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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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2
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Gupta R, Singh M, Pathania R. Chemical genetic approaches for the discovery of bacterial cell wall inhibitors. RSC Med Chem 2023; 14:2125-2154. [PMID: 37974958 PMCID: PMC10650376 DOI: 10.1039/d3md00143a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 08/10/2023] [Indexed: 11/19/2023] Open
Abstract
Antimicrobial resistance (AMR) in bacterial pathogens is a worldwide health issue. The innovation gap in discovering new antibiotics has remained a significant hurdle in combating the AMR problem. Currently, antibiotics target various vital components of the bacterial cell envelope, nucleic acid and protein biosynthesis machinery and metabolic pathways essential for bacterial survival. The critical role of the bacterial cell envelope in cell morphogenesis and integrity makes it an attractive drug target. While a significant number of in-clinic antibiotics target peptidoglycan biosynthesis, several components of the bacterial cell envelope have been overlooked. This review focuses on various antibacterial targets in the bacterial cell wall and the strategies employed to find their novel inhibitors. This review will further elaborate on combining forward and reverse chemical genetic approaches to discover antibacterials that target the bacterial cell envelope.
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Affiliation(s)
- Rinki Gupta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee Roorkee - 247 667 Uttarakhand India
| | - Mangal Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee Roorkee - 247 667 Uttarakhand India
| | - Ranjana Pathania
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee Roorkee - 247 667 Uttarakhand India
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3
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Shoaib M, Shehzadi I, Asif MU, Shen Y, Ni J. Identification of fungus-growing termite-associated halogenated-PKS maduralactomycin a as a potential inhibitor of MurF protein of multidrug-resistant Acinetobacter baumannii. Front Mol Biosci 2023; 10:1183073. [PMID: 37152898 PMCID: PMC10160657 DOI: 10.3389/fmolb.2023.1183073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 04/13/2023] [Indexed: 05/09/2023] Open
Abstract
Multidrug-resistant Acinetobacter baumannii infections have become a major public health concern globally. Inhibition of its essential MurF protein has been proposed as a potential target for broad-spectrum drugs. This study aimed to evaluate the potential of a novel ecological niche of 374 fungus-growing termite associated Natural Products (NPs). The molecular docking and computational pharmacokinetics screened four compounds, i.e., Termstrin B, Fridamycin A, Maduralactomycin A, and Natalenamide C, as potential compounds that have higher binding affinities and favourable protein-ligand interactions. The compound Maduralactomycin A induced more stability based on its lowest average RMSD value (2.31 Å) and low standard deviation (0.35) supported by the consistent flexibility and β-factor during the protein's time-dependent motion. While hydrogen bond analysis indicated that Termstrin B has formed the strongest intra-protein interaction, solvent accessibility was in good agreement with Maduralactomycin A compactness. Maduralactomycin A has the strongest binding energy among all the compounds (-348.48 kcal/mol) followed by Termstrin B (-321.19 kcal/mol). Since these findings suggest Maduralactomycin A and Termstrin B as promising candidates for inhibition of MurF protein, the favourable binding energies of Maduralactomycin A make it a more important compound to warrant further investigation. However, experimental validation using animal models and clinical trials is recommended before reaching any final conclusions.
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Affiliation(s)
- Muhammad Shoaib
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, Shandong, China
| | | | | | - Yulong Shen
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, Shandong, China
- *Correspondence: Yulong Shen, ; Jinfeng Ni,
| | - Jinfeng Ni
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, Shandong, China
- *Correspondence: Yulong Shen, ; Jinfeng Ni,
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4
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Gaur V, Bera S. Recent developments on UDP-N-acetylmuramoyl-L-alanine-D-gutamate ligase (Mur D) enzyme for antimicrobial drug development: An emphasis on in-silico approaches. CURRENT RESEARCH IN PHARMACOLOGY AND DRUG DISCOVERY 2022; 3:100137. [PMID: 36568273 PMCID: PMC9780078 DOI: 10.1016/j.crphar.2022.100137] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 10/09/2022] [Accepted: 10/26/2022] [Indexed: 11/06/2022] Open
Abstract
Introduction The rapid emergence of antibiotic resistance among various bacterial pathogens has been one of the major concerns of health organizations across the world. In this context, for the development of novel inhibitors against antibiotic-resistant bacterial pathogens, UDP-N-Acetylmuramoyl-L-Alanine-D-Glutamate Ligase (MurD) enzyme represents one of the most apposite targets. Body The present review focuses on updated advancements on MurD-targeted inhibitors in recent years along with genetic regulation, structural and functional characteristics of the MurD enzyme from various bacterial pathogens. A concise account of various crystal structures of MurD enzyme, submitted into Protein Data Bank is also discussed. Discussion MurD, an ATP dependent cytoplasmic enzyme is an important target for drug discovery. The genetic organization of MurD enzyme is well elucidated and many crystal structures of MurD enzyme are submitted into Protein Data bank. Various inhibitors against MurD enzyme have been developed so far with an increase in the use of in-silico methods in the recent past. But cell permeability barriers and conformational changes of MurD enzyme during catalytic reaction need to be addressed for effective drug development. So, a combination of in-silico methods along with experimental work is proposed to counter the catalytic machinery of MurD enzyme.
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Key Words
- Antibiotic resistance
- HTS, High Throughput Screening
- In-silico
- MD, Molecular Dynamics
- MIC, Minimum Inhibitory Concentration
- MurD
- PDB, Protein Data Bank
- PEP, Phosphoenolpyruvate
- PG, Peptidoglycan
- Peptidoglycan
- SAR, Structural Activity Relationship
- UDP-GlcNAc, UDP-N-acetylglucosamine
- UDP-Mpp, UDP-N-acetylmuramylpentapeptide
- UDP-MurNAc, UDP-N-acetylmuramicacid
- UMA, UDP N-acetylmuramoyl-l-alanine
- UNAG, UDP- N-acetylglucosamine
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5
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Zhou J, Cai Y, Liu Y, An H, Deng K, Ashraf MA, Zou L, Wang J. Breaking down the cell wall: Still an attractive antibacterial strategy. Front Microbiol 2022; 13:952633. [PMID: 36212892 PMCID: PMC9544107 DOI: 10.3389/fmicb.2022.952633] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/18/2022] [Indexed: 11/17/2022] Open
Abstract
Since the advent of penicillin, humans have known about and explored the phenomenon of bacterial inhibition via antibiotics. However, with changes in the global environment and the abuse of antibiotics, resistance mechanisms have been selected in bacteria, presenting huge threats and challenges to the global medical and health system. Thus, the study and development of new antimicrobials is of unprecedented urgency and difficulty. Bacteria surround themselves with a cell wall to maintain cell rigidity and protect against environmental insults. Humans have taken advantage of antibiotics to target the bacterial cell wall, yielding some of the most widely used antibiotics to date. The cell wall is essential for bacterial growth and virulence but is absent from humans, remaining a high-priority target for antibiotic screening throughout the antibiotic era. Here, we review the extensively studied targets, i.e., MurA, MurB, MurC, MurD, MurE, MurF, Alr, Ddl, MurI, MurG, lipid A, and BamA in the cell wall, starting from the very beginning to the latest developments to elucidate antimicrobial screening. Furthermore, recent advances, including MraY and MsbA in peptidoglycan and lipopolysaccharide, and tagO, LtaS, LspA, Lgt, Lnt, Tol-Pal, MntC, and OspA in teichoic acid and lipoprotein, have also been profoundly discussed. The review further highlights that the application of new methods such as macromolecular labeling, compound libraries construction, and structure-based drug design will inspire researchers to screen ideal antibiotics.
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Affiliation(s)
- Jingxuan Zhou
- The People’s Hospital of China Three Gorges University, Yichang, Hubei, China
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
- The Institute of Infection and Inflammation, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Yi Cai
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
- The Institute of Infection and Inflammation, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Ying Liu
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
- The Institute of Infection and Inflammation, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Haoyue An
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
- The Institute of Infection and Inflammation, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Kaihong Deng
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
- The Institute of Infection and Inflammation, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Muhammad Awais Ashraf
- Department of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Lili Zou
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
- The Institute of Infection and Inflammation, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Jun Wang
- The People’s Hospital of China Three Gorges University, Yichang, Hubei, China
- *Correspondence: Jun Wang,
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Azam MA, Singh A. Molecular insight into the binding mode of thieno[3,2-c]pyrazol-3-ols with Streptococcus pneumoniae MurF enzyme by combined molecular modeling approach. Struct Chem 2022. [DOI: 10.1007/s11224-021-01866-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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7
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Shinde Y, Ahmad I, Surana S, Patel H. The Mur Enzymes Chink in the Armour of Mycobacterium tuberculosis cell wall. Eur J Med Chem 2021; 222:113568. [PMID: 34118719 DOI: 10.1016/j.ejmech.2021.113568] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 02/02/2023]
Abstract
TUBERCULOSIS: (TB) transmitted by Mycobacterium tuberculosis (Mtb) is one of the top 10 causes of death globally. Currently, the widespread occurrence of resistance toward Mtb strains is becoming a significant concern to public health. This scenario exaggerated the need for the discovery of novel targets and their inhibitors. Targeting the "Mtb cell wall peptidoglycan synthesis" is an attractive strategy to overcome drug resistance. Mur enzymes (MurA-MurF) play essential roles in the peptidoglycan synthesis by catalyzing the ligation of key amino acid residues to the stem peptide. These enzymes are unique and confined to the eubacteria and are absent in humans, representing potential targets for anti-tubercular drug discovery. Mtb Mur ligases with the same catalytic mechanism share conserved amino acid regions and structural features that can conceivably exploit for the designing of the inhibitors, which can simultaneously target more than one isoforms (MurC-MurF) of the enzyme. In light of these findings in the current review, we have discussed the recent advances in medicinal chemistry of Mtb Mur enzymes (MurA-MurF) and their inhibitors, offering attractive multi-targeted strategies to combat the problem of drug-resistant in M. tuberculosis.
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Affiliation(s)
- Yashodeep Shinde
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, District Dhule, 425405, Maharashtra, India
| | - Iqrar Ahmad
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, District Dhule, 425405, Maharashtra, India
| | - Sanjay Surana
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, District Dhule, 425405, Maharashtra, India
| | - Harun Patel
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, District Dhule, 425405, Maharashtra, India.
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8
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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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9
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Azam MA, Manoj VCV. An explorative study on diarylquinoline-based inhibitor targeting Enterococcus faecium MurF. Struct Chem 2020. [DOI: 10.1007/s11224-020-01622-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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10
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Maitra A, Munshi T, Healy J, Martin LT, Vollmer W, Keep NH, Bhakta S. Cell wall peptidoglycan in Mycobacterium tuberculosis: An Achilles' heel for the TB-causing pathogen. FEMS Microbiol Rev 2020; 43:548-575. [PMID: 31183501 PMCID: PMC6736417 DOI: 10.1093/femsre/fuz016] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 06/07/2019] [Indexed: 02/06/2023] Open
Abstract
Tuberculosis (TB), caused by the intracellular pathogen Mycobacterium tuberculosis, remains one of the leading causes of mortality across the world. There is an urgent requirement to build a robust arsenal of effective antimicrobials, targeting novel molecular mechanisms to overcome the challenges posed by the increase of antibiotic resistance in TB. Mycobacterium tuberculosis has a unique cell envelope structure and composition, containing a peptidoglycan layer that is essential for maintaining cellular integrity and for virulence. The enzymes involved in the biosynthesis, degradation, remodelling and recycling of peptidoglycan have resurfaced as attractive targets for anti-infective drug discovery. Here, we review the importance of peptidoglycan, including the structure, function and regulation of key enzymes involved in its metabolism. We also discuss known inhibitors of ATP-dependent Mur ligases, and discuss the potential for the development of pan-enzyme inhibitors targeting multiple Mur ligases.
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Affiliation(s)
- Arundhati Maitra
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Tulika Munshi
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Jess Healy
- Department of Pharmaceutical and Biological Chemistry, UCL School of Pharmacy, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Liam T Martin
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Waldemar Vollmer
- The Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
| | - Nicholas H Keep
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Sanjib Bhakta
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
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11
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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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12
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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: 10] [Impact Index Per Article: 2.5] [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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14
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Eniyan K, Rani J, Ramachandran S, Bhat R, Khan IA, Bajpai U. Screening of Antitubercular Compound Library Identifies Inhibitors of Mur Enzymes in Mycobacterium tuberculosis. SLAS DISCOVERY 2019; 25:70-78. [PMID: 31597510 DOI: 10.1177/2472555219881148] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The rapid rise in the emergence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains of Mycobacterium tuberculosis (Mtb) mandates the discovery of novel tuberculosis (TB) drugs. Mur enzymes, which are identified as essential proteins in Mtb and catalyze the cytoplasmic steps in the peptidoglycan biosynthetic pathway, are considered potential drug targets. However, none of the clinical drugs have yet been developed against these enzymes. Hence, the aim of this study was to identify novel inhibitors of Mur enzymes in Mycobacterium tuberculosis. We screened an antitubercular compound library of 684 compounds, using MurB and MurE enzymes of the Mtb Mur pathway as drug targets. For experimental validation, the top hits obtained on in silico screening were screened in vitro, using Mtb Mur enzyme-specific assays. In all, seven compounds were found to show greater than 50% inhibition, with the highest inhibition observed at 77%, and the IC50 for these compounds was found to be in the range of 28-50 μM. Compound 5175112 showed the lowest IC50 (28.69 ± 1.17 μM), and on the basis of (1) the binding affinity, (2) the stability of interaction noted on molecular dynamics simulation, and (3) an in vitro assay, MurE appeared to be its target enzyme. We believe that the overall strategy followed in this study and the results obtained are a good starting point for developing Mur enzyme-specific Mtb inhibitors.
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Affiliation(s)
- Kandasamy Eniyan
- Department of Biomedical Science, Acharya Narendra Dev College, University of Delhi, New Delhi, India
| | - Jyoti Rani
- Department of Biomedical Science, Acharya Narendra Dev College, University of Delhi, New Delhi, India.,Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Srinivasan Ramachandran
- Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Rahul Bhat
- Clinical Microbiology Division, Council of Scientific and Industrial Research-Indian Institute of Integrative Medicine (CSIR-IIIM), Jammu, India
| | - Inshad Ali Khan
- Clinical Microbiology Division, Council of Scientific and Industrial Research-Indian Institute of Integrative Medicine (CSIR-IIIM), Jammu, India
| | - Urmi Bajpai
- Department of Biomedical Science, Acharya Narendra Dev College, University of Delhi, New Delhi, India
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15
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Helal AM, Sayed AM, Omara M, Elsebaei MM, Mayhoub AS. Peptidoglycan pathways: there are still more! RSC Adv 2019; 9:28171-28185. [PMID: 35530449 PMCID: PMC9071014 DOI: 10.1039/c9ra04518j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Accepted: 08/22/2019] [Indexed: 11/21/2022] Open
Abstract
The discovery of 3rd and 4th generations of currently existing classes of antibiotics has not hindered bacterial resistance, which is escalating at an alarming global level. This review follows WHO recommendations through implementing new criteria for newly discovered antibiotics. These recommendations focus on abandoning old scaffolds and hitting new targets. In light of these recommendations, this review discusses seven bacterial proteins that no commercial antibiotics have targeted yet, alongside their reported chemical scaffolds.
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Affiliation(s)
- Ahmed M Helal
- Department of Pharmaceutical Organic Chemistry, College of Pharmacy, Al-Azhar University Cairo 11884 Egypt
| | - Ahmed M Sayed
- Department of Pharmaceutical Organic Chemistry, College of Pharmacy, Al-Azhar University Cairo 11884 Egypt
| | - Mariam Omara
- Department of Pharmaceutical Organic Chemistry, College of Pharmacy, Al-Azhar University Cairo 11884 Egypt
| | - Mohamed M Elsebaei
- Department of Pharmaceutical Organic Chemistry, College of Pharmacy, Al-Azhar University Cairo 11884 Egypt
| | - Abdelrahman S Mayhoub
- Department of Pharmaceutical Organic Chemistry, College of Pharmacy, Al-Azhar University Cairo 11884 Egypt
- University of Science and Technology, Zewail City of Science and Technology Giza Egypt
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16
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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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17
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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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18
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Abstract
Ras converting enzyme 1 (Rce1) is an integral membrane endoprotease localized to the endoplasmic reticulum that mediates the cleavage of the carboxyl-terminal three amino acids from CaaX proteins, whose members play important roles in cell signaling processes. Examples include the Ras family of small GTPases, the γ-subunit of heterotrimeric GTPases, nuclear lamins, and protein kinases and phosphatases. CaaX proteins, especially Ras, have been implicated in cancer, and understanding the post-translational modifications of CaaX proteins would provide insight into their biological function and regulation. Many proteolytic mechanisms have been proposed for Rce1, but sequence alignment, mutational studies, topology, and recent crystallographic data point to a novel mechanism involving a glutamate-activated water and an oxyanion hole. Studies using in vivo and in vitro reporters of Rce1 activity have revealed that the enzyme cleaves only prenylated substrates and the identity of the a2 amino residue in the Ca1a2X sequence is most critical for recognition, preferring Ile, Leu, or Val. Substrate mimetics can be somewhat effective inhibitors of Rce1 in vitro. Small-molecule inhibitor discovery is currently limited by the lack of structural information on a eukaryotic enzyme, but a set of 8-hydroxyquinoline derivatives has demonstrated an ability to mislocalize all three mammalian Ras isoforms, giving optimism that potent, selective inhibitors might be developed. Much remains to be discovered regarding cleavage specificity, the impact of chemical inhibition, and the potential of Rce1 as a therapeutic target, not only for cancer, but also for other diseases.
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Affiliation(s)
| | - Timothy M Dore
- a New York University Abu Dhabi , Abu Dhabi , United Arab Emirates.,b Department of Chemistry , University of Georgia , Athens , GA , USA
| | - Walter K Schmidt
- c Department of Biochemistry & Molecular Biology , University of Georgia , Athens , GA , USA
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19
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Ahmad S, Raza S, Uddin R, Azam SS. Binding mode analysis, dynamic simulation and binding free energy calculations of the MurF ligase from Acinetobacter baumannii. J Mol Graph Model 2017; 77:72-85. [DOI: 10.1016/j.jmgm.2017.07.024] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 07/20/2017] [Accepted: 07/21/2017] [Indexed: 01/16/2023]
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20
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Azam MA, Jupudi S. Insight into the structural requirements of thiophene-3-carbonitriles-based MurF inhibitors by 3D-QSAR, molecular docking and molecular dynamics study. J Recept Signal Transduct Res 2017; 37:522-534. [PMID: 28768454 DOI: 10.1080/10799893.2017.1360354] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The discovery of clinically relevant inhibitors against MurF enzyme has proven to be a challenging task. In order to get further insight into the structural features required for the MurF inhibitory activity, we performed pharmacophore and atom-based three-dimensional quantitative structure-activity relationship studies for novel thiophene-3-carbonitriles based MurF inhibitors. The five-feature pharmacophore model was generated using 48 inhibitors having IC50 values ranging from 0.18 to 663 μm. The best-fitted model showed a higher coefficient of determination (R2 = 0.978), cross-validation coefficient (Q2 = 0.8835) and Pearson coefficient (0.9406) at four component partial least-squares factor. The model was validated with external data set and enrichment study. The effectiveness of the docking protocol was validated by docking the co-crystallized ligand into the catalytic pocket of MurF enzyme. Further, binding free energy calculated by the molecular mechanics generalized Born surface area approach showed that van der Waals and non-polar solvation energy terms are the main contributors to ligand binding in the active site of MurF enzyme. A 10-ns molecular dynamic simulation was performed to confirm the stability of the 3ZM6-ligand complex. Four new molecules are also designed as potent MurF inhibitors. These results provide insights regarding the development of novel MurF inhibitors with better binding affinity.
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Affiliation(s)
- Mohammed Afzal Azam
- a Department of Pharmaceutical Chemistry , JSS College of Pharmacy (A Constituent College of Jagadguru Sri Sivarathreeswara University, Mysuru) , Udhagamandalam , India
| | - Srikanth Jupudi
- a Department of Pharmaceutical Chemistry , JSS College of Pharmacy (A Constituent College of Jagadguru Sri Sivarathreeswara University, Mysuru) , Udhagamandalam , India
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21
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Šink R, Kotnik M, Zega A, Barreteau H, Gobec S, Blanot D, Dessen A, Contreras-Martel C. Crystallographic Study of Peptidoglycan Biosynthesis Enzyme MurD: Domain Movement Revisited. PLoS One 2016; 11:e0152075. [PMID: 27031227 PMCID: PMC4816537 DOI: 10.1371/journal.pone.0152075] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 03/08/2016] [Indexed: 11/30/2022] Open
Abstract
The biosynthetic pathway of peptidoglycan, an essential component of bacterial cell wall, is a well-recognized target for antibiotic development. Peptidoglycan precursors are synthesized in the bacterial cytosol by various enzymes including the ATP-hydrolyzing Mur ligases, which catalyze the stepwise addition of amino acids to a UDP-MurNAc precursor to yield UDP-MurNAc-pentapeptide. MurD catalyzes the addition of D-glutamic acid to UDP-MurNAc-L-Ala in the presence of ATP; structural and biochemical studies have suggested the binding of the substrates with an ordered kinetic mechanism in which ligand binding inevitably closes the active site. In this work, we challenge this assumption by reporting the crystal structures of intermediate forms of MurD either in the absence of ligands or in the presence of small molecules. A detailed analysis provides insight into the events that lead to the closure of MurD and reveals that minor structural modifications contribute to major overall conformation alterations. These novel insights will be instrumental in the development of new potential antibiotics designed to target the peptidoglycan biosynthetic pathway.
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Affiliation(s)
- Roman Šink
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, Ljubljana, Slovenia
| | - Miha Kotnik
- Lek Pharmaceuticals d. d., Verovškova 57, Ljubljana, Slovenia
| | - Anamarija Zega
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, Ljubljana, Slovenia
| | - Hélène Barreteau
- Laboratoire des Enveloppes Bactériennes et Antibiotiques, Institut de Biologie Intégrative de la Cellule (I2BC), CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette, France
| | - Stanislav Gobec
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, Ljubljana, Slovenia
| | - Didier Blanot
- Laboratoire des Enveloppes Bactériennes et Antibiotiques, Institut de Biologie Intégrative de la Cellule (I2BC), CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette, France
| | - Andréa Dessen
- Univ. Grenoble Alpes, Institut de Biologie Structurale, Grenoble, France
- CNRS, IBS, Grenoble, France
- CEA, IBS, Grenoble, France
- Brazilian National Laboratory for Biosciences (LNBio), CNPEM, Campinas, São Paulo, Brazil
| | - Carlos Contreras-Martel
- Univ. Grenoble Alpes, Institut de Biologie Structurale, Grenoble, France
- CNRS, IBS, Grenoble, France
- CEA, IBS, Grenoble, France
- * E-mail:
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22
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Šink R, Barreteau H, Patin D, Mengin-Lecreulx D, Gobec S, Blanot D. MurD enzymes: some recent developments. Biomol Concepts 2015; 4:539-56. [PMID: 25436755 DOI: 10.1515/bmc-2013-0024] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 09/10/2013] [Indexed: 12/21/2022] Open
Abstract
The synthesis of the peptide stem of bacterial peptidoglycan involves four enzymes, the Mur ligases (MurC, D, E and F). Among them, MurD is responsible for the ATP-dependent addition of d-glutamic acid to UDP-MurNAc-l-Ala, a reaction which involves acyl-phosphate and tetrahedral intermediates. Like most enzymes of peptidoglycan biosynthesis, MurD constitutes an attractive target for the design and synthesis of new antibacterial agents. Escherichia coli MurD has been the first Mur ligase for which the tridimensional (3D) structure was solved. Thereafter, several co-crystal structures with different ligands or inhibitors were released. In the present review, we will deal with work performed on substrate specificity, reaction mechanism and 3D structure of E. coli MurD. Then, a part of the review will be devoted to recent work on MurD orthologs from species other than E. coli and to cellular organization of Mur ligases and in vivo regulation of the MurD activity. Finally, we will review the different classes of MurD inhibitors that have been designed and assayed to date with the hope of obtaining new antibacterial compounds.
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23
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Hrast M, Sosič I, Sink R, Gobec S. Inhibitors of the peptidoglycan biosynthesis enzymes MurA-F. Bioorg Chem 2014; 55:2-15. [PMID: 24755374 DOI: 10.1016/j.bioorg.2014.03.008] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 03/23/2014] [Accepted: 03/24/2014] [Indexed: 01/12/2023]
Abstract
The widespread emergence of resistant bacterial strains is becoming a serious threat to public health. This thus signifies the need for the development of new antibacterial agents with novel mechanisms of action. Continuous efforts in the design of novel antibacterials remain one of the biggest challenges in drug development. In this respect, the Mur enzymes, MurA-F, that are involved in the formation of UDP-N-acetylmuramyl-pentapeptide can be genuinely considered as promising antibacterial targets. This review provides an in-depth insight into the recent developments in the field of inhibitors of the MurA-F enzymes. Special attention is also given to compounds that act as multiple inhibitors of two, three or more of the Mur enzymes. Moreover, the reasons for the lack of preclinically successful inhibitors and the challenges to overcome these hurdles in the next years are also debated.
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Affiliation(s)
- Martina Hrast
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Izidor Sosič
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Roman Sink
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia.
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24
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Pastierik T, Šebej P, Medalová J, Štacko P, Klán P. Near-Infrared Fluorescent 9-Phenylethynylpyronin Analogues for Bioimaging. J Org Chem 2014; 79:3374-82. [DOI: 10.1021/jo500140y] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
| | | | - Jiřina Medalová
- Department
of Animal Physiology and Immunology, Institute of Experimental Biology,
Faculty of Science, Masaryk University, Kotlarska 2, 611 37 Brno, Czech Republic
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25
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Hrast M, Anderluh M, Knez D, Randall CP, Barreteau H, O'Neill AJ, Blanot D, Gobec S. Design, synthesis and evaluation of second generation MurF inhibitors based on a cyanothiophene scaffold. Eur J Med Chem 2014; 73:83-96. [DOI: 10.1016/j.ejmech.2013.11.031] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 11/15/2013] [Accepted: 11/24/2013] [Indexed: 11/29/2022]
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26
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Hrast M, Turk S, Sosič I, Knez D, Randall CP, Barreteau H, Contreras-Martel C, Dessen A, O'Neill AJ, Mengin-Lecreulx D, Blanot D, Gobec S. Structure-activity relationships of new cyanothiophene inhibitors of the essential peptidoglycan biosynthesis enzyme MurF. Eur J Med Chem 2013; 66:32-45. [PMID: 23786712 DOI: 10.1016/j.ejmech.2013.05.013] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Revised: 05/10/2013] [Accepted: 05/13/2013] [Indexed: 10/26/2022]
Abstract
Peptidoglycan is an essential component of the bacterial cell wall, and enzymes involved in its biosynthesis represent validated targets for antibacterial drug discovery. MurF catalyzes the final intracellular peptidoglycan biosynthesis step: the addition of D-Ala-D-Ala to the nucleotide precursor UDP-MurNAc-L-Ala-γ-D-Glu-meso-DAP (or L-Lys). As MurF has no human counterpart, it represents an attractive target for the development of new antibacterial drugs. Using recently published cyanothiophene inhibitors of MurF from Streptococcus pneumoniae as a starting point, we designed and synthesized a series of structurally related derivatives and investigated their inhibition of MurF enzymes from different bacterial species. Systematic structural modifications of the parent compounds resulted in a series of nanomolar inhibitors of MurF from S. pneumoniae and micromolar inhibitors of MurF from Escherichia coli and Staphylococcus aureus. Some of the inhibitors also show antibacterial activity against S. pneumoniae R6. These findings, together with two new co-crystal structures, represent an excellent starting point for further optimization toward effective novel antibacterials.
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Affiliation(s)
- Martina Hrast
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
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27
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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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28
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Šebej P, Wintner J, Müller P, Slanina T, Al Anshori J, Antony LAP, Klán P, Wirz J. Fluorescein Analogues as Photoremovable Protecting Groups Absorbing at ∼520 nm. J Org Chem 2012; 78:1833-43. [DOI: 10.1021/jo301455n] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peter Šebej
- Department of Chemistry, Faculty
of Science, Masaryk University, Kamenice
5, 625 00, Brno, Czech Republic
- Research Centre for Toxic Compounds
in the Environment, Faculty of Science, Masaryk University, Kamenice 3, 625 00 Brno, Czech Republic
| | - Jürgen Wintner
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056
Basel, Switzerland
| | - Pavel Müller
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056
Basel, Switzerland
| | - Tomáš Slanina
- Department of Chemistry, Faculty
of Science, Masaryk University, Kamenice
5, 625 00, Brno, Czech Republic
| | - Jamaludin Al Anshori
- Department of Chemistry, Faculty
of Science, Masaryk University, Kamenice
5, 625 00, Brno, Czech Republic
| | | | - Petr Klán
- Department of Chemistry, Faculty
of Science, Masaryk University, Kamenice
5, 625 00, Brno, Czech Republic
- Research Centre for Toxic Compounds
in the Environment, Faculty of Science, Masaryk University, Kamenice 3, 625 00 Brno, Czech Republic
| | - Jakob Wirz
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056
Basel, Switzerland
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29
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Sivaramakrishnan V, Thiyagarajan C, Kalaivanan S, Selvakumar R, Anusuyadevi M, Jayachandran KS. Homology modeling, molecular docking and electrostatic potential analysis of MurF ligase from Klebsiella pneumonia. Bioinformation 2012; 8:466-73. [PMID: 22715301 PMCID: PMC3374357 DOI: 10.6026/97320630008466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2012] [Accepted: 05/24/2012] [Indexed: 11/23/2022] Open
Abstract
In spite of availability of moderately protective vaccine and antibiotics, new antibacterial agents are urgently needed to decrease the global incidence of Klebsiella pneumonia infections. MurF ligase, a key enzyme, which participates in the bacterial cell wall assembly, is indispensable to existence of K. pneumonia. MurF ligase lack mammalian vis-à-vis and have high specificity, uniqueness, and occurrence only in eubacteria, epitomizing them as promising therapeutic targets for intervention. In this study, we present a unified approach involving homology modeling and molecular docking studies on MurF ligase enzyme. As part of this study, a homology model of K. pneumonia (MurF ligase) enzyme was predicted for the first time in order to carry out structurebased drug design. The accuracy of the model was further validated using different computational approaches. The comparative molecular docking study on this enzyme was undertaken using different phyto-ligands from Desmodium sp. and a known antibiotic Ciprofloxacin. The docking analysis indicated the importance of hotspots (HIS 281 and ASN 282) within the MurF binding pocket. The Lipinski's rule of five was analyzed for all ligands considered for this study by calculating the ADME/Tox, drug likeliness using Qikprop simulation. Only ten ligands were found to comply with the Lipinski rule of five. Based on the molecular docking results and Lipinki values 6-Methyltetrapterol A was confirmed as a promising lead compound. The present study should therefore play a guiding role in the experimental design and development of 6-Methyltetrapterol A as a bactericidal agent.
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Affiliation(s)
| | - Chinnaiyan Thiyagarajan
- Department of Bioinformatics, Bharathidasan University, Palkalaiperur, Tiruchirapalli-620024,
Tamilnadu, India
| | - Sivakumaran Kalaivanan
- Department of Bioinformatics, Bharathidasan University, Palkalaiperur, Tiruchirapalli-620024,
Tamilnadu, India
| | - Raj Selvakumar
- Department of Bioinformatics, Bharathidasan University, Palkalaiperur, Tiruchirapalli-620024,
Tamilnadu, India
| | - Muthuswamy Anusuyadevi
- Department of Biochemistry, Bharathidasan University, Palkalaiperur, Tiruchirapalli-620024, Tamilnadu, India
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30
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Osman K, Evangelopoulos D, Basavannacharya C, Gupta A, McHugh TD, Bhakta S, Gibbons S. An antibacterial from Hypericum acmosepalum inhibits ATP-dependent MurE ligase from Mycobacterium tuberculosis. Int J Antimicrob Agents 2011; 39:124-9. [PMID: 22079533 PMCID: PMC3657136 DOI: 10.1016/j.ijantimicag.2011.09.018] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Revised: 09/05/2011] [Accepted: 09/21/2011] [Indexed: 11/28/2022]
Abstract
In a project to characterise new antibacterial chemotypes from plants, hyperenone A and hypercalin B were isolated from the hexane and chloroform extracts of the aerial parts of Hypericum acmosepalum. The structures of both compounds were characterised by extensive one- and two-dimensional nuclear magnetic resonance (NMR) spectroscopy and were confirmed by mass spectrometry. Hyperenone A and hypercalin B exhibited antibacterial activity against multidrug-resistant strains of Staphylococcus aureus, with minimum inhibition concentration ranges of 2–128 mg/L and 0.5–128 mg/L, respectively. Hyperenone A also showed growth-inhibitory activity against Mycobacterium tuberculosis H37Rv and Mycobacterium bovis BCG at 75 mg/L and 100 mg/L. Neither hyperenone A nor hypercalin B inhibited the growth of Escherichia coli and both were non-toxic to cultured mammalian macrophage cells. Both compounds were tested for their ability to inhibit the ATP-dependent MurE ligase of M. tuberculosis, a crucial enzyme in the cytoplasmic steps of peptidoglycan biosynthesis. Hyperenone A inhibited MurE selectively, whereas hypercalin B did not have any effect on enzyme activity.
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Affiliation(s)
- Khadijo Osman
- Department of Pharmaceutical and Biological Chemistry, The School of Pharmacy, University of London, 29-39 Brunswick Square, Bloomsbury, London WC1N 1AX, UK
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Zidar N, Tomašić T, Šink R, Kovač A, Patin D, Blanot D, Contreras-Martel C, Dessen A, Premru MM, Zega A, Gobec S, Mašič LP, Kikelj D. New 5-benzylidenethiazolidin-4-one inhibitors of bacterial MurD ligase: design, synthesis, crystal structures, and biological evaluation. Eur J Med Chem 2011; 46:5512-23. [PMID: 21963114 DOI: 10.1016/j.ejmech.2011.09.017] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Revised: 09/02/2011] [Accepted: 09/08/2011] [Indexed: 11/19/2022]
Abstract
Mur ligases (MurC-MurF), a group of bacterial enzymes that catalyze four consecutive steps in the formation of cytoplasmic peptidoglycan precursor, are becoming increasingly adopted as targets in antibacterial drug design. Based on the crystal structure of MurD cocrystallized with thiazolidine-2,4-dione inhibitor I, we have designed, synthesized, and evaluated a series of improved glutamic acid containing 5-benzylidenerhodanine and 5-benzylidenethiazolidine-2,4-dione inhibitors of MurD with IC(50) values up to 28 μM. Inhibitor 37, with an IC(50) of 34 μM, displays a weak antibacterial activity against S. aureus ATCC 29213 and E. faecalis ATCC 29212 with minimal inhibitory concentrations of 128 μg/mL. High-resolution crystal structures of MurD in complex with two new inhibitors (compounds 23 and 51) reveal details of their binding modes within the active site and provide valuable information for further structure-based optimization.
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Affiliation(s)
- Nace Zidar
- Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia
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32
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Tomašić T, Kovač A, Simčič M, Blanot D, Grdadolnik SG, Gobec S, Kikelj D, Peterlin Mašič L. Novel 2-thioxothiazolidin-4-one inhibitors of bacterial MurD ligase targeting d-Glu- and diphosphate-binding sites. Eur J Med Chem 2011; 46:3964-75. [DOI: 10.1016/j.ejmech.2011.05.070] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Revised: 05/11/2011] [Accepted: 05/28/2011] [Indexed: 12/27/2022]
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33
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Virtual screening for potential inhibitors of bacterial MurC and MurD ligases. J Mol Model 2011; 18:1063-72. [PMID: 21667288 DOI: 10.1007/s00894-011-1139-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Accepted: 05/25/2011] [Indexed: 12/24/2022]
Abstract
Mur ligases are bacterial enzymes involved in the cytoplasmic steps of peptidoglycan biosynthesis and are viable targets for antibacterial drug discovery. We have performed virtual screening for potential ATP-competitive inhibitors targeting MurC and MurD ligases, using a protocol of consecutive hierarchical filters. Selected compounds were evaluated for inhibition of MurC and MurD ligases, and weak inhibitors possessing dual inhibitory activity have been identified. These compounds represent new scaffolds for further optimisation towards multiple Mur ligase inhibitors with improved inhibitory potency.
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34
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Tomašić T, Zidar N, Šink R, Kovač A, Blanot D, Contreras-Martel C, Dessen A, Müller-Premru M, Zega A, Gobec S, Kikelj D, Peterlin Mašič L. Structure-Based Design of a New Series of d-Glutamic Acid Based Inhibitors of Bacterial UDP-N-acetylmuramoyl-l-alanine:d-glutamate Ligase (MurD). J Med Chem 2011; 54:4600-10. [DOI: 10.1021/jm2002525] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Tihomir Tomašić
- Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Nace Zidar
- Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Roman Šink
- Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Andreja Kovač
- Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Didier Blanot
- Enveloppes Bactériennes et Antibiotiques, IBBMC, UMR 8619 CNRS, Université Paris-Sud, 91405 Orsay, France
| | | | | | - Manica Müller-Premru
- Medical Faculty, Institute of Microbiology and Immunology, University of Ljubljana, 1105 Ljubljana, Slovenia
| | - Anamarija Zega
- Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Danijel Kikelj
- Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia
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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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Simmons KJ, Chopra I, Fishwick CWG. Structure-based discovery of antibacterial drugs. Nat Rev Microbiol 2011; 8:501-10. [PMID: 20551974 DOI: 10.1038/nrmicro2349] [Citation(s) in RCA: 108] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The modern era of antibacterial chemotherapy began in the 1930s, and the next four decades saw the discovery of almost all the major classes of antibacterial agents that are currently in use. However, bacterial resistance to many of these drugs is becoming an increasing problem. As such, the discovery of drugs with novel modes of action will be vital to meet the threats created by the emergence of resistance. Success in discovering inhibitors using high-throughput screening of chemical libraries is rare. In this Review we explore the exciting opportunities for antibacterial-drug discovery arising from structure-based drug design.
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Affiliation(s)
- Katie J Simmons
- Antimicrobial Research Centre, University of Leeds, Leeds, UK
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37
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Derouaux A, Turk S, Olrichs NK, Gobec S, Breukink E, Amoroso A, Offant J, Bostock J, Mariner K, Chopra I, Vernet T, Zervosen A, Joris B, Frère JM, Nguyen-Distèche M, Terrak M. Small molecule inhibitors of peptidoglycan synthesis targeting the lipid II precursor. Biochem Pharmacol 2011; 81:1098-105. [PMID: 21356201 DOI: 10.1016/j.bcp.2011.02.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Revised: 02/10/2011] [Accepted: 02/14/2011] [Indexed: 11/19/2022]
Abstract
Bacterial peptidoglycan glycosyltransferases (GTs) of family 51 catalyze the polymerization of the lipid II precursor into linear peptidoglycan strands. This activity is essential to bacteria and represents a validated target for the development of new antibacterials. Application of structure-based virtual screening to the National Cancer Institute library using eHits program and the structure of the glycosyltransferase domain of the Staphylococcus aureus penicillin-binding protein 2 resulted in the identification of two small molecules analogues 5, a 2-[1-[(2-chlorophenyl)methyl]-2-methyl-5-methylsulfanylindol-3-yl]ethanamine and 5b, a 2-[1-[(3,4-dichlorophenyl)methyl]-2-methyl-5-methylsulfanylindol-3-yl]ethanamine that exhibit antibacterial activity against several Gram-positive bacteria but were less active on Gram-negative bacteria. The two compounds inhibit the activity of five GTs in the micromolar range. Investigation of the mechanism of action shows that the compounds specifically target peptidoglycan synthesis. Unexpectedly, despite the fact that the compounds were predicted to bind to the GT active site, compound 5b was found to interact with the lipid II substrate via the pyrophosphate motif. In addition, this compound showed a negatively charged phospholipid-dependent membrane depolarization and disruption activity. These small molecules are promising leads for the development of more active and specific compounds to target the essential GT step in cell wall synthesis.
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Affiliation(s)
- Adeline Derouaux
- Centre d'Ingénierie des Protéines, Université de Liège, Allée de la chimie, B6a, B-4000, Sart Tilman, Liège, Belgium
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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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41
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Zidar N, Tomasić T, Sink R, Rupnik V, Kovac A, Turk S, Patin D, Blanot D, Contreras Martel C, Dessen A, Müller Premru M, Zega A, Gobec S, Peterlin Masic L, Kikelj D. Discovery of novel 5-benzylidenerhodanine and 5-benzylidenethiazolidine-2,4-dione inhibitors of MurD ligase. J Med Chem 2010; 53:6584-94. [PMID: 20804196 DOI: 10.1021/jm100285g] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have designed, synthesized, and evaluated 5-benzylidenerhodanine- and 5-benzylidenethiazolidine-2,4-dione-based compounds as inhibitors of bacterial enzyme MurD with E. coli IC(50) in the range 45-206 μM. The high-resolution crystal structure of MurD in complex with (R,Z)-2-(3-[{4-([2,4-dioxothiazolidin-5-ylidene]methyl)phenylamino}methyl)benzamido)pentanedioic acid [(R)-32] revealed details of the binding mode of the inhibitor within the active site and provides a good foundation for structure-based design of a novel generation of MurD inhibitors.
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Affiliation(s)
- Nace Zidar
- Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia
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42
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Tomasić T, Zidar N, Kovac A, Turk S, Simcic M, Blanot D, Müller-Premru M, Filipic M, Grdadolnik SG, Zega A, Anderluh M, Gobec S, Kikelj D, Peterlin Masic L. 5-Benzylidenethiazolidin-4-ones as multitarget inhibitors of bacterial Mur ligases. ChemMedChem 2010; 5:286-95. [PMID: 20024979 DOI: 10.1002/cmdc.200900449] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Mur ligases participate in the intracellular path of bacterial peptidoglycan biosynthesis and constitute attractive, although so far underexploited, targets for antibacterial drug discovery. A series of hydroxy-substituted 5-benzylidenethiazolidin-4-ones were synthesized and tested as inhibitors of Mur ligases. The most potent compound 5 a was active against MurD-F with IC(50) values between 2 and 6 microm, making it a promising multitarget inhibitor of Mur ligases. Antibacterial activity against different strains, inhibitory activity against protein kinases, mutagenicity and genotoxicity of 5 a were also investigated, and kinetic and NMR studies were conducted.
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Affiliation(s)
- Tihomir Tomasić
- University of Ljubljana, Faculty of Pharmacy, Askerceva 7, 1000 Ljubljana, Slovenia
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Krüger DM, Evers A. Comparison of structure- and ligand-based virtual screening protocols considering hit list complementarity and enrichment factors. ChemMedChem 2010; 5:148-58. [PMID: 19908272 DOI: 10.1002/cmdc.200900314] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Structure- and ligand-based virtual-screening methods (docking, 2D- and 3D-similarity searching) were analysed for their effectiveness in virtual screening against four different targets: angiotensin-converting enzyme (ACE), cyclooxygenase 2 (COX-2), thrombin and human immunodeficiency virus 1 (HIV-1) protease. The relative performance of the tools was compared by examining their ability to recognise known active compounds from a set of actives and nonactives. Furthermore, we investigated whether the application of different virtual-screening methods in parallel provides complementary or redundant hit lists. Docking was performed with GOLD, Glide, FlexX and Surflex. The obtained docking poses were rescored by using nine different scoring functions in addition to the scoring functions implemented as objective functions in the docking algorithms. Ligand-based virtual screening was done with ROCS (3D-similarity searching), Feature Trees and Scitegic Functional Fingerprints (2D-similarity searching). The results show that structure- and ligand-based virtual-screening methods provide comparable enrichments in detecting active compounds. Interestingly, the hit lists that are obtained from different virtual-screening methods are generally highly complementary. These results suggest that a parallel application of different structure- and ligand-based virtual-screening methods increases the chance of identifying more (and more diverse) active compounds from a virtual-screening campaign.
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Affiliation(s)
- Dennis M Krüger
- Institut für pharmazeutische und medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
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Štefane B, Gobec S, Sosič I, Kovač A, Turk S, Blanot D. The Synthesis of Novel 2,4,6-Trisubstituted 1,3,5-Triazines: A Search for Potential MurF Enzyme Inhibitors. HETEROCYCLES 2010. [DOI: 10.3987/com-09-11839] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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45
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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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46
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Functional and biochemical analysis of the Chlamydia trachomatis ligase MurE. J Bacteriol 2009; 191:7430-5. [PMID: 19820100 DOI: 10.1128/jb.01029-09] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Chlamydiae are unusual obligately intracellular bacteria that do not synthesize detectable peptidoglycan. However, they possess genes that appear to encode products with peptidoglycan biosynthetic activity. Bioinformatic analysis predicts that chlamydial MurE possesses UDP-MurNAc-L-Ala-D-Glu:meso-diaminopimelic acid (UDP-MurNAc-L-Ala-D-Glu:meso-A(2)pm) ligase activity. Nevertheless, there are no experimental data to confirm this hypothesis. In this paper we demonstrate that the murE gene from Chlamydia trachomatis is capable of complementing a conditional Escherichia coli mutant impaired in UDP-MurNAc-L-Ala-D-Glu:meso-A(2)pm ligase activity. Recombinant MurE from C. trachomatis (MurE(Ct)) was overproduced in and purified from E. coli in order to investigate its kinetic parameters in vitro. By use of UDP-MurNAc-L-Ala-D-Glu as the nucleotide substrate, MurE(Ct) demonstrated ATP-dependent meso-A(2)pm ligase activity with pH and magnesium ion optima of 8.6 and 30 mM, respectively. Other amino acids (meso-lanthionine, the ll and dd isomers of A(2)pm, D-lysine) were also recognized by MurE(Ct.) However, the activities for these amino acid substrates were weaker than that for meso-A(2)pm. The specificity of MurE(Ct) for three possible C. trachomatis peptidoglycan nucleotide substrates was also determined in order to deduce which amino acid might be present at the first position of the UDP-MurNAc-pentapeptide. Relative k(cat)/K(m) ratios for UDP-MurNAc-L-Ala-D-Glu, UDP-MurNAc-L-Ser-D-Glu, and UDP-MurNAc-Gly-D-Glu were 100, 115, and 27, respectively. Our results are consistent with the synthesis in chlamydiae of a UDP-MurNAc-pentapeptide in which the third amino acid is meso-A(2)pm. However, due to the lack of specificity of MurE(Ct) for nucleotide substrates in vitro, it is not obvious which amino acid is present at the first position of the pentapeptide.
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47
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Falconer SB, Brown ED. New screens and targets in antibacterial drug discovery. Curr Opin Microbiol 2009; 12:497-504. [DOI: 10.1016/j.mib.2009.07.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2009] [Revised: 06/30/2009] [Accepted: 07/06/2009] [Indexed: 11/15/2022]
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48
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Perdih A, Kovac A, Wolber G, Blanot D, Gobec S, Solmajer T. Discovery of novel benzene 1,3-dicarboxylic acid inhibitors of bacterial MurD and MurE ligases by structure-based virtual screening approach. Bioorg Med Chem Lett 2009; 19:2668-73. [PMID: 19369074 DOI: 10.1016/j.bmcl.2009.03.141] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2009] [Revised: 03/25/2009] [Accepted: 03/27/2009] [Indexed: 01/17/2023]
Abstract
The peptidoglycan biosynthetic pathway provides an array of potential targets for antibacterial drug design, attractive especially with respect to selective toxicity. Within this pathway, the members of the Mur ligase family are considered as promising emerging targets for novel antibacterial drug design. Based on the available MurD crystal structures co-crystallised with N-sulfonyl glutamic acid inhibitors, a virtual screening campaign was performed, combining three-dimensional structure-based pharmacophores and molecular docking calculations. A novel class of glutamic acid surrogates-benzene 1,3-dicarboxylic acid derivatives-were identified and compounds 14 and 16 found to possess dual MurD and MurE inhibitory activity.
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Affiliation(s)
- Andrej Perdih
- National Institute of Chemistry, Hajdrihova, Ljubljana, Slovenia
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