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Gaur V, Kumar N, Vyas A, Chowdhury D, Singh J, Bera S. Identification of potential inhibitors against Escherichia coli Mur D enzyme to combat rising drug resistance: an in-silico approach. J Biomol Struct Dyn 2023:1-11. [PMID: 38149858 DOI: 10.1080/07391102.2023.2297007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 12/13/2023] [Indexed: 12/28/2023]
Abstract
Indiscriminate use of anti-microbial agents has resulted in the inception, frequency, and spread of antibiotic resistance among targeted bacterial pathogens and the commensal flora. Mur enzymes, playing a crucial role in cell-wall synthesis, are one of the most appropriate targets for developing novel inhibitors against antibiotic-resistant bacterial pathogens. In the present study, in-silico high-throughput virtual (HTVS) and Standard-Precision (SP) screening was carried out with 0.3 million compounds from several small-molecule libraries against the E. coli Mur D enzyme (PDB ID 2UUP). The docked complexes were further subjected to extra-precision (XP) docking calculations, and highest Glide-score compound was further subjected to molecular simulation studies. The top six virtual hits (S1-S6) displayed a glide score (G-score) within the range of -9.013 to -7.126 kcal/mol and compound S1 was found to have the highest stable interactions with the Mur D enzyme (2UUP) of E. coli. The stability of compound S1 with the Mur D (2UUP) complex was validated by a 100-ns molecular dynamics simulation. Binding free energy calculation by the MM-GBSA strategy of the S1-2UUP (Mur D) complex established van der Waals, hydrogen bonding, lipophilic, and Coulomb energy terms as significant favorable contributors for ligand binding. The final lead molecules were subjected to ADMET predictions to study their pharmacokinetic properties and displayed promising results, except for certain modifications required to improve QPlogHERG values. So, the compounds screened against the Mur D enzyme can be further studied as preparatory points for in-vivo studies to develop potential drugs. HIGHLIGHTSE.coli is a common cause of urinary tract infections.E.coli MurD enzyme is a suitable target for drug development.Novel inhibitors against E.coli MurD enzyme were identified.Molecular dynamics studies identified in-silico potential of identified compound.ADMET predictions and Lipinski's rule of five studies showed promising results.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Vinita Gaur
- Department of Microbiology, School of Bioengineering and Biosciences, Lovely Professional University, Punjab, India
| | - Neeraj Kumar
- Department of Pharmaceutical Chemistry, Bhupal Nobles' University, Udaipur, Rajasthan, India
| | - Ashish Vyas
- Department of Microbiology, School of Bioengineering and Biosciences, Lovely Professional University, Punjab, India
| | - Debabrata Chowdhury
- School of Medicine - Infectious Diseases, Stanford University, Stanford, CA, USA
| | - Joginder Singh
- Department of Microbiology, School of Bioengineering and Biosciences, Lovely Professional University, Punjab, India
| | - Surojit Bera
- Department of Microbiology, School of Bioengineering and Biosciences, Lovely Professional University, Punjab, India
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2
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Hervin V, Roy V, Agrofoglio LA. Antibiotics and Antibiotic Resistance-Mur Ligases as an Antibacterial Target. Molecules 2023; 28:8076. [PMID: 38138566 PMCID: PMC10745416 DOI: 10.3390/molecules28248076] [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: 07/29/2023] [Revised: 11/09/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
The emergence of Multidrug Resistance (MDR) strains of bacteria has accelerated the search for new antibacterials. The specific bacterial peptidoglycan biosynthetic pathway represents opportunities for the development of novel antibacterial agents. Among the enzymes involved, Mur ligases, described herein, and especially the amide ligases MurC-F are key targets for the discovery of multi-inhibitors, as they share common active sites and structural features.
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Affiliation(s)
| | - Vincent Roy
- ICOA UMR CNRS 7311, Université d’Orléans et CNRS, Rue de Chartres, 45067 Orléans, France;
| | - Luigi A. Agrofoglio
- ICOA UMR CNRS 7311, Université d’Orléans et CNRS, Rue de Chartres, 45067 Orléans, France;
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3
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Zhuang Z, Cummings SW, Roll-Mecak A, Tanner ME. Phosphinic acid-based inhibitors of tubulin polyglycylation. Chem Commun (Camb) 2022; 58:6530-6533. [PMID: 35579270 DOI: 10.1039/d2cc01783k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Tubulin polyglycylation is a posttranslational modification that occurs primarily on the axonemes of flagella and cilia and has been shown to be essential for proper sperm motility. Inhibitors of both the initiase and elongase ligases (TTLL8 and TTLL10) are shown to inhibit tubulin glycylation in the low micromolar range.
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Affiliation(s)
- Zaile Zhuang
- Department of Chemistry, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada.
| | - Steven W Cummings
- Cell Biology and Biophysics Unit, National Institute of Neurological Disorders and Stroke, and Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD, 20892, USA.
| | - Antonina Roll-Mecak
- Cell Biology and Biophysics Unit, National Institute of Neurological Disorders and Stroke, and Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD, 20892, USA.
| | - Martin E Tanner
- Department of Chemistry, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada.
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4
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Design, synthesis and molecular modelling of phenoxyacetohydrazide derivatives as Staphylococcus aureus MurD inhibitors. CHEMICAL PAPERS 2021. [DOI: 10.1007/s11696-020-01380-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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5
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Li W, Yu B. Temporary ether protecting groups at the anomeric center in complex carbohydrate synthesis. Adv Carbohydr Chem Biochem 2020; 77:1-69. [PMID: 33004110 DOI: 10.1016/bs.accb.2019.10.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The synthesis of a carbohydrate building block usually starts with introduction of a temporary protecting group at the anomeric center and ends with its selective cleavage for further transformation. Thus, the choice of the anomeric temporary protecting group must be carefully considered because it should retain intact during the whole synthetic manipulation, and it should be chemoselectively removable without affecting other functional groups at a late stage in the synthesis. Etherate groups are the most widely used temporary protecting groups at the anomeric center, generally including allyl ethers, MP (p-methoxyphenyl) ethers, benzyl ethers, PMB (p-methoxybenzyl) eithers, and silyl ethers. This chapter provides a comprehensive review on their formation, cleavage, and applications in the synthesis of complex carbohydrates.
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Affiliation(s)
- Wei Li
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China.
| | - Biao Yu
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China.
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6
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MurE inhibitors as antibacterial agents: a review. J INCL PHENOM MACRO 2020. [DOI: 10.1007/s10847-020-01018-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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7
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Azam MA, Jupudi S. MurD inhibitors as antibacterial agents: a review. CHEMICAL PAPERS 2020. [DOI: 10.1007/s11696-020-01057-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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8
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Jupudi S, Azam MA, Wadhwani A. Synthesis, molecular docking, binding free energy calculation and molecular dynamics simulation studies of benzothiazol-2-ylcarbamodithioates as Staphylococcus aureus MurD inhibitors. J Recept Signal Transduct Res 2020; 39:283-293. [PMID: 31538846 DOI: 10.1080/10799893.2019.1663538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
A new series of benzothiazol-2-ylcarbamodithioate functional compounds 5a-f has been designed, synthesized and characterized by spectral data. These compounds were screened for their in vitro antibacterial activity against strains of Staphylococcus aureus (NCIM 5021, NCIM 5022 and methicillin-resistant isolate 43300), Bacillus subtilis (NCIM 2545), Escherichia coli (NCIM 2567), Klebsiella pneumoniae (NCIM 2706) and Psudomonas aeruginosa (NCIM 2036). Compounds 5a and 5d exhibited significant activity against all the tested bacterial strains. Specifically, compounds 5a and 5d showed potent activity against K. pneumoniae (NCIM 2706), while compound 5a also displayed potent activity against S. aureus (NCIM 5021). Compound 5d showed minimum IC50 value of 13.37 μM against S. aureus MurD enzyme. Further, the binding interactions of compounds 5a-f in the catalytic pocket have been investigated using the extra-precision molecular docking and binding free energy calculation by MM-GBSA approach. A 30 ns molecular dynamics simulation of 5d/modeled S. aureus MurD enzyme was performed to determine the stability of the predicted binding conformation.
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Affiliation(s)
- Srikanth Jupudi
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy , Ooty , India
| | - Mohammed Afzal Azam
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy , Ooty , India
| | - Ashish Wadhwani
- Department of Biotechnology, JSS College of Pharmacy , Ooty , India
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Shan L, Wenling Q, Mauro P, Stefano B. Antibacterial Agents Targeting the Bacterial Cell Wall. Curr Med Chem 2020; 27:2902-2926. [PMID: 32003656 DOI: 10.2174/0929867327666200128103653] [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] [Received: 08/06/2019] [Revised: 10/16/2019] [Accepted: 10/23/2019] [Indexed: 11/22/2022]
Abstract
The introduction of antibiotics to treat bacterial infections either by killing or blocking their growth has been accompanied by the studies of mechanism that allows the drugs to kill the bacteria or to stop their proliferation. In such a scenario, the emergence of antibacterial agents active on the bacterial cell wall has been of fundamental importance in the fight against bacterial agents responsible for severe diseases. As a matter of fact, the cell wall, which plays many roles during the lifecycle, is an essential constituent of most bacteria. This overview focuses on the intracellular steps of peptidoglycan biosynthesis and the research of new antibacterial agents based on the enzymes involved in these early steps of the formation of cell membrane components.
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Affiliation(s)
- Li Shan
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, China
| | - Qin Wenling
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, China
| | - Panunzio Mauro
- Isof-CNR Chemistry Department, Via Selmi, 2, 40126 Bologna, Italy
| | - Biondi Stefano
- BioVersys AG, C/o Technologiepark Basel, Hochbergerstrasse 60c, CH- 4057 Basel, Switzerland
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10
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Structure-based virtual screening to identify inhibitors against Staphylococcus aureus MurD enzyme. Struct Chem 2019. [DOI: 10.1007/s11224-019-01330-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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11
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Azam MA, Jupudi S, Saha N, Paul RK. Combining molecular docking and molecular dynamics studies for modelling Staphylococcus aureus MurD inhibitory activity. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2019; 30:1-20. [PMID: 30406684 DOI: 10.1080/1062936x.2018.1539034] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Indexed: 06/08/2023]
Abstract
The ATP-dependent bacterial MurD enzyme catalyses the formation of the peptide bond between cytoplasmic intermediate UDP-N-acetylmuramoyl-L-alanine and D-glutamic acid. This is essential for bacterial cell wall peptidoglycan synthesis in both Gram-positive and Gram-negative bacteria. MurD is recognized as an important target for the development of new antibacterial agents. In the present study we prepared the 3D-stucture of the catalytic pocket of the Staphylococcus aureus MurD enzyme by homology modelling. Extra-precision docking, binding free energy calculation by the MM-GBSA approach and a 40 ns molecular dynamics (MD) simulation of 2-thioxothiazolidin-4-one based inhibitor $1 was carried out to elucidate its inhibition potential for the S. aureus MurD enzyme. Molecular docking results showed that Lys19, Gly147, Tyr148, Lys328, Thr330 and Phe431 residues are responsible for the inhibitor-protein complex stabilization. Binding free energy calculation revealed electrostatic solvation and van der Waals energy components as major contributors for the inhibitor binding. The inhibitor-modelled S. aureus protein complex had a stable conformation in response to the atomic flexibility and interaction, when subjected to MD simulation at 40 ns in aqueous solution. We designed some molecules as potent inhibitors of S. aureus MurD, and to validate the stability of the designed molecule D1-modelled protein complex we performed a 20 ns MD simulation. Results obtained from this study can be utilized for the design of potent S. aureus MurD inhibitors.
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Affiliation(s)
- M A Azam
- a Department of Pharmaceutical Chemistry , JSS College of Pharmacy, Tamil Nadu (A Constituent College of JSS Academy of Higher Education and Research, Mysuru) , India
| | - S Jupudi
- a Department of Pharmaceutical Chemistry , JSS College of Pharmacy, Tamil Nadu (A Constituent College of JSS Academy of Higher Education and Research, Mysuru) , India
| | - N Saha
- a Department of Pharmaceutical Chemistry , JSS College of Pharmacy, Tamil Nadu (A Constituent College of JSS Academy of Higher Education and Research, Mysuru) , India
| | - R K Paul
- a Department of Pharmaceutical Chemistry , JSS College of Pharmacy, Tamil Nadu (A Constituent College of JSS Academy of Higher Education and Research, Mysuru) , India
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12
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Viveros-Ceballos JL, Ordóñez M, Sayago FJ, Cativiela C. Stereoselective Synthesis of α-Amino-C-phosphinic Acids and Derivatives. Molecules 2016; 21:molecules21091141. [PMID: 27589703 PMCID: PMC6274224 DOI: 10.3390/molecules21091141] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 08/25/2016] [Accepted: 08/25/2016] [Indexed: 11/29/2022] Open
Abstract
α-Amino-C-phosphinic acids and derivatives are an important group of compounds of synthetic and medicinal interest and particular attention has been dedicated to their stereoselective synthesis in recent years. Among these, phosphinic pseudopeptides have acquired pharmacological importance in influencing physiologic and pathologic processes, primarily acting as inhibitors for proteolytic enzymes where molecular stereochemistry has proven to be critical. This review summarizes the latest developments in the asymmetric synthesis of acyclic and phosphacyclic α-amino-C-phosphinic acids and derivatives, following in the first case an order according to the strategy used, whereas for cyclic compounds the nitrogen embedding in the heterocyclic core is considered. In addition selected examples of pharmacological implications of title compounds are also disclosed.
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Affiliation(s)
- José Luis Viveros-Ceballos
- Secretaría Académica, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, 62209 Cuernavaca, Morelos, Mexico.
| | - Mario Ordóñez
- Centro de Investigaciones Químicas-IICBA, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, 62209 Cuernavaca, Morelos, Mexico.
| | - Francisco J Sayago
- Departamento de Química Orgánica, Universidad de Zaragoza-CSIC, ISQCH, 50009 Zaragoza, Spain.
| | - Carlos Cativiela
- Departamento de Química Orgánica, Universidad de Zaragoza-CSIC, ISQCH, 50009 Zaragoza, Spain.
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13
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References. Antibiotics (Basel) 2015. [DOI: 10.1128/9781555819316.refs] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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14
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A novel 2-oxoindolinylidene inhibitor of bacterial MurD ligase: Enzyme kinetics, protein-inhibitor binding by NMR and a molecular dynamics study. Eur J Med Chem 2014; 83:92-101. [PMID: 24952377 DOI: 10.1016/j.ejmech.2014.06.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Revised: 05/30/2014] [Accepted: 06/10/2014] [Indexed: 11/24/2022]
Abstract
N-(5-(5-nitro-2-oxo-1,2-dihydro-3H-indol-3-ylidene)4-oxo-2-thioxo-1,3-thiazolidin-3-yl)nicotinamide, a 2-oxoindolinylidene derivative with novel structure scaffold, was evaluated for inhibition potency against the MurD enzyme from Escherichia coli using an enzyme steady-state kinetics study. The compound exerted competitive inhibition with respect to UMA, a MurD substrate, and affected bacterial growth. Furthermore, we isolated and purified (13)C selectively labeled MurD enzyme from E. coli and evaluated the binding interactions of the new compound using the (1)H/(13)C-HSQC 2D NMR method. Molecular dynamics calculations showed stable structure for the MurD-inhibitor complex. The binding mode of novel inhibitor was determined and compared to naphthalene-N-sulfonamide-d-Glu derivatives, transition state mimicking inhibitors, UMA and AMP-PCP, an ATP analog. It binds to the UDP/MurNAc binding region. In contrast to transition state mimicking inhibitors, it does not interact with the enzyme's C-terminal domain, which can be beneficial for ligand binding. A pharmacophore pattern was established for the design of novel drugs having a propensity to inhibit a broad spectrum of Mur enzymes.
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15
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Liu Y, Garnham CP, Roll-Mecak A, Tanner ME. Phosphinic acid-based inhibitors of tubulin polyglutamylases. Bioorg Med Chem Lett 2013; 23:4408-12. [PMID: 23777780 DOI: 10.1016/j.bmcl.2013.05.069] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 05/16/2013] [Accepted: 05/20/2013] [Indexed: 10/26/2022]
Abstract
Tubulin is subject to a reversible post-translational modification involving polyglutamylation and deglutamylation of glutamate residues in its C-terminal tail. This process plays key roles in regulating the function of microtubule associated proteins, neuronal development, and metastatic progression. This study describes the synthesis and testing of three phosphinic acid-based inhibitors that have been designed to inhibit both the glutamylating and deglutamylating enzymes. The compounds were tested against the polyglutamylase TTLL7 using tail peptides as substrates (100 μM) and the most potent inhibitor displayed an IC₅₀ value of 150 μM. The incorporation of these compounds into tubulin C-terminal tail peptides may lead to more potent TTLL inhibitors.
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Affiliation(s)
- Yanjie Liu
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z1
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16
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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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17
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Simčič M, Sosič I, Hodošček M, Barreteau H, Blanot D, Gobec S, Grdadolnik SG. The binding mode of second-generation sulfonamide inhibitors of MurD: clues for rational design of potent MurD inhibitors. PLoS One 2012; 7:e52817. [PMID: 23285193 PMCID: PMC3527612 DOI: 10.1371/journal.pone.0052817] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 11/23/2012] [Indexed: 11/19/2022] Open
Abstract
A series of optimized sulfonamide derivatives was recently reported as novel inhibitors of UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase (MurD). These are based on naphthalene-N-sulfonyl-D-glutamic acid and have the D-glutamic acid replaced with rigidified mimetics. Here we have defined the binding site of these novel ligands to MurD using (1)H/(13)C heteronuclear single quantum correlation. The MurD protein was selectively (13)C-labeled on the methyl groups of Ile (δ1 only), Leu and Val, and was isolated and purified. Crucial Ile, Leu and Val methyl groups in the vicinity of the ligand binding site were identified by comparison of chemical shift perturbation patterns among the ligands with various structural elements and known binding modes. The conformational and dynamic properties of the bound ligands and their binding interactions were examined using the transferred nuclear Overhauser effect and saturation transfer difference. In addition, the binding mode of these novel inhibitors was thoroughly examined using unrestrained molecular dynamics simulations. Our results reveal the complex dynamic behavior of ligand-MurD complexes and its influence on ligand-enzyme contacts. We further present important findings for the rational design of potent Mur ligase inhibitors.
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Affiliation(s)
- Mihael Simčič
- EN-FIST Centre of Excellence, Ljubljana, Slovenia
- Laboratory of Biomolecular Structure, National Institute of Chemistry, Ljubljana, Slovenia
| | - Izidor Sosič
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Milan Hodošček
- Laboratory of Molecular Modeling, National Institute of Chemistry, Ljubljana, Slovenia
| | - Hélène Barreteau
- Laboratoire des Enveloppes Bactériennes et Antibiotiques, Université Paris-Sud, Orsay, France
| | - Didier Blanot
- Laboratoire des Enveloppes Bactériennes et Antibiotiques, Université Paris-Sud, Orsay, France
- Centre National de la Recherche Scientifique, Orsay, France
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Simona Golič Grdadolnik
- EN-FIST Centre of Excellence, Ljubljana, Slovenia
- Laboratory of Biomolecular Structure, National Institute of Chemistry, Ljubljana, Slovenia
- * E-mail:
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Synthesis and modifications of phosphinic dipeptide analogues. Molecules 2012; 17:13530-68. [PMID: 23154272 PMCID: PMC6268094 DOI: 10.3390/molecules171113530] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Revised: 11/09/2012] [Accepted: 11/12/2012] [Indexed: 01/01/2023] Open
Abstract
Pseudopeptides containing the phosphinate moiety (-P(O)(OH)CH2-) have been studied extensively, mainly as transition state analogue inhibitors of metalloproteases. The key synthetic aspect of their chemistry is construction of phosphinic dipeptide derivatives bearing appropriate side-chain substituents. Typically, this synthesis involves a multistep preparation of two individual building blocks, which are combined in the final step. As this methodology does not allow simple variation of the side-chain structure, many efforts have been dedicated to the development of alternative approaches. Recent achievements in this field are summarized in this review. Improved methods for the formation of the phosphinic peptide backbone, including stereoselective and multicomponent reactions, are presented. Parallel modifications leading to the structurally diversified substituents are also described. Finally, selected examples of the biomedical applications of the title compounds are given.
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Anusuya S, Natarajan J. Multi-targeted therapy for leprosy: insilico strategy to overcome multi drug resistance and to improve therapeutic efficacy. INFECTION GENETICS AND EVOLUTION 2012; 12:1899-910. [PMID: 22981928 DOI: 10.1016/j.meegid.2012.08.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2012] [Revised: 08/01/2012] [Accepted: 08/17/2012] [Indexed: 02/02/2023]
Abstract
Leprosy remains a major public health problem, since single and multi-drug resistance has been reported worldwide over the last two decades. In the present study, we report the novel multi-targeted therapy for leprosy to overcome multi drug resistance and to improve therapeutic efficacy. If multiple enzymes of an essential metabolic pathway of a bacterium were targeted, then the therapy would become more effective and can prevent the occurrence of drug resistance. The MurC, MurD, MurE and MurF enzymes of peptidoglycan biosynthetic pathway were selected for multi targeted therapy. The conserved or class specific active site residues important for function or stability were predicted using evolutionary trace analysis and site directed mutagenesis studies. Ten such residues which were present in at least any three of the four Mur enzymes (MurC, MurD, MurE and MurF) were identified. Among the ten residues G125, K126, T127 and G293 (numbered based on their position in MurC) were found to be conserved in all the four Mur enzymes of the entire bacterial kingdom. In addition K143, T144, T166, G168, H234 and Y329 (numbered based on their position in MurE) were significant in binding substrates and/co-factors needed for the functional events in any three of the Mur enzymes. These are the probable residues for designing newer anti-leprosy drugs in an attempt to reduce drug resistance.
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Affiliation(s)
- Shanmugam Anusuya
- Department of Bioinformatics, VMKV Engineering College, Vinayaka Missions University, Salem 636 308, India.
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Virtual screening of phenylsulfonamido-3-morpholinopropan-2-yl dihydrogen phosphate derivatives as novel inhibitors of MurC–MurF ligases from Mycobacterium leprae. Med Chem Res 2012. [DOI: 10.1007/s00044-011-9958-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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21
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Second-generation sulfonamide inhibitors of D-glutamic acid-adding enzyme: activity optimisation with conformationally rigid analogues of D-glutamic acid. Eur J Med Chem 2011; 46:2880-94. [PMID: 21524830 DOI: 10.1016/j.ejmech.2011.04.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Revised: 03/24/2011] [Accepted: 04/03/2011] [Indexed: 01/06/2023]
Abstract
D-Glutamic acid-adding enzyme (MurD) catalyses the essential addition of d-glutamic acid to the cytoplasmic peptidoglycan precursor UDP-N-acetylmuramoyl-l-alanine, and as such it represents an important antibacterial drug-discovery target enzyme. Based on a series of naphthalene-N-sulfonyl-d-Glu derivatives synthesised recently, we synthesised two series of new, optimised sulfonamide inhibitors of MurD that incorporate rigidified mimetics of d-Glu. The compounds that contained either constrained d-Glu or related rigid d-Glu mimetics showed significantly better inhibitory activities than the parent compounds, thereby confirming the advantage of molecular rigidisation in the design of MurD inhibitors. The binding modes of the best inhibitors were examined with high-resolution NMR spectroscopy and X-ray crystallography. We have solved a new crystal structure of the complex of MurD with an inhibitor bearing a 4-aminocyclohexane-1,3-dicarboxyl moiety. These data provide an additional step towards the development of sulfonamide inhibitors with potential antibacterial activities.
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Abstract
The discovery of novel small-molecule antibacterial drugs has been stalled for many years. The purpose of this review is to underscore and illustrate those scientific problems unique to the discovery and optimization of novel antibacterial agents that have adversely affected the output of the effort. The major challenges fall into two areas: (i) proper target selection, particularly the necessity of pursuing molecular targets that are not prone to rapid resistance development, and (ii) improvement of chemical libraries to overcome limitations of diversity, especially that which is necessary to overcome barriers to bacterial entry and proclivity to be effluxed, especially in Gram-negative organisms. Failure to address these problems has led to a great deal of misdirected effort.
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Affiliation(s)
- Lynn L Silver
- LL Silver Consulting, LLC, 955 S. Springfield Ave., Unit C403, Springfield, NJ 07081, USA.
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Gautam A, Vyas R, Tewari R. Peptidoglycan biosynthesis machinery: a rich source of drug targets. Crit Rev Biotechnol 2010; 31:295-336. [PMID: 21091161 DOI: 10.3109/07388551.2010.525498] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The range of antibiotic therapy for the control of bacterial infections is becoming increasingly limited because of the rapid rise in multidrug resistance in clinical bacterial isolates. A few diseases, such as tuberculosis, which were once thought to be under control, have re-emerged as serious health threats. These problems have resulted in intensified research to look for new inhibitors for bacterial pathogens. Of late, the peptidoglycan (PG) layer, the most important component of the bacterial cell wall has been the subject of drug targeting because, first, it is essential for the survivability of eubacteria and secondly, it is absent in humans. The last decade has seen tremendous inputs in deciphering the 3-D structures of the PG biosynthetic enzymes. Many inhibitors against these enzymes have been developed using virtual and high throughput screening techniques. This review discusses the mechanistic and structural properties of the PG biosynthetic enzymes and inhibitors developed in the last decade.
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Affiliation(s)
- Ankur Gautam
- Department of Biotechnology, Panjab University, Chandigarh, India
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Basavannacharya C, Robertson G, Munshi T, Keep NH, Bhakta S. ATP-dependent MurE ligase in Mycobacterium tuberculosis: biochemical and structural characterisation. Tuberculosis (Edinb) 2009; 90:16-24. [PMID: 19945347 DOI: 10.1016/j.tube.2009.10.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Revised: 10/10/2009] [Accepted: 10/26/2009] [Indexed: 01/30/2023]
Abstract
New therapies are required against Mycobacterium tuberculosis and its cell wall peptidoglycan biosynthesis is a potential therapeutic target. UDP-MurNAc-tripeptide ligase (MurE) is a member of the ATP-dependent ligase family, which incorporate amino acids including meso-diaminopimelic acid (m-DAP) into peptidoglycan during synthesis in a species-specific manner. In the present study, we have cloned, over-expressed, and characterised MurE from M. tuberculosis (Mtb-MurE). The crystal structure has been determined at 3.0A resolution in the presence of the substrate UDP-MurNAc-l-Ala-d-Glu (UAG). The activity of the enzyme was measured through estimating inorganic phosphate released in a non-radioactive high-throughput colourimetric assay. UDP-MurNAc-l-Ala-d-Glu-m-DAP (UMT) formation coupled to inorganic phosphate release was confirmed by HPLC and mass spectrometric analyses. Kinetic constants were determined for a range of natural substrates using optimised conditions. From our findings, it is evident that Mtb-MurE is highly specific in adding m-DAP to UDP-MurNAc-dipeptide and ATP-hydrolysis is an absolute requirement for its activity.
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Affiliation(s)
- Chandrakala Basavannacharya
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
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Sova M, Kovac A, Turk S, Hrast M, Blanot D, Gobec S. Phosphorylated hydroxyethylamines as novel inhibitors of the bacterial cell wall biosynthesis enzymes MurC to MurF. Bioorg Chem 2009; 37:217-22. [PMID: 19804894 DOI: 10.1016/j.bioorg.2009.09.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2009] [Revised: 09/03/2009] [Accepted: 09/04/2009] [Indexed: 10/20/2022]
Abstract
Enzymes involved in the biosynthesis of bacterial peptidoglycan represent important targets for development of new antibacterial drugs. Among them, Mur ligases (MurC to MurF) catalyze the formation of the final cytoplasmic precursor UDP-N-acetylmuramyl-pentapeptide from UDP-N-acetylmuramic acid. We present the design, synthesis and biological evaluation of a series of phosphorylated hydroxyethylamines as new type of small-molecule inhibitors of Mur ligases. We show that the phosphate group attached to the hydroxyl moiety of the hydroxyethylamine core is essential for good inhibitory activity. The IC(50) values of these inhibitors were in the micromolar range, which makes them a promising starting point for the development of multiple inhibitors of Mur ligases as potential antibacterial agents. In addition, 1-(4-methoxyphenylsulfonamido)-3-morpholinopropan-2-yl dihydrogen phosphate 7a was discovered as one of the best inhibitors of MurE described so far.
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Affiliation(s)
- Matej Sova
- Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia
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Turk S, Kovac A, Boniface A, Bostock JM, Chopra I, Blanot D, Gobec S. Discovery of new inhibitors of the bacterial peptidoglycan biosynthesis enzymes MurD and MurF by structure-based virtual screening. Bioorg Med Chem 2009; 17:1884-9. [PMID: 19223185 DOI: 10.1016/j.bmc.2009.01.052] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2008] [Revised: 01/19/2009] [Accepted: 01/22/2009] [Indexed: 11/18/2022]
Abstract
The ATP-dependent Mur ligases (MurC, MurD, MurE and MurF) successively add L-Ala, D-Glu, meso-A(2)pm or L-Lys, and D-Ala-D-Ala to the nucleotide precursor UDP-MurNAc, and they represent promising targets for antibacterial drug discovery. We have used the molecular docking programme eHiTS for the virtual screening of 1990 compounds from the National Cancer Institute 'Diversity Set' on MurD and MurF. The 50 top-scoring compounds from screening on each enzyme were selected for experimental biochemical evaluation. Our approach of virtual screening and subsequent in vitro biochemical evaluation of the best ranked compounds has provided four novel MurD inhibitors (best IC(50)=10 microM) and one novel MurF inhibitor (IC(50)=63 microM).
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Affiliation(s)
- Samo Turk
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
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Humljan J, Kotnik M, Contreras-Martel C, Blanot D, Urleb U, Dessen A, Šolmajer T, Gobec S. Novel Naphthalene-N-sulfonyl-d-glutamic Acid Derivatives as Inhibitors of MurD, a Key Peptidoglycan Biosynthesis Enzyme,. J Med Chem 2008; 51:7486-94. [DOI: 10.1021/jm800762u] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jan Humljan
- Drug Discovery, Lek Pharmaceuticals d.d., Verovškova 57, 1526 Ljubljana, Slovenia, Laboratoire des Protéines Membranaires, Institut de Biologie Structurale Jean-Pierre Ebel, CEA, CNRS, UJF, UMR5075, 41 Rue Jules Horowitz, F-38027 Grenoble, France, Enveloppes Bactériennes et Antibiotiques, IBBMC, UMR 8619 CNRS, Univ Paris-Sud, 91405 Orsay, France, and Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Miha Kotnik
- Drug Discovery, Lek Pharmaceuticals d.d., Verovškova 57, 1526 Ljubljana, Slovenia, Laboratoire des Protéines Membranaires, Institut de Biologie Structurale Jean-Pierre Ebel, CEA, CNRS, UJF, UMR5075, 41 Rue Jules Horowitz, F-38027 Grenoble, France, Enveloppes Bactériennes et Antibiotiques, IBBMC, UMR 8619 CNRS, Univ Paris-Sud, 91405 Orsay, France, and Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Carlos Contreras-Martel
- Drug Discovery, Lek Pharmaceuticals d.d., Verovškova 57, 1526 Ljubljana, Slovenia, Laboratoire des Protéines Membranaires, Institut de Biologie Structurale Jean-Pierre Ebel, CEA, CNRS, UJF, UMR5075, 41 Rue Jules Horowitz, F-38027 Grenoble, France, Enveloppes Bactériennes et Antibiotiques, IBBMC, UMR 8619 CNRS, Univ Paris-Sud, 91405 Orsay, France, and Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Didier Blanot
- Drug Discovery, Lek Pharmaceuticals d.d., Verovškova 57, 1526 Ljubljana, Slovenia, Laboratoire des Protéines Membranaires, Institut de Biologie Structurale Jean-Pierre Ebel, CEA, CNRS, UJF, UMR5075, 41 Rue Jules Horowitz, F-38027 Grenoble, France, Enveloppes Bactériennes et Antibiotiques, IBBMC, UMR 8619 CNRS, Univ Paris-Sud, 91405 Orsay, France, and Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Uroš Urleb
- Drug Discovery, Lek Pharmaceuticals d.d., Verovškova 57, 1526 Ljubljana, Slovenia, Laboratoire des Protéines Membranaires, Institut de Biologie Structurale Jean-Pierre Ebel, CEA, CNRS, UJF, UMR5075, 41 Rue Jules Horowitz, F-38027 Grenoble, France, Enveloppes Bactériennes et Antibiotiques, IBBMC, UMR 8619 CNRS, Univ Paris-Sud, 91405 Orsay, France, and Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Andréa Dessen
- Drug Discovery, Lek Pharmaceuticals d.d., Verovškova 57, 1526 Ljubljana, Slovenia, Laboratoire des Protéines Membranaires, Institut de Biologie Structurale Jean-Pierre Ebel, CEA, CNRS, UJF, UMR5075, 41 Rue Jules Horowitz, F-38027 Grenoble, France, Enveloppes Bactériennes et Antibiotiques, IBBMC, UMR 8619 CNRS, Univ Paris-Sud, 91405 Orsay, France, and Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Tom Šolmajer
- Drug Discovery, Lek Pharmaceuticals d.d., Verovškova 57, 1526 Ljubljana, Slovenia, Laboratoire des Protéines Membranaires, Institut de Biologie Structurale Jean-Pierre Ebel, CEA, CNRS, UJF, UMR5075, 41 Rue Jules Horowitz, F-38027 Grenoble, France, Enveloppes Bactériennes et Antibiotiques, IBBMC, UMR 8619 CNRS, Univ Paris-Sud, 91405 Orsay, France, and Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Stanislav Gobec
- Drug Discovery, Lek Pharmaceuticals d.d., Verovškova 57, 1526 Ljubljana, Slovenia, Laboratoire des Protéines Membranaires, Institut de Biologie Structurale Jean-Pierre Ebel, CEA, CNRS, UJF, UMR5075, 41 Rue Jules Horowitz, F-38027 Grenoble, France, Enveloppes Bactériennes et Antibiotiques, IBBMC, UMR 8619 CNRS, Univ Paris-Sud, 91405 Orsay, France, and Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
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Šink R, Kovač A, Tomašić T, Rupnik V, Boniface A, Bostock J, Chopra I, Blanot D, Mašič LP, Gobec S, Zega A. Synthesis and Biological Evaluation ofN-Acylhydrazones as Inhibitors of MurC and MurD Ligases. ChemMedChem 2008; 3:1362-70. [DOI: 10.1002/cmdc.200800087] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Zawadzke LE, Norcia M, Desbonnet CR, Wang H, Freeman-Cook K, Dougherty TJ. Identification of an inhibitor of the MurC enzyme, which catalyzes an essential step in the peptidoglycan precursor synthesis pathway. Assay Drug Dev Technol 2008; 6:95-103. [PMID: 18315498 DOI: 10.1089/adt.2007.114] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The pathway for synthesis of the peptidoglycan precursor UDP-N-acetylmuramyl pentapeptide is essential in Gram-positive and Gram-negative bacteria. This pathway has been exploited in the recent past to identify potential new antibiotics as inhibitors of one or more of the Mur enzymes. In the present study, a high-throughput screen was employed to identify potential inhibitors of the Escherichia coli MurC (UDP-N-acetylmuramic acid:L-alanine ligase), the first of four paralogous amino acid-adding enzymes. Inhibition of ATP consumed during the MurC reaction, using an adaptation of a kinase assay format, identified a number of potential inhibitory chemotypes. After nonspecific inhibition testing and chemical attractiveness were assessed, C-1 emerged as a compound for further characterization. The inhibition of MurC by this compound was confirmed in both a kinetic-coupled enzyme assay and a direct nuclear magnetic resonance product detection assay. C-1 was found to be a low micromolar inhibitor of the E. coli MurC reaction, with preferential inhibition by one of two enantiomeric forms. Experiments indicated that it was a competitive inhibitor of ATP binding to the MurC enzyme. Further work with MurC enzymes from several bacterial sources revealed that while the compound was equally effective at inhibiting MurC from genera (Proteus mirabilis and Klebsiella pneumoniae) closely related to E. coli, MurC enzymes from more distant Gram-negative species such as Haemophilus influenzae, Acinetobacter baylyi, and Pseudomonas aeruginosa were not inhibited.
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Affiliation(s)
- Laura E Zawadzke
- HTS Center of Emphasis, Pfizer Global Research & Development, Groton, CT, USA.
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Barreteau H, Kovac A, Boniface A, Sova M, Gobec S, Blanot D. Cytoplasmic steps of peptidoglycan biosynthesis. FEMS Microbiol Rev 2008; 32:168-207. [PMID: 18266853 DOI: 10.1111/j.1574-6976.2008.00104.x] [Citation(s) in RCA: 479] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The biosynthesis of bacterial cell wall peptidoglycan is a complex process that involves enzyme reactions that take place in the cytoplasm (synthesis of the nucleotide precursors) and on the inner side (synthesis of lipid-linked intermediates) and outer side (polymerization reactions) of the cytoplasmic membrane. This review deals with the cytoplasmic steps of peptidoglycan biosynthesis, which can be divided into four sets of reactions that lead to the syntheses of (1) UDP-N-acetylglucosamine from fructose 6-phosphate, (2) UDP-N-acetylmuramic acid from UDP-N-acetylglucosamine, (3) UDP-N-acetylmuramyl-pentapeptide from UDP-N-acetylmuramic acid and (4) D-glutamic acid and dipeptide D-alanyl-D-alanine. Recent data concerning the different enzymes involved are presented. Moreover, special attention is given to (1) the chemical and enzymatic synthesis of the nucleotide precursor substrates that are not commercially available and (2) the search for specific inhibitors that could act as antibacterial compounds.
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Affiliation(s)
- Hélène Barreteau
- Laboratoire des Enveloppes Bactériennes et Antibiotiques, Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Univ Paris-Sud, Orsay, France
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31
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Structural and functional characterization of enantiomeric glutamic acid derivatives as potential transition state analogue inhibitors of MurD ligase. J Mol Biol 2007; 370:107-15. [PMID: 17507028 DOI: 10.1016/j.jmb.2007.04.048] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2007] [Revised: 04/06/2007] [Accepted: 04/17/2007] [Indexed: 10/23/2022]
Abstract
Mur ligases play an essential role in the intracellular biosynthesis of bacterial peptidoglycan, the main component of the bacterial cell wall, and represent attractive targets for the design of novel antibacterials. UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase (MurD) catalyses the addition of D-glutamic acid to the cytoplasmic intermediate UDP-N-acetylmuramoyl-L-alanine (UMA) and is the second in the series of Mur ligases. MurD ligase is highly stereospecific for its substrate, D-glutamic acid (D-Glu). Here, we report the high resolution crystal structures of MurD in complexes with two novel inhibitors designed to mimic the transition state of the reaction, which contain either the D-Glu or the L-Glu moiety. The binding modes of N-sulfonyl-D-Glu and N-sulfonyl-L-Glu derivatives were also characterised kinetically. The results of this study represent an excellent starting point for further development of novel inhibitors of this enzyme.
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Humljan J, Kotnik M, Boniface A, Šolmajer T, Urleb U, Blanot D, Gobec S. A new approach towards peptidosulfonamides: synthesis of potential inhibitors of bacterial peptidoglycan biosynthesis enzymes MurD and MurE. Tetrahedron 2006. [DOI: 10.1016/j.tet.2006.08.030] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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34
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Noble M, Sinha Y, Kolupaev A, Demin O, Earnshaw D, Tobin F, West J, Martin JD, Qiu C, Liu WS, DeWolf WE, Tew D, Goryanin II. The kinetic model of the shikimate pathway as a tool to optimize enzyme assays for high-throughput screening. Biotechnol Bioeng 2006; 95:560-73. [PMID: 16921527 DOI: 10.1002/bit.20772] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Four-enzyme section of the shikimate pathway (Aro B, D, E, and K) of Streptococcus pneumoniae has been studied. Kinetic properties of the individual enzymes and three- and four-enzyme linked reactions have been characterized in vitro. On the basis of the data measured in spectrophotometric and LC-MS experiments, kinetic mechanisms of the enzymes have been suggested and all kinetic parameters have been identified. Kinetic models for these three- and four-enzyme sections of the shikimate pathway have been constructed and validated. The model of the four-enzyme section of shikimate pathway has been employed to design an inhibition-sensitive reconstituted pathway for a high-throughput screening effort on the shikimate pathway. It was demonstrated that using the model it was possible to optimize this reconstituted pathway in such a way to provide equal sensitivity of the enzymes to inhibition.
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Affiliation(s)
- Michael Noble
- Assay Methodology Development, GlaxoSmithKline, New Frontiers Science Park, Harlow, Essex, United Kingdom
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Silver LL. Does the cell wall of bacteria remain a viable source of targets for novel antibiotics? Biochem Pharmacol 2005; 71:996-1005. [PMID: 16290173 DOI: 10.1016/j.bcp.2005.10.029] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2005] [Revised: 10/13/2005] [Accepted: 10/17/2005] [Indexed: 11/19/2022]
Abstract
Whether the bacterial cell wall remains a viable source of novel antibacterials is addressed here by reviewing screen and design strategies for discovery of antibacterials with a focus on their output. Inhibitors for which antibacterial activity has been shown to be due to specific inhibition of a reaction (antibacterially validated inhibitors) are known for 8 of the 14 conserved essential steps of the pathway. Antibacterially validated enzyme inhibitors exist for six of these steps. The possible obstacles to finding validated inhibitors of the remaining enzymes are discussed and some strategies are suggested.
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Affiliation(s)
- Lynn L Silver
- LL Silver Consulting (LLC), 3403 Park Place, Springfield, NJ 07081, USA.
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Strancar K, Blanot D, Gobec S. Design, synthesis and structure-activity relationships of new phosphinate inhibitors of MurD. Bioorg Med Chem Lett 2005; 16:343-8. [PMID: 16271472 DOI: 10.1016/j.bmcl.2005.09.086] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2005] [Accepted: 09/28/2005] [Indexed: 11/24/2022]
Abstract
A series of new phosphinate compounds were designed and synthesized as inhibitors of the d-glutamic acid-adding enzyme (MurD) involved in peptidoglycan biosynthesis. They were tested against the MurD enzyme from Escherichia coli, allowing initial structure-activity relationships to be deduced. Two compounds had IC(50) values near 100 microM and constitute a promising starting point for further development.
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Affiliation(s)
- Katja Strancar
- University of Ljubljana, Faculty of Pharmacy, Askerceva 7, 1000 Ljubljana, Slovenia
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Hiratake J. Enzyme inhibitors as chemical tools to study enzyme catalysis: rational design, synthesis, and applications. CHEM REC 2005; 5:209-28. [PMID: 16041744 DOI: 10.1002/tcr.20045] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Carefully designed molecules that are intimately related to the reaction mechanism of enzymes are often highly selective and potent inhibitors that serve as extremely useful chemical probes for understanding the reaction mechanism and structure of enzymes. This article describes the design, synthesis, and applications of specific inhibitors of two mechanistically distinct groups of enzymes, ATP-dependent amide ligases and Ser- and Thr-hydrolases. Our strategy is based on the premise that stable analogues of the transition state (transition-state analogues) are highly potent inhibitors that serve as good mechanistic probes, and that a key structure of a good inhibitor of one enzyme is also utilized for the inhibitors of other enzymes that share the same chemistry in their catalyzed reactions, irrespective of the degree of structural similarity and evolutionary link between the enzymes. According to these principles, we designed and synthesized a series of phosphinate- and sulfoximine-based transition-state analogue inhibitors of glutathione synthetase, gamma-glutamylcysteine synthetase and asparagine synthetase. For the second group of enzymes, we synthesized a gamma-monofluorophosphono glutamate analogue for mechanism-based affinity labeling of gamma-glutamyltranspeptidase and fluorescent phosphonic acid esters for the active-site titration of lipase. These inhibitors were used successfully as ligands for detailed kinetic analyses, X-ray crystallography, and mass analysis of the enzymes to identify the key amino acid residues responsible for catalysis and substrate recognition in the transition state.
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Affiliation(s)
- Jun Hiratake
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.
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A De Novo Designed Inhibitor ofD-Ala-D-Ala Ligase fromE. coli. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200501662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Besong GE, Bostock JM, Stubbings W, Chopra I, Roper DI, Lloyd AJ, Fishwick CWG, Johnson AP. A De Novo Designed Inhibitor ofD-Ala-D-Ala Ligase fromE. coli. Angew Chem Int Ed Engl 2005; 44:6403-6. [PMID: 16158456 DOI: 10.1002/anie.200501662] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Abstract
Over the past forty years, efforts to discover antibacterials have yielded a wide variety of chemical structures, almost exclusively natural products, which inhibit many steps in cell wall synthesis. Although screening for new cell wall inhibitors has been continuous during that period, there have been few reports of new drugs. With the advent of genomics, high resolution X-ray crystallography and the recognition of the need for new antibiotics to combat resistant organisms, there has been a resurgence in interest in this validated target area.
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Affiliation(s)
- Lynn L Silver
- Department of Human and Animal Infectious Diseases, Merck & Co., Rahway, NJ 07065, USA.
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41
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Su W, McLeod D, Verkade JG. P(RNCH2CH2)3N: Catalysts for the Head-to-Tail Dimerization of Methyl Acrylate. J Org Chem 2003; 68:9499-501. [PMID: 14629181 DOI: 10.1021/jo034815c] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The dimerization of methyl acrylate to the head-to-tail 2-methylene-pentanedioic acid dimethyl ester product was realized in 82 and 85% yield in only 4 h at room temperature in THF in the presence of catalytic amounts of P(RNCH2CH2)3N (R = i-Bu and Bn, respectively). These phosphines are to our knowledge the best nonmetallic catalysts so far reported for this reaction. In contrast, less sterically hindered P(MeNCH2CH2)3N failed to catalyze this dimerization, giving oligomer or polymer instead.
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Affiliation(s)
- Weiping Su
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA
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42
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References. Antibiotics (Basel) 2003. [DOI: 10.1128/9781555817886.refs] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Horton JR, Bostock JM, Chopra I, Hesse L, Phillips SEV, Adams DJ, Johnson AP, Fishwick CWG. Macrocyclic inhibitors of the bacterial cell wall biosynthesis enzyme MurD. Bioorg Med Chem Lett 2003; 13:1557-60. [PMID: 12699754 DOI: 10.1016/s0960-894x(03)00176-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Computer-based molecular design has been used to produce a series of new macrocyclic systems targeted against the bacterial cell wall biosynthetic enzyme MurD. Following their preparation, which involved a novel metathesis-based cyclisation as the key step, these systems were found to show good inhibition when assayed against the MurD enzyme.
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Affiliation(s)
- James R Horton
- Departments of Chemistry, University of Leeds, Leeds LS2 9JT, UK
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El Zoeiby A, Beaumont M, Dubuc E, Sanschagrin F, Voyer N, Levesque RC. Combinatorial enzymatic assay for the screening of a new class of bacterial cell wall inhibitors. Bioorg Med Chem 2003; 11:1583-92. [PMID: 12628682 DOI: 10.1016/s0968-0896(02)00447-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
We have developed a screening assay by thin-layer chromatography (TLC) to identify inhibitors for the bacterial essential enzymes MurA, -B, and -C. Libraries of compounds were synthesized using the mix-and-split combinatorial chemistry approach. Screening of the pooled compounds using the developed assay revealed the presence of many pools active in vitro. Pools of interest were tested for antibacterial activity. Individual molecules in the active pools were synthesized and retested with the TLC assay and with bacteria. We focused on the best five compounds for further analysis. They were tested for inhibition on each of the three enzymes separately, and showed no inhibition of MurA or MurB activity but were all inhibitors of MurC enzyme. This approach yielded interesting lead compounds for the development of novel antibacterial agents.
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Affiliation(s)
- Ahmed El Zoeiby
- Centre de recherche sur la fonction, structure et ingénierie des protéines, Faculté de médecine, pavillon Charles-Eugène-Marchand, Université Laval, Sainte-Foy, Québec, G1K 7P4, Canada
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Maletic M, Antonic J, Leeman A, Santorelli G, Waddell S. Preparation of potential inhibitors of the mur-pathway enzymes on solid support using an acetal linker. Bioorg Med Chem Lett 2003; 13:1125-8. [PMID: 12643926 DOI: 10.1016/s0960-894x(03)00043-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Here, we report a novel strategy for the combinatorial or parallel solid-phase synthesis of potential inhibitors of the mur-pathway enzymes. The strategy involves the efficient use of p-alkoxybenzylidene acetal linker for reversible immobilization of sugar scaffolds to solid phase. This methodology was used to synthesize several glycopeptides on solid phase in good yields.
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Affiliation(s)
- Milana Maletic
- Department of Medicinal Chemistry, Merck Research Laboratories, PO Box 2000, Rahway, NJ 07065, USA
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46
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Bouhss A, Dementin S, van Heijenoort J, Parquet C, Blanot D. MurC and MurD synthetases of peptidoglycan biosynthesis: borohydride trapping of acyl-phosphate intermediates. Methods Enzymol 2003; 354:189-96. [PMID: 12418226 DOI: 10.1016/s0076-6879(02)54015-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Ahmed Bouhss
- UMR 8619 CNRS, Université de Paris-Sud, 91405 Orsay, France
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47
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El Zoeiby A, Sanschagrin F, Levesque RC. Structure and function of the Mur enzymes: development of novel inhibitors. Mol Microbiol 2003; 47:1-12. [PMID: 12492849 DOI: 10.1046/j.1365-2958.2003.03289.x] [Citation(s) in RCA: 253] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
One of the biggest challenges for recent medical research is the continuous development of new antibiotics interacting with bacterial essential mechanisms. The machinery for peptidoglycan biosynthesis is a rich source of crucial targets for antibacterial chemotherapy. The cytoplasmic steps of the biosynthesis of peptidoglycan precursor, catalysed by a series of Mur enzymes, are excellent candidates for drug development. There has been growing interest in these bacterial enzymes over the last decade. Many studies attempted to understand the detailed mechanisms and structural features of the key enzymes MurA to MurF. Only MurA is inhibited by a known antibiotic, fosfomycin. Several attempts made to develop novel inhibitors of this pathway are discussed in this review. Three novel inhibitors of MurA were identified recently. 4-Thiazolidinone compounds were designed as MurB inhibitors. Many phosphinic acid derivatives and substrate analogues were identified as inhibitors of the MurC to MurF amino acid ligases.
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Affiliation(s)
- Ahmed El Zoeiby
- Centre de Recherche sur la Fonction, Structure et Ingénierie des Protéines, Faculté de Médecine, Pavillon Charles-Eugène Marchand, Université Laval, Ste-Foy, Québec, Canada, G1K 7P4
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48
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Chopra I, Hesse L, O'Neill A. Exploiting current understanding of antibiotic action for discovery of new drugs. J Appl Microbiol 2002. [DOI: 10.1046/j.1365-2672.92.5s1.13.x] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Abstract
This review focuses on target-based approaches for developing new chemical classes of antibacterial agents aimed at the bacterial cell wall. The clinical success of antibiotics such as beta-lactams and glycopeptides validates this chemotherapeutic strategy and emerging resistance to these agents warrants the development of new antibacterial drugs. Understanding the mechanism of action and resistance to beta-lactams and glycopeptides at a molecular level has supported the development of new agents that prevent transpeptidation and transglycosylation reactions of peptidoglycan polymerisation. The enzymes involved in the synthesis of the peptidoglycan structural unit have also been targeted for antibacterial discovery. The influence of bacterial genetics and genomics, structural biology, assay development and the properties of known inhibitors on these approaches will be discussed in the context of drug discovery.
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Affiliation(s)
- David W Green
- Cubist Pharmaceuticals, Inc., 65 Hayden Ave., Lexington, MA 02421, USA.
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Dementin S, Bouhss A, Auger G, Parquet C, Mengin-Lecreulx D, Dideberg O, van Heijenoort J, Blanot D. Evidence of a functional requirement for a carbamoylated lysine residue in MurD, MurE and MurF synthetases as established by chemical rescue experiments. EUROPEAN JOURNAL OF BIOCHEMISTRY 2001; 268:5800-7. [PMID: 11722566 DOI: 10.1046/j.0014-2956.2001.02524.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Enzymes MurD, MurE, MurF, folylpolyglutamate synthetase and cyanophycin synthetase, which belong to the Mur synthetase superfamily, possess an invariant lysine residue (K198 in the Escherichia coli MurD numbering). Crystallographic analysis of MurD and MurE has recently shown that this residue is present as a carbamate derivative, a modification presumably essential for Mg(2+) binding and acyl phosphate formation. In the present work, the importance of the carbamoylated residue was investigated in MurD, MurE and MurF by site-directed mutagenesis and chemical rescue experiments. Mutant proteins MurD K198A/F, MurE K224A and MurF K202A, which displayed low enzymatic activity, were rescued by incubation with short-chain carboxylic acids, but not amines. The best rescuing agent was acetate for MurD K198A, formate for K198F, and propionate for MurE K224A and MurF K202A. In the last of these, wild-type levels of activity were recovered. A complementarity between the volume of the residue replacing lysine and the length of the carbon chain of the acid was noted. These observations support a functional role for the carbamate in the three Mur synthetases. Experiments aimed at recovering an active enzyme by introducing an acidic residue in place of the invariant lysine residue were also undertaken. Mutant protein MurD K198E was weakly active and was rescued by formate, indicating the necessity of correct positioning of the acidic function with respect to the peptide backbone. Attempts at covalent rescue of mutant protein MurD K198C failed because of its lack of reactivity towards haloacids.
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Affiliation(s)
- S Dementin
- Enveloppes Bactériennes et Antibiotiques, UMR 8619 CNRS, Université de Paris-Sud, Orsay, France
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