1
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Dashti Y, Errington J. Chemistry and biology of specialized metabolites produced by Actinomadura. Nat Prod Rep 2024; 41:370-401. [PMID: 38099919 PMCID: PMC10951976 DOI: 10.1039/d3np00047h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Indexed: 03/21/2024]
Abstract
Covering: up to the end of 2022In recent years rare Actinobacteria have become increasingly recognised as a rich source of novel bioactive metabolites. Actinomadura are Gram-positive bacteria that occupy a wide range of ecological niches. This review highlights about 230 secondary metabolites produced by Actinomadura spp., reported until the end of 2022, including their bioactivities and selected biosynthetic pathways. Notably, the bioactive compounds produced by Actinomadura spp. demonstrate a wide range of activities, including antimicrobial, antitumor and anticoccidial effects, highlighting their potential in various fields.
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Affiliation(s)
- Yousef Dashti
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2015, Australia.
| | - Jeff Errington
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2015, Australia.
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2
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Stephanie F, Tambunan USF, Siahaan TJ. M. tuberculosis Transcription Machinery: A Review on the Mycobacterial RNA Polymerase and Drug Discovery Efforts. Life (Basel) 2022; 12:1774. [PMID: 36362929 PMCID: PMC9695777 DOI: 10.3390/life12111774] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 10/24/2022] [Accepted: 11/01/2022] [Indexed: 09/08/2023] Open
Abstract
Mycobacterium tuberculosis (MTB) is the main source of tuberculosis (TB), one of the oldest known diseases in the human population. Despite the drug discovery efforts of past decades, TB is still one of the leading causes of mortality and claimed more than 1.5 million lives worldwide in 2020. Due to the emergence of drug-resistant strains and patient non-compliance during treatments, there is a pressing need to find alternative therapeutic agents for TB. One of the important areas for developing new treatments is in the inhibition of the transcription step of gene expression; it is the first step to synthesize a copy of the genetic material in the form of mRNA. This further translates to functional protein synthesis, which is crucial for the bacteria living processes. MTB contains a bacterial DNA-dependent RNA polymerase (RNAP), which is the key enzyme for the transcription process. MTB RNAP has been targeted for designing and developing antitubercular agents because gene transcription is essential for the mycobacteria survival. Initiation, elongation, and termination are the three important sequential steps in the transcription process. Each step is complex and highly regulated, involving multiple transcription factors. This review is focused on the MTB transcription machinery, especially in the nature of MTB RNAP as the main enzyme that is regulated by transcription factors. The mechanism and conformational dynamics that occur during transcription are discussed and summarized. Finally, the current progress on MTB transcription inhibition and possible drug target in mycobacterial RNAP are also described to provide insight for future antitubercular drug design and development.
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Affiliation(s)
- Filia Stephanie
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok 16424, Indonesia
| | - Usman Sumo Friend Tambunan
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok 16424, Indonesia
| | - Teruna J. Siahaan
- Department of Pharmaceutical Chemistry, School of Pharmacy, The University of Kansas, Lawrence, KS 66045, USA
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3
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Kirsch SH, Haeckl FPJ, Müller R. Beyond the approved: target sites and inhibitors of bacterial RNA polymerase from bacteria and fungi. Nat Prod Rep 2022; 39:1226-1263. [PMID: 35507039 DOI: 10.1039/d1np00067e] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Covering: 2016 to 2022RNA polymerase (RNAP) is the central enzyme in bacterial gene expression representing an attractive and validated target for antibiotics. Two well-known and clinically approved classes of natural product RNAP inhibitors are the rifamycins and the fidaxomycins. Rifampicin (Rif), a semi-synthetic derivative of rifamycin, plays a crucial role as a first line antibiotic in the treatment of tuberculosis and a broad range of bacterial infections. However, more and more pathogens such as Mycobacterium tuberculosis develop resistance, not only against Rif and other RNAP inhibitors. To overcome this problem, novel RNAP inhibitors exhibiting different target sites are urgently needed. This review includes recent developments published between 2016 and today. Particular focus is placed on novel findings concerning already known bacterial RNAP inhibitors, the characterization and development of new compounds isolated from bacteria and fungi, and providing brief insights into promising new synthetic compounds.
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Affiliation(s)
- Susanne H Kirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany. .,German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - F P Jake Haeckl
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany. .,German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany. .,German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.,Department of Pharmacy, Saarland University, 66123 Saarbrücken, Germany
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4
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Ma S, Chen H, Li H, Ji X, Deng Z, Ding W, Zhang Q. Post-Translational Formation of Aminomalonate by a Promiscuous Peptide-Modifying Radical SAM Enzyme. Angew Chem Int Ed Engl 2021; 60:19957-19964. [PMID: 34164914 DOI: 10.1002/anie.202107192] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 06/23/2021] [Indexed: 11/12/2022]
Abstract
Aminomalonate (Ama) is a widespread structural motif in Nature, whereas its biosynthetic route is only partially understood. In this study, we show that a radical S-adenosylmethionine (rSAM) enzyme involved in cyclophane biosynthesis exhibits remarkable catalytic promiscuity. This enzyme, named three-residue cyclophane forming enzyme (3-CyFE), mainly produces cyclophane in vivo, whereas it produces formylglycine (FGly) as a major product and barely produce cyclophane in vitro. Importantly, the enzyme can further oxidize FGly to produce Ama. Bioinformatic study revealed that 3-CyFEs have evolved from a common ancestor with anaerobic sulfatase maturases (anSMEs), and possess a similar set of catalytic residues with anSMEs. Remarkably, the enzyme does not need leader peptide for activity and is fully active on a truncated peptide containing only 5 amino acids of the core sequence. Our work discloses the first ribosomal path towards Ama formation, providing a possible hint for the rich occurrence of Ama in Nature.
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Affiliation(s)
- Suze Ma
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Heng Chen
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - He Li
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Xinjian Ji
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wei Ding
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qi Zhang
- Department of Chemistry, Fudan University, Shanghai, 200433, China
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5
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Ma S, Chen H, Li H, Ji X, Deng Z, Ding W, Zhang Q. Post‐Translational Formation of Aminomalonate by a Promiscuous Peptide‐Modifying Radical SAM Enzyme. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202107192] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Suze Ma
- Department of Chemistry Fudan University Shanghai 200433 China
| | - Heng Chen
- Department of Chemistry Fudan University Shanghai 200433 China
| | - He Li
- Department of Chemistry Fudan University Shanghai 200433 China
| | - Xinjian Ji
- Department of Chemistry Fudan University Shanghai 200433 China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology Shanghai Jiao Tong University Shanghai 200240 China
| | - Wei Ding
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology Shanghai Jiao Tong University Shanghai 200240 China
| | - Qi Zhang
- Department of Chemistry Fudan University Shanghai 200433 China
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6
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Kaur G, Kapoor S, Kaundal S, Dutta D, Thakur KG. Structure-Guided Designing and Evaluation of Peptides Targeting Bacterial Transcription. Front Bioeng Biotechnol 2020; 8:797. [PMID: 33014990 PMCID: PMC7505949 DOI: 10.3389/fbioe.2020.00797] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 06/22/2020] [Indexed: 11/17/2022] Open
Abstract
The mycobacterial RNA polymerase (RNAP) is an essential and validated drug target for developing antibacterial drugs. The β-subunit of Mycobacterium tuberculosis (Mtb) RNAP (RpoB) interacts with an essential and global transcription factor, CarD, and confers antibiotic and oxidative stress resistance to Mtb. Compromising the RpoB/CarD interactions results in the killing of mycobacteria, hence disrupting the RpoB/CarD interaction has been proposed as a novel strategy for the development of anti-tubercular drugs. Here, we describe the first approach to rationally design and test the efficacy of the peptide-based inhibitors which specifically target the conserved PPI interface between the bacterial RNAP β/transcription factor complex. We performed in silico protein-peptide docking studies along with biochemical assays to characterize the novel peptide-based inhibitors. Our results suggest that the top ranked peptides are highly stable, soluble in aqueous buffer, and capable of inhibiting transcription with IC50 > 50 μM concentration. Using peptide-based molecules, our study provides the first piece of evidence to target the conserved RNAP β/transcription factor interface for designing new inhibitors. Our results may hence form the basis to further improve the potential of these novel peptides in modulating bacterial gene expression, thus inhibiting bacterial growth and combating bacterial infections.
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Affiliation(s)
- Gundeep Kaur
- Structural Biology Laboratory, G. N. Ramachandran Protein Centre, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
| | - Srajan Kapoor
- Structural Biology Laboratory, G. N. Ramachandran Protein Centre, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
| | - Soni Kaundal
- Structural Biology Laboratory, G. N. Ramachandran Protein Centre, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
| | - Dipak Dutta
- Molecular Microbiology Laboratory, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
| | - Krishan Gopal Thakur
- Structural Biology Laboratory, G. N. Ramachandran Protein Centre, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
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7
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Dalmastri C, Gastaldo L, Berini F, Marinelli F, Marcone GL. Description of the bacterial RNA polymerase inhibitor GE23077-producer Actinomadura sp. NRRL B-65521 T as Actinomadura lepetitiana sp. nov. Int J Syst Evol Microbiol 2020; 70:4782-4790. [PMID: 32701429 DOI: 10.1099/ijsem.0.004348] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The filamentous actinomycete that produces the antibiotic GE23077 was isolated by the Lepetit Research Group from a soil sample collected in Thailand, and it was classified as a member of the genus Actinomadura on the basis of its morphology and cell-wall composition. Phylogenetic analysis based on 16S rRNA gene sequences indicated that this strain formed a distinct monophyletic line within the genus Actinomadura, and it was most closely related to Actinomadura bangladeshensis DSM 45347T (99.31 % similarity) and Actinomadura mexicana DSM 44485T (98.94 %). The GE23077-producing strain formed an extensively branched, non-fragmented vegetative mycelium; no pseudosporangia were formed and the arthrospores were organized in slightly twisted chains. The cell wall contained meso-2,6-diaminopimelic acid and the diagnostic sugar was madurose. The predominant menaquinone was MK-9(H6), with minor amounts of MK-9(H8) and MK-9(H4). The diagnostic phospholipids were phosphatidylinositol and diphosphatidylglycerol. The major cellular fatty acids were C16 : 0 and tuberculostearic acid (10-methyloctadecanoic acid), followed by minor amounts of C18:1ω9c, C16:1ω7c and 10-methylheptadecanoic acid. The genomic DNA G+C content was 71.77 mol%. Significant differences in the morphological, chemotaxonomic and biochemical data, and the low DNA-DNA relatedness between the GE23077-producing strain and closely related type strains clearly demonstrate that it represents a novel species of the genus Actinomadura, for which the name Actinomadura lepetitiana sp. nov. is proposed. The type strain is NRRL B-65521T(=LMG 31258T=DSM 109019T).
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Affiliation(s)
- Claudia Dalmastri
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development, ENEA, Department for Sustainability, C.R. Casaccia, 00123 Rome, Italy
| | - Luciano Gastaldo
- University of Insubria, Department of Biotechnology and Life Sciences, 21100 Varese, Italy
| | - Francesca Berini
- University of Insubria, Department of Biotechnology and Life Sciences, 21100 Varese, Italy
| | - Flavia Marinelli
- University of Insubria, Department of Biotechnology and Life Sciences, 21100 Varese, Italy
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8
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Malde AK, Hill TA, Iyer A, Fairlie DP. Crystal Structures of Protein-Bound Cyclic Peptides. Chem Rev 2019; 119:9861-9914. [DOI: 10.1021/acs.chemrev.8b00807] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Alpeshkumar K. Malde
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Timothy A. Hill
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Abishek Iyer
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - David P. Fairlie
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
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9
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Mechanisms of antibiotics inhibiting bacterial RNA polymerase. Biochem Soc Trans 2019; 47:339-350. [PMID: 30647141 DOI: 10.1042/bst20180499] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 12/18/2018] [Accepted: 12/20/2018] [Indexed: 12/21/2022]
Abstract
Transcription, the first phase of gene expression, is performed by the multi-subunit RNA polymerase (RNAP). Bacterial RNAP is a validated target for clinical antibiotics. Many natural and synthetic compounds are now known to target RNAP, inhibiting various stages of the transcription cycle. However, very few RNAP inhibitors are used clinically. A detailed knowledge of inhibitors and their mechanisms of action (MOA) is vital for the future development of efficacious antibiotics. Moreover, inhibitors of RNAP are often useful tools with which to dissect RNAP function. Here, we review the MOA of antimicrobial transcription inhibitors.
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10
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Lin W, Das K, Degen D, Mazumder A, Duchi D, Wang D, Ebright YW, Ebright RY, Sineva E, Gigliotti M, Srivastava A, Mandal S, Jiang Y, Liu Y, Yin R, Zhang Z, Eng ET, Thomas D, Donadio S, Zhang H, Zhang C, Kapanidis AN, Ebright RH. Structural Basis of Transcription Inhibition by Fidaxomicin (Lipiarmycin A3). Mol Cell 2018; 70:60-71.e15. [PMID: 29606590 PMCID: PMC6205224 DOI: 10.1016/j.molcel.2018.02.026] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 02/14/2018] [Accepted: 02/23/2018] [Indexed: 12/16/2022]
Abstract
Fidaxomicin is an antibacterial drug in clinical use for treatment of Clostridium difficile diarrhea. The active ingredient of fidaxomicin, lipiarmycin A3 (Lpm), functions by inhibiting bacterial RNA polymerase (RNAP). Here we report a cryo-EM structure of Mycobacterium tuberculosis RNAP holoenzyme in complex with Lpm at 3.5-Å resolution. The structure shows that Lpm binds at the base of the RNAP "clamp." The structure exhibits an open conformation of the RNAP clamp, suggesting that Lpm traps an open-clamp state. Single-molecule fluorescence resonance energy transfer experiments confirm that Lpm traps an open-clamp state and define effects of Lpm on clamp dynamics. We suggest that Lpm inhibits transcription by trapping an open-clamp state, preventing simultaneous interaction with promoter -10 and -35 elements. The results account for the absence of cross-resistance between Lpm and other RNAP inhibitors, account for structure-activity relationships of Lpm derivatives, and enable structure-based design of improved Lpm derivatives.
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Affiliation(s)
- Wei Lin
- Waksman Institute and Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA
| | - Kalyan Das
- Rega Institute and Department of Microbiology and Immunology, KU Leuven, 3000 Leuven, Belgium.
| | - David Degen
- Waksman Institute and Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA
| | - Abhishek Mazumder
- Waksman Institute and Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA
| | - Diego Duchi
- Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Dongye Wang
- Waksman Institute and Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA
| | - Yon W Ebright
- Waksman Institute and Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA
| | - Richard Y Ebright
- Waksman Institute and Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA
| | - Elena Sineva
- Waksman Institute and Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA
| | - Matthew Gigliotti
- Waksman Institute and Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA
| | - Aashish Srivastava
- Waksman Institute and Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA
| | - Sukhendu Mandal
- Waksman Institute and Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA
| | - Yi Jiang
- Waksman Institute and Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA
| | - Yu Liu
- Waksman Institute and Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA
| | - Ruiheng Yin
- Waksman Institute and Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA
| | - Zhening Zhang
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York NY 10027, USA
| | - Edward T Eng
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York NY 10027, USA
| | - Dennis Thomas
- Center for Integrative Proteomics, Rutgers University, Piscataway, NJ 08854, USA
| | | | - Haibo Zhang
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Changsheng Zhang
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | | | - Richard H Ebright
- Waksman Institute and Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA.
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11
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Orientia tsutsugamushi Is Highly Susceptible to the RNA Polymerase Switch Region Inhibitor Corallopyronin A In Vitro and In Vivo. Antimicrob Agents Chemother 2018; 62:AAC.01732-17. [PMID: 29358295 DOI: 10.1128/aac.01732-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 01/12/2018] [Indexed: 01/19/2023] Open
Abstract
Scrub typhus is a potentially lethal infection caused by the obligate intracellular bacterium Orientia tsutsugamushi Reports on the emergence of doxycycline-resistant strains highlight the urgent need to develop novel antiinfectives against scrub typhus. Corallopyronin A (CorA) is a novel α-pyrone compound synthesized by the myxobacterium Corallococcus coralloides that was characterized as a noncompetitive inhibitor of the switch region of the bacterial RNA polymerase (RNAP). We investigated the antimicrobial action of CorA against the human-pathogenic Karp strain of O. tsutsugamushiin vitro and in vivo The MIC of CorA against O. tsutsugamushi was remarkably low (0.0078 μg/ml), 16-fold lower than that against Rickettsia typhi In the lethal intraperitoneal O. tsutsugamushi mouse infection model, a minimum daily dose of 100 μg CorA protected 100% of infected mice. Two days of treatment were sufficient to confer protection. In contrast to BALB/c mice, SCID mice succumbed to the infection despite treatment with CorA or tetracycline, suggesting that antimicrobial treatment required synergistic action of the adaptive immune response. Similar to tetracycline, CorA did not prevent latent infection of O. tsutsugamushiin vivo However, latency was not caused by acquisition of antimicrobial resistance, since O. tsutsugamushi reisolated from latently infected BALB/c mice remained fully susceptible to CorA. No mutations were found in the CorA-binding regions of the β and β' RNAP subunit genes rpoB and rpoC Inhibition of the RNAP switch region of O. tsutsugamushi by CorA is therefore a novel and highly potent target for antimicrobial therapy for scrub typhus.
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12
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Maffioli SI, Zhang Y, Degen D, Carzaniga T, Del Gatto G, Serina S, Monciardini P, Mazzetti C, Guglierame P, Candiani G, Chiriac AI, Facchetti G, Kaltofen P, Sahl HG, Dehò G, Donadio S, Ebright RH. Antibacterial Nucleoside-Analog Inhibitor of Bacterial RNA Polymerase. Cell 2017. [PMID: 28622509 DOI: 10.1016/j.cell.2017.05.042] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Drug-resistant bacterial pathogens pose an urgent public-health crisis. Here, we report the discovery, from microbial-extract screening, of a nucleoside-analog inhibitor that inhibits bacterial RNA polymerase (RNAP) and exhibits antibacterial activity against drug-resistant bacterial pathogens: pseudouridimycin (PUM). PUM is a natural product comprising a formamidinylated, N-hydroxylated Gly-Gln dipeptide conjugated to 6'-amino-pseudouridine. PUM potently and selectively inhibits bacterial RNAP in vitro, inhibits bacterial growth in culture, and clears infection in a mouse model of Streptococcus pyogenes peritonitis. PUM inhibits RNAP through a binding site on RNAP (the NTP addition site) and mechanism (competition with UTP for occupancy of the NTP addition site) that differ from those of the RNAP inhibitor and current antibacterial drug rifampin (Rif). PUM exhibits additive antibacterial activity when co-administered with Rif, exhibits no cross-resistance with Rif, and exhibits a spontaneous resistance rate an order-of-magnitude lower than that of Rif. PUM is a highly promising lead for antibacterial therapy.
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Affiliation(s)
- Sonia I Maffioli
- NAICONS Srl, 20139 Milan, Italy; Vicuron Pharmaceuticals, 21040 Gerenzano, Italy
| | - Yu Zhang
- Waksman Institute and Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA
| | - David Degen
- Waksman Institute and Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA
| | - Thomas Carzaniga
- Department of Bioscience, University of Milan, 20122 Milan, Italy
| | | | - Stefania Serina
- NAICONS Srl, 20139 Milan, Italy; Vicuron Pharmaceuticals, 21040 Gerenzano, Italy
| | - Paolo Monciardini
- NAICONS Srl, 20139 Milan, Italy; Vicuron Pharmaceuticals, 21040 Gerenzano, Italy
| | | | | | | | - Alina Iulia Chiriac
- Institute of Medical Microbiology, Immunology, and Parasitology, University of Bonn, D-53012 Bonn, Germany
| | | | | | - Hans-Georg Sahl
- Institute of Medical Microbiology, Immunology, and Parasitology, University of Bonn, D-53012 Bonn, Germany
| | - Gianni Dehò
- Department of Bioscience, University of Milan, 20122 Milan, Italy
| | - Stefano Donadio
- NAICONS Srl, 20139 Milan, Italy; Vicuron Pharmaceuticals, 21040 Gerenzano, Italy.
| | - Richard H Ebright
- Waksman Institute and Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA.
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13
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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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14
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Growing the seeds sown by Piero Sensi. J Antibiot (Tokyo) 2014; 67:613-7. [PMID: 25118102 DOI: 10.1038/ja.2014.110] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Revised: 07/08/2014] [Accepted: 07/16/2014] [Indexed: 11/08/2022]
Abstract
Piero Sensi is probably known primarily for his role in the discovery of rifamycin and for developing it to be a drug of fundamental importance in the treatment of tuberculosis. He has also contributed to promote screening programs of microbial products and research approaches for antibacterial agents that have been further developed up to the present day. This paper reports a sequence of discovery approaches, failures and successes that spans for about 50 years and is still in progress.
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15
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Zhang Y, Degen D, Ho MX, Sineva E, Ebright KY, Ebright YW, Mekler V, Vahedian-Movahed H, Feng Y, Yin R, Tuske S, Irschik H, Jansen R, Maffioli S, Donadio S, Arnold E, Ebright RH. GE23077 binds to the RNA polymerase 'i' and 'i+1' sites and prevents the binding of initiating nucleotides. eLife 2014; 3:e02450. [PMID: 24755292 PMCID: PMC3994528 DOI: 10.7554/elife.02450] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Using a combination of genetic, biochemical, and structural approaches, we show that the cyclic-peptide antibiotic GE23077 (GE) binds directly to the bacterial RNA polymerase (RNAP) active-center ‘i’ and ‘i+1’ nucleotide binding sites, preventing the binding of initiating nucleotides, and thereby preventing transcription initiation. The target-based resistance spectrum for GE is unusually small, reflecting the fact that the GE binding site on RNAP includes residues of the RNAP active center that cannot be substituted without loss of RNAP activity. The GE binding site on RNAP is different from the rifamycin binding site. Accordingly, GE and rifamycins do not exhibit cross-resistance, and GE and a rifamycin can bind simultaneously to RNAP. The GE binding site on RNAP is immediately adjacent to the rifamycin binding site. Accordingly, covalent linkage of GE to a rifamycin provides a bipartite inhibitor having very high potency and very low susceptibility to target-based resistance. DOI:http://dx.doi.org/10.7554/eLife.02450.001 As increasing numbers of bacteria become resistant to antibiotics, new drugs are needed to fight bacterial infections. To develop new antibacterial drugs, researchers need to understand how existing antibiotics work. There are many ways to kill bacteria, but one of the most effective is to target an enzyme called bacterial RNA polymerase. If bacterial RNA polymerase is prevented from working, bacteria cannot synthesize RNA and cannot survive. GE23077 (GE for short) is an antibiotic produced by bacteria found in soil. Although GE stops bacterial RNA polymerase from working, and thereby kills bacteria, it does not affect mammalian RNA polymerases, and so does not kill mammalian cells. Understanding how GE works could help with the development of new antibacterial drugs. Zhang et al. present results gathered from a range of techniques to show how GE inhibits bacterial RNA polymerase. These show that GE works by binding to a site on RNA polymerase that is different from the binding sites of previously characterized antibacterial drugs. The mechanism used to inhibit the RNA polymerase is also different. The newly identified binding site has several features that make it an unusually attractive target for development of antibacterial compounds. Bacteria can become resistant to an antibiotic if genetic mutations lead to changes in the site the antibiotic binds to. However, the site that GE binds to on RNA polymerase is essential for RNA polymerase to function and so cannot readily be changed without crippling the enzyme. Therefore, this type of antibiotic resistance is less likely to develop. In addition, the newly identified binding site for GE on RNA polymerase is located next to the binding site for a current antibacterial drug, rifampin. Zhang et al. therefore linked GE and rifampin to form a two-part (‘bipartite’) compound designed to bind simultaneously to the GE and the rifampin binding sites. This compound was able to inhibit drug-resistant RNA polymerases tens to thousands of times more potently than GE or rifampin alone. DOI:http://dx.doi.org/10.7554/eLife.02450.002
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Affiliation(s)
- Yu Zhang
- Waksman Institute, Rutgers University, Piscataway, United States
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16
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Arnvig KB, Werner F. A new spanner in the works of bacterial transcription. eLife 2014; 3:e02840. [PMID: 24755293 PMCID: PMC3994527 DOI: 10.7554/elife.02840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
A promising molecular target that is unlikely to develop antibiotic resistance has been identified in bacteria.
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Affiliation(s)
- Kristine B Arnvig
- Kristine B Arnvig is in the Institute for Structural and Molecular Biology, University College London, London, United Kingdom
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17
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18
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Singh SB, Young K, Miesel L. Screening strategies for discovery of antibacterial natural products. Expert Rev Anti Infect Ther 2013; 9:589-613. [PMID: 21819327 DOI: 10.1586/eri.11.81] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Microbial-derived natural products have been a traditional source of antibiotics and antibiotic leads and continue to be effective sources of antibiotics today. The most important of these discoveries were made about 50 years ago. Chemical modifications of natural products discovered during those years continue to produce new clinical agents but their value is now, unfortunately, fading away owing to the exhaustion of opportunities of chemical modifications. The discovery of new natural antibiotics is directly linked to new screening technologies, particularly technologies that can help to eliminate the rediscovery of known antibiotics. In this article, we have reviewed the screening technologies from recent literature as well as originating from authors laboratories that were used for the screening of natural products. The article covers the entire spectrum of screening strategies, including classical empiric whole-cell assays to more sophisticated antisense based hypersensitive Staphylococcus aureus Fitness Test assays designed to screen all targets simultaneously. These technologies have led to the discovery of a series of natural product antibiotics, which have been summarized, including the discovery of platensimycin, platencin, nocathiacins, philipimycin, cyclothialidine and muryamycins. It is quite clear that natural products provide a tremendous opportunity to discover new antibiotics when combined with new hyper-sensitive whole-cell technologies.
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Affiliation(s)
- Sheo B Singh
- Merck Research Laboratories, Rahway, NJ 07065, USA.
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19
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Mazzei E, Iorio M, Maffioli SI, Sosio M, Donadio S. Characterization of madurastatin C1, a novel siderophore from Actinomadura sp. J Antibiot (Tokyo) 2012; 65:267-9. [DOI: 10.1038/ja.2012.10] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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20
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Saleem M, Nazir M, Ali MS, Hussain H, Lee YS, Riaz N, Jabbar A. Antimicrobial natural products: an update on future antibiotic drug candidates. Nat Prod Rep 2009; 27:238-54. [PMID: 20111803 DOI: 10.1039/b916096e] [Citation(s) in RCA: 263] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Over the last decade, it has become clear that antimicrobial drugs are losing their effectiveness due to the evolution of pathogen resistance. There is therefore a continuing need to search for new antibiotics, especially as new drugs only rarely reach the market. Natural products are both fundamental sources of new chemical diversity and integral components of today's pharmaceutical compendium, and the aim of this review is to explore and highlight the diverse natural products that have potential to lead to more effective and less toxic antimicrobial drugs. Although more than 300 natural metabolites with antimicrobial activity have been reported in the period 2000-2008, this review will describe only those with potentially useful antimicrobial activity, viz. with MICs in the range 0.02-10 microg mL(-1). A total of 145 compounds from 13 structural classes are discussed, and over 100 references are cited.
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Affiliation(s)
- Muhammad Saleem
- Department of Chemistry, Baghdad-ul-Jadeed Campus, The Islamia University of Bahawalpur, 63000 Bahawalpur, Pakistan
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21
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Villain-Guillot P, Bastide L, Gualtieri M, Leonetti JP. Progress in targeting bacterial transcription. Drug Discov Today 2007; 12:200-8. [PMID: 17331884 DOI: 10.1016/j.drudis.2007.01.005] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2006] [Revised: 01/05/2007] [Accepted: 01/23/2007] [Indexed: 01/25/2023]
Abstract
The bacterial RNA polymerase (RNAP) is an essential enzyme that is responsible for making RNA from a DNA template and is targeted by several antibiotics. Rifampicin was the first of such antibiotics to be described and is one of the most efficient anti-tuberculosis drugs in use. In the past five years, structural studies of bacterial RNAP and the resolution of several complexes of drugs bound to RNAP subunits have revealed molecular details of the drug-binding sites and the mechanism of drug action. This knowledge opens avenues for the development of antibiotics. Here these drugs are reviewed, together with their mechanisms and their potential interest for therapeutic applications.
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Affiliation(s)
- Philippe Villain-Guillot
- CNRS UMR 5236, UM1 UM2, Centre d'études d'agents pathogènes et Biotechnologies our la Santé, Av Charles Flahault, 34093 Montpellier, France
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22
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Chan YA, Boyne MT, Podevels AM, Klimowicz AK, Handelsman J, Kelleher NL, Thomas MG. Hydroxymalonyl-acyl carrier protein (ACP) and aminomalonyl-ACP are two additional type I polyketide synthase extender units. Proc Natl Acad Sci U S A 2006; 103:14349-54. [PMID: 16983083 PMCID: PMC1599966 DOI: 10.1073/pnas.0603748103] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Combinatorial biosynthesis of type I polyketide synthases is a promising approach for the generation of new structural derivatives of polyketide-containing natural products. A target of this approach has been to change the extender units incorporated into a polyketide backbone to alter the structure and activity of the natural product. One limitation to these efforts is that only four extender units were known: malonyl-CoA, methylmalonyl-CoA, ethylmalonyl-CoA, and methoxymalonyl-acyl carrier protein (ACP). The chemical attributes of these extender units are quite similar, with the exception of the potential hydrogen bonding interactions by the oxygen of the methoxy moiety. Furthermore, the incorporated extender units are not easily modified by using simple chemical approaches when combinatorial biosynthesis is coupled to semisynthetic chemistry. We recently proposed the existence of two additional extender units, hydroxymalonyl-ACP and aminomalonyl-ACP, involved in the biosynthesis of zwittermicin A. These extender units offer unique possibilities for combinatorial biosynthesis and semisynthetic chemistry because of the introduction of free hydroxyl and amino moieties into a polyketide structure. Here, we present the biochemical and mass spectral evidence for the formation of these extender units. This evidence shows the formation of ACP-linked extender units for polyketide synthesis. Interestingly, aminomalonyl-ACP formation involves enzymology typically found in nonribosomal peptide synthesis.
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Affiliation(s)
- Yolande A. Chan
- *Departments of Bacteriology and
- Microbiology Doctoral Training Program, University of Wisconsin, Madison, WI 53706; and
| | - Michael T. Boyne
- Department of Chemistry, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | | | | | - Jo Handelsman
- Plant Pathology and
- Microbiology Doctoral Training Program, University of Wisconsin, Madison, WI 53706; and
| | - Neil L. Kelleher
- Department of Chemistry, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Michael G. Thomas
- *Departments of Bacteriology and
- Microbiology Doctoral Training Program, University of Wisconsin, Madison, WI 53706; and
- To whom correspondence should be addressed. E-mail:
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Leeds JA, Schmitt EK, Krastel P. Recent developments in antibacterial drug discovery: microbe-derived natural products – from collection to the clinic. Expert Opin Investig Drugs 2006; 15:211-26. [PMID: 16503759 DOI: 10.1517/13543784.15.3.211] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The pharmaceutical industry has historically relied on nature to provide compounds for antibacterial drug discovery. In recent years, several pharmaceutical companies have scaled back their efforts in natural product research. Nevertheless, the screening of natural products for antibacterial activity continues to provide excellent sources of biologically and chemically informative leads for new drugs. New technologies in high-throughput cultivation, genetic approaches to biodiversity and discovery of relatively untapped sources of natural products are expanding the ability to find novel, potent and highly selective antibacterial structures. Advances in purification, dereplication and structure elucidation, combined with the ability to chemically or biologically derivatise hits, aim to make the timeline for natural product-derived drug discovery similar or shorter than that expected for small synthetic molecules. This review addresses the strengths and shortcomings of technologies focused on microbe-derived natural products for antibacterial drug discovery and stresses the need for commitment to these approaches in order to achieve the goal of delivering safe, efficacious and high-quality medicines in the long run.
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Affiliation(s)
- Jennifer A Leeds
- Infectious Diseases Area, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA.
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Mariani R, Granata G, Maffioli SI, Serina S, Brunati C, Sosio M, Marazzi A, Vannini A, Patel D, White R, Ciabatti R. Antibiotics GE23077, novel inhibitors of bacterial RNA polymerase. Part 3: Chemical derivatization. Bioorg Med Chem Lett 2005; 15:3748-52. [PMID: 15990299 DOI: 10.1016/j.bmcl.2005.05.060] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2005] [Revised: 05/16/2005] [Accepted: 05/17/2005] [Indexed: 11/29/2022]
Abstract
GE23077 is a novel RNA polymerase inhibitor that is isolated from the fermentation broth of an Actinomadura sp. It is a cyclic heptapeptide complex made up of four factors, differing in the structure of acyl group connected to the side chain of an alpha,beta-diaminopropanoic acid moiety and in the configuration of the stereocenter of an alpha-amino-malonic acid residue. Although GE23077 shows strong inhibitory activity on both Rifampicin-sensitive and -resistant polymerases, it exhibits poor antimicrobial activity. The most reasonable explanation for this property has been based on the lack of penetration of the molecule across the bacterial membrane, owing to its strong hydrophilic character. To improve penetration, several parts of the molecule were accordingly modified with the aim of altering the physico-chemical properties of GE23077. The current SAR study has identified moieties important for RNA polymerase activity.
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Affiliation(s)
- Riccardo Mariani
- Vicuron Pharmaceuticals via R. Lepetit 34, 21040, Gerenzano (Varese), Italy.
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Butler MS, Buss AD. Natural products--the future scaffolds for novel antibiotics? Biochem Pharmacol 2005; 71:919-29. [PMID: 16289393 DOI: 10.1016/j.bcp.2005.10.012] [Citation(s) in RCA: 209] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2005] [Revised: 09/30/2005] [Accepted: 10/05/2005] [Indexed: 11/27/2022]
Abstract
Natural products have played a pivotal role in antibiotic drug discovery with most antibacterial drugs being derived from a natural product or natural product lead. However, the rapid onset of resistance to most antibacterial drugs diminishes their effectiveness considerably and necessitates a constant supply of new antibiotics for effective treatment of infections. The natural product templates of actinonin, pleuromutilin, ramoplanin and tiacumicin B, which are compounds undergoing clinical evaluation, represent templates not found in currently marketed antibacterial drugs. In addition, the new templates present in the recently discovered lead antibacterials arylomycin, GE23077, mannopeptimycin, muraymycin/caprazamycin, nocathiacin and ECO-0501, are discussed. Despite extensive efforts to identify antibiotic leads from molecular targets, only the peptide deformylase inhibitor LBM-415 is currently in clinical trials. It is proposed that new antibacterial assays which combine cell-based screening with molecular targets could offer better prospects for lead discovery.
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Affiliation(s)
- Mark S Butler
- MerLion Pharmaceuticals, 1 Science Park Road, The Capricorn #05-01, Singapore Science Park II, Singapore 117528, Singapore.
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26
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Sarubbi E, Monti F, Corti E, Miele A, Selva E. Mode of action of the microbial metabolite GE23077, a novel potent and selective inhibitor of bacterial RNA polymerase. ACTA ACUST UNITED AC 2004; 271:3146-54. [PMID: 15265034 DOI: 10.1111/j.1432-1033.2004.04244.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
GE23077, a novel microbial metabolite recently isolated from Actinomadura sp. culture media, is a potent and selective inhibitor of bacterial RNA polymerase (RNAP). It inhibits Gram-positive (Bacillus subtilis) and Gram-negative (Escherichia coli) RNAPs with IC50 values (i.e. the concentration at which the enzyme activity is inhibited by 50%) in the 10(-8) m range, whereas it is not active on E. coli DNA polymerase or on eukaryotic (wheat germ) RNAP II (IC50 values > 10(-4) m in both cases). In spite of its potent activity on purified bacterial RNAPs, GE23077 shows a narrow spectrum of antimicrobial activity on Gram-positive and Gram-negative bacteria. To investigate the molecular basis of this behaviour, the effects of GE23077 on macromolecular biosynthesis were tested in E. coli cells permeabilized under different conditions. The addition of GE23077 to plasmolyzed cells resulted in an immediate and specific inhibition of intracellular RNA biosynthesis, in a dose-response manner, strongly suggesting that cell penetration is the main obstacle for effective antimicrobial activity of the antibiotic. Biochemical studies were also conducted with purified enzymes to obtain further insights into the mode of action of GE23077. Interestingly, the compound displays a behaviour similar to that of rifampicin, an antibiotic structurally unrelated to GE23077: both compounds act at the level of transcription initiation, but not on the sigma subunit and not on the formation of the promoter DNA-RNAP complex. Tests on different rifampicin-resistant E. coli RNAPs did not show any cross-resistance between the two compounds, indicating distinct binding sites on the target enzyme. In conclusion, GE23077 is an interesting new molecule for future mechanistic studies on bacterial RNAP and for its potential in anti-infective drug discovery.
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