1
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Ragab A, Ibrahim SA, Aboul-Magd DS, Baren MH. One-pot synthesis of pyrazolo[4,3- d]thiazole derivatives containing α-aminophosphonate as potential Mur A inhibitors against MDR pathogens with radiosterilization and molecular modeling simulation. RSC Adv 2023; 13:34756-34771. [PMID: 38035237 PMCID: PMC10685179 DOI: 10.1039/d3ra07040a] [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: 10/16/2023] [Accepted: 11/14/2023] [Indexed: 12/02/2023] Open
Abstract
The present study involves the synthesis of a new series of α-aminophosphonate derivatives in good yields with a simple workup via the Kabachnik-Fields reaction using lithium perchlorate (LiClO4) as a catalyst to facilitate the reaction. All the newly synthesized compounds were confirmed using various physical, spectroscopic, and analytical data, and the obtained results correlated with the proposed molecular structure. The in vitro antimicrobial activities of each compound were evaluated against different clinical isolates. The results indicated that among these derivatives, two compounds (5a and 5b) were the most active and displayed potent activity with MICs in the range from 0.06 to 0.25 μg mL-1 compared with fosfomycin and fluconazole as standard antibiotics. Moreover, the synthesized phosphonates displayed a broad spectrum of bactericidal and fungicidal activities depending on MICs, MBCs/MFCs, and the time-kill kinetics. In addition, the checkerboard assay showed synergistic and partial synergistic activities between the active compounds combined with fosfomycin and fluconazole. Furthermore, the SEM images showed distinct ruptures of the OM integrity of the FOS-R E. coli at their MICs, which was further indicated by the increased EtBr accumulation within the bacterial cells. Moreover, active derivatives revealed MurA inhibitory activity with IC50 values of 3.8 ± 0.39 and 4.5 ± 0.23 μM compared with fosfomycin (IC50 = 12.7 ± 0.27 μM). To our surprise, exposing 5a and 5b compounds to different gamma radiation doses revealed that 7.0 kGy eradicated the microbial load completely. Finally, the results of quantum chemical study supported the binding mode obtained from the docking study performed inside the active site of MurA (PDB: 1UAE), suggesting that these phosphonates may be promising safe candidates for MDR infection therapy clinical trials with no toxic effects on the normal human cells.
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Affiliation(s)
- Ahmed Ragab
- Chemistry Department, Faculty of Science (Boys), Al-Azhar University Nasr City Cairo 11884 Egypt
| | - Seham A Ibrahim
- Chemistry Department, Faculty of Science, Tanta University Tanta 31527 Egypt
| | - Dina S Aboul-Magd
- Drug Radiation Research Department, National Center for Radiation Research and Technology (NCRRT), Egyptian Atomic Energy Authority Egypt
| | - Mohamed H Baren
- Chemistry Department, Faculty of Science, Tanta University Tanta 31527 Egypt
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2
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Tiwari H, Raina D, Gupta M, Barik MR, Khan IA, Khan F, Nargotra A. Identification of novel MurA inhibitors using in silico approach, their validation and elucidation of mode of inhibition. J Biomol Struct Dyn 2023; 41:457-468. [PMID: 34866550 DOI: 10.1080/07391102.2021.2007793] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
UDP-N-acetylglucosamine enolpyruvyl transferase (MurA) is an important enzyme involved in the first cytosolic step of bacterial cell wall synthesis. In this study a combination of ligand based and structure based in silico virtual screening methods were utilised for screening of more than 50,000 drug-like compounds from CSIR-IIIM in-house compound library in order to identify potent inhibitors of MurA. The identified hits were validated in vitro under various incubation conditions using Malachite green phosphate assay, and two potent hits viz 3772-9534 and D396-0012 were identified. Among these hits, compound 3772-9534 showed significant changes in the activity values in different assay conditions. The MD simulation study of 3772-9534 suggested a novel binding site in MurA enzyme, independent of the two-substrate binding sites. Binding of inhibitors at the allosteric site induces conformational changes in the enzyme, which leads to inhibition of enzymatic activity. Overall, the study offers new insight for targeting MurA, which may promote the discovery of novel MurA allosteric site inhibitors.
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Affiliation(s)
- Harshita Tiwari
- Discovery Informatics, NPMC Division, CSIR-Indian Institute of Integrative Medicine, Jammu, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Diksha Raina
- Clinical Microbiology, CSIR-Indian Institute of Integrative Medicine, Jammu, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Monika Gupta
- Discovery Informatics, NPMC Division, CSIR-Indian Institute of Integrative Medicine, Jammu, India
| | - Manas Ranjan Barik
- Discovery Informatics, NPMC Division, CSIR-Indian Institute of Integrative Medicine, Jammu, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Inshad Ali Khan
- Clinical Microbiology, CSIR-Indian Institute of Integrative Medicine, Jammu, India.,Department of Microbiology, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - Farrah Khan
- Clinical Microbiology, CSIR-Indian Institute of Integrative Medicine, Jammu, India
| | - Amit Nargotra
- Discovery Informatics, NPMC Division, CSIR-Indian Institute of Integrative Medicine, Jammu, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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3
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Dewachter L, Brooks AN, Noon K, Cialek C, Clark-ElSayed A, Schalck T, Krishnamurthy N, Versées W, Vranken W, Michiels J. Deep mutational scanning of essential bacterial proteins can guide antibiotic development. Nat Commun 2023; 14:241. [PMID: 36646716 PMCID: PMC9842644 DOI: 10.1038/s41467-023-35940-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 01/09/2023] [Indexed: 01/18/2023] Open
Abstract
Deep mutational scanning is a powerful approach to investigate a wide variety of research questions including protein function and stability. Here, we perform deep mutational scanning on three essential E. coli proteins (FabZ, LpxC and MurA) involved in cell envelope synthesis using high-throughput CRISPR genome editing, and study the effect of the mutations in their original genomic context. We use more than 17,000 variants of the proteins to interrogate protein function and the importance of individual amino acids in supporting viability. Additionally, we exploit these libraries to study resistance development against antimicrobial compounds that target the selected proteins. Among the three proteins studied, MurA seems to be the superior antimicrobial target due to its low mutational flexibility, which decreases the chance of acquiring resistance-conferring mutations that simultaneously preserve MurA function. Additionally, we rank anti-LpxC lead compounds for further development, guided by the number of resistance-conferring mutations against each compound. Our results show that deep mutational scanning studies can be used to guide drug development, which we hope will contribute towards the development of novel antimicrobial therapies.
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Affiliation(s)
- Liselot Dewachter
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium. .,VIB-KU Leuven Center for Microbiology, Leuven, Belgium.
| | | | | | | | | | - Thomas Schalck
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium.,VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | | | - Wim Versées
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,VIB-VUB Center for Structural Biology, Brussels, Belgium
| | - Wim Vranken
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,VIB-VUB Center for Structural Biology, Brussels, Belgium.,Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Brussels, Belgium
| | - Jan Michiels
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium. .,VIB-KU Leuven Center for Microbiology, Leuven, Belgium.
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4
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Chen T, Zhao L, Liu Y, Wang Y, Jian Y, Zhao N, Yang Z, Wang X, Liu Q, Li M. Mechanisms of high-level fosfomycin resistance in Staphylococcus aureus epidemic lineage ST5. J Antimicrob Chemother 2022; 77:2816-2826. [PMID: 35848785 PMCID: PMC9525092 DOI: 10.1093/jac/dkac236] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 06/19/2022] [Indexed: 11/17/2022] Open
Abstract
Objectives Fosfomycin resistance has become a clinical concern. In this study, we analysed the dynamic change of fosfomycin MIC in the epidemic Staphylococcus aureus lineages in a teaching hospital in Shanghai for 12 years and sought to elucidate the major underlying mechanisms. Methods MLST was conducted for 4580 S. aureus isolates recovered from 2008 to 2019. Fosfomycin MIC was determined by the agar dilution method. The genome data of 230 S. aureus epidemic lineage isolates were acquired from a next-generation sequencing (NGS) platform. Gene deletion and corresponding complementation mutants were constructed to confirm the mechanism of fosfomycin resistance. Results The predominant S. aureus lineages during the past 12 years were ST5 and ST239 (45.6%; 2090/4580). However, ST5 has been spreading clinically, while ST239 has gradually disappeared recently. Consistent with epidemic trends, fosfomycin-resistant ST5 increased from 19.5% to 67.3%. Most fosfomycin-resistant ST5 isolates (92.7%; 647/698) possessed high-level resistance (MIC > 1024 mg/L) with combined mutations mainly in glpT and uhpT. In contrast, fosfomycin-resistant ST239 isolates (76.8%; 149/194) mainly acquired low-level resistance (MIC = 64–128 mg/L) with mutation primarily in hptA. Deletion of a single resistant gene merely resulted in low-level fosfomycin resistance, while double-gene mutants ΔglpTΔuhpT, ΔglpTΔhptA and ΔglpTΔhptR acquired high-level fosfomycin resistance. Conclusions The high-level fosfomycin resistance of S. aureus epidemic lineage ST5 is mainly due to the accumulation of mutations in the resistant genes related to membrane transporter systems, and partly contributes to its persistent prevalence under clinical antibiotic pressure.
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Affiliation(s)
- Tianchi Chen
- Department of Laboratory Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Lin Zhao
- Department of Laboratory Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Yao Liu
- Department of Laboratory Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Ya'nan Wang
- Department of Laboratory Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Ying Jian
- Department of Laboratory Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Na Zhao
- Department of Laboratory Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Ziyu Yang
- Department of Laboratory Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Xi Wang
- Department of Laboratory Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Qian Liu
- Department of Laboratory Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Min Li
- Department of Laboratory Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China.,Faculty of Medical Laboratory Science, College of Health Science and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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5
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Raina D, Khan FG, Tiwari H, Sangwan PL, Nargotra A, Kumar V, Khan IA, Saran S. Boswellic acids, as novel inhibitor targeting peptidoglycan biosynthetic enzyme UDP-N-acetylglucosamine enolpyruvyl transferase (MurA) in Escherichia coli. Arch Microbiol 2022; 204:472. [PMID: 35819545 DOI: 10.1007/s00203-022-03066-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 06/13/2022] [Indexed: 11/29/2022]
Abstract
UDP-N-acetylglucosamine enolpyruvyl transferase (MurA) is an essential cytosolic enzyme in the biosynthesis of peptidoglycan. It becomes a potential bacterial target for screening promising antibacterial compounds as it is associated with the early phases of peptidoglycan production. MurA enzyme is conserved and necessary for bacterial viability with no mammalian homolog, which is a well-proven therapeutic research target. The present study reports the natural compounds from Boswellia serrata targeting the MurA enzyme. The identified inhibitors against MurA Escherichia coli (E. coli): β-boswellic acid (IC50 33.65 µM), Acetyl-β-boswellic acid (IC50 30.17 µM), and Acetyl-11-keto-β-boswellic acid (IC50 37.67 µM). Inhibitors showed a fourfold decrease in IC50 values on pre-incubation with substrate-UDP-N-acetyl-glucosamine (UDP-GlcNAc). Mode-of-inhibition studies revealed their uncompetitive nature with both the substrates. Although these boswellic acids have been explored for their pharmacological potential, this is the first study reporting these compounds' E. coli MurA inhibiting potential.
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Affiliation(s)
- Diksha Raina
- Clinical Microbiology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India
- Fermentation Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India
- Academy of Scientific and Innovative Research, (AcSIR), Ghaziabad, 201002, India
| | - Farrah Gul Khan
- Clinical Microbiology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India
| | - Harshita Tiwari
- Discovery Informatics, NPMC Division, CSIR-Indian Institute of Integrative Medicine (CSIR), Canal Road, Jammu, 180001, India
- Academy of Scientific and Innovative Research, (AcSIR), Ghaziabad, 201002, India
| | - Payare L Sangwan
- Natural Products and Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
| | - Amit Nargotra
- Discovery Informatics, NPMC Division, CSIR-Indian Institute of Integrative Medicine (CSIR), Canal Road, Jammu, 180001, India
- Academy of Scientific and Innovative Research, (AcSIR), Ghaziabad, 201002, India
| | - Vinod Kumar
- Fermentation Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India
- Academy of Scientific and Innovative Research, (AcSIR), Ghaziabad, 201002, India
| | - Inshad Ali Khan
- Clinical Microbiology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India.
- Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, 305817, India.
| | - Saurabh Saran
- Fermentation Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India.
- Academy of Scientific and Innovative Research, (AcSIR), Ghaziabad, 201002, India.
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6
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Zhang F, Graham J, Zhai T, Liu Y, Huang Z. Discovery of MurA Inhibitors as Novel Antimicrobials through an Integrated Computational and Experimental Approach. Antibiotics (Basel) 2022; 11:antibiotics11040528. [PMID: 35453279 PMCID: PMC9031695 DOI: 10.3390/antibiotics11040528] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/09/2022] [Accepted: 04/12/2022] [Indexed: 11/16/2022] Open
Abstract
The bacterial cell wall is essential for protecting bacteria from the surrounding environment and maintaining the integrity of bacteria cells. The MurA enzyme, which is an essential enzyme involved in bacterial cell wall synthesis, could be a good drug target for antibiotics. Although fosfomycin is used clinically as a MurA inhibitor, resistance to this antibiotic is a concern. Here we used molecular docking-based virtual screening approaches to identify potential MurA inhibitors from 1.412 million compounds from three databases. Thirty-three top compounds from virtual screening were experimentally tested in Listeria innocua (Gram-positive bacterium) and Escherichia coli (Gram-negative bacterium). Compound 2-Amino-5-bromobenzimidazole (S17) showed growth inhibition effect in both L. innocua and E. coli, with the same Minimum Inhibitory Concentration (MIC) value of 0.5 mg/mL. Compound 2-[4-(dimethylamino)benzylidene]-n-nitrohydrazinecarboximidamide (C1) had growth inhibition effect only in L. innocua, with a MIC value of 0.5 mg/mL. Two FDA-approved drugs, albendazole (S4) and diflunisal (S8), had a growth inhibition effect only in E. coli, with a MIC value of 0.0625 mg/mL. The identified MurA inhibitors could be potential novel antibiotics. Furthermore, they could be potential fosfomycin substitutes for the fosfomycin-resistant strains.
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Affiliation(s)
- Fangyuan Zhang
- Department of Chemical and Biological Engineering, Villanova University, Villanova, PA 19085, USA; (F.Z.); (J.G.); (T.Z.)
| | - Joshua Graham
- Department of Chemical and Biological Engineering, Villanova University, Villanova, PA 19085, USA; (F.Z.); (J.G.); (T.Z.)
| | - Tianhua Zhai
- Department of Chemical and Biological Engineering, Villanova University, Villanova, PA 19085, USA; (F.Z.); (J.G.); (T.Z.)
| | - Yanhong Liu
- Molecular Characterization of Foodborne Pathogens Research Unit, Eastern Regional Research Center, U.S. Department of Agriculture, Wyndmoor, PA 19038, USA
- Correspondence: (Y.L.); (Z.H.); Tel.: +1-215-233-6587 (Y.L.); +1-610-519-4848 (Z.H.)
| | - Zuyi Huang
- Department of Chemical and Biological Engineering, Villanova University, Villanova, PA 19085, USA; (F.Z.); (J.G.); (T.Z.)
- Correspondence: (Y.L.); (Z.H.); Tel.: +1-215-233-6587 (Y.L.); +1-610-519-4848 (Z.H.)
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7
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In Silico Study on the Inhibition of UDP-N-Acetylglucosamine 1-Carboxy Vinyl Transferase from Salmonella typhimurium by the Lipopeptide Produced from Bacillus aryabhattai. Int J Pept Res Ther 2022. [DOI: 10.1007/s10989-022-10388-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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8
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Raina D, Kumar C, Kumar V, Khan IA, Saran S. Potential Inhibitors Targeting Escherichia coli UDP-N-Acetylglucosamine Enolpyruvyl Transferase (MurA): An Overview. Indian J Microbiol 2022; 62:11-22. [PMID: 35068599 PMCID: PMC8758813 DOI: 10.1007/s12088-021-00988-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 10/12/2021] [Indexed: 11/28/2022] Open
Abstract
Antibiotic resistance is one of the biggest challenges that is escalating and affecting humanity across the globe. To overcome this increasing burden of resistance, discovering novel hits by targeting the enzymes involved in peptidoglycan (murein) biosynthesis has always been considered better in antimicrobial drug discovery. UDP-N-acetylglucosamine enolpyruvyl transferase (MurA) enzyme has been identified as essential for Escherichia coli survival and catalyzes the early-stage step in bacterial cell wall synthesis. The present article gives a brief overview of the role of enzymes in peptidoglycan synthesis and MurA enzyme (previously known as MurZ in E. coli), in particular, including its structural and active site features. This review also provides an insight into the current knowledge of the reported MurA inhibitors, their mechanism of action and drawbacks of these hits that hinder their clinical trials, which would be helpful for synthesis and discovering potent molecules. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12088-021-00988-6.
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Affiliation(s)
- Diksha Raina
- Fermentation and Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001 India ,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Chetan Kumar
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India ,Natural Product and Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001 India
| | - Vinod Kumar
- Fermentation and Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001 India ,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Inshad Ali Khan
- Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan 305817 India
| | - Saurabh Saran
- Fermentation and Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001 India ,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
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9
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Funes Chabán M, Hrast M, Frlan R, Graikioti DG, Athanassopoulos CM, Carpinella MC. Inhibition of MurA Enzyme from Escherichia coli and Staphylococcus aureus by Diterpenes from Lepechinia meyenii and Their Synthetic Analogs. Antibiotics (Basel) 2021; 10:1535. [PMID: 34943747 PMCID: PMC8698320 DOI: 10.3390/antibiotics10121535] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/07/2021] [Accepted: 12/09/2021] [Indexed: 12/11/2022] Open
Abstract
Enzymes MurA and MurF, involved in bacterial cell wall synthesis, have been validated as targets for the discovery of novel antibiotics. A panel of plant-origin antibacterial diterpenes and synthetic analogs derived therefrom were investigated for their inhibitory properties on these enzymes from Escherichia coli and Staphylococcus aureus. Six compounds were proven to be effective for inhibiting MurA from both bacteria, with IC50 values ranging from 1.1 to 25.1 µM. To further mechanistically investigate the nature of binding and to explain the activity, these compounds were docked into the active site of MurA from E. coli. The aromatic ring of the active compounds showed a T-shaped π-π interaction with the phenyl ring of Phe328, and at least one hydrogen bond was formed between the hydroxy groups and Arg120 and/or Arg91. The results disclosed here establish new chemical scaffolds for the development of novel entities targeting MurA as potential antibiotics to combat the threat of pathogenic bacteria, particularly resistant strains.
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Affiliation(s)
- Macarena Funes Chabán
- Fine Chemical and Natural Products Laboratory, IRNASUS CONICET-UCC, Universidad Católica de Córdoba, Córdoba 5016, Argentina;
| | - Martina Hrast
- Faculty of Pharmacy, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (M.H.); (R.F.)
| | - Rok Frlan
- Faculty of Pharmacy, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (M.H.); (R.F.)
| | - Dafni G. Graikioti
- Synthetic Organic Chemistry Laboratory, Department of Chemistry, University of Patras, 26504 Patras, Greece; (D.G.G.); (C.M.A.)
| | - Constantinos M. Athanassopoulos
- Synthetic Organic Chemistry Laboratory, Department of Chemistry, University of Patras, 26504 Patras, Greece; (D.G.G.); (C.M.A.)
| | - María Cecilia Carpinella
- Fine Chemical and Natural Products Laboratory, IRNASUS CONICET-UCC, Universidad Católica de Córdoba, Córdoba 5016, Argentina;
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10
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Screening of compound library identifies novel inhibitors against the MurA enzyme of Escherichia coli. Appl Microbiol Biotechnol 2021; 105:3611-3623. [PMID: 33860835 DOI: 10.1007/s00253-021-11272-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 03/27/2021] [Accepted: 04/05/2021] [Indexed: 11/27/2022]
Abstract
Bacterial cell has always been an attractive target for anti-infective drug discovery. MurA (UDP-N-acetylglucosamine enolpyruvyl transferase) enzyme of Escherichia coli (E.coli) is crucial for peptidoglycan biosynthetic pathway, as it is involved in the early stages of bacterial cell wall biosynthesis. In the present study we aim to identify novel chemical structures targeting the MurA enzyme. For screening purpose, we used in silico approach (pharmacophore based strategy) for 52,026 library compounds (Chembridge, Chemdiv and in house synthetics) which resulted in identification of 50 compounds. These compounds were screened in vitro against MurA enzyme and release of inorganic phosphate (Pi) was estimated. Two compounds (IN00152 and IN00156) were found to inhibit MurA enzyme > 70% in primary screening and IC50 of 14.03 to 32.30 μM respectively. These two hits were further evaluated for their mode of inhibition studies and whole-cell activity where we observed 2-4 folds increase in activity in presence of Permeabilizer EDTA (Ethylenediaminetetraacetic acid). Combination studies were also performed with known antibiotics in presence of EDTA. Hits are reported for the first time against this target and our report also support the use of OM permeabilizer in combination with antibacterial compounds to address the permeability and efficacy issue. These lead hits can be further optimized for drug discovery. KEY POINTS: • Emerging Gram negative resistant strains is a matter of concern. • Need for new screening strategies to cope with drying up antibiotics pipeline. • Outer membrane permeabilizers could be useful to improve potency of molecules to reach its target.
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11
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Šrajer Gajdošik M, Andjelković U, Gašo-Sokač D, Pavlović H, Shevchuk O, Martinović T, Clifton J, Begić M, Josić D. Proteomic analysis of pyridoxal oxime derivatives treated Listeria monocytogenes reveals down-regulation of the main virulence factor, Listeriolysin O. Food Res Int 2020; 131:108951. [DOI: 10.1016/j.foodres.2019.108951] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 12/20/2019] [Accepted: 12/22/2019] [Indexed: 12/12/2022]
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12
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Mihalovits LM, Ferenczy GG, Keserű GM. Catalytic Mechanism and Covalent Inhibition of UDP- N-Acetylglucosamine Enolpyruvyl Transferase (MurA): Implications to the Design of Novel Antibacterials. J Chem Inf Model 2019; 59:5161-5173. [PMID: 31715096 DOI: 10.1021/acs.jcim.9b00691] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
UDP-N-acetylglucosamine enolpyruvyl transferase (MurA) catalyzes the first step in the biosynthesis of the bacterial cell wall. This pathway is essential for the growth of bacteria but missing in mammals, that nominates MurA as an attractive antibacterial target. MurA has a flexible loop whose conformational change is known to be part of the activation mechanism of the enzyme. We have shown that the loop closed conformation makes the proton transfer from Cys115 to His394 possible by a low barrier exothermic process. QM/MM MD simulations revealed that the activated thiolate is able to react with phosphoenolpyruvate (PEP), the natural substrate of MurA. The binding free energy profile of several covalent inhibitors with various warheads reacting with the activated Cys115 was calculated by QM/MM MD simulations and confirmed that reaction barrier heights tend to separate active from inactive compounds. Our results give new insight into the catalytic mechanism and covalent inhibition of MurA and suggest that QM/MM MD simulations are able to support ligand design by providing sensible relative free energy barriers for covalent inhibitors with various warheads reacting with thiolate nucleophiles.
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Affiliation(s)
- Levente M Mihalovits
- Medicinal Chemistry Research Group , Research Centre for Natural Sciences , Magyar tudósok körútja 2 , Budapest 1117 , Hungary
| | - György G Ferenczy
- Medicinal Chemistry Research Group , Research Centre for Natural Sciences , Magyar tudósok körútja 2 , Budapest 1117 , Hungary
| | - György M Keserű
- Medicinal Chemistry Research Group , Research Centre for Natural Sciences , Magyar tudósok körútja 2 , Budapest 1117 , Hungary
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13
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Sharma D, Sharma A, Verma SK, Singh B. Targeting metabolic pathways proteins of Orientia tsutsugamushi using combined hierarchical approach to combat scrub typhus. J Mol Recognit 2018; 32:e2766. [DOI: 10.1002/jmr.2766] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 09/04/2018] [Accepted: 09/15/2018] [Indexed: 01/08/2023]
Affiliation(s)
- Dixit Sharma
- Centre for Computational Biology and Bioinformatics, School of Life Sciences; Central University of Himachal Pradesh; Shahpur, District-Kangra Himachal Pradesh India
| | - Ankita Sharma
- Centre for Computational Biology and Bioinformatics, School of Life Sciences; Central University of Himachal Pradesh; Shahpur, District-Kangra Himachal Pradesh India
| | - Shailender Kumar Verma
- Centre for Computational Biology and Bioinformatics, School of Life Sciences; Central University of Himachal Pradesh; Shahpur, District-Kangra Himachal Pradesh India
| | - Birbal Singh
- ICAR-Indian Veterinary Research Institute, Regional Station; Palampur Himachal Pradesh India
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14
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Lessons on enzyme kinetics from quantitative proteomics. Curr Opin Biotechnol 2017; 46:81-89. [DOI: 10.1016/j.copbio.2017.02.007] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Accepted: 02/15/2017] [Indexed: 11/24/2022]
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15
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Hrast M, Rožman K, Jukič M, Patin D, Gobec S, Sova M. Synthesis and structure-activity relationship study of novel quinazolinone-based inhibitors of MurA. Bioorg Med Chem Lett 2017; 27:3529-3533. [PMID: 28579123 DOI: 10.1016/j.bmcl.2017.05.064] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Revised: 05/18/2017] [Accepted: 05/21/2017] [Indexed: 11/26/2022]
Abstract
MurA is an intracellular bacterial enzyme that is essential for peptidoglycan biosynthesis, and is therefore an important target for antibacterial drug discovery. We report the synthesis, in silico studies and extensive structure-activity relationships of a series of quinazolinone-based inhibitors of MurA from Escherichia coli. 3-Benzyloxyphenylquinazolinones showed promising inhibitory potencies against MurA, in the low micromolar range, with an IC50 of 8µM for the most potent derivative (58). Furthermore, furan-substituted quinazolinones (38, 46) showed promising antibacterial activities, with MICs from 1µg/mL to 8µg/mL, concomitant with their MurA inhibitory potencies. These data represent an important step towards the development of novel antimicrobial agents to combat increasing bacterial resistance.
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Affiliation(s)
- Martina Hrast
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia
| | - Kaja Rožman
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia
| | - Marko Jukič
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia
| | - Delphine Patin
- Bacterial Cell Envelopes and Antibiotics Group, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University of Paris Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia
| | - Matej Sova
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia.
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16
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Mondal SI, Mahmud Z, Elahi M, Akter A, Jewel NA, Muzahidul Islam M, Ferdous S, Kikuchi T. Study of intra-inter species protein-protein interactions for potential drug targets identification and subsequent drug design for Escherichia coli O104:H4 C277-11. In Silico Pharmacol 2017; 5:1. [PMID: 28401513 DOI: 10.1007/s40203-017-0021-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 03/20/2017] [Indexed: 11/29/2022] Open
Abstract
Protein-protein interaction (PPI) and host-pathogen interactions (HPI) proteomic analysis has been successfully practiced for potential drug target identification in pathogenic infections. In this research, we attempted to identify new drug target based on PPI and HPI computation approaches and subsequently design new drug against devastating enterohemorrhagic Escherichia coli O104:H4 C277-11 (Broad), which causes life-threatening food borne disease outbreak in Germany and other countries in Europe in 2011. Our systematic in silico analysis on PPI and HPI of E. coli O104:H4 was able to identify bacterial D-galactose-binding periplasmic and UDP-N-acetylglucosamine 1-carboxyvinyltransferase as attractive candidates for new drug targets. Furthermore, computational three-dimensional structure modeling and subsequent molecular docking finally proposed [3-(5-Amino-7-Hydroxy-[1,2,3]Triazolo[4,5-D]Pyrimidin-2-Yl)-N-(3,5-Dichlorobenzyl)-Benzamide)] and (6-amino-2-[(1-naphthylmethyl)amino]-3,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one) as promising candidate drugs for further evaluation and development for E. coli O104:H4 mediated diseases. Identification of new drug target would be of great utility for humanity as the demand for designing new drugs to fight infections is increasing due to the developing resistance and side effects of current treatments. This research provided the basis for computer aided drug design which might be useful for new drug target identification and subsequent drug design for other infectious organisms.
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Affiliation(s)
- Shakhinur Islam Mondal
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh. .,Division of Microbiology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki, 889-1692, Japan.
| | - Zabed Mahmud
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Montasir Elahi
- Department of Diagnosis, Prevention and Treatment of Dementia, Juntendo University Graduate School of Medicine, Bunkyō, Tokyo, Japan
| | - Arzuba Akter
- Division of Microbiology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki, 889-1692, Japan.,Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Nurnabi Azad Jewel
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Md Muzahidul Islam
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Sabiha Ferdous
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Taisei Kikuchi
- Division of Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki, 889-1692, Japan
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17
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Rožman K, Lešnik S, Brus B, Hrast M, Sova M, Patin D, Barreteau H, Konc J, Janežič D, Gobec S. Discovery of new MurA inhibitors using induced-fit simulation and docking. Bioorg Med Chem Lett 2017; 27:944-949. [DOI: 10.1016/j.bmcl.2016.12.082] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Revised: 12/26/2016] [Accepted: 12/29/2016] [Indexed: 11/15/2022]
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18
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Kumar A, Saranathan R, Prashanth K, Tiwary BK, Krishna R. Inhibition of the MurA enzyme in Fusobacterium nucleatum by potential inhibitors identified through computational and in vitro approaches. MOLECULAR BIOSYSTEMS 2017; 13:939-954. [DOI: 10.1039/c7mb00074j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Inhibition of MurA in open conformation by orientin and in closed conformation by quercetin-3-O-d-glucuronide with efficient inhibitory constant values.
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Affiliation(s)
- Amit Kumar
- Centre for Bioinformatics
- Pondicherry University
- Puducherry-605014
- India
| | | | - K. Prashanth
- Department of Biotechnology
- Pondicherry University
- Puducherry-605014
- India
| | - Basant K. Tiwary
- Centre for Bioinformatics
- Pondicherry University
- Puducherry-605014
- India
| | - Ramadas Krishna
- Centre for Bioinformatics
- Pondicherry University
- Puducherry-605014
- India
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19
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de Carvalho MP, Gulotta G, do Amaral MW, Lünsdorf H, Sasse F, Abraham WR. Coprinuslactone protects the edible mushroom Coprinus comatus against biofilm infections by blocking both quorum-sensing and MurA. Environ Microbiol 2016; 18:4254-4264. [PMID: 27696655 DOI: 10.1111/1462-2920.13560] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 09/28/2016] [Indexed: 12/23/2022]
Abstract
Pathogens embedded in biofilms are involved in many infections and are very difficult to treat with antibiotics because of higher resistance compared with planktonic cells. Therefore, new approaches for their control are urgently needed. One way to search for biofilm dispersing compounds is to look at defense strategies of organisms exposed to wet environments, which makes them prone to biofilm infections. It is reasonable to assume that mushrooms have developed mechanisms to control biofilms on their sporocarps (fruiting bodies). A preliminary screening for biofilms on sporocarps revealed several species with few or no bacteria on their sporocarps. From the edible mushroom Coprinus comatus where no bacteria on the sporocarp could be detected (3R,4S)-2-methylene-3,4-dihydroxypentanoic acid 1,4-lactone, named coprinuslactone, was isolated. Coprinuslactone interfered with quorum-sensing and dispersed biofilms of Pseudomonas aeruginosa, where it also reduced the formation of the pathogenicity factors pyocyanin and rhamnolipid B. Coprinuslactone also damaged Staphylococcus aureus cells in biofilms at subtoxic concentrations. Furthermore, it inhibited UDP-N-acetylglucosamine enolpyruvyl transferase (MurA), essential for bacterial cell wall synthesis. These two modes of action ensure the inhibition of a broad spectrum of pathogens on the fruiting body but may also be useful for future clinical applications.
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Affiliation(s)
- Maira P de Carvalho
- Chemical Microbiology, Helmholtz Center for Infection Research, Braunschweig, 38124, Germany
| | - Giuseppe Gulotta
- Microbial Interactions and Processes, Helmholtz Center for Infection Research, Braunschweig, 38124, Germany
| | - Matheus W do Amaral
- Chemical Microbiology, Helmholtz Center for Infection Research, Braunschweig, 38124, Germany
| | - Heinrich Lünsdorf
- Central Facility for Microscopy, Helmholtz Center for Infection Research, Braunschweig, 38124, Germany
| | - Florenz Sasse
- Chemical Biology, Helmholtz Center for Infection Research, Braunschweig, 38124, Germany
| | - Wolf-Rainer Abraham
- Chemical Microbiology, Helmholtz Center for Infection Research, Braunschweig, 38124, Germany
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20
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Lamsa A, Lopez-Garrido J, Quach D, Riley EP, Pogliano J, Pogliano K. Rapid Inhibition Profiling in Bacillus subtilis to Identify the Mechanism of Action of New Antimicrobials. ACS Chem Biol 2016; 11:2222-31. [PMID: 27193499 DOI: 10.1021/acschembio.5b01050] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Increasing antimicrobial resistance has become a major public health crisis. New antimicrobials with novel mechanisms of action (MOA) are desperately needed. We previously developed a method, bacterial cytological profiling (BCP), which utilizes fluorescence microscopy to rapidly identify the MOA of antimicrobial compounds. BCP is based upon our discovery that cells treated with antibiotics affecting different metabolic pathways generate different cytological signatures, providing quantitative information that can be used to determine a compound's MOA. Here, we describe a system, rapid inhibition profiling (RIP), for creating cytological profiles of new antibiotic targets for which there are currently no chemical inhibitors. RIP consists of the fast, inducible degradation of a target protein followed by BCP. We demonstrate that degrading essential proteins in the major metabolic pathways for DNA replication, transcription, fatty acid biosynthesis, and peptidoglycan biogenesis in Bacillus subtilis rapidly produces cytological profiles closely matching that of antimicrobials targeting the same pathways. Additionally, RIP and antibiotics targeting different steps in fatty acid biosynthesis can be differentiated from each other. We utilize RIP and BCP to show that the antibacterial MOA of four nonsteroidal anti-inflammatory antibiotics differs from that proposed based on in vitro data. RIP is a versatile method that will extend our knowledge of phenotypes associated with inactivating essential bacterial enzymes and thereby allow for screening for molecules that inhibit novel essential targets.
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Affiliation(s)
- Anne Lamsa
- Division
of Biological Sciences, University of California, San Diego, La Jolla, California, United States
| | - Javier Lopez-Garrido
- Division
of Biological Sciences, University of California, San Diego, La Jolla, California, United States
| | - Diana Quach
- Department
of Bioengineering, University of California, San Diego, La Jolla, California, United States
| | - Eammon P. Riley
- Division
of Biological Sciences, University of California, San Diego, La Jolla, California, United States
| | - Joe Pogliano
- Division
of Biological Sciences, University of California, San Diego, La Jolla, California, United States
| | - Kit Pogliano
- Division
of Biological Sciences, University of California, San Diego, La Jolla, California, United States
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21
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Global characterization of in vivo enzyme catalytic rates and their correspondence to in vitro kcat measurements. Proc Natl Acad Sci U S A 2016; 113:3401-6. [PMID: 26951675 DOI: 10.1073/pnas.1514240113] [Citation(s) in RCA: 142] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Turnover numbers, also known as kcat values, are fundamental properties of enzymes. However, kcat data are scarce and measured in vitro, thus may not faithfully represent the in vivo situation. A basic question that awaits elucidation is: how representative are kcat values for the maximal catalytic rates of enzymes in vivo? Here, we harness omics data to calculate kmax(vivo), the observed maximal catalytic rate of an enzyme inside cells. Comparison with kcat values from Escherichia coli, yields a correlation ofr(2)= 0.62 in log scale (p < 10(-10)), with a root mean square difference of 0.54 (3.5-fold in linear scale), indicating that in vivo and in vitro maximal rates generally concur. By accounting for the degree of saturation of enzymes and the backward flux dictated by thermodynamics, we further refine the correspondence between kmax(vivo) and kcat values. The approach we present here characterizes the quantitative relationship between enzymatic catalysis in vitro and in vivo and offers a high-throughput method for extracting enzyme kinetic constants from omics data.
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22
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Overexpression of the Lactobacillus plantarum peptidoglycan biosynthesis murA2 gene increases the tolerance of Escherichia coli to alcohols and enhances ethanol production. Appl Microbiol Biotechnol 2014; 98:8399-411. [DOI: 10.1007/s00253-014-6004-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 07/28/2014] [Accepted: 08/03/2014] [Indexed: 10/24/2022]
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23
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Cloning, expression and characterization of UDP-N-acetylglucosamine enolpyruvyl transferase (MurA) from Wolbachia endosymbiont of human lymphatic filarial parasite Brugia malayi. PLoS One 2014; 9:e99884. [PMID: 24941309 PMCID: PMC4062475 DOI: 10.1371/journal.pone.0099884] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 05/19/2014] [Indexed: 12/21/2022] Open
Abstract
Wolbachia, an endosymbiont of filarial nematode, is considered a promising target for treatment of lymphatic filariasis. Although functional characterization of the Wolbachia peptidoglycan assembly has not been fully explored, the Wolbachia genome provides evidence for coding all of the genes involved in lipid II biosynthesis, a part of peptidoglycan biosynthesis pathway. UDP-N-acetylglucosamine enolpyruvyl transferase (MurA) is one of the lipid II biosynthesis pathway enzymes and it has inevitably been recognized as an antibiotic target. In view of the vital role of MurA in bacterial viability and survival, MurA ortholog from Wolbachia endosymbiont of Brugia malayi (wBm-MurA) was cloned, expressed and purified for further molecular characterization. The enzyme kinetics and inhibition studies were undertaken using fosfomycin. wBm-MurA was found to be expressed in all the major life stages of B. malayi and was immunolocalized in Wolbachia within the microfilariae and female adults by the confocal microscopy. Sequence analysis suggests that the amino acids crucial for enzymatic activity are conserved. The purified wBm-MurA was shown to possess the EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase) like activity at a broad pH range with optimal activity at pH 7.5 and 37°C temperature. The apparent affinity constant (Km) for the substrate UDP-N-acetylglucosamine was found to be 0.03149 mM and for phosphoenolpyruvate 0.009198 mM. The relative enzymatic activity was inhibited ∼2 fold in presence of fosfomycin. Superimposition of the wBm-MurA homology model with the structural model of Haemophilus influenzae (Hi-MurA) suggests binding of fosfomycin at the same active site. The findings suggest wBm-MurA to be a putative antifilarial drug target for screening of novel compounds.
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24
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Khokhar M, Kaur N, Jain V, Sandhir R, Gautam A, Bharatam PV, Tewari R. Comparative modeling of pivotal enzymes, MurA and MurZ, of Enterococcus faecalis and identification of potential inhibitors by computational methods. Med Chem Res 2014. [DOI: 10.1007/s00044-013-0785-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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25
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Characterization of mycobacterial UDP-N-acetylglucosamine enolpyruvyle transferase (MurA). Res Microbiol 2014; 165:91-101. [PMID: 24463011 DOI: 10.1016/j.resmic.2014.01.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 01/13/2014] [Indexed: 11/23/2022]
Abstract
The mycobacterial peptidoglycan has structure and biosynthetic pathways to similar those of other bacteria. UDP-N-acetylglucosamine enolpyruvyle transferase (MurA) catalyzes the first reaction in the biosynthesis of peptidoglycan. The MurA enzyme has been identified from various bacterial species, but the in-depth biochemical properties of mycobacterial MurA have not been characterized. In this study, both Mycobacterium tuberculosis MurA protein and Mycobacterium smegmatis MurA protein were overexpressed in Escherichia coli and purified by affinity chromatography. MurA activity was detected by HPLC. A colorimetric assay of MurA activity was also developed and the kinetic properties of Mtb MurA and Msm MurA were determined using this colorimetric assay. A conditional murA gene knockout strain was constructed by DNA homologous recombination. The disruption of murA in the genome of M. smegmatis led to loss of viability at a non-permissive temperature. Drastic morphological and structural alterations in the M. smegmatis murA knockout strain were observed by scanning electron microscopy and transmission electron microscopy. These results demonstrated that murA was an essential gene for growth of M. smegmatis. Therefore, MurA is a potential target for developing new anti-tuberculosis drugs.
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26
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Nikolaidis I, Favini-Stabile S, Dessen A. Resistance to antibiotics targeted to the bacterial cell wall. Protein Sci 2014; 23:243-59. [PMID: 24375653 DOI: 10.1002/pro.2414] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 12/21/2013] [Accepted: 12/23/2013] [Indexed: 11/10/2022]
Abstract
Peptidoglycan is the main component of the bacterial cell wall. It is a complex, three-dimensional mesh that surrounds the entire cell and is composed of strands of alternating glycan units crosslinked by short peptides. Its biosynthetic machinery has been, for the past five decades, a preferred target for the discovery of antibacterials. Synthesis of the peptidoglycan occurs sequentially within three cellular compartments (cytoplasm, membrane, and periplasm), and inhibitors of proteins that catalyze each stage have been identified, although not all are applicable for clinical use. A number of these antimicrobials, however, have been rendered inactive by resistance mechanisms. The employment of structural biology techniques has been instrumental in the understanding of such processes, as well as the development of strategies to overcome them. This review provides an overview of resistance mechanisms developed toward antibiotics that target bacterial cell wall precursors and its biosynthetic machinery. Strategies toward the development of novel inhibitors that could overcome resistance are also discussed.
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Affiliation(s)
- I Nikolaidis
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, 6 rue Jules Horowitz, 38027, Grenoble, France; Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Grenoble, France; Centre National de la Recherche Scientifique (CNRS), UMR 5075, Grenoble, France; Bijvoet Center for Biomolecular Research, Department of Biochemistry of Membranes, Utrecht University, Utrecht, The Netherlands
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27
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Abstract
The synthesis of the bacterial peptidoglycan has been recognized for over 50 years as fertile ground for antibacterial discovery. Initially, empirical screening of natural products for inhibition of bacterial growth detected many chemical classes of antibiotics whose specific mechanisms of action were eventually dissected and defined. Of the nontoxic antibiotics discovered, most were found to be inhibitors of either protein synthesis or cell wall synthesis, which led to more directed screening for inhibitors of these pathways. Directed screening and design programs for cell wall inhibitors have been undertaken since the 1960s. In that time it has become clear that, while certain steps and intermediates have yielded selective inhibitors and are established targets, other potential targets have not yielded inhibitors whose antibacterial activity is proven to be solely due to that inhibition. Why has this search been so problematic? Are the established targets still worth pursuing? This review will attempt to answer these and other questions and evaluate the viability of targets related to peptidoglycan synthesis.
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Affiliation(s)
- Lynn L Silver
- LL Silver Consulting, LLC, Springfield, New Jersey 07081, USA.
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28
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Singh S, Phillips GN, Thorson JS. The structural biology of enzymes involved in natural product glycosylation. Nat Prod Rep 2012; 29:1201-37. [PMID: 22688446 DOI: 10.1039/c2np20039b] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The glycosylation of microbial natural products often dramatically influences the biological and/or pharmacological activities of the parental metabolite. Over the past decade, crystal structures of several enzymes involved in the biosynthesis and attachment of novel sugars found appended to natural products have emerged. In many cases, these studies have paved the way to a better understanding of the corresponding enzyme mechanism of action and have served as a starting point for engineering variant enzymes to facilitate to production of differentially-glycosylated natural products. This review specifically summarizes the structural studies of bacterial enzymes involved in biosynthesis of novel sugar nucleotides.
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Affiliation(s)
- Shanteri Singh
- Laboratory for Biosynthetic Chemistry, Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
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