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Yao J, Wang ZN, Liu H, Jin H, Zhang Y. Survey of Acetylation for Thermoanaerobacter tengcongensis. Appl Biochem Biotechnol 2023; 195:6081-6097. [PMID: 36809429 DOI: 10.1007/s12010-023-04361-9] [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] [Accepted: 01/10/2023] [Indexed: 02/23/2023]
Abstract
Non-histone protein acetylation is involved in key cellular processes both in eukaryotes and prokaryotes. Acetylation in bacteria is used to modify proteins involved in metabolism and allow the bacteria to adapt to their environment. TTE (Thermoanaerobacter tengcongensis) is an anaerobic, thermophilic saccharolytic bacterium that grows at extreme temperature range between 50 and 80 ℃. The annotated TTE proteome contains less than 3000 proteins. We analyzed the proteome and acetylome of TTE using 2DLC-MS/MS (2-dimensional liquid chromatography mass spectrum). We evaluated the ability of mass spectrometry technology to cover a relatively small proteome as much as possible. And we also observed wide spread of acetylation in TTE, which changed under different temperatures. A total of 2082 proteins were identified, which accounts for about 82% of the database. A total of 2050 (~ 98%) proteins were quantified in at least one culture condition and 1818 proteins were quantified in all 4 conditions. The result also consisted 3457 acetylation sites corresponding to 827 distinct proteins, which covered 40% of the proteins identified. Bioinformatics analysis reported that proteins related to replication, recombination, repair, and extracellular structure cell wall biogenesis had more than half members acetylated, while energy production, carbohydrate transport, and metabolism related proteins were least acetylated. Our result suggested that acetylation affects the ATP-related energy metabolism and energy-dependent biosynthesis process. Comparing the enzymes related with lysine acetylation and acetyl-CoA (acetyl-coenzyme A) metabolism, we suggested that the acetylation of TTE took a non-enzymatic mechanism and affected by abundance of acetyl-CoA.
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Affiliation(s)
- Jun Yao
- Department of Chemistry, Shanghai Stomatological Hospital & Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China
| | - Ze-Ning Wang
- Department of Chemistry, Shanghai Stomatological Hospital & Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China
| | - Hang Liu
- Department of Chemistry, Shanghai Stomatological Hospital & Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China
| | - Hong Jin
- Department of Chemistry, Shanghai Stomatological Hospital & Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China.
| | - Yang Zhang
- Department of Chemistry, Shanghai Stomatological Hospital & Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China.
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2
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Patel KD, Gulick AM. Structural and functional insights into δ-poly-L-ornithine polymer biosynthesis from Acinetobacter baumannii. Commun Biol 2023; 6:982. [PMID: 37752201 PMCID: PMC10522769 DOI: 10.1038/s42003-023-05362-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 09/15/2023] [Indexed: 09/28/2023] Open
Abstract
Cationic homo-polyamino acid (CHPA) peptides containing isopeptide bonds of diamino acids have been identified from Actinomycetes strains. However, none has been reported from other bacteria. Here, we report a δ-poly-L-ornithine synthetase from Acinetobacter baumannii, which we name PosA. Surprisingly, structural analysis of the adenylation domain and biochemical assay shows L-ornithine as the substrate for PosA. The product from the enzymatic reaction was purified and identified as poly-L-ornithine composed of 7-12 amino acid units. Chemical labeling of the polymer confirmed the isopeptide linkage of δ-poly-L-ornithine. We examine the biological activity of chemically synthesized 12-mer δ-poly-L-ornithine, illustrating that the polymer may act as an anti-fungal agent. Structures of the isolated adenylation domain from PosA are presented with several diamino acids and biochemical assays identify important substrate binding residues. Structurally-guided genome-mining led to the identification of homologs with different substrate binding residues that could activate additional substrates. A homolog from Bdellovibrionales sp. shows modest activity with L-arginine but not with any diamino acids observed to be substrates for previously examined CHPA synthetases. Our study indicates the possibility that additional CHPAs may be produced by various microbes, supporting the further exploration of uncharacterized natural products.
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Affiliation(s)
- Ketan D Patel
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, SUNY, Buffalo, NY, 14203, USA
| | - Andrew M Gulick
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, SUNY, Buffalo, NY, 14203, USA.
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3
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Soni V, Rosenn EH, Venkataraman R. Insights into the central role of N-acetyl-glucosamine-1-phosphate uridyltransferase (GlmU) in peptidoglycan metabolism and its potential as a therapeutic target. Biochem J 2023; 480:1147-1164. [PMID: 37498748 DOI: 10.1042/bcj20230173] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/07/2023] [Accepted: 07/14/2023] [Indexed: 07/29/2023]
Abstract
Several decades after the discovery of the first antibiotic (penicillin) microbes have evolved novel mechanisms of resistance; endangering not only our abilities to combat future bacterial pandemics but many other clinical challenges such as acquired infections during surgeries. Antimicrobial resistance (AMR) is attributed to the mismanagement and overuse of these medications and is complicated by a slower rate of the discovery of novel drugs and targets. Bacterial peptidoglycan (PG), a three-dimensional mesh of glycan units, is the foundation of the cell wall that protects bacteria against environmental insults. A significant percentage of drugs target PG, however, these have been rendered ineffective due to growing drug resistance. Identifying novel druggable targets is, therefore, imperative. Uridine diphosphate N-acetylglucosamine (UDP-GlcNAc) is one of the key building blocks in PG production, biosynthesized by the bifunctional enzyme N-acetyl-glucosamine-1-phosphate uridyltransferase (GlmU). UDP-GlcNAc metabolism has been studied in many organisms, but it holds some distinctive features in bacteria, especially regarding the bacterial GlmU enzyme. In this review, we provide an overview of different steps in PG biogenesis, discuss the biochemistry of GlmU, and summarize the characteristic structural elements of bacterial GlmU vital to its catalytic function. Finally, we will discuss various studies on the development of GlmU inhibitors and their significance in aiding future drug discoveries.
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Affiliation(s)
- Vijay Soni
- Division of Infectious Diseases, Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10065, U.S.A
| | - Eric H Rosenn
- Tel Aviv University School of Medicine, Tel Aviv 6997801, Israel
| | - Ramya Venkataraman
- Laboratory of Innate Immunity, National Institute of Immunology, New Delhi 110067, India
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4
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Wyllie JA, McKay MV, Barrow AS, Soares da Costa TP. Biosynthesis of uridine diphosphate N-Acetylglucosamine: An underexploited pathway in the search for novel antibiotics? IUBMB Life 2022; 74:1232-1252. [PMID: 35880704 PMCID: PMC10087520 DOI: 10.1002/iub.2664] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 07/04/2022] [Indexed: 11/06/2022]
Abstract
Although the prevalence of antibiotic resistance is increasing at an alarming rate, there are a dwindling number of effective antibiotics available. Thus, the development of novel antibacterial agents should be of utmost importance. Peptidoglycan biosynthesis has been and is still an attractive source for antibiotic targets; however, there are several components that remain underexploited. In this review, we examine the enzymes involved in the biosynthesis of one such component, UDP-N-acetylglucosamine, an essential building block and precursor of bacterial peptidoglycan. Furthermore, given the presence of a similar biosynthesis pathway in eukaryotes, we discuss the current knowledge on the differences and similarities between the bacterial and eukaryotic enzymes. Finally, this review also summarises the recent advances made in the development of inhibitors targeting the bacterial enzymes.
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Affiliation(s)
- Jessica A Wyllie
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Mirrin V McKay
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Andrew S Barrow
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Tatiana P Soares da Costa
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, South Australia, Australia
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5
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Zheng M, Zheng M, Epstein S, Harnagel AP, Kim H, Lupoli TJ. Chemical Biology Tools for Modulating and Visualizing Gram-Negative Bacterial Surface Polysaccharides. ACS Chem Biol 2021; 16:1841-1865. [PMID: 34569792 DOI: 10.1021/acschembio.1c00341] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Bacterial cells present a wide diversity of saccharides that decorate the cell surface and help mediate interactions with the environment. Many Gram-negative cells express O-antigens, which are long sugar polymers that makeup the distal portion of lipopolysaccharide (LPS) that constitutes the surface of the outer membrane. This review highlights chemical biology tools that have been developed in recent years to facilitate the modulation of O-antigen synthesis and composition, as well as related bacterial polysaccharide pathways, and the detection of unique glycan sequences. Advances in the biochemistry and structural biology of O-antigen biosynthetic machinery are also described, which provide guidance for the design of novel chemical and biomolecular probes. Many of the tools noted here have not yet been utilized in biological systems and offer researchers the opportunity to investigate the complex sugar architecture of Gram-negative cells.
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Affiliation(s)
- Meng Zheng
- Department of Chemistry, New York University, New York, 10003 New York, United States
| | - Maggie Zheng
- Department of Chemistry, New York University, New York, 10003 New York, United States
| | - Samuel Epstein
- Department of Chemistry, New York University, New York, 10003 New York, United States
| | - Alexa P. Harnagel
- Department of Chemistry, New York University, New York, 10003 New York, United States
| | - Hanee Kim
- Department of Chemistry, New York University, New York, 10003 New York, United States
| | - Tania J. Lupoli
- Department of Chemistry, New York University, New York, 10003 New York, United States
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6
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Prabha A, Balaji PV. Characterization of left-handed beta helix-domains, and identification and functional annotation of proteins containing such domains. Proteins 2020; 89:6-20. [PMID: 32748987 DOI: 10.1002/prot.25990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 05/12/2020] [Accepted: 07/26/2020] [Indexed: 11/12/2022]
Abstract
Only about 0.3% of the entries in UniProt database have manually curated annotation. Annotation at the molecular level often relies on low-throughput one-protein-at-a-time approach. Computational methods bridge this gap by assigning function based on sequence and/or fold similarity. Left-handed beta helix (LbH) consists of three repeating six-stranded beta-strands forming an 18-mer turn of the helix. Analysis of LbH-domains showed that variations are found in the number of residues in a beta-strand (5-7, 6 being the most common), number of turns (4-10) of the helix, insertions of one or more loops of variable length (0-36 residues), and the location of loop insertion. An 18-mer HMM profile was created which identifies LbH-domain containing proteins using sequence as the only input; the number of false positives is zero when proteins tested were those with known 3D structures. 136 474 entries of TrEMBL database were found to contain LbH-domain. Rules developed by analyzing LbH-domain containing acyltransferases, gamma-class carbonic anhydrases, and nucleotidyltransferases have led to the annotation of 17 389 TrEMBL entries which currently have no functional tag.
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Affiliation(s)
- Anu Prabha
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Petety V Balaji
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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7
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Enhancement of Production of D-Glucosamine in Escherichia coli by Blocking Three Pathways Involved in the Consumption of GlcN and GlcNAc. Mol Biotechnol 2020; 62:387-399. [PMID: 32572810 DOI: 10.1007/s12033-020-00257-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2020] [Indexed: 10/24/2022]
Abstract
D-Glucosamine is a commonly used dietary supplement that promotes cartilage health in humans. Metabolic flux analysis showed that D-glucosamine production could be increased by blocking three pathways involved in the consumption of glucosamine-6-phosphate and acetylglucosamine-6-phosphate. By homologous single-exchange, two key genes (nanE and murQ) of Escherichia coli BL21 were knocked out, respectively. The D-glucosamine yields of the engineered strains E. coli BL21ΔmurQ and E. coli BL21ΔnanE represented increases by factors of 2.14 and 1.79, respectively. Meanwhile, for bifunctional gene glmU, we only knocked out its glucosamine-1-phosphate acetyltransferase domain by 3D structural analysis to keep the engineered strain E. coli BL21glmU-Δgpa survival, which resulted in an increase in the production of D-glucosamine by a factor of 2.16. Moreover, for further increasing D-glucosamine production, two genes encoding rate-limiting enzymes, named glmS and gna1, were coexpressed by an RBS sequence in those engineered strains. The total concentrations of D-glucosamine in E. coli BL21 glmU-Δgpa', E. coli BL21ΔmurQ', and E. coli BL21ΔnanE' were 2.65 g/L, 1.73 g/L, and 1.38 g/L, which represented increases by factors of 8.83, 5.76, and 3.3, respectively.
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8
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Han X, Chen C, Yan Q, Jia L, Taj A, Ma Y. Action of Dicumarol on Glucosamine-1-Phosphate Acetyltransferase of GlmU and Mycobacterium tuberculosis. Front Microbiol 2019; 10:1799. [PMID: 31481936 PMCID: PMC6710349 DOI: 10.3389/fmicb.2019.01799] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 07/22/2019] [Indexed: 11/13/2022] Open
Abstract
Mycobacterium tuberculosis is one of most pathogenic microorganisms in the world. Previously, the bifunctional enzyme GlmU with glucosamine-1-phosphate acetyltransferase activity and N-acetylglucosamine-1-phosphate uridyltransferase activity has been suggested as a potential drug target; therefore, discovering compounds targeting GlmU acetyltransferase is necessary. The natural products were tested for inhibition of GlmU acetyltransferase activity. We found that dicumarol exhibited inhibitory effects on GlmU acetyltransferase, with a concentration achieving a 50% inhibition (IC50) value of 4.608 μg/ml (13.7 μM). The inhibition kinetics indicated that dicumarol uncompetitively inhibited acetyl CoA and showed mixed-type inhibition for glucosamine-1-phosphate (GlcN-1-P). The activity of dicumarol against M. tuberculosis H37Ra was evaluated with a minimum inhibitory concentration (MIC) value of 6.25 μg/ml (18.55 μM) in the Alamar blue assay. Dicumarol also exhibited inhibitory effects on several clinically sensitive M. tuberculosis strains and drug-resistant strains, with a range of MIC value of 6.25 to >100 μg/ml. Dicumarol increased the sensitivity of anti-tuberculosis drugs (isoniazid and rifampicin) when dicumarol was present at a low concentration. The transcriptome and proteome data of M. tuberculosis H37Ra treated by dicumarol showed that the affected genes were associated with cell wall synthesis, DNA damage and repair, metabolic processes, and signal transduction. These results provided the mechanism of dicumarol inhibition against GlmU acetyltransferase and M. tuberculosis and also suggested that dicumarol is a potential candidate for TB treatment.
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Affiliation(s)
- Xiuyan Han
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Changming Chen
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Qiulong Yan
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Liqiu Jia
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Ayaz Taj
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Yufang Ma
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China.,Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
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9
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Martinez SR, Pavani CC, Baptista MS, Becerra MC, Quevedo MA, Ribone SR. Identification of the potential biological target of N-benzenesulfonyl-1,2,3,4-tetrahydroquinoline compounds active against gram-positive and gram-negative bacteria. J Biomol Struct Dyn 2019; 38:2412-2421. [PMID: 31215842 DOI: 10.1080/07391102.2019.1633410] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The development of new antibiotics with activity towards a broad spectrum of bacteria, including multiresistant strains, is a very important topic for global public health. As part of previous works, N-benzenesulfonyl-1,2,3,4-tetrahydroquinoline (BSTHQ) derivatives were described as antimicrobial agents active against gram-positive and gram-negative pathogens. In this work, experimental and molecular modelling studies were performed in order to identify their potential biological target in the light of structure-based design efforts towards further BSTHQ derivatives. First, a carboxyfluorescein leakage assay was performed using liposomes to mimic bacterial membranes, which found no significative membrane disruption effects with respect to control samples. These results support a non-surfactant antimicrobial activity of the tested compounds. In a second stage, the inhibition of potential antimicrobial targets was screened using molecular modelling methods, taking into account previously reported druggable targets deposited in the ChEMBL database for Escherichia coli and Staphylococcus aureus. Two enzymes, namely D-glutamic acid-adding enzyme (MurD) and N-acetylglucosamine-1-phophate-uridyltransferase (GlmU), both involved in bacterial membrane synthesis, were identified as potential targets. Pharmacodynamic interaction models were developed using known MurD and GlmU inhibitors by applying state-of-the-art chemoinformatic methods (molecular docking, molecular dynamics and free energy of interaction analyses). These models were further extended to the analysis of the studied BSTHQ derivatives. Overall, our results demonstrated that the studied BSTHQ derivatives elicit their antibacterial activity by interacting with a specific molecular target, GlmU being the highly feasible one. Based on the presented results, further structure-aided design efforts towards the obtaining of novel BSTHQ derivatives are envisioned.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sol R Martinez
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET and Departamento de Ciencias Farmacéuticas, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina.,Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, SP, Brazil
| | - Christiane C Pavani
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, SP, Brazil.,Biophotonics Applied to Health Sciences, University Nove de Jullho, São Paulo, SP, Brazil
| | - Mauricio S Baptista
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, SP, Brazil
| | - María C Becerra
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET and Departamento de Ciencias Farmacéuticas, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Mario A Quevedo
- Unidad de Investigación y Desarrollo en Tecnología Farmacéutica (UNITEFA), CONICET and Departamento de Ciencias Farmacéuticas, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Sergio R Ribone
- Unidad de Investigación y Desarrollo en Tecnología Farmacéutica (UNITEFA), CONICET and Departamento de Ciencias Farmacéuticas, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
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10
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Skarbek K, Gabriel I, Szweda P, Wojciechowski M, Khan MA, Görke B, Milewski S, Milewska MJ. Synthesis and antimicrobial activity of 6-sulfo-6-deoxy-D-glucosamine and its derivatives. Carbohydr Res 2017. [PMID: 28628891 DOI: 10.1016/j.carres.2017.06.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
6-Sulfo-6-deoxy-D-glucosamine (GlcN6S), 6-sulfo-6-deoxy-D-glucosaminitol (ADGS) and their N-acetyl and methyl ester derivatives have been synthesized and tested as inhibitors of enzymes catalyzing reactions of the UDP-GlcNAc pathway in bacteria and yeasts. GlcN6S and ADGS at micromolar concentrations inhibited glucosamine-6-phosphate (GlcN6P) synthase of microbial origin. The former was also inhibitory towards fungal GlcN6P N-acetyl transferase, but at millimolar concentrations. Both compounds and their N-acetyl derivatives exhibited antimicrobial in vitro activity, with MICs in the 0.125-2.0 mg mL-1 range. Antibacterial but not antifungal activity of GlcN6S was potentiated by D-glucosamine and a synergistic antibacterial effect was observed for combination of ADGP and a dipeptide Nva-FMDP.
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Affiliation(s)
- Kornelia Skarbek
- Department of Organic Chemistry, Gdańsk University of Technology, Gdańsk, Poland
| | - Iwona Gabriel
- Department of Pharmaceutical Technology and Biochemistry, Gdańsk University of Technology, Gdańsk, Poland
| | - Piotr Szweda
- Department of Pharmaceutical Technology and Biochemistry, Gdańsk University of Technology, Gdańsk, Poland
| | - Marek Wojciechowski
- Department of Pharmaceutical Technology and Biochemistry, Gdańsk University of Technology, Gdańsk, Poland
| | - Muna A Khan
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Boris Görke
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Sławomir Milewski
- Department of Pharmaceutical Technology and Biochemistry, Gdańsk University of Technology, Gdańsk, Poland.
| | - Maria J Milewska
- Department of Organic Chemistry, Gdańsk University of Technology, Gdańsk, Poland
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Mehra R, Rani C, Mahajan P, Vishwakarma RA, Khan IA, Nargotra A. Computationally Guided Identification of Novel Mycobacterium tuberculosis GlmU Inhibitory Leads, Their Optimization, and in Vitro Validation. ACS COMBINATORIAL SCIENCE 2016; 18:100-16. [PMID: 26812086 DOI: 10.1021/acscombsci.5b00019] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Mycobacterium tuberculosis (Mtb) infections are causing serious health concerns worldwide. Antituberculosis drug resistance threatens the current therapies and causes further need to develop effective antituberculosis therapy. GlmU represents an interesting target for developing novel Mtb drug candidates. It is a bifunctional acetyltransferase/uridyltransferase enzyme that catalyzes the biosynthesis of UDP-N-acetyl-glucosamine (UDP-GlcNAc) from glucosamine-1-phosphate (GlcN-1-P). UDP-GlcNAc is a substrate for the biosynthesis of lipopolysaccharide and peptidoglycan that are constituents of the bacterial cell wall. In the current study, structure and ligand based computational models were developed and rationally applied to screen a drug-like compound repository of 20,000 compounds procured from ChemBridge DIVERSet database for the identification of probable inhibitors of Mtb GlmU. The in vitro evaluation of the in silico identified inhibitor candidates resulted in the identification of 15 inhibitory leads of this target. Literature search of these leads through SciFinder and their similarity analysis with the PubChem training data set (AID 1376) revealed the structural novelty of these hits with respect to Mtb GlmU. IC50 of the most potent identified inhibitory lead (5810599) was found to be 9.018 ± 0.04 μM. Molecular dynamics (MD) simulation of this inhibitory lead (5810599) in complex with protein affirms the stability of the lead within the binding pocket and also emphasizes on the key interactive residues for further designing. Binding site analysis of the acetyltransferase pocket with respect to the identified structural moieties provides a thorough analysis for carrying out the lead optimization studies.
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Affiliation(s)
- Rukmankesh Mehra
- Discovery
Informatics, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India
| | - Chitra Rani
- Clinical
Microbiology, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India
- Academy
of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India
| | - Priya Mahajan
- Discovery
Informatics, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India
- Academy
of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India
| | - Ram Ashrey Vishwakarma
- Discovery
Informatics, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India
| | - Inshad Ali Khan
- Clinical
Microbiology, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India
- Academy
of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India
| | - Amit Nargotra
- Discovery
Informatics, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India
- Academy
of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India
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12
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UDP-GlcNAc pathway: Potential target for inhibitor discovery against M. tuberculosis. Eur J Pharm Sci 2016; 83:62-70. [DOI: 10.1016/j.ejps.2015.12.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 11/29/2015] [Accepted: 12/08/2015] [Indexed: 11/23/2022]
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13
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Sharma R, Lambu MR, Jamwal U, Rani C, Chib R, Wazir P, Mukherjee D, Chaubey A, Khan IA. Escherichia coli N-Acetylglucosamine-1-Phosphate-Uridyltransferase/Glucosamine-1-Phosphate-Acetyltransferase (GlmU) Inhibitory Activity of Terreic Acid Isolated from Aspergillus terreus. ACTA ACUST UNITED AC 2016; 21:342-53. [PMID: 26762501 DOI: 10.1177/1087057115625308] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 11/19/2015] [Indexed: 11/16/2022]
Abstract
Secondary metabolite of Aspergillus terreus, terreic acid, is a reported potent antibacterial that was identified more than 60 years ago, but its cellular target(s) are still unknown. Here we screen its activity against the acetyltransferase domain of a bifunctional enzyme, Escherichia coli N-acetylglucosamine-1-phosphate-uridyltransferase/glucosamine-1-phosphate-acetyltransferase (GlmU). An absorbance-based assay was used to screen terreic acid against the acetyltransferase activity of E. coli GlmU. Terreic acid was found to inhibit the acetyltransferase domain of E. coli GlmU with an IC50 of 44.24 ± 1.85 µM. Mode of inhibition studies revealed that terreic acid was competitive with AcCoA and uncompetitive with GlcN-1-P. It also exhibited concentration-dependent killing of E. coli ATCC 25922 up to 4× minimum inhibitory concentration and inhibited the growth of biofilms generated by E. coli. Characterization of resistant mutants established mutation in the acetyltransferase domain of GlmU. Terreic acid was also found to be metabolically stable in the in vitro incubations with rat liver microsome in the presence of a NADPH regenerating system. The studies reported here suggest that terreic acid is a potent antimicrobial agent and support that E. coli GlmU acetyltransferase is a molecular target of terreic acid, resulting in its antibacterial activity.
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Affiliation(s)
- Rashmi Sharma
- Clinical Microbiology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, India Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, India
| | - Mallikharjuna Rao Lambu
- Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, India Natural Products Chemistry: Microbes, CSIR-Indian Institute of Integrative Medicine (CSIR), Canal Road, Jammu, India
| | - Urmila Jamwal
- Fermentation Technology Division, CSIR-Indian Institute of Integrative Medicine (CSIR), Canal Road, Jammu Tawi, India
| | - Chitra Rani
- Clinical Microbiology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, India Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, India
| | - Reena Chib
- Clinical Microbiology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, India
| | - Priya Wazir
- Instrumentation Division, CSIR-Indian Institute of Integrative Medicine (CSIR), Canal Road, Jammu Tawi, India
| | - Debaraj Mukherjee
- Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, India Natural Products Chemistry: Microbes, CSIR-Indian Institute of Integrative Medicine (CSIR), Canal Road, Jammu, India
| | - Asha Chaubey
- Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, India Fermentation Technology Division, CSIR-Indian Institute of Integrative Medicine (CSIR), Canal Road, Jammu Tawi, India
| | - Inshad Ali Khan
- Clinical Microbiology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, India Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, India
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14
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Sharma R, Rani C, Mehra R, Nargotra A, Chib R, Rajput VS, Kumar S, Singh S, Sharma PR, Khan IA. Identification and characterization of novel small molecule inhibitors of the acetyltransferase activity of Escherichia coli N-acetylglucosamine-1-phosphate-uridyltransferase/glucosamine-1-phosphate-acetyltransferase (GlmU). Appl Microbiol Biotechnol 2015; 100:3071-85. [PMID: 26563552 DOI: 10.1007/s00253-015-7123-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 08/19/2015] [Accepted: 10/26/2015] [Indexed: 10/22/2022]
Abstract
This study aims at identifying novel chemical scaffolds as inhibitors specific to the acetyltransferase domain of a bifunctional enzyme, Escherichia coli GlmU, involved in the cell wall biosynthesis of Gram-negative organisms. A two-pronged approach was used to screen a 50,000 small-molecule library. Using the first approach, the library was in silico screened by docking the library against acetyltransferase domain of E. coli GlmU studies. In the second approach, complete library was screened against Escherichia coli ATCC 25922 to identify the whole cell active compounds. Active compounds from both the screens were screened in a colorimetric absorbance-based assay to identify inhibitors of acetyltransferase domain of E. coli GlmU which resulted in the identification of 1 inhibitor out of 56 hits identified by in silico screening and 4 inhibitors out of 35 whole cell active compounds on Gram-negative bacteria with the most potent inhibitor showing IC50 of 1.40 ± 0.69 μM. Mode of inhibition studies revealed these inhibitors to be competitive with AcCoA and uncompetitive with GlcN-1-P. These selected inhibitors were also tested for their antibacterial and cytotoxic activities. Compounds 5175178 and 5215319 exhibited antibacterial activity that co-related with GlmU inhibition. These compounds, therefore, represent novel chemical scaffolds targeting acetyltransferase activity of E. coli GlmU.
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Affiliation(s)
- Rashmi Sharma
- Clinical Microbiology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India.,Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
| | - Chitra Rani
- Clinical Microbiology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India.,Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
| | - Rukmankesh Mehra
- Discovery Informatics Division, CSIR-Indian Institute of Integrative Medicine (CSIR), Canal Road, Jammu, 180001, India
| | - Amit Nargotra
- Discovery Informatics Division, CSIR-Indian Institute of Integrative Medicine (CSIR), Canal Road, Jammu, 180001, India.,Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
| | - Reena Chib
- Clinical Microbiology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India
| | - Vikrant S Rajput
- Clinical Microbiology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India.,Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
| | - Sunil Kumar
- Clinical Microbiology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India.,Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
| | - Samsher Singh
- Clinical Microbiology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India.,Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
| | - Parduman R Sharma
- Cancer Pharmacology Division, CSIR-Indian Institute of Integrative Medicine (CSIR), Canal Road, Jammu Tawi, 180001, India.,Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
| | - Inshad A Khan
- Clinical Microbiology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India. .,Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India.
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15
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Gonen S, DiMaio F, Gonen T, Baker D. Design of ordered two-dimensional arrays mediated by noncovalent protein-protein interfaces. Science 2015; 348:1365-8. [PMID: 26089516 DOI: 10.1126/science.aaa9897] [Citation(s) in RCA: 179] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
We describe a general approach to designing two-dimensional (2D) protein arrays mediated by noncovalent protein-protein interfaces. Protein homo-oligomers are placed into one of the seventeen 2D layer groups, the degrees of freedom of the lattice are sampled to identify configurations with shape-complementary interacting surfaces, and the interaction energy is minimized using sequence design calculations. We used the method to design proteins that self-assemble into layer groups P 3 2 1, P 4 2(1) 2, and P 6. Projection maps of micrometer-scale arrays, assembled both in vitro and in vivo, are consistent with the design models and display the target layer group symmetry. Such programmable 2D protein lattices should enable new approaches to structure determination, sensing, and nanomaterial engineering.
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Affiliation(s)
- Shane Gonen
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA. Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. Institute for Protein Design, University of Washington, Seattle, WA 98195, USA. Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Tamir Gonen
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA.
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. Institute for Protein Design, University of Washington, Seattle, WA 98195, USA. Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
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16
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Edwards TE, Gardberg AS, Phan IQH, Zhang Y, Staker BL, Myler PJ, Lorimer DD. Structure of uridine diphosphate N-acetylglucosamine pyrophosphorylase from Entamoeba histolytica. Acta Crystallogr F Struct Biol Commun 2015; 71:560-5. [PMID: 25945709 PMCID: PMC4427165 DOI: 10.1107/s2053230x1500179x] [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: 12/01/2014] [Accepted: 01/27/2015] [Indexed: 11/10/2022] Open
Abstract
Uridine diphosphate N-acetylglucosamine pyrophosphorylase (UAP) catalyzes the final step in the synthesis of UDP-GlcNAc, which is involved in cell-wall biogenesis in plants and fungi and in protein glycosylation. Small-molecule inhibitors have been developed against UAP from Trypanosoma brucei that target an allosteric pocket to provide selectivity over the human enzyme. A 1.8 Å resolution crystal structure was determined of UAP from Entamoeba histolytica, an anaerobic parasitic protozoan that causes amoebic dysentery. Although E. histolytica UAP exhibits the same three-domain global architecture as other UAPs, it appears to lack three α-helices at the N-terminus and contains two amino acids in the allosteric pocket that make it appear more like the enzyme from the human host than that from the other parasite T. brucei. Thus, allosteric inhibitors of T. brucei UAP are unlikely to target Entamoeba UAPs.
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Affiliation(s)
- Thomas E. Edwards
- Seattle Structural Genomics Center for Infectious Disease, USA
- Beryllium, Bainbridge Island, WA 98110, USA
| | - Anna S. Gardberg
- Seattle Structural Genomics Center for Infectious Disease, USA
- Beryllium, Bainbridge Island, WA 98110, USA
| | - Isabelle Q. H. Phan
- Seattle Structural Genomics Center for Infectious Disease, USA
- Seattle Biomedical Research Institute, Seattle, WA 98109, USA
| | - Yang Zhang
- Seattle Structural Genomics Center for Infectious Disease, USA
- Seattle Biomedical Research Institute, Seattle, WA 98109, USA
| | - Bart L. Staker
- Seattle Structural Genomics Center for Infectious Disease, USA
- Seattle Biomedical Research Institute, Seattle, WA 98109, USA
| | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease, USA
- Seattle Biomedical Research Institute, Seattle, WA 98109, USA
- Departments of Global Health and Medical Education and Biomedical Informatics, University of Washington, Seattle, WA 98195, USA
| | - Donald D. Lorimer
- Seattle Structural Genomics Center for Infectious Disease, USA
- Beryllium, Bainbridge Island, WA 98110, USA
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17
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Mehra R, Sharma R, Khan IA, Nargotra A. Identification and optimization of Escherichia coli GlmU inhibitors: An in silico approach with validation thereof. Eur J Med Chem 2015; 92:78-90. [DOI: 10.1016/j.ejmech.2014.12.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 11/21/2014] [Accepted: 12/18/2014] [Indexed: 12/25/2022]
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18
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Purification and biochemical characterisation of GlmU from Yersinia pestis. Arch Microbiol 2014; 197:371-8. [PMID: 25417006 DOI: 10.1007/s00203-014-1065-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 11/12/2014] [Accepted: 11/16/2014] [Indexed: 12/22/2022]
Abstract
Antibiotic resistance has emerged as a real threat to mankind, rendering many compounds ineffective in the fight against bacterial infection, including for significant diseases such as plague caused by Yersinia pestis. Essential genes have been identified as promising targets for inhibiting with new classes of compounds. Previously, the gene encoding the bifunctional UDP-N-acetylglucosamine pyrophosphorylase/glucosamine-1-phosphate N-acetyltransferase enzyme GlmU was confirmed as an essential gene in Yersinia. As a step towards exploiting this target for antimicrobial screening, we undertook a biochemical characterisation of the Yersinia GlmU. Effects of pH and magnesium concentration on the acetyltransferase and uridyltransferase activities were analysed, and kinetic parameters were determined. The acetyltransferase activity, which is strongly increased in the presence of reducing agent, was shown to be susceptible to oxidation and thiol-specific reagents.
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19
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Abstract
The synthesis of the bacterial peptidoglycan has been recognized for over 50 years as fertile ground for antibacterial discovery. Initially, empirical screening of natural products for inhibition of bacterial growth detected many chemical classes of antibiotics whose specific mechanisms of action were eventually dissected and defined. Of the nontoxic antibiotics discovered, most were found to be inhibitors of either protein synthesis or cell wall synthesis, which led to more directed screening for inhibitors of these pathways. Directed screening and design programs for cell wall inhibitors have been undertaken since the 1960s. In that time it has become clear that, while certain steps and intermediates have yielded selective inhibitors and are established targets, other potential targets have not yielded inhibitors whose antibacterial activity is proven to be solely due to that inhibition. Why has this search been so problematic? Are the established targets still worth pursuing? This review will attempt to answer these and other questions and evaluate the viability of targets related to peptidoglycan synthesis.
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Affiliation(s)
- Lynn L Silver
- LL Silver Consulting, LLC, Springfield, New Jersey 07081, USA.
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20
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Inhibitors of the acetyltransferase domain of N-acetylglucosamine-1-phosphate-uridylyltransferase/glucosamine-1-phosphate-acetyltransferase (GlmU). Part 2: Optimization of physical properties leading to antibacterial aryl sulfonamides. Bioorg Med Chem Lett 2012; 22:7019-23. [DOI: 10.1016/j.bmcl.2012.10.003] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Revised: 09/24/2012] [Accepted: 10/01/2012] [Indexed: 11/22/2022]
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21
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An aminoquinazoline inhibitor of the essential bacterial cell wall synthetic enzyme GlmU has a unique non-protein-kinase-like binding mode. Biochem J 2012; 446:405-13. [PMID: 22721802 DOI: 10.1042/bj20120596] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
GlmU is a bifunctional enzyme with acetyltransferase and uridyltransferase activities, and is essential for the biosynthesis of the bacterial cell wall. Inhibition results in a loss of cell viability. GlmU is therefore considered a potential target for novel antibacterial agents. A HTS (high-throughput screen) identified a series of aminoquinazolines with submicromolar potency against the uridyltransferase reaction. Biochemical and biophysical characterization showed competition with UTP binding. We determined the crystal structure of a representative aminoquinazoline bound to the Haemophilus influenzae isoenzyme at a resolution of 2.0 Å. The inhibitor occupies part of the UTP site, skirts the outer perimeter of the GlcNAc1-P (N-acetylglucosamine-1-phosphate) pocket and anchors a hydrophobic moiety into a lipophilic pocket. Our SAR (structure-activity relationship) analysis shows that all of these interactions are essential for inhibitory activity in this series. The crystal structure suggests that the compound would block binding of UTP and lock GlmU in an apo-enzyme-like conformation, thus interfering with its enzymatic activity. Our lead generation effort provides ample scope for further optimization of these compounds for antibacterial drug discovery.
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