modeling based on known lumazine synthase/inhibitor crystal structures suggests that the main forces stabilizing the present benzindolone/enzyme complexes involve pi-pi stacking interactions with Trp27 and hydrogen bonding of the phosphates with Arg128, the backbone nitrogens of Gly85 and Gln86, and the side chain hydroxyl of Thr87.
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Affiliation(s)
- Arindam Talukdar
- Department of Medicinal Chemistry and Molecular Pharmacology, School of Pharmacy and Pharmaceutical Sciences, and The Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Ekaterina Morgunova
- Karolinska Institute, Department of Bioscience, Hälsovägen 7-9, S-14157 Huddinge, Sweden
| | - Jianxin Duan
- Anterio Consult & Research GmbH, Augustaanlage 23, 68165 Mannheim, Germany
| | - Winfried Meining
- Lehrstuhl für Biologische Chemie, Technische Universität München, 85350 Freising-Weihenstephan, Germany
| | - Nicolas Foloppe
- Karolinska Institute, Department of Bioscience, Hälsovägen 7-9, S-14157 Huddinge, Sweden
| | - Lennart Nilsson
- Karolinska Institute, Department of Bioscience, Hälsovägen 7-9, S-14157 Huddinge, Sweden
| | - Adelbert Bacher
- Institute of Biochemistry and Food Chemistry, Food Chemistry Division, University of Hamburg, Grindelallee 117, D-20146 Hamburg, Germany
| | - Boris Illarionov
- Institute of Biochemistry and Food Chemistry, Food Chemistry Division, University of Hamburg, Grindelallee 117, D-20146 Hamburg, Germany
| | - Markus Fischer
- Institute of Biochemistry and Food Chemistry, Food Chemistry Division, University of Hamburg, Grindelallee 117, D-20146 Hamburg, Germany
| | - Rudolf Ladenstein
- Karolinska Institute, Department of Bioscience, Hälsovägen 7-9, S-14157 Huddinge, Sweden
| | - Mark Cushman
- Department of Medicinal Chemistry and Molecular Pharmacology, School of Pharmacy and Pharmaceutical Sciences, and The Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana, 47907, USA
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23
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Long Q, Ji L, Wang H, Xie J. Riboflavin Biosynthetic and Regulatory Factors as Potential Novel Anti-Infective Drug Targets. Chem Biol Drug Des 2010; 75:339-47. [DOI: 10.1111/j.1747-0285.2010.00946.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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24
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Sun HL, Wang TT, Lv ZL, Feng JL, Geng DP, Li YM, Li K. Synthesis, chiral resolution, and determination of novel furan lignan derivatives with potent anti-tumor activity. Bioorg Med Chem Lett 2010; 20:1961-4. [DOI: 10.1016/j.bmcl.2010.01.122] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2009] [Revised: 01/18/2010] [Accepted: 01/22/2010] [Indexed: 11/27/2022]
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25
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Ameen MA, Karsten S, Liebscher J. A convenient method for constructing novel tetrahydropyrido[4′,3′:4,5]thieno[2,3-d]-pyrimidinones-carbohydrate and amino acid conjugates via copper(I)-catalyzed alkyne-azide ‘Click Chemistry’. Tetrahedron 2010. [DOI: 10.1016/j.tet.2010.01.071] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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26
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Discovery and development of the covalent hydrates of trifluoromethylated pyrazoles as riboflavin synthase inhibitors with antibiotic activity against Mycobacterium tuberculosis. J Org Chem 2009; 74:5297-303. [PMID: 19545132 DOI: 10.1021/jo900768c] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A high-throughput screening (HTS) hit compound displayed moderate inhibition of Mycobacterium tuberculosis and Escherichia coli riboflavin synthases. The structure of the hit compound provided by the commercial vendor was reassigned as [3-(4-chlorophenyl)-5-hydroxy-5-(trifluoromethyl)-4,5-dihydro-1H-pyrazol-1-yl](o-tolyl)methanone (18). The hit compound had a k(is) of 8.7 microM vs. M. tuberculosis riboflavin synthase and moderate antibiotic activity against both M. tuberculosis replicating phenotype and nonreplicating persistent phenotype. Molecular modeling studies suggest that two inhibitor molecules bind in the active site of the enzyme, and that the binding is stabilized by stacking between the benzene rings of two adjacent ligands. The most potent antibiotic in the series proved to be [5-(4-chlorophenyl)-5-hydroxy-3-(trifluoromethyl)-4,5-dihydro-1H-pyrazol-1-yl](m-tolyl)methanone (16), which displayed a minimum inhibitory concentration (MIC) of 36.6 microM vs. M. tuberculosis replicating phenotype and 48.9 microM vs. M. tuberculosis nonreplicating phenotype. The HTS hit compound and its analogues provide the first examples of riboflavin synthase inhibitors with antibiotic activity.
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27
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Wang HQ, Zhou WP, Wang YY, Lin CR, Liu ZJ. Regioselective synthesis and bioactivity of new 5-amino-6-arylamino-pyrazolo[3,4-d]-pyrimidin-4(5H)-one derivatives. J Heterocycl Chem 2009. [DOI: 10.1002/jhet.26] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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28
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Boudet N, Dubbaka SR, Knochel P. Oxidative Amination of Cuprated Pyrimidine and Purine Derivatives. Org Lett 2008; 10:1715-8. [DOI: 10.1021/ol800353s] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nadège Boudet
- Department Chemie and Biochemie, Ludwig-Maximilians-Universität, Butenandtstrasse 5-13, 81377 München, Germany
| | - Srinivas Reddy Dubbaka
- Department Chemie and Biochemie, Ludwig-Maximilians-Universität, Butenandtstrasse 5-13, 81377 München, Germany
| | - Paul Knochel
- Department Chemie and Biochemie, Ludwig-Maximilians-Universität, Butenandtstrasse 5-13, 81377 München, Germany
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29
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Fischer M, Bacher A. Biosynthesis of vitamin B2: Structure and mechanism of riboflavin synthase. Arch Biochem Biophys 2008; 474:252-65. [PMID: 18298940 DOI: 10.1016/j.abb.2008.02.008] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2007] [Revised: 02/05/2008] [Accepted: 02/06/2008] [Indexed: 11/30/2022]
Abstract
The biosynthesis of one riboflavin molecule requires one molecule of GTP and two molecules of ribulose 5-phosphate as substrates. GTP is hydrolytically opened, converted into 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione by a sequence of deamination, side chain reduction and dephosphorylation. Condensation with 3,4-dihydroxy-2-butanone 4-phosphate obtained from ribulose 5-phosphate leads to 6,7-dimethyl-8-ribityllumazine. The final step in the biosynthesis of the vitamin involves the dismutation of 6,7-dimethyl-8-ribityllumazine catalyzed by riboflavin synthase. The mechanistically unusual reaction involves the transfer of a four-carbon fragment between two identical substrate molecules. The second product, 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione, is recycled in the biosynthetic pathway by 6,7-dimethyl-8-ribityllumazine synthase. This article will review structures and reaction mechanisms of riboflavin synthases and related proteins up to 2007 and 122 references are cited.
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Affiliation(s)
- Markus Fischer
- Institute of Food Chemistry, University of Hamburg, Grindelallee 117, D-20146 Hamburg, Germany.
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30
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Bhat RG, Kumar NS, Pinto BM. Synthesis of phosphate derivatives related to the glycosidase inhibitor salacinol. Carbohydr Res 2007; 342:1934-42. [PMID: 17572396 DOI: 10.1016/j.carres.2007.05.030] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2007] [Revised: 05/23/2007] [Accepted: 05/25/2007] [Indexed: 10/23/2022]
Abstract
The syntheses of polyhydroxylated imino- and anhydro thio-alditol compounds related to the naturally occurring glycosidase inhibitor, salacinol, containing a phosphate group in the side chain are described. The compounds lack hydroxyl groups on the acyclic side chain and are prototypes of the exact salacinol analogue. The synthetic strategy relies on the Mitsunobu reaction of N- and S-hydroxyalkyl derivatives of 2,3,5-tri-O-benzyl-1,4-dideoxy-1,4-imino-D-arabinitol and 1,4-anhydro-2,3,5-tri-O-benzyl-1-thio-D-arabinitol with dibenzyl phosphate to yield the corresponding protected heteroalditol phosphates. Screening of these compounds against recombinant human maltase glucoamylase (MGA), a critical intestinal glucosidase involved in the processing of oligosaccharides of glucose into glucose itself, shows that they are not effective inhibitors of MGA and demonstrates the importance of the hydroxyl and/or sulfate substituents present on the side chain for effective inhibition. The attempted synthesis of the exact analogue of salacinol by opening of cyclic phosphates is also described.
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Affiliation(s)
- Ramakrishna G Bhat
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
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31
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Zhang Y, Jin G, Illarionov B, Bacher A, Fischer M, Cushman M. A New Series of 3-Alkyl Phosphate Derivatives of 4,5,6,7-Tetrahydro-1-d-ribityl-1H-pyrazolo[3,4-d]pyrimidinedione as Inhibitors of Lumazine Synthase: Design, Synthesis, and Evaluation. J Org Chem 2007; 72:7176-84. [PMID: 17705537 DOI: 10.1021/jo070982r] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Lumazine synthase catalyzes the penultimate step in the biosynthesis of riboflavin. A homologous series of three pyrazolopyrimidine analogues of a hypothetical intermediate in the lumazine synthase-catalyzed reaction were synthesized and evaluated as lumazine synthase inhibitors. The key steps of the synthesis were C-5 deprotonation of 4-chloro-2,6-dimethoxypyrimidine, acylation of the resulting anion, and conversion of the product to a pyrazolopyrimidine with hydrazine. Alkylation of the pyrazolopyrimidine with a substituted ribityl iodide and deprotection of the ribityl chain afforded the final set of three products. All three compounds were extremely potent inhibitors of the lumazine synthases of Mycobacterium tuberculosis, Magnaporthe grisea, Candida albicans, and Schizosaccharomyces pombe lumazine synthase, with inhibition constants in the low nanomolar to subnanomolar range. Molecular modeling of one of the homologues bound to Mycobacterium tuberculosis lumazine synthase suggests that both the hypothetical intermediate in the lumazine synthase-catalyzed reaction pathway and the metabolically stable analogues bind similarly.
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Affiliation(s)
- Yanlei Zhang
- Department of Medicinal Chemistry and Molecular Pharmacology, School of Pharmacy and Pharmaceutical Sciences, and the Purdue Cancer Center, Purdue University, West Lafayette, IN 47907, USA
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32
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Talukdar A, Illarionov B, Bacher A, Fischer M, Cushman M. Synthesis and Enzyme Inhibitory Activity of the S-Nucleoside Analogue of the Ribitylaminopyrimidine Substrate of Lumazine Synthase and Product of Riboflavin Synthase. J Org Chem 2007; 72:7167-75. [PMID: 17696548 DOI: 10.1021/jo0709495] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Lumazine synthase and riboflavin synthase catalyze the last two steps in the biosynthesis of riboflavin. To obtain structural and mechanistic probes of these two enzymes, as well as inhibitors of potential value as antibiotics, a sulfur analogue of the pyrimidine substrate of the lumazine synthase-catalyzed reaction and product of the riboflavin synthase-catalyzed reaction was designed. Facile syntheses of the S-nucleoside 5-amino-6-(D-ribitylthio)pyrimidine-2,4(1H,3H)-dione hydrochloride (15) and its nitro precursor 5-nitro-6-(D-ribitylthio)pyrimidine-2,4(1H,3H)-dione (14) are described. These compounds were tested against lumazine synthase and riboflavin synthase obtained from a variety of microorganisms. Compounds 14 and 15 were found to be inhibitors of both riboflavin synthase and lumazine synthase. Compound 14 is an inhibitor of Bacillus subtilis lumazine synthase (Ki 26 microM), Schizosaccharomyces pombe lumazine synthase (Ki 2.0 microM), Mycobacterium tuberculosis lumazine synthase (Ki 11 microM), Escherichia coli riboflavin synthase (Ki 2.7 microM), and Mycobacterium tuberculosis riboflavin synthase (Ki 0.56 muM), while compound 15 is an inhibitor of B. subtilis lumazine synthase (Ki 2.6 microM), S. pombe lumazine synthase (Ki 0.16 microM), M. tuberculosis lumazine synthase (Ki 31 microM), E. coli riboflavin synthase (Ki 47 microM), and M. tuberculosis riboflavin synthase (Ki 2.5 microM).
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Affiliation(s)
- Arindam Talukdar
- Department of Medicinal Chemistry and Molecular Pharmacology, School of Pharmacy and Pharmaceutical Sciences, and Purdue Cancer Center, Purdue University, West Lafayette, IN 47907, USA
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33
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Romanenko VD, Kukhar VP. Fluorinated phosphonates: synthesis and biomedical application. Chem Rev 2007; 106:3868-935. [PMID: 16967924 DOI: 10.1021/cr051000q] [Citation(s) in RCA: 287] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Vadim D Romanenko
- Institute of Bioorganic Chemistry and Petrochemistry, National Academy of Sciences of the Ukraine, 1 Murmanska Street, Kyiv-94 02660, Ukraine
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34
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Kaiser J, Illarionov B, Rohdich F, Eisenreich W, Saller S, den Brulle JV, Cushman M, Bacher A, Fischer M. A high-throughput screening platform for inhibitors of the riboflavin biosynthesis pathway. Anal Biochem 2007; 365:52-61. [PMID: 17400171 DOI: 10.1016/j.ab.2007.02.033] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2007] [Revised: 02/21/2007] [Accepted: 02/26/2007] [Indexed: 10/23/2022]
Abstract
3,4-Dihydroxy-2-butanone 4-phosphate synthase, 6,7-dimethyl-8-ribityllumazine synthase, and riboflavin synthase of the riboflavin biosynthetic pathway are potential targets for novel antiinfective drugs. This article describes a platform for high-throughput screening for inhibitors of these enzymes. The assays can be monitored photometrically and have been shown to be robust, as indicated by Z factors 0.87. A (13)C NMR assay for hit verification of 3,4-dihydroxy-2-butanone 4-phosphate synthase inhibitors is also reported.
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Affiliation(s)
- Johannes Kaiser
- Lehrstuhl für Organische Chemie und Biochemie, Technische Universität München, D-85748 München, Germany
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35
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Morgunova E, Saller S, Haase I, Cushman M, Bacher A, Fischer M, Ladenstein R. Lumazine synthase from Candida albicans as an anti-fungal target enzyme: structural and biochemical basis for drug design. J Biol Chem 2007; 282:17231-41. [PMID: 17446177 DOI: 10.1074/jbc.m701724200] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Lumazine synthase is an enzyme involved in riboflavin biosynthesis in many plants and microorganisms, including numerous human pathogens. The fact that the enzymes of the riboflavin biosynthesis pathway are not present in the human or animal host makes them potential targets for anti-infective agents. The crystal structure of lumazine synthase from Candida albicans was solved by molecular replacement and refined at 2.5-Angstrom resolution. The results of crystallographic investigations and sedimentation equilibrium experiments clearly indicated the presence of pentameric assemblies of the enzyme either in crystals or in solution. Isothermal titration calorimetry measurements of the binding reactions of four different inhibitors revealed high affinity for all four compounds with binding constants in the micromolar range. Structural comparison with previously determined structures of the enzyme.ligand complexes of other orthologue allowed modeling of the binding of four different inhibitors into the active site of lumazine synthase from Candida albicans.
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Affiliation(s)
- Ekaterina Morgunova
- Karolinska Institutet, NOVUM, Centre for Structural Biochemistry, Halsovagen 7-9, S-14157 Huddinge, Sweden.
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36
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Liu H, Wang HQ, Liu ZJ. Synthesis and herbicidal activity of novel pyrazolo[3,4-d]pyrimidin-4-one derivatives containing aryloxyphenoxypropionate moieties. Bioorg Med Chem Lett 2007; 17:2203-9. [PMID: 17337186 DOI: 10.1016/j.bmcl.2007.01.083] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2006] [Revised: 01/04/2007] [Accepted: 01/23/2007] [Indexed: 11/22/2022]
Abstract
The 6-(4-alkoxycarbonylalkoxy)phenoxy-3-alkylthio(alkylsulfonyl)-1-phenyl-5-(substituted phenyl)pyrazolo[3,4-d]pyrimidin-4-ones 6 and 7 have been synthesized via the tandem aza-Wittig and annulation reactions of the corresponding iminophosphoranes 4, aromatic isocyanates, and substituted phenols 2 in 52-98% yields. Their structures were clearly verified by spectroscopic data (IR, (1)H NMR, (13)C NMR, MS, and elemental analysis or X-ray diffraction crystallography). And the results of preliminary bioassay indicated that these title compounds possess potential herbicidal activity against the root of rape and barnyard grass.
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Affiliation(s)
- Hui Liu
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, 152 Luoyu Road, Wuhan, Hubei 430079, China
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37
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Blanco G, Quintela JM, Peinador C. Efficient one-pot preparation of bis(pyrazino[2′,3′:4,5]thieno[3,2-d]pyrimidin-4-yl)benzenes based on an aza–Wittig/mediated annulation strategy. Tetrahedron 2007. [DOI: 10.1016/j.tet.2006.12.049] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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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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A practical one-pot procedure for the synthesis of pyrazino[2′,3′:4,5]thieno[3,2-d]pyrimidinones by a tandem aza-Wittig/heterocumulene-mediated annulation strategy. Tetrahedron 2006. [DOI: 10.1016/j.tet.2006.09.028] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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40
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Morgunova E, Illarionov B, Sambaiah T, Haase I, Bacher A, Cushman M, Fischer M, Ladenstein R. Structural and thermodynamic insights into the binding mode of five novel inhibitors of lumazine synthase from Mycobacterium tuberculosis. FEBS J 2006; 273:4790-804. [PMID: 16984393 DOI: 10.1111/j.1742-4658.2006.05481.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Recently published genomic investigations of the human pathogen Mycobacterium tuberculosis have revealed that genes coding the proteins involved in riboflavin biosynthesis are essential for the growth of the organism. Because the enzymes involved in cofactor biosynthesis pathways are not present in humans, they appear to be promising candidates for the development of therapeutic drugs. The substituted purinetrione compounds have demonstrated high affinity and specificity to lumazine synthase, which catalyzes the penultimate step of riboflavin biosynthesis in bacteria and plants. The structure of M. tuberculosis lumazine synthase in complex with five different inhibitor compounds is presented, together with studies of the binding reactions by isothermal titration calorimetry. The inhibitors showed the association constants in the micromolar range. The analysis of the structures demonstrated the specific features of the binding of different inhibitors. The comparison of the structures and binding modes of five different inhibitors allows us to propose the ribitylpurinetrione compounds with C4-C5 alkylphosphate chains as most promising leads for further development of therapeutic drugs against M. tuberculosis.
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Affiliation(s)
- Ekaterina Morgunova
- Karolinska Institutet, NOVUM, Centre for Structural Biochemistry, Huddinge, Sweden.
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41
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Mack M, Grill S. Riboflavin analogs and inhibitors of riboflavin biosynthesis. Appl Microbiol Biotechnol 2006; 71:265-75. [PMID: 16607521 DOI: 10.1007/s00253-006-0421-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2006] [Revised: 03/06/2006] [Accepted: 03/06/2006] [Indexed: 11/30/2022]
Abstract
Flavins are active components of many enzymes. In most cases, riboflavin (vitamin B(2)) as a coenzyme represents the catalytic part of the holoenzyme. Riboflavin is an amphiphatic molecule and allows a large variety of different interactions with the enzyme itself and also with the substrate. A great number of active riboflavin analogs can readily be synthesized by chemical methods and, thus, a large number of possible inhibitors for many different enzyme targets is conceivable. As mammalian and especially human biochemistry depends on flavins as well, the target of the inhibiting flavin analog has to be carefully selected to avoid unwanted effects. In addition to flavoproteins, enzymes, which are involved in the biosynthesis of flavins, are possible targets for anti-infectives. Only a few flavin analogs or inhibitors of flavin biosynthesis have been subjected to detailed studies to evaluate their biological activity. Nevertheless, flavin analogs certainly have the potential to serve as basic structures for the development of novel anti-infectives and it is possible that, in the future, the urgent need for new molecules to fight multiresistant microorganisms will be met.
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Affiliation(s)
- Matthias Mack
- Institute for Technical Microbiology, Mannheim University of Applied Sciences, Germany.
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42
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Cushman M, Jin G, Sambaiah T, Illarionov B, Fischer M, Ladenstein R, Bacher A. Design, synthesis, and biochemical evaluation of 1,5,6,7-tetrahydro-6,7-dioxo-9-D-ribitylaminolumazines bearing alkyl phosphate substituents as inhibitors of lumazine synthase and riboflavin synthase. J Org Chem 2005; 70:8162-70. [PMID: 16277343 PMCID: PMC2548293 DOI: 10.1021/jo051332v] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The last two steps in the biosynthesis of riboflavin, an essential metabolite that is involved in electron transport, are catalyzed by lumazine synthase and riboflavin synthase. To obtain structural probes and inhibitors of these two enzymes, two ribityllumazinediones bearing alkyl phosphate substituents were synthesized. The synthesis involved the generation of the ribityl side chain, the phosphate side chain, and the lumazine system in protected form, followed by the simultaneous removal of three different types of protecting groups. The products were designed as intermediate analogue inhibitors of lumazine synthase that would bind to its phosphate-binding site as well as its lumazine binding site. Both compounds were found to be effective inhibitors of Bacillus subtilislumazine synthase as well as Escherichia coli riboflavin synthase. Molecular modeling of the binding of one of the two compounds provided a structural explanation for how these compounds are able to effectively inhibit both enzymes. In phosphate-free buffer, the phosphate moieties of the inhibitors were found to contribute positively to their binding to Mycobacterium tuberculosis lumazine synthase, resulting in very potent inhibitors with Ki values in the low nanomolar range. The additional carbonyl in the dioxolumazine system versus the purinetrione system was found to make a positive contribution to its binding to E. coli riboflavin synthase.
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Affiliation(s)
- Mark Cushman
- Department of Medicinal Chemistry and Molecular Pharmacology, School of Pharmacy and Pharmaceutical Sciences, Purdue University, West Lafayette, Indiana 47907, USA.
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Morgunova E, Meining W, Illarionov B, Haase I, Jin G, Bacher A, Cushman M, Fischer M, Ladenstein R. Crystal structure of lumazine synthase from Mycobacterium tuberculosis as a target for rational drug design: binding mode of a new class of purinetrione inhibitors. Biochemistry 2005; 44:2746-58. [PMID: 15723519 DOI: 10.1021/bi047848a] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The enzymes involved in the biosynthesis of riboflavin represent attractive targets for the development of drugs against bacterial pathogens, because the inhibitors of these enzymes are not likely to interfere with enzymes of the mammalian metabolism. Lumazine synthase catalyzes the penultimate step in the riboflavin biosynthesis pathway. A number of substituted purinetrione compounds represent a new class of highly specific inhibitors of lumazine synthase from Mycobacterium tuberculosis. To develop potent antibiotics for the treatment of tuberculosis, we have determined the structure of lumazine synthase from M. tuberculosis in complex with two purinetrione inhibitors and have studied binding via isothermal titration calorimetry. The structures were determined by molecular replacement using lumazine synthase from Saccharomyces cerevisiae as a search model and refined at 2 and 2.3 A resolution. The R-factors were 14.7 and 17.4%, respectively, and the R(free) values were 19.3 and 26.3%, respectively. The enzyme was found to be a pentamer consisting of five subunits related by 5-fold local symmetry. The comparison of the active site architecture with the active site of previously determined lumazine synthase structures reveals a largely conserved topology with the exception of residues Gln141 and Glu136, which participate in different charge-charge interactions in the core space of the active site. The impact of structural changes in the active site on the altered binding and catalytic properties of the enzyme is discussed. Isothermal titration calorimetry measurements indicate highly specific binding of the purinetrione inhibitors to the M. tuberculosis enzyme with dissociation constants in micromolar range.
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Affiliation(s)
- Ekaterina Morgunova
- Karolinska Institutet, NOVUM, Centre for Structural Biochemistry, S-14157 Huddinge, Sweden.
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Becker SA, Palsson BØ. Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation. BMC Microbiol 2005; 5:8. [PMID: 15752426 PMCID: PMC1079855 DOI: 10.1186/1471-2180-5-8] [Citation(s) in RCA: 170] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2005] [Accepted: 03/07/2005] [Indexed: 11/30/2022] Open
Abstract
Background Several strains of bacteria have sequenced and annotated genomes, which have been used in conjunction with biochemical and physiological data to reconstruct genome-scale metabolic networks. Such reconstruction amounts to a two-dimensional annotation of the genome. These networks have been analyzed with a constraint-based formalism and a variety of biologically meaningful results have emerged. Staphylococcus aureus is a pathogenic bacterium that has evolved resistance to many antibiotics, representing a significant health care concern. We present the first manually curated elementally and charge balanced genome-scale reconstruction and model of S. aureus' metabolic networks and compute some of its properties. Results We reconstructed a genome-scale metabolic network of S. aureus strain N315. This reconstruction, termed iSB619, consists of 619 genes that catalyze 640 metabolic reactions. For 91% of the reactions, open reading frames are explicitly linked to proteins and to the reaction. All but three of the metabolic reactions are both charge and elementally balanced. The reaction list is the most complete to date for this pathogen. When the capabilities of the reconstructed network were analyzed in the context of maximal growth, we formed hypotheses regarding growth requirements, the efficiency of growth on different carbon sources, and potential drug targets. These hypotheses can be tested experimentally and the data gathered can be used to improve subsequent versions of the reconstruction. Conclusion iSB619 represents comprehensive biochemically and genetically structured information about the metabolism of S. aureus to date. The reconstructed metabolic network can be used to predict cellular phenotypes and thus advance our understanding of a troublesome pathogen.
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Affiliation(s)
- Scott A Becker
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
| | - Bernhard Ø Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
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Chen J, Illarionov B, Bacher A, Fischer M, Haase I, Georg G, Ye QZ, Ma Z, Cushman M. A high-throughput screen utilizing the fluorescence of riboflavin for identification of lumazine synthase inhibitors. Anal Biochem 2005; 338:124-30. [PMID: 15707942 DOI: 10.1016/j.ab.2004.11.033] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2004] [Indexed: 11/20/2022]
Abstract
A high-throughput screening method based on the competitive binding of a lumazine synthase inhibitor and riboflavin to the active site of Schizosaccharomyces pombe lumazine synthase was developed. This assay is sensitive, simple, and robust. During assay development, all of the known active inhibitors tested were positively identified. Preliminary high-throughput screening in 384-well format resulted in a Z factor of 0.7. The approach utilizes a thermodynamic assay to bypass the problems associated with the instabilities of both lumazine synthase substrates that complicate the use of a kinetic assay in a high-throughput format, and it removes the time element from the assay, thus simplifying the procedure.
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Affiliation(s)
- Jinhua Chen
- Department of Medicinal Chemistry and Molecular Pharmacology, School of Pharmacy and Pharmaceutical Sciences, Purdue University, West Lafayette, IN 47907, USA
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Abstract
The biosynthesis of one riboflavin molecule requires one molecule of GTP and two molecules of ribulose 5-phosphate. The imidazole ring of GTP is hydrolytically opened, yielding a 2,5-diaminopyrimidine that is converted to 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione by a sequence of deamination, side chain reduction, and dephosphorylation. Condensation of 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione with 3,4-dihydroxy-2-butanone 4-phosphate obtained from ribulose 5-phosphate affords 6,7-dimethyl-8-ribityllumazine. Dismutation of the lumazine derivative yields riboflavin and 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione, which is recycled in the biosynthetic pathway. The enzymes of the riboflavin pathway are potential targets for antibacterial agents.
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Affiliation(s)
- Markus Fischer
- Lehrstuhl für Organische Chemie und Biochemie, Technische Universität München, Lichtenbergstr. 4, D-85747, Garching, Germany.
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Ding MW, Xu SZ, Zhao JF. Application of Bis(iminophosphorane) in Heterocyclic Synthesis: New Entries to Symmetrically or Unsymmetrically Substituted Thieno[2,3-d:5,4-d‘]dipyrimidine-4,5(3H,6H)-diones. J Org Chem 2004; 69:8366-71. [PMID: 15549808 DOI: 10.1021/jo048691v] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The bis(carbodiimides) 4, obtained from bis-aza-Wittig reactions of bis(iminophosphorane) 3 with 2 equiv of aromatic isocyanates, were reacted with secondary amine to give symmetrically substituted 2,7-diaminothieno[2,3-d:5,4-d']dipyrimidine-4,5(3H,6H)-dione 6 in the presence of a catalytic amount of EtO(-)Na(+). Reactions of 4 with phenols or ROH in the presence of a catalytic amount of potassium carbonate or RO(-)Na(+) gave symmetrically substituted 2,7-diaryl(alkyl)oxythieno[2,3-d:5,4-d']dipyrimidine-4,5(3H,6H)-diones 6 in satisfactory yields. However, iminophosphoranes 9 were obtained via reaction of bis(iminophosphorane) 3 with 1 equiv of aromatic isocyanate and subsequent reaction with an amine in the presence of a catalytic amount of EtO(-)Na(+). Further reaction of iminophosphoranes 9 with aromatic isocyanates and various nucleophile generated unsymmetrically substituted thieno[2,3-d:5,4-d']dipyrimidine-4,5(3H,6H)-diones 12 in good yields.
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Affiliation(s)
- Ming-Wu Ding
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, 430079, P. R. China.
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