1
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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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2
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First-In-Class Inhibitors Targeting the Interaction between Bacterial RNA Polymerase and Sigma Initiation Factor Affect the Viability and Toxin Release of Streptococcus pneumoniae. Molecules 2019; 24:molecules24162902. [PMID: 31405060 PMCID: PMC6719014 DOI: 10.3390/molecules24162902] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/07/2019] [Accepted: 08/08/2019] [Indexed: 11/16/2022] Open
Abstract
Novel antimicrobial classes are in desperate need for clinical management of infections caused by increasingly prevalent multi-drug resistant pathogens. The protein-protein interaction between bacterial RNA polymerase (RNAP) and the housekeeping sigma initiation factor is essential to transcription and bacterial viability. It also presents a potential target for antimicrobial discovery, for which a hit compound (C3) was previously identified from a pharmacophore model-based in silico screen. In this study, the hit compound was experimentally assessed with some rationally designed derivatives for the antimicrobial activities, in particular against Streptococcus pneumoniae and other pathogens. One compound, C3-005, shows dramatically improved activity against pneumococci compared to C3. C3-005 also attenuates S. pneumoniae toxin production more strongly than existing classes of antibiotics tested. Here we demonstrate a newly validated antimicrobial agent to address an overlooked target in the hit-to-lead process, which may pave the way for further antimicrobial development.
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3
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Discovery and development of novel rhodanine derivatives targeting enoyl-acyl carrier protein reductase. Bioorg Med Chem 2019; 27:1509-1516. [DOI: 10.1016/j.bmc.2019.02.043] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/18/2019] [Accepted: 02/20/2019] [Indexed: 12/12/2022]
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4
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Sun ZG, Xu YJ, Xu JF, Liu QX, Yang YS, Zhu HL. Introducing Broadened Antibacterial Activity to Rhodanine Derivatives Targeting Enoyl-Acyl Carrier Protein Reductase. Chem Pharm Bull (Tokyo) 2019; 67:125-129. [PMID: 30713272 DOI: 10.1248/cpb.c18-00663] [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: 11/22/2022]
Abstract
Broadened antibacterial activity was introduced to rhodanine derivatives targeting Mycobacterial tuberculosis enoyl-acyl carrier protein reductase (Mtb InhA) by recruiting feature of xacins to bring DNA Gyrase B inhibitory capability. This is significant for preventing further bacterial injections in the tuberculosis treatment. The most potent compound Cy14 suggested comparable bioactivity (IC50 = 3.18 µM for Mtb InhA; IC50 = 10 nM for DNA Gyrase B) with positive controls. Structure-activity relationship discussion and molecular docking model revealed the significance of rhodanine moiety and derived methoxyl on meta-position, pointing out orientations for future modification.
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Affiliation(s)
- Zhi-Gang Sun
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University.,Central Laboratory, Linyi Central Hospital
| | - Yun-Jie Xu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University
| | - Jian-Fei Xu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University
| | - Qi-Xing Liu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University
| | - Yu-Shun Yang
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University
| | - Hai-Liang Zhu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University
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5
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Wenholz DS, Zeng M, Ma C, Mielczarek M, Yang X, Bhadbhade M, Black DSC, Lewis PJ, Griffith R, Kumar N. Small molecule inhibitors of bacterial transcription complex formation. Bioorg Med Chem Lett 2017; 27:4302-4308. [PMID: 28866270 DOI: 10.1016/j.bmcl.2017.08.036] [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: 07/19/2017] [Revised: 08/16/2017] [Accepted: 08/16/2017] [Indexed: 11/26/2022]
Abstract
Knoevenagel condensation was employed to generate a set of molecules potentially capable of inhibiting the RNA polymerase-σ70/σA interaction in bacteria. Synthesis was achieved via reactions between a variety of indole-7-carbaldehydes and rhodanine, N-allylrhodanine, barbituric acid or thiobarbituric acid. A library of structurally diverse compounds was examined by enzyme-linked immunosorbent assay (ELISA) to assess the inhibition of the targeted protein-protein interaction. Inhibition of bacterial growth was also evaluated using Bacillus subtilis and Escherichia coli cultures. The structure-activity relationship studies demonstrated the significance of particular structural features of the synthesized molecules for RNA polymerase-σ70/σA interaction inhibition and antibacterial activity. Docking was investigated as an in silico method for the further development of the compounds.
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Affiliation(s)
- Daniel S Wenholz
- School of Chemistry, UNSW Sydney, Kensington, NSW 2052, Australia
| | - Ming Zeng
- School of Chemistry, UNSW Sydney, Kensington, NSW 2052, Australia
| | - Cong Ma
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia; Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong
| | | | - Xiao Yang
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia; Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong
| | - Mohan Bhadbhade
- School of Chemistry, UNSW Sydney, Kensington, NSW 2052, Australia
| | - David St C Black
- School of Chemistry, UNSW Sydney, Kensington, NSW 2052, Australia
| | - Peter J Lewis
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Renate Griffith
- School of Medical Sciences, UNSW Sydney, Kensington, NSW 2052, Australia
| | - Naresh Kumar
- School of Chemistry, UNSW Sydney, Kensington, NSW 2052, Australia; Australian Centre for Nanomedicine, UNSW Sydney, Kensington, NSW 2052, Australia.
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6
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Slepikas L, Chiriano G, Perozzo R, Tardy S, Kranjc A, Patthey-Vuadens O, Ouertatani-Sakouhi H, Kicka S, Harrison CF, Scrignari T, Perron K, Hilbi H, Soldati T, Cosson P, Tarasevicius E, Scapozza L. In Silico Driven Design and Synthesis of Rhodanine Derivatives as Novel Antibacterials Targeting the Enoyl Reductase InhA. J Med Chem 2016; 59:10917-10928. [DOI: 10.1021/acs.jmedchem.5b01620] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Liudas Slepikas
- School
of Pharmaceutical Sciences, Department of Pharmaceutical Biochemistry, University of Geneva and University of Lausanne, 30 Quai Ernest Ansermet, CH-1211 Geneva, Switzerland
- Faculty
of Pharmacy, Lithuanian University of Health Sciences, LT 44307 Kaunas, Lithuania
| | - Gianpaolo Chiriano
- School
of Pharmaceutical Sciences, Department of Pharmaceutical Biochemistry, University of Geneva and University of Lausanne, 30 Quai Ernest Ansermet, CH-1211 Geneva, Switzerland
| | - Remo Perozzo
- School
of Pharmaceutical Sciences, Department of Pharmaceutical Biochemistry, University of Geneva and University of Lausanne, 30 Quai Ernest Ansermet, CH-1211 Geneva, Switzerland
| | - Sébastien Tardy
- School
of Pharmaceutical Sciences, Department of Pharmaceutical Biochemistry, University of Geneva and University of Lausanne, 30 Quai Ernest Ansermet, CH-1211 Geneva, Switzerland
| | - Agata Kranjc
- School
of Pharmaceutical Sciences, Department of Pharmaceutical Biochemistry, University of Geneva and University of Lausanne, 30 Quai Ernest Ansermet, CH-1211 Geneva, Switzerland
| | - Ophélie Patthey-Vuadens
- School
of Pharmaceutical Sciences, Department of Pharmaceutical Biochemistry, University of Geneva and University of Lausanne, 30 Quai Ernest Ansermet, CH-1211 Geneva, Switzerland
| | - Hajer Ouertatani-Sakouhi
- Department
of Cell Physiology and Metabolism, CMU, Rue Michel-Servet 1 CH-1211 Geneva, Switzerland
| | - Sébastien Kicka
- Department
of Biochemistry, University of Geneva, 30 Quai Ernest Ansermet, CH-1211 Geneva, Switzerland
| | - Christopher F. Harrison
- Max
von Pettenkofer Institute, Department of Medicine, Ludwig-Maximilians University Munich, 80336 Munich, Germany
| | - Tiziana Scrignari
- Microbiology
Unit, Department of Botany and Plant Biology, University of Geneva, CH-1211 Geneva, Switzerland
| | - Karl Perron
- Microbiology
Unit, Department of Botany and Plant Biology, University of Geneva, CH-1211 Geneva, Switzerland
| | - Hubert Hilbi
- Max
von Pettenkofer Institute, Department of Medicine, Ludwig-Maximilians University Munich, 80336 Munich, Germany
- Institute
of Medical Microbiology, Department of Medicine, University of Zürich, Gloriastrasse 30/32, CH-8006 Zürich, Switzerland
| | - Thierry Soldati
- Department
of Biochemistry, University of Geneva, 30 Quai Ernest Ansermet, CH-1211 Geneva, Switzerland
| | - Pierre Cosson
- Department
of Cell Physiology and Metabolism, CMU, Rue Michel-Servet 1 CH-1211 Geneva, Switzerland
| | - Eduardas Tarasevicius
- Faculty
of Pharmacy, Lithuanian University of Health Sciences, LT 44307 Kaunas, Lithuania
| | - Leonardo Scapozza
- School
of Pharmaceutical Sciences, Department of Pharmaceutical Biochemistry, University of Geneva and University of Lausanne, 30 Quai Ernest Ansermet, CH-1211 Geneva, Switzerland
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7
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Bacterial Transcription as a Target for Antibacterial Drug Development. Microbiol Mol Biol Rev 2016; 80:139-60. [PMID: 26764017 DOI: 10.1128/mmbr.00055-15] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Transcription, the first step of gene expression, is carried out by the enzyme RNA polymerase (RNAP) and is regulated through interaction with a series of protein transcription factors. RNAP and its associated transcription factors are highly conserved across the bacterial domain and represent excellent targets for broad-spectrum antibacterial agent discovery. Despite the numerous antibiotics on the market, there are only two series currently approved that target transcription. The determination of the three-dimensional structures of RNAP and transcription complexes at high resolution over the last 15 years has led to renewed interest in targeting this essential process for antibiotic development by utilizing rational structure-based approaches. In this review, we describe the inhibition of the bacterial transcription process with respect to structural studies of RNAP, highlight recent progress toward the discovery of novel transcription inhibitors, and suggest additional potential antibacterial targets for rational drug design.
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8
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Perdih A, Hrast M, Pureber K, Barreteau H, Grdadolnik SG, Kocjan D, Gobec S, Solmajer T, Wolber G. Furan-based benzene mono- and dicarboxylic acid derivatives as multiple inhibitors of the bacterial Mur ligases (MurC-MurF): experimental and computational characterization. J Comput Aided Mol Des 2015; 29:541-60. [PMID: 25851408 DOI: 10.1007/s10822-015-9843-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 03/28/2015] [Indexed: 01/05/2023]
Abstract
Bacterial resistance to the available antibiotic agents underlines an urgent need for the discovery of novel antibacterial agents. Members of the bacterial Mur ligase family MurC-MurF involved in the intracellular stages of the bacterial peptidoglycan biosynthesis have recently emerged as a collection of attractive targets for novel antibacterial drug design. In this study, we have first extended the knowledge of the class of furan-based benzene-1,3-dicarboxylic acid derivatives by first showing a multiple MurC-MurF ligase inhibition for representatives of the extended series of this class. Steady-state kinetics studies on the MurD enzyme were performed for compound 1, suggesting a competitive inhibition with respect to ATP. To the best of our knowledge, compound 1 represents the first ATP-competitive MurD inhibitor reported to date with concurrent multiple inhibition of all four Mur ligases (MurC-MurF). Subsequent molecular dynamic (MD) simulations coupled with interaction energy calculations were performed for two alternative in silico models of compound 1 in the UMA/D-Glu- and ATP-binding sites of MurD, identifying binding in the ATP-binding site as energetically more favorable in comparison to the UMA/D-Glu-binding site, which was in agreement with steady-state kinetic data. In the final stage, based on the obtained MD data novel furan-based benzene monocarboxylic acid derivatives 8-11, exhibiting multiple Mur ligase (MurC-MurF) inhibition with predominantly superior ligase inhibition over the original series, were discovered and for compound 10 it was shown to possess promising antibacterial activity against S. aureus. These compounds represent novel leads that could by further optimization pave the way to novel antibacterial agents.
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Affiliation(s)
- Andrej Perdih
- National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia,
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9
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Surface plasmon resonance – more than a screening technology: insights in the binding mode of σ70:core RNAP inhibitors. Future Med Chem 2014; 6:1551-65. [DOI: 10.4155/fmc.14.105] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Aim: Antibiotic resistance has become a major health problem. The σ70:core interface of bacterial RNA polymerase is a promising drug target. Recently, the coiled-coil and lid-rudder-system of the β’ subunit has been identified as an inhibition hot spot. Materials & methods & Results: By using surface plasmon resonance-based assays, inhibitors of the protein–protein interaction were identified and competition with σ70 was shown. Effective inhibition was verified in an in vitro transcription and a σ70:core assembly assay. For one hit series, we found a correlation between activity and affinity. Mutant interaction studies suggest the inhibitors’ binding site. Conclusion: Surface plasmon resonance is a valuable technology in drug design, that has been used in this study to identify and evaluate σ70:core RNA polymerase inhibitors.
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10
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Nasiri F, Zolali A, Azimian Z. A novel one-pot solvent-free synthesis of 3-alkyl-2-thioxo-1,3-thiazolidine-4-ones. J Sulphur Chem 2013. [DOI: 10.1080/17415993.2013.789518] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Farough Nasiri
- Department of Applied Chemistry, University of Mohaghegh Ardabili, PO Box 56199-11367, Ardabil, Iran
| | - Amin Zolali
- Department of Chemistry, Faculty of Science, University of Kurdistan, Sanandaj, Iran
| | - Zeinab Azimian
- Department of Chemistry, Faculty of Science, University of Kurdistan, Sanandaj, Iran
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11
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Hüsecken K, Negri M, Fruth M, Boettcher S, Hartmann RW, Haupenthal J. Peptide-based investigation of the Escherichia coli RNA polymerase σ(70):core interface as target site. ACS Chem Biol 2013; 8:758-66. [PMID: 23330640 DOI: 10.1021/cb3005758] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The number of bacterial strains that are resistant against antibiotics increased dramatically during the past decades. This fact stresses the urgent need for the development of new antibacterial agents with novel modes of action targeting essential enzymes such as RNA polymerase (RNAP). Bacterial RNAP is a large multi-subunit complex consisting of a core enzyme (subunits: α(2)ββ'ω) and a dissociable sigma factor (σ(70); holo enzyme: α(2)ββ'ωσ(70)) that is responsible for promoter recognition and transcription initiation. The interface between core RNAP and σ(70) represents a promising binding site. Nevertheless, detailed studies investigating its druggability are rare. Compounds binding to this region could inhibit this protein-protein interaction and thus holo enzyme formation, resulting in inhibition of transcription initiation. Sixteen peptides covering different regions of the Escherichia coli σ(70):core interface were designed; some of them-all derived from σ(70) 2.2 region-led to a strong RNAP inhibition. Indeed, an ELISA-based experiment confirmed the most active peptide P07 to inhibit the σ(70):core interaction. Furthermore, an abortive transcription assay revealed that P07 impedes transcription initiation. In order to study the mechanism of action of P07 in more detail, molecular dynamics simulations and a rational amino acid replacement study were performed, leading to the conclusion that P07 binds to the coiled-coil region in β' and that its flexible N-terminus inhibits the enzyme by interaction with the β' lid-rudder-system (LRS). This work revisits the β' coiled-coil as a hot spot for the protein-protein interaction inhibition and expands it by introduction of the LRS as target site.
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Affiliation(s)
- Kristina Hüsecken
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Department
of Drug Design and Optimization and ‡Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2_3, D-66123
Saarbrücken, Germany
| | - Matthias Negri
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Department
of Drug Design and Optimization and ‡Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2_3, D-66123
Saarbrücken, Germany
| | - Martina Fruth
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Department
of Drug Design and Optimization and ‡Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2_3, D-66123
Saarbrücken, Germany
| | - Stefan Boettcher
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Department
of Drug Design and Optimization and ‡Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2_3, D-66123
Saarbrücken, Germany
| | - Rolf W. Hartmann
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Department
of Drug Design and Optimization and ‡Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2_3, D-66123
Saarbrücken, Germany
| | - Joerg Haupenthal
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Department
of Drug Design and Optimization and ‡Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2_3, D-66123
Saarbrücken, Germany
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12
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Chopra I. The 2012 Garrod lecture: discovery of antibacterial drugs in the 21st century. J Antimicrob Chemother 2012; 68:496-505. [PMID: 23134656 DOI: 10.1093/jac/dks436] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The discovery and development of antibacterial drugs in the twentieth century were major scientific and medical achievements that have had profound benefits for human society. However, in the twenty-first century the widespread global occurrence of bacteria resistant to the antibiotics and synthetic drugs discovered in the previous century threatens to reverse our ability to treat infectious diseases. Although some new drugs are in development they do not adequately cover growing medical needs. Furthermore, these drugs are mostly derivatives of older classes already in use and therefore prone to existing bacterial resistance mechanisms. Thus, new drug classes are urgently needed. Despite investment in antibacterial drug discovery, no new drug class has been discovered in the past 20 years. In this review, based upon my career as a research scientist in the field of antibacterial drug discovery, I consider some of the technical reasons for the recent failure and look to the future developments that may help to reverse the poor current success rate. Diversification of screening libraries to include new natural products will be important as well as ensuring that the promising drug hits arising from structure-based drug design can achieve effective concentrations at their target sites within the bacterial cell.
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Affiliation(s)
- Ian Chopra
- School of Molecular and Cellular Biology and Antimicrobial Research Centre, University of Leeds, Leeds LS2 9JT, UK.
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13
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Influence of DNA template choice on transcription and inhibition of Escherichia coli RNA polymerase. Antimicrob Agents Chemother 2012; 56:4536-9. [PMID: 22664971 DOI: 10.1128/aac.00198-12] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
In recent decades, quantitative transcription assays using bacterial RNA polymerase (RNAP) have been performed under widely diverse experimental conditions. We demonstrate that the template choice can influence the inhibitory potency of RNAP inhibitors. Furthermore, we illustrate that the sigma factor (σ(70)) surprisingly increases the transcription efficiency of templates with nonphysiological nonprokaryotic promoters. Our results might be a useful guideline in the early stages of using RNAP for drug discovery.
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14
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McPhillie MJ, Trowbridge R, Mariner KR, O’Neill AJ, Johnson AP, Chopra I, Fishwick CWG. Structure-based ligand design of novel bacterial RNA polymerase inhibitors. ACS Med Chem Lett 2011; 2:729-34. [PMID: 24900260 DOI: 10.1021/ml200087m] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Accepted: 07/29/2011] [Indexed: 11/28/2022] Open
Abstract
Bacterial RNA polymerase (RNAP) is essential for transcription and is an antibacterial target for small molecule inhibitors. The binding region of myxopyronin B (MyxB), a bacterial RNAP inhibitor, offers the possibility of new inhibitor design. The molecular design program SPROUT has been used in conjunction with the X-ray cocrystal structure of Thermus thermophilus RNAP with MyxB to design novel inhibitors based on a substituted pyridyl-benzamide scaffold. A series of molecules, with molecular masses <350 Da, have been prepared using a simple synthetic approach. A number of these compounds inhibited Escherichia coli RNAP.
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Affiliation(s)
- Martin J. McPhillie
- School of Chemistry and ‡Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Rachel Trowbridge
- School of Chemistry and ‡Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Katherine R. Mariner
- School of Chemistry and ‡Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Alex J. O’Neill
- School of Chemistry and ‡Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - A. Peter Johnson
- School of Chemistry and ‡Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Ian Chopra
- School of Chemistry and ‡Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Colin W. G. Fishwick
- School of Chemistry and ‡Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
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15
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Derouaux A, Turk S, Olrichs NK, Gobec S, Breukink E, Amoroso A, Offant J, Bostock J, Mariner K, Chopra I, Vernet T, Zervosen A, Joris B, Frère JM, Nguyen-Distèche M, Terrak M. Small molecule inhibitors of peptidoglycan synthesis targeting the lipid II precursor. Biochem Pharmacol 2011; 81:1098-105. [PMID: 21356201 DOI: 10.1016/j.bcp.2011.02.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Revised: 02/10/2011] [Accepted: 02/14/2011] [Indexed: 11/19/2022]
Abstract
Bacterial peptidoglycan glycosyltransferases (GTs) of family 51 catalyze the polymerization of the lipid II precursor into linear peptidoglycan strands. This activity is essential to bacteria and represents a validated target for the development of new antibacterials. Application of structure-based virtual screening to the National Cancer Institute library using eHits program and the structure of the glycosyltransferase domain of the Staphylococcus aureus penicillin-binding protein 2 resulted in the identification of two small molecules analogues 5, a 2-[1-[(2-chlorophenyl)methyl]-2-methyl-5-methylsulfanylindol-3-yl]ethanamine and 5b, a 2-[1-[(3,4-dichlorophenyl)methyl]-2-methyl-5-methylsulfanylindol-3-yl]ethanamine that exhibit antibacterial activity against several Gram-positive bacteria but were less active on Gram-negative bacteria. The two compounds inhibit the activity of five GTs in the micromolar range. Investigation of the mechanism of action shows that the compounds specifically target peptidoglycan synthesis. Unexpectedly, despite the fact that the compounds were predicted to bind to the GT active site, compound 5b was found to interact with the lipid II substrate via the pyrophosphate motif. In addition, this compound showed a negatively charged phospholipid-dependent membrane depolarization and disruption activity. These small molecules are promising leads for the development of more active and specific compounds to target the essential GT step in cell wall synthesis.
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Affiliation(s)
- Adeline Derouaux
- Centre d'Ingénierie des Protéines, Université de Liège, Allée de la chimie, B6a, B-4000, Sart Tilman, Liège, Belgium
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16
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Activity of and development of resistance to corallopyronin A, an inhibitor of RNA polymerase. Antimicrob Agents Chemother 2011; 55:2413-6. [PMID: 21321139 DOI: 10.1128/aac.01742-10] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We explored the properties of corallopyronin A (CorA), a poorly characterized inhibitor of bacterial RNA polymerase (RNAP). It displayed a 50% inhibitory concentration of 0.73 μM against RNAP, compared with 11.5 nM for rifampin. The antibacterial activity of CorA was also inferior to rifampin, and resistant mutants of Staphylococcus aureus were easily selected. The mutations conferring resistance resided in the rpoB and rpoC subunits of RNAP. We conclude that CorA is not a promising antibacterial drug candidate.
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17
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Further characterization of Bacillus subtilis antibiotic biosensors and their use for antibacterial mode-of-action studies. Antimicrob Agents Chemother 2011; 55:1784-6. [PMID: 21282422 DOI: 10.1128/aac.01710-10] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We further examined the usefulness of previously reported Bacillus subtilis biosensors for antibacterial mode-of-action studies. The biosensors could not detect the tRNA synthetase inhibitors mupirocin, indolmycin, and borrelidin, some inhibitors of peptidoglycan synthesis, and most membrane-damaging agents. However, the biosensors confirmed the modes of action of several RNA polymerase inhibitors and DNA intercalators and provided new insights into the possible modes of action of ciprofloxacin, anhydrotetracycline, corralopyronin, 8-hydroxyquinoline, and juglone.
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