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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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Anti-Tuberculosis Mur Inhibitors: Structural Insights and the Way Ahead for Development of Novel Agents. Pharmaceuticals (Basel) 2023; 16:ph16030377. [PMID: 36986477 PMCID: PMC10058398 DOI: 10.3390/ph16030377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 02/20/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
Mur enzymes serve as critical molecular devices for the synthesis of UDP-MurNAc-pentapeptide, the main building block of bacterial peptidoglycan polymer. These enzymes have been extensively studied for bacterial pathogens such as Escherichia coli and Staphylococcus aureus. Various selective and mixed Mur inhibitors have been designed and synthesized in the past few years. However, this class of enzymes remains relatively unexplored for Mycobacterium tuberculosis (Mtb), and thus offers a promising approach for drug design to overcome the challenges of battling this global pandemic. This review aims to explore the potential of Mur enzymes of Mtb by systematically scrutinizing the structural aspects of various reported bacterial inhibitors and implications concerning their activity. Diverse chemical scaffolds such as thiazolidinones, pyrazole, thiazole, etc., as well as natural compounds and repurposed compounds, have been reviewed to understand their in silico interactions with the receptor or their enzyme inhibition potential. The structural diversity and wide array of substituents indicate the scope of the research into developing varied analogs and providing valuable information for the purpose of modifying reported inhibitors of other multidrug-resistant microorganisms. Therefore, this provides an opportunity to expand the arsenal against Mtb and overcome multidrug-resistant tuberculosis.
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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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Nowak MG, Skwarecki AS, Milewska MJ. Amino Acid Based Antimicrobial Agents - Synthesis and Properties. ChemMedChem 2021; 16:3513-3544. [PMID: 34596961 PMCID: PMC9293202 DOI: 10.1002/cmdc.202100503] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 09/02/2021] [Indexed: 12/20/2022]
Abstract
Structures of several dozen of known antibacterial, antifungal or antiprotozoal agents are based on the amino acid scaffold. In most of them, the amino acid skeleton is of a crucial importance for their antimicrobial activity, since very often they are structural analogs of amino acid intermediates of different microbial biosynthetic pathways. Particularly, some aminophosphonate or aminoboronate analogs of protein amino acids are effective enzyme inhibitors, as structural mimics of tetrahedral transition state intermediates. Synthesis of amino acid antimicrobials is a particular challenge, especially in terms of the need for enantioselective methods, including the asymmetric synthesis. All these issues are addressed in this review, summing up the current state‐of‐the‐art and presenting perspectives fur further progress.
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Affiliation(s)
- Michał G Nowak
- Department of Organic Chemistry and BioTechMed Center, Gdańsk University of Technology, 11/12 Gabriela Narutowicza Street, 80-233, Gdańsk, Poland
| | - Andrzej S Skwarecki
- Department of Pharmaceutical Technology and Biochemistry and BioTechMed Center, Gdańsk University of Technology, 11/12 Gabriela Narutowicza Street, 80-233, Gdańsk, Poland
| | - Maria J Milewska
- Department of Organic Chemistry and BioTechMed Center, Gdańsk University of Technology, 11/12 Gabriela Narutowicza Street, 80-233, Gdańsk, Poland
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Poopandi S, Sundaraj R, Rajmichael R, Thangaraj S, Dhamodharan P, Biswal J, Malaisamy V, Jeyaraj Pandian C, Jeyaraman J. Computational screening of potential inhibitors targeting MurF of Brugia malayi Wolbachia through multi-scale molecular docking, molecular dynamics and MM-GBSA analysis. Mol Biochem Parasitol 2021; 246:111427. [PMID: 34666103 DOI: 10.1016/j.molbiopara.2021.111427] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 10/08/2021] [Accepted: 10/13/2021] [Indexed: 01/19/2023]
Abstract
Lymphatic filariasis is a parasitic disease caused by the worms Wuchereria bancrofti, Brugia malayi and Brugia timori. Three anti-filarial drugs namely Diethylcarbamazine, Ivermectin and Albendazole and their combinations are used as the control strategies for filariasis. The disease has received much attention in drug discovery due to the unavailability of vaccines and the toxic pharmaceutical properties of the existing drugs. In Wolbachia endosymbiont Brugia malayi, the UDP-N-acetylmuramoyl-tripeptide-d-alanyl-d-alanine ligase (MurF) plays a key role in peptidoglycan biosynthesis pathway and therefore can be considered as effective drug target against filariasis disease. Therefore, in the present study, MurF was selected as the therapeutic target to identify specific inhibitors against filariasis. Homology modeling was performed to predict the three-dimensional structure of MurF due to the absence of the experimental structure. Further molecular dynamics simulation and structure-based high throughput virtual screening with three different chemical databases (Zinc, Maybridge and Specs) were carried out to identify potent inhibitors and also to check their conformations inside the binding site of MurF, respectively. Top three compounds with high docking score and high relative binding affinity against MurF were selected. Further, validation studies, including predicted ADME (Absorption, Distribution, Metabolism, Excretion) assessment, binding free energy using MM-GBSA (Molecular Mechanics Generalized Born Surface Area) and DFT (Density Functional Theory) calculations were performed for the top three compounds. From the results, it was observed that all the three compounds were predicted to show high reactivity, acceptable range of pharmacokinetic properties and high binding affinity with the drug target MurF. Overall, the results could provide more understanding on the inhibition of MurF enzyme and the screened compounds could lead to the development of new specific anti-filarial drugs.
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Affiliation(s)
- Saritha Poopandi
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, 630 003, Tamil Nadu, India.
| | - Rajamanikandan Sundaraj
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, 630 003, Tamil Nadu, India.
| | - Raji Rajmichael
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, 630 003, Tamil Nadu, India.
| | - Sindhu Thangaraj
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, 560 012, Karnataka, India.
| | - Prabhu Dhamodharan
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, 630 003, Tamil Nadu, India.
| | - Jayashree Biswal
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, 630 003, Tamil Nadu, India.
| | - Veerapandiyan Malaisamy
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, 630 003, Tamil Nadu, India.
| | - Chitra Jeyaraj Pandian
- Department of Biotechnology, Dr. Umayal Ramanathan College for Women, Alagappa University, Karaikudi, 630 003, Tamil Nadu, India.
| | - Jeyakanthan Jeyaraman
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, 630 003, Tamil Nadu, India.
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Xu J. Synthesis of sulfonopeptides. J Pept Sci 2021; 27:e3331. [PMID: 33913204 DOI: 10.1002/psc.3331] [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: 02/10/2021] [Revised: 03/25/2021] [Accepted: 03/26/2021] [Indexed: 11/07/2022]
Abstract
Sulfonopeptides as the sulfur analogues of natural peptides have been widely used as enzyme inhibitors due to their tetrahedral sulfonamide moiety, which can mimic the transition-state analogues of hydrolysis of the ester and amide bonds. Synthetic methods of sulfonopeptides are reviewed. The synthetic methods of sulfonopeptides include the condensation of N-protected amino acid/peptide acids and 2-aminoalkanesulfonic acids, coupling of N-protected 2-aminoalkanesulfonyl chlorides and amino acid esters/peptide esters, sulfinylation of amino acid esters/peptide esters with N-protected 2-aminoalkanesulfinyl chlorides and subsequent oxidation, the alkylation of taurine-containing peptides, and the displacement of N-aminoacyl/peptidyl 2-aminoalkyl halides/methanesulfonates with sulfites. Hybrid sulfonophosphinopeptides are prepared through the Mannich-type reaction of N-protected 2-aminoalkanesulfonamides/peptidylsulfonamides, aldehydes, and aryldichlorophosphines/phosphorus trichloride followed by the aminolysis with amino acid/peptide esters or hydrolysis. The developed synthetic methods provide diverse synthetic routes for biologically important sulfonopeptides as the candidates of medicinal agents.
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Affiliation(s)
- Jiaxi Xu
- State Key Laboratory of Chemical Resource Engineering, Department of Organic Chemistry, College of Chemistry, Beijing University of Chemical Technology, Beijing, China
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7
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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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8
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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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9
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Amera GM, Khan RJ, Pathak A, Jha RK, Muthukumaran J, Singh AK. Computer aided ligand based screening for identification of promising molecules against enzymes involved in peptidoglycan biosynthetic pathway from Acinetobacter baumannii. Microb Pathog 2020; 147:104205. [PMID: 32353580 DOI: 10.1016/j.micpath.2020.104205] [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] [Received: 03/23/2020] [Revised: 04/14/2020] [Accepted: 04/15/2020] [Indexed: 12/30/2022]
Abstract
A. baumannii has been considered as Priority-I as suggested by the World Health Organization (WHO) and the most critical pathogenic microorganism for causing nosocomial infection in imunno-compromised hospital-acquired patients due to multi-drug resistance (MDR). In the current study, we utilized "Computer-aided ligand-based virtual screening approach" for identification of promising molecules against Mur family proteins based on the known inhibitor (Naphthyl Tetronic Acids ((5Z)-3-(4-chlorophenyl)-4-hydroxy-5-(1-naphthylmethylene) furan-2(5H)-one)) of MurB from E. coli. The in-house library was prepared using a similarity search of a known inhibitor (Drug Bank ID: DB07296) against several relevant chemical databases. The molecules obtained from virtual screening of Naphthyl Tetronic Acids in-house library were successively subjected to physicochemical and ADMET screening. After this, the molecules which passed all the filters, subsequently subjected into interaction analysis with the drug target proteins (MurB, MurD, MurE and MurG) of A. baumanni and the results explained that four molecules were promising (CHEMBL468144, DB07296, Enamine_T5956969 and 54723243) for further molecular dynamics simulations. The free and ligand bounded proteins that undergone MD simulation are listed as follows: MurB, MurB-CHEMBL468144, MurB-DB07296, MurE, MurE-54723243, MurE-DB07296, MurD, MurD-Enamine_T5956969, MurD-DB07296, MurG, MurG-CHEMBL468144, and MurG-DB07296. Based on global and essential dynamics analysis, the stability order of molecules towards MurB (CHEMBL468144 > DB07296); MurD (Enamine_T5956969 > DB07296); MurE (54723243 > DB07296) and MurG (CHEMBL468144 > DB07296) indicates that the newly identified molecules are more promising one in comparison with the existing inhibitor. Based on all the docking and MD simulation results, the stability order of the free and ligand bounded protein are as follows; MurB and MurB-ligand complexes > MurD and MurD-ligand complexes > MurG and MurG-ligand complexes > MurE and MurE-ligand complexes. Finally, the selected compounds would be recommended for further experimental investigations and used as promising inhibitors of the infection caused by A. baumannii.
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Affiliation(s)
- Gizachew Muluneh Amera
- Department of Biotechnology, School of Engineering and Technology, Sharda University, P.C, 201310, Greater Noida, U.P, India
| | - Rameez Jabeer Khan
- Department of Biotechnology, School of Engineering and Technology, Sharda University, P.C, 201310, Greater Noida, U.P, India
| | - Amita Pathak
- Department of Chemistry, Indian Institute of Technology, HauzKhas, New Delhi, 110016, India
| | - Rajat Kumar Jha
- Department of Biotechnology, School of Engineering and Technology, Sharda University, P.C, 201310, Greater Noida, U.P, India
| | - Jayaraman Muthukumaran
- Department of Biotechnology, School of Engineering and Technology, Sharda University, P.C, 201310, Greater Noida, U.P, India
| | - Amit Kumar Singh
- Department of Biotechnology, School of Engineering and Technology, Sharda University, P.C, 201310, Greater Noida, U.P, India.
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10
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Torosyan SA, Nuriakhmetova ZF, Gimalova FA, Miftakhov MS. 4H-Thieno[3,2-b]pyrrole-5-carboxylate Conjugates with Taurine and Its Tetrabutylammonium Salt. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2020. [DOI: 10.1134/s1070428019120157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Azam MA, Saha N, Jupudi S. An explorative study on Staphylococcus aureus MurE inhibitor: induced fit docking, binding free energy calculation, and molecular dynamics. J Recept Signal Transduct Res 2019; 39:45-54. [PMID: 31162992 DOI: 10.1080/10799893.2019.1605528] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Staphylococcus aureus MurE enzyme catalyzes the addition of l-lysine as third residue of the peptidoglycan peptide moiety. Due to the high substrate specificity and its ubiquitous nature among bacteria, MurE enzyme is considered as one of the potential target for the development of new therapeutic agents. In the present work, induced fit docking (IFD), binding free energy calculation, and molecular dynamics (MD) simulation were carried out to elucidate the inhibition potential of 2-thioxothiazolidin-4-one based inhibitor 1 against S. aureus MurE enzyme. The inhibitor 1 formed majority of hydrogen bonds with the central domain residues Asn151, Thr152, Ser180, Arg187, and Lys219. Binding free-energy calculation by MM-GBSA approach showed that van der Waals (ΔGvdW, -57.30 kcal/mol) and electrostatic solvation (ΔGsolv, -36.86 kcal/mol) energy terms are major contributors for the inhibitor binding. Further, 30-ns MD simulation was performed to validate the stability of ligand-protein complex and also to get structural insight into mode of binding. Based on the IFD and MD simulation results, we designed four new compounds D1-D4 with promising binding affinity for the S. aureus MurE enzyme. The designed compounds were subjected to the extra-precision docking and binding free energy was calculated for complexes. Further, a 30-ns MD simulation was performed for D1/4C13 complex.
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Affiliation(s)
- Mohammed Afzal Azam
- a Department of Pharmaceutical Chemistry, JSS College of Pharmacy , Ooty , Tamil Nadu , India
| | - Niladri Saha
- a Department of Pharmaceutical Chemistry, JSS College of Pharmacy , Ooty , Tamil Nadu , India
| | - Srikanth Jupudi
- a Department of Pharmaceutical Chemistry, JSS College of Pharmacy , Ooty , Tamil Nadu , India
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Pertel SS, Seryi SA, Kakayan ES. A new approach to the synthesis of lactams of muramic, isomuramic and normuramic acids via intramolecular O-alkylation: Stereochemical features of the intramolecular nucleophilic substitution. Tetrahedron 2018. [DOI: 10.1016/j.tet.2018.07.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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13
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Grygorenko OO, Biitseva AV, Zhersh S. Amino sulfonic acids, peptidosulfonamides and other related compounds. Tetrahedron 2018. [DOI: 10.1016/j.tet.2018.01.033] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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14
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Extra precision docking, free energy calculation and molecular dynamics studies on glutamic acid derivatives as MurD inhibitors. Comput Biol Chem 2017; 69:55-63. [DOI: 10.1016/j.compbiolchem.2017.05.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Revised: 04/18/2017] [Accepted: 05/20/2017] [Indexed: 01/28/2023]
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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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16
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Vertesaljai P, Biswas S, Lebedyeva I, Broggi E, Asiri AM, Katritzky AR. Synthesis of taurine-containing peptides, sulfonopeptides, and N- and O-conjugates. J Org Chem 2014; 79:2688-93. [PMID: 24568296 DOI: 10.1021/jo500181g] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Taurine-containing water-soluble peptidomimetics were designed and synthesized. N-terminal taurine acylations allowed synthesis of a number of taurine-containing peptides. N-protection of taurine with Cbz and SO2-activation with benzotriazole followed by coupling with various amino esters, dipeptides and nucleophiles provided taurine N- and O-conjugates and sulfonopeptides.
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Affiliation(s)
- Peter Vertesaljai
- Center for Heterocyclic Compounds, Department of Chemistry, University of Florida , Gainesville, Florida 32611-7200, United States
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17
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Yudakhina TS, Moreva YV, Zarubin YP, Purygin PP. Synthesis of 2-phthalimidoethanesulfonic acid imidazolides. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2013. [DOI: 10.1134/s1070428013060250] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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18
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Sharma A, Pan A. Identification of potential drug targets in Yersinia pestis using metabolic pathway analysis: MurE ligase as a case study. Eur J Med Chem 2012; 57:185-95. [DOI: 10.1016/j.ejmech.2012.09.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Revised: 09/07/2012] [Accepted: 09/11/2012] [Indexed: 01/14/2023]
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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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Tomašić T, Šink R, Zidar N, Fic A, Contreras-Martel C, Dessen A, Patin D, Blanot D, Müller-Premru M, Gobec S, Zega A, Kikelj D, Mašič LP. Dual Inhibitor of MurD and MurE Ligases from Escherichia coli and Staphylococcus aureus. ACS Med Chem Lett 2012; 3:626-30. [PMID: 24900523 DOI: 10.1021/ml300047h] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Accepted: 06/27/2012] [Indexed: 01/16/2023] Open
Abstract
MurD and MurE ligases, consecutive enzymes participating in the intracellular steps of bacterial peptidoglycan biosynthesis, are important targets for antibacterial drug discovery. We have designed, synthesized, and evaluated the first d-glutamic acid-containing dual inhibitor of MurD and MurE ligases from Escherichia coli and Staphylococcus aureus (IC50 values between 6.4 and 180 μM) possessing antibacterial activity against Gram-positive S. aureus and its methicillin-resistant strain (MRSA) with minimal inhibitory concentration (MIC) values of 8 μg/mL. The inhibitor was also found to be noncytotoxic for human HepG2 cells at concentrations below 200 μM.
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Affiliation(s)
- Tihomir Tomašić
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7,
1000 Ljubljana, Slovenia
| | - Roman Šink
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7,
1000 Ljubljana, Slovenia
| | - Nace Zidar
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7,
1000 Ljubljana, Slovenia
| | - Anja Fic
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7,
1000 Ljubljana, Slovenia
| | - Carlos Contreras-Martel
- Institut de Biologie Structurale,
Bacterial Pathogenesis Group, Université Grenoble I, 38027 Grenoble, France
- Commissariat à l'Energie Atomique (CEA), IBS, 38027 Grenoble, France
- Centre National de la Recherche Scientifique (CNRS), IBS, 41 rue Jules
Horowitz, 38027 Grenoble, France
| | - Andréa Dessen
- Institut de Biologie Structurale,
Bacterial Pathogenesis Group, Université Grenoble I, 38027 Grenoble, France
- Commissariat à l'Energie Atomique (CEA), IBS, 38027 Grenoble, France
- Centre National de la Recherche Scientifique (CNRS), IBS, 41 rue Jules
Horowitz, 38027 Grenoble, France
| | - Delphine Patin
- Univ Paris-Sud, Laboratoire des Enveloppes
Bactériennes et Antibiotiques,
Institut de Biochimie et Biophysique Moléculaire et Cellulaire,
UMR 8619, 91405 Orsay, France
- CNRS, 91405
Orsay, France
| | - Didier Blanot
- Univ Paris-Sud, Laboratoire des Enveloppes
Bactériennes et Antibiotiques,
Institut de Biochimie et Biophysique Moléculaire et Cellulaire,
UMR 8619, 91405 Orsay, France
- CNRS, 91405
Orsay, France
| | - Manica Müller-Premru
- Institute
of Microbiology and
Immunology, Medical Faculty, University of Ljubljana, 1105 Ljubljana, Slovenia
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7,
1000 Ljubljana, Slovenia
| | - Anamarija Zega
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7,
1000 Ljubljana, Slovenia
| | - Danijel Kikelj
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7,
1000 Ljubljana, Slovenia
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21
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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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22
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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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23
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Patin D, Boniface A, Kovač A, Hervé M, Dementin S, Barreteau H, Mengin-Lecreulx D, Blanot D. Purification and biochemical characterization of Mur ligases from Staphylococcus aureus. Biochimie 2010; 92:1793-800. [PMID: 20659527 DOI: 10.1016/j.biochi.2010.07.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Accepted: 07/15/2010] [Indexed: 10/19/2022]
Abstract
The Mur ligases (MurC, MurD, MurE and MurF) catalyze the stepwise synthesis of the UDP-N-acetylmuramoyl-pentapeptide precursor of peptidoglycan. The murC, murD, murE and murF genes from Staphylococcus aureus, a major pathogen, were cloned and the corresponding proteins were overproduced in Escherichia coli and purified as His(6)-tagged forms. Their biochemical properties were investigated and compared to those of the E. coli enzymes. Staphylococcal MurC accepted L-Ala, L-Ser and Gly as substrates, as the E. coli enzyme does, with a strong preference for L-Ala. S. aureus MurE was very specific for L-lysine and in particular did not accept meso-diaminopimelic acid as a substrate. This mirrors the E. coli MurE specificity, for which meso-diaminopimelic acid is the preferred substrate and L-lysine a very poor one. S. aureus MurF appeared less specific and accepted both forms (L-lysine and meso-diaminopimelic acid) of UDP-MurNAc-tripeptide, as the E. coli MurF does. The inverse and strict substrate specificities of the two MurE orthologues is thus responsible for the presence of exclusively meso-diaminopimelic acid and L-lysine at the third position of the peptide in the peptidoglycans of E. coli and S. aureus, respectively. The specific activities of the four Mur ligases were also determined in crude extracts of S. aureus and compared to cell requirements for peptidoglycan biosynthesis.
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Affiliation(s)
- Delphine Patin
- Univ Paris-Sud, Laboratoire des Enveloppes Bactériennes et Antibiotiques, Institut de Biochimie et Biophysique Moléculaire et Cellulaire, UMR 8619, Orsay F-91405, France
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24
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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: 38] [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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25
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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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26
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Perdih A, Hodoscek M, Solmajer T. MurD ligase from E. coli: Tetrahedral intermediate formation study by hybrid quantum mechanical/molecular mechanical replica path method. Proteins 2009; 74:744-59. [PMID: 18704940 DOI: 10.1002/prot.22188] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
MurD (UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase), a three-domain bacterial protein, catalyses a highly specific incorporation of D-glutamate to the cytoplasmic intermediate UDP-N-acetyl-muramoyl-L-alanine (UMA) utilizing ATP hydrolysis to ADP and P(i). This reaction is part of a biosynthetic path yielding bacterial peptidoglycan. On the basis of structural studies of MurD complexes, a stepwise catalytic mechanism was proposed that commences with a formation of the acyl-phosphate intermediate, followed by a nucleophilic attack of D-glutamate that, through the formation of a tetrahedral reaction intermediate and subsequent phosphate dissociation, affords the final product, UDP-N-acetyl-muramoyl-L-alanine-D-glutamate (UMAG). A hybrid quantum mechanical/molecular mechanical (QM/MM) molecular modeling approach was utilized, combining the B3LYP QM level of theory with empirical force field simulations to evaluate three possible reaction pathways leading to tetrahedral intermediate formation. Geometries of the starting structures based on crystallographic experimental data and tetrahedral intermediates were carefully examined together with a role of crucial amino acids and water molecules. The replica path method was used to generate the reaction pathways between the starting structures and the corresponding tetrahedral reaction intermediates, offering direct comparisons with a sequential kinetic mechanism and the available structural data for this enzyme. The acquired knowledge represents new and valuable information to assist in the ongoing efforts leading toward novel inhibitors of MurD as potential antibacterial drugs.
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Affiliation(s)
- Andrej Perdih
- Laboratory for Molecular Modeling and NMR Spectroscopy, National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia
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27
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Perdih A, Bren U, Solmajer T. Binding free energy calculations of N-sulphonyl-glutamic acid inhibitors of MurD ligase. J Mol Model 2009; 15:983-96. [PMID: 19198900 DOI: 10.1007/s00894-009-0455-8] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2008] [Accepted: 01/06/2009] [Indexed: 10/21/2022]
Abstract
The increasing incidence of bacterial resistance to most available antibiotics has underlined the urgent need for the discovery of novel efficacious antibacterial agents. The biosynthesis of bacterial peptidoglycan, where the MurD enzyme is involved in the intracellular phase of UDP-MurNAc-pentapeptide formation, represents a collection of highly selective targets for novel antibacterial drug design. Structural studies of N-sulfonyl-glutamic acid inhibitors of MurD have made possible the examination of binding modes of this class of compounds, providing valuable information for the lead optimization phase of the drug discovery cycle. Binding free energies were calculated for a series of MurD N-sulphonyl-Glu inhibitors using the linear interaction energy (LIE) method. Analysis of interaction energy during the 20-ns MD trajectories revealed non-polar van der Waals interactions as the main driving force for the binding of these inhibitors, and excellent agreement with the experimental free energies was obtained. Calculations of binding free energies for selected moieties of compounds in this structural class substantiated even deeper insight into the source of inhibitory activity. These results constitute new valuable information to further assist the lead optimization process.
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Affiliation(s)
- Andrej Perdih
- Laboratory for Molecular Modeling and NMR Spectroscopy, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia
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28
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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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29
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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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30
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Mansour TS, Caufield CE, Rasmussen B, Chopra R, Krishnamurthy G, Morris KM, Svenson K, Bard J, Smeltzer C, Naughton S, Antane S, Yang Y, Severin A, Quagliato D, Petersen PJ, Singh G. Naphthyl tetronic acids as multi-target inhibitors of bacterial peptidoglycan biosynthesis. ChemMedChem 2008; 2:1414-7. [PMID: 17600795 DOI: 10.1002/cmdc.200700094] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Tarek S Mansour
- Medicinal Chemistry, Wyeth Research, 401 North Middletown Road, Pearl River, NY 10965, USA.
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31
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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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32
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Tang XY, Yan XL, Zhang P, Qin L, Yin Y. (S)-1-Hydroxy-propan-2-aminium (2R,3R)-3-carb-oxy-2,3-dihydroxy-propanoate monohydrate. Acta Crystallogr Sect E Struct Rep Online 2008; 64:o422. [PMID: 21201449 PMCID: PMC2960284 DOI: 10.1107/s1600536808000391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2008] [Accepted: 01/06/2008] [Indexed: 11/10/2022]
Abstract
The chiral title compound, C(4)H(10)NO(+)·C(4)H(5)O(6) (-)·H(2)O, is a hydrated mol-ecular salt in which the tartaric acid has transferred one proton to the (S)-2-amino-propan-1-ol mol-ecule. The crystal structure is stabilized by a three-dimensional network of N-H⋯O and O-H⋯O hydrogen bonds. The absolute configuration was assigned on the basis of the starting materials.
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33
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Abstract
Peptidomimetic modifications or cyclization of linear peptides are frequently used as attractive methods to provide more conformationally constrained and thus more stable and bioactive peptides. Among numerous peptidomimetic approaches described recently in the literature, particularly attractive are pseudopeptides or peptide bond surrogates in which peptide bonds have been replaced with other chemical groups. In these peptidomimetics the amide bond surrogates possess three-dimensional structures similar to those of natural peptides, yet with significant differences in polarity, hydrogen bonding capability, and acid-base character. The introduction of such modifications to the peptide sequence is expected to completely prevent protease cleavage of amide bond and significantly improve peptides' metabolic stability. In this chapter we consider Fmoc solid-phase synthesis of peptide analogs containing the amide surrogate that tend to be isosteric with the natural amide. This includes synthesis of peptidosulfonamides, phosphonopeptides, oligoureas, depsides, depsipeptides, and peptoids.
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Affiliation(s)
- Predrag Cudic
- Department of Chemistry and Biochemistry Florida, Atlantic University, Boca Raton, FL, USA
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34
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35
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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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36
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Strancar K, Boniface A, Blanot D, Gobec S. Phosphinate Inhibitors of UDP-N-Acetylmuramoyl-L-Alanyl-D-Glutamate:L-Lysine Ligase (MurE). Arch Pharm (Weinheim) 2007; 340:127-34. [PMID: 17335103 DOI: 10.1002/ardp.200600191] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The increasing emergence of pathogenic bacterial strains with high resistance to antibiotic therapy has created an urgent need for the development of new antibacterial agents that are directed towards novel targets. We have focused our attention on the Mur ligases (MurC-F), which catalyze the early steps of bacterial peptidoglycan biosynthesis, and which to date represent under-exploited targets for antibacterial drug design. We show that some of our phosphinate inhibitors of UDP-N-acetylmuramoyl-L-alanyl:D-glutamate ligase (MurD) also inhibits UDP-N-acetylmuramoyl-L-alanyl-D-glutamate:L-lysine ligase (MurE). To obtain new information on their structure-activity relationships, three new, structurally related phosphinates were synthesized and evaluated for inhibition of MurD and MurE.
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Affiliation(s)
- Katja Strancar
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
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37
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Kovac A, Majce V, Lenarsic R, Bombek S, Bostock JM, Chopra I, Polanc S, Gobec S. Diazenedicarboxamides as inhibitors of D-alanine-D-alanine ligase (Ddl). Bioorg Med Chem Lett 2007; 17:2047-54. [PMID: 17267218 DOI: 10.1016/j.bmcl.2007.01.015] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2006] [Revised: 12/27/2006] [Accepted: 01/05/2007] [Indexed: 10/23/2022]
Abstract
D-Alanine-D-alanine ligase (Ddl) catalyzes the biosynthesis of an essential bacterial peptidoglycan precursor D-alanyl-D-alanine and it represents an important target for development of new antibacterial drugs. A series of semicarbazides, aminocarbonyldiazenecarboxylates, diazenedicarboxamides, and hydrazinedicarboxamides was synthesized and screened for inhibition of DdlB from Escherichia coli. Compounds with good inhibitory activity were identified, enabling us to deduce initial structure-activity relationships. Thirteen diazenedicarboxamides were better inhibitors than D-cycloserine and some of them also possess antibacterial activity, which makes them a promising starting point for further development.
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Affiliation(s)
- Andreja Kovac
- University of Ljubljana, Faculty of Pharmacy, Askerceva 7, 1000 Ljubljana, Slovenia
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