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Singh M, Dhanwal A, Verma A, Augustin L, Kumari N, Chakraborti S, Agarwal N, Sriram D, Dey RJ. Discovery of potent antimycobacterial agents targeting lumazine synthase (RibH) of Mycobacterium tuberculosis. Sci Rep 2024; 14:12170. [PMID: 38806590 PMCID: PMC11133327 DOI: 10.1038/s41598-024-63051-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 05/24/2024] [Indexed: 05/30/2024] Open
Abstract
Tuberculosis (TB) continues to be a global health crisis, necessitating urgent interventions to address drug resistance and improve treatment efficacy. In this study, we validate lumazine synthase (RibH), a vital enzyme in the riboflavin biosynthetic pathway, as a potential drug target against Mycobacterium tuberculosis (M. tb) using a CRISPRi-based conditional gene knockdown strategy. We employ a high-throughput molecular docking approach to screen ~ 600,000 compounds targeting RibH. Through in vitro screening of 55 shortlisted compounds, we discover 3 compounds that exhibit potent antimycobacterial activity. These compounds also reduce intracellular burden of M. tb during macrophage infection and prevent the resuscitation of the nutrient-starved persister bacteria. Moreover, these three compounds enhance the bactericidal effect of first-line anti-TB drugs, isoniazid and rifampicin. Corroborating with the in silico predicted high docking scores along with favourable ADME and toxicity profiles, all three compounds demonstrate binding affinity towards purified lumazine synthase enzyme in vitro, in addition these compounds exhibit riboflavin displacement in an in vitro assay with purified lumazine synthase indicative of specificity of these compounds to the active site. Further, treatment of M. tb with these compounds indicate reduced production of flavin adenine dinucleotide (FAD), the ultimate end product of the riboflavin biosynthetic pathway suggesting the action of these drugs on riboflavin biosynthesis. These compounds also show acceptable safety profile in mammalian cells, with a high selective index. Hence, our study validates RibH as an important drug target against M. tb and identifies potent antimycobacterial agents.
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Affiliation(s)
- Monica Singh
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Hyderabad Campus, Hyderabad, Telangana, 500078, India
| | - Anannya Dhanwal
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Hyderabad Campus, Hyderabad, Telangana, 500078, India
| | - Arpita Verma
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Hyderabad Campus, Hyderabad, Telangana, 500078, India
| | - Linus Augustin
- Translational Health Science and Technology Institute, Faridabad, Haryana, 121001, India
| | - Niti Kumari
- National Institute of Animal Biotechnology (NIAB), Hyderabad, Telangana, 500032, India
| | - Soumyananda Chakraborti
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Hyderabad Campus, Hyderabad, Telangana, 500078, India
- National Institute of Malaria Research, Indian Council of Medical Research (ICMR), New Delhi, 110077, India
| | - Nisheeth Agarwal
- Translational Health Science and Technology Institute, Faridabad, Haryana, 121001, India
| | - Dharmarajan Sriram
- Department of Pharmacy, Birla Institute of Technology and Science Pilani, Hyderabad Campus, Hyderabad, Telangana, 500078, India
| | - Ruchi Jain Dey
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Hyderabad Campus, Hyderabad, Telangana, 500078, India.
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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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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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Shingare RD, MacMillan JB, Reddy DS. Antibiotic natural product hunanamycin A: Lead identification towards anti-Salmonella agents. Eur J Med Chem 2022; 236:114245. [DOI: 10.1016/j.ejmech.2022.114245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 02/10/2022] [Accepted: 02/26/2022] [Indexed: 11/30/2022]
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Kondrashova SA, Polyancev FM, Latypov SK. Tautomeric preference in lumazines, deazalumazines, isoalloxazines and pyrimidines and its effect on the reactivity of alkyl groups. Bioorg Chem 2021; 109:104725. [PMID: 33611139 DOI: 10.1016/j.bioorg.2021.104725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 02/02/2021] [Accepted: 02/03/2021] [Indexed: 11/30/2022]
Abstract
In lumazines, deazalumazines and pyrimidines, there are extremely low-energy "rare" tautomers (<2.3 kcal/mol), this fact perfectly explains the observed mobility of usually "non-labile" protons of methyl groups in such systems. In general, the dependence of tautomeric preference on structure correlates well with experimental findings. Thus, the activity of alkyl groups during biological transformations may be due to the presence of the corresponding thermodynamically stable tautomers.
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Affiliation(s)
- Svetlana A Kondrashova
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of RAS, Russia
| | - Fedor M Polyancev
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of RAS, Russia
| | - Shamil K Latypov
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of RAS, Russia.
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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, 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: 7] [Impact Index Per Article: 1.0] [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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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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Ma L, He L, Lei L, Liang X, Lei K, Zhang R, Yang Z, Chen L. Synthesis and biological evaluation of 5-nitropyrimidine-2,4-dione analogues as inhibitors of nitric oxide and iNOS activity. Chem Biol Drug Des 2014; 85:296-9. [PMID: 24985766 DOI: 10.1111/cbdd.12386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2014] [Revised: 05/12/2014] [Accepted: 06/18/2014] [Indexed: 02/05/2023]
Abstract
Fifty two compounds based on 5-nitropyrimidine-2,4-dione moiety have been synthesized and evaluated for their inhibitory potency on the production of nitric oxide. Among them, compound 36 inhibited the production of nitric oxide (IC50 : 8.6 μm) on lipopolysaccharide-induced RAW 264.7 cells and inducible nitric oxide synthase activity (IC50 : 6.2 μm), as well as exerted no potential cytotoxicity (IC50 > 80.0 μm). Docking study confirmed that compound 36 was an inducible nitric oxide synthase inhibitor with perfect binding to the active site of inducible nitric oxide synthase. At a dose of 10 mg/kg, oral administration of 36 possessed protective properties in carrageenan-induced paw edema of male ICR mice.
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Affiliation(s)
- Liang Ma
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, 610041, China
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Reddy PS, Reddy PVG, Reddy SM. Phosphomolybdic acid promoted Kabachnik–Fields reaction: an efficient one-pot synthesis of α-aminophosphonates from 2-cyclopropylpyrimidine-4-carbaldehyde. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2014.04.053] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Sura MR, Peddiahgari VGR, Bhoomireddy RPR, Vadde RK. Synthesis of New 2,4-Diaryl-6-methyl-5-nitropyrimidines as Antibacterial and Antioxidant Agents. J Heterocycl Chem 2013. [DOI: 10.1002/jhet.1645] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | | | | | - Rama Krishna Vadde
- Department of Biotechnology & Bioinformatics; Yogi Vemana University; Kadapa 516003 Andhra Pradesh India
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Shankar M, Wilbanks SM, Nakatani Y, Monk BC, Tyndall JDA. Catalysis product captured in lumazine synthase from the fungal pathogenCandida glabrata. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1580-6. [DOI: 10.1107/s0907444913010949] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 04/23/2013] [Indexed: 02/05/2023]
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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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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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Brücher K, Illarionov B, Held J, Tschan S, Kunfermann A, Pein MK, Bacher A, Gräwert T, Maes L, Mordmüller B, Fischer M, Kurz T. α-Substituted β-oxa isosteres of fosmidomycin: synthesis and biological evaluation. J Med Chem 2012; 55:6566-75. [PMID: 22731758 DOI: 10.1021/jm300652f] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Specific inhibition of enzymes of the non-mevalonate pathway is a promising strategy for the development of novel antiplasmodial drugs. α-Aryl-substituted β-oxa isosteres of fosmidomycin with a reverse orientation of the hydroxamic acid group were synthesized and evaluated for their inhibitory activity against recombinant 1-deoxy-d-xylulose 5-phosphate reductoisomerase (IspC) of Plasmodium falciparum and for their in vitro antiplasmodial activity against chloroquine-sensitive and resistant strains of P. falciparum . The most active derivative inhibits IspC protein of P. falciparum (PfIspC) with an IC(50) value of 12 nM and shows potent in vitro antiplasmodial activity. In addition, lipophilic ester prodrugs demonstrated improved P. falciparum growth inhibition in vitro.
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Affiliation(s)
- Karin Brücher
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich Heine Universität, Universitätsstr. 1, 40225 Düsseldorf, Germany
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Abbas CA, Sibirny AA. Genetic control of biosynthesis and transport of riboflavin and flavin nucleotides and construction of robust biotechnological producers. Microbiol Mol Biol Rev 2011; 75:321-60. [PMID: 21646432 PMCID: PMC3122625 DOI: 10.1128/mmbr.00030-10] [Citation(s) in RCA: 239] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Riboflavin [7,8-dimethyl-10-(1'-d-ribityl)isoalloxazine, vitamin B₂] is an obligatory component of human and animal diets, as it serves as the precursor of flavin coenzymes, flavin mononucleotide, and flavin adenine dinucleotide, which are involved in oxidative metabolism and other processes. Commercially produced riboflavin is used in agriculture, medicine, and the food industry. Riboflavin synthesis starts from GTP and ribulose-5-phosphate and proceeds through pyrimidine and pteridine intermediates. Flavin nucleotides are synthesized in two consecutive reactions from riboflavin. Some microorganisms and all animal cells are capable of riboflavin uptake, whereas many microorganisms have distinct systems for riboflavin excretion to the medium. Regulation of riboflavin synthesis in bacteria occurs by repression at the transcriptional level by flavin mononucleotide, which binds to nascent noncoding mRNA and blocks further transcription (named the riboswitch). In flavinogenic molds, riboflavin overproduction starts at the stationary phase and is accompanied by derepression of enzymes involved in riboflavin synthesis, sporulation, and mycelial lysis. In flavinogenic yeasts, transcriptional repression of riboflavin synthesis is exerted by iron ions and not by flavins. The putative transcription factor encoded by SEF1 is somehow involved in this regulation. Most commercial riboflavin is currently produced or was produced earlier by microbial synthesis using special selected strains of Bacillus subtilis, Ashbya gossypii, and Candida famata. Whereas earlier RF overproducers were isolated by classical selection, current producers of riboflavin and flavin nucleotides have been developed using modern approaches of metabolic engineering that involve overexpression of structural and regulatory genes of the RF biosynthetic pathway as well as genes involved in the overproduction of the purine precursor of riboflavin, GTP.
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Affiliation(s)
| | - Andriy A. Sibirny
- Institute of Cell Biology, NAS of Ukraine, Lviv 79005, Ukraine
- University of Rzeszow, Rzeszow 35-601, Poland
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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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Abstract
About 20 proteins are known to modify their activity upon interaction with C60. Their structures are present in a database that includes more than 1200 protein structures selected as possible targets for drugs and to represent the entire Protein Data Bank. The set was examined with an algorithm that appraises quantitatively the interaction of C60 and the surface of each protein. The redundancy of the set allows to establish the predictive power of the approach that finds explicitly the most probable site where C60 docks on each protein. About 80% of the known fullerene binding proteins fall in the top 10% of scorers. The close match between the model and experiments vouches for the accuracy of the model and validates its predictions. The sites of docking are shown and discussed in view of the existing experimental data available for protein-C60 interaction. A closer exam of the 10 top scorers is discussed in detail. New proteins that can interact with C60 are identified and discussed for possible future applications as drug targets and fullerene derivatives bioconjugate materials.
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Affiliation(s)
- Matteo Calvaresi
- Dipartimento di Chimica "G. Ciamician", Universita' di Bologna, V. F. Selmi 2, 40126 Bologna, Italy.
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