1
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Ye J, Kan CH, Yang X, Ma C. Inhibition of bacterial RNA polymerase function and protein-protein interactions: a promising approach for next-generation antibacterial therapeutics. RSC Med Chem 2024; 15:1471-1487. [PMID: 38784472 PMCID: PMC11110800 DOI: 10.1039/d3md00690e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 03/25/2024] [Indexed: 05/25/2024] Open
Abstract
The increasing prevalence of multidrug-resistant pathogens necessitates the urgent development of new antimicrobial agents with innovative modes of action for the next generation of antimicrobial therapy. Bacterial transcription has been identified and widely studied as a viable target for antimicrobial development. The main focus of these studies has been the discovery of inhibitors that bind directly to the core enzyme of RNA polymerase (RNAP). Over the past two decades, substantial advancements have been made in understanding the properties of protein-protein interactions (PPIs) and gaining structural insights into bacterial RNAP and its associated factors. This has led to the crucial role of computational methods in aiding the identification of new PPI inhibitors to affect the RNAP function. In this context, bacterial transcriptional PPIs present promising, albeit challenging, targets for the creation of new antimicrobials. This review will succinctly outline the structural foundation of bacterial transcription networks and provide a summary of the known small molecules that target transcription PPIs.
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Affiliation(s)
- Jiqing Ye
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University Kowloon Hong Kong SAR China
- School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University Hefei 230032 China
| | - Cheuk Hei Kan
- Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital Shatin Hong Kong SAR China
| | - Xiao Yang
- Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital Shatin Hong Kong SAR China
| | - Cong Ma
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University Kowloon Hong Kong SAR China
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2
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Ye J, Kan CH, Zheng Y, Tsang TF, Chu AJ, Chan KH, Yang X, Ma C. Sulfonamidyl derivatives of sigmacidin: Protein-protein interaction inhibitors targeting bacterial RNA polymerase and sigma factor interaction exhibiting antimicrobial activity against antibiotic-resistant bacteria. Bioorg Chem 2024; 143:106983. [PMID: 38016396 DOI: 10.1016/j.bioorg.2023.106983] [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: 09/28/2023] [Revised: 11/12/2023] [Accepted: 11/16/2023] [Indexed: 11/30/2023]
Abstract
RNA polymerase is an essential enzyme involved in bacterial transcription, playing a crucial role in RNA synthesis. However, it requires the association with sigma factors to initiate this process. In our previous work, we utilized a structure-based drug discovery approach to create benzoyl and benzyl benzoic acid compounds. These compounds were designed based on the amino acid residues within the key binding site of sigma factors, which are crucial for their interaction with RNA polymerase. By inhibiting bacterial transcription, these compounds exhibited notable antimicrobial activity, and we coined them as sigmacidins to highlight their resemblance to sigma factors and the benzoic acid structure. In this study, we further modified the compound scaffolds and developed a series of sulfonamidyl benzoic acid derivatives. These derivatives displayed potent antimicrobial activity, with minimum inhibitory concentrations (MICs) as low as 1 µg/mL, demonstrating their efficacy against bacteria. Furthermore, these compounds demonstrated low cytotoxicity, indicating their potential as safe antimicrobial agents. To ascertain their mechanism of action in interfering with bacterial transcription, we conducted biochemical and cellular assays. Overall, this study showcases the effectiveness of sulfonamidyl benzoic acid derivatives as antimicrobial agents by targeting protein-protein interactions involving RNA polymerase and sigma factors. Their strong antimicrobial activity and low cytotoxicity implicate their potential in combating antibiotic-resistant bacteria.
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Affiliation(s)
- Jiqing Ye
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region; School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, China
| | - Cheuk Hei Kan
- Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong Special Administrative Region
| | - Yingbo Zheng
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region
| | - Tsz Fung Tsang
- Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong Special Administrative Region
| | - Adrian Jun Chu
- Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong Special Administrative Region
| | - King Hong Chan
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region
| | - Xiao Yang
- Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong Special Administrative Region.
| | - Cong Ma
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region.
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3
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Ye J, Yang X, Ma C. Ligand-Based Drug Design of Novel Antimicrobials against Staphylococcus aureus by Targeting Bacterial Transcription. Int J Mol Sci 2022; 24:ijms24010339. [PMID: 36613782 PMCID: PMC9820117 DOI: 10.3390/ijms24010339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022] Open
Abstract
Staphylococcus aureus is a common human commensal pathogen that causes a wide range of infectious diseases. Due to the generation of antimicrobial resistance, the pathogen becomes resistant to more and more antibiotics, resulting in methicillin-resistant S. aureus (MRSA) and even multidrug-resistant S. aureus (MDRSA), namely 'superbugs'. This situation highlights the urgent need for novel antimicrobials. Bacterial transcription, which is responsible for bacterial RNA synthesis, is a valid but underutilized target for developing antimicrobials. Previously, we reported a novel class of antimicrobials, coined nusbiarylins, that inhibited bacterial transcription by interrupting the protein-protein interaction (PPI) between two transcription factors NusB and NusE. In this work, we developed a ligand-based workflow based on the chemical structures of nusbiarylins and their activity against S. aureus. The ligand-based models-including the pharmacophore model, 3D QSAR, AutoQSAR, and ADME/T calculation-were integrated and used in the following virtual screening of the ChemDiv PPI database. As a result, four compounds, including J098-0498, 1067-0401, M013-0558, and F186-026, were identified as potential antimicrobials against S. aureus, with predicted pMIC values ranging from 3.8 to 4.2. The docking study showed that these molecules bound to NusB tightly with the binding free energy ranging from -58 to -66 kcal/mol.
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Affiliation(s)
- Jiqing Ye
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
- School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei 230032, China
| | - Xiao Yang
- Department of Microbiology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Correspondence: (X.Y.); (C.M.)
| | - Cong Ma
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
- Correspondence: (X.Y.); (C.M.)
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4
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Qiu Y, Chu AJ, Tsang TF, Zheng Y, Lam NM, Li KSL, Ip M, Yang X, Ma C. Synthesis and biological evaluation of nusbiarylin derivatives as bacterial rRNA synthesis inhibitor with potent antimicrobial activity against MRSA and VRSA. Bioorg Chem 2022; 124:105863. [DOI: 10.1016/j.bioorg.2022.105863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/09/2022] [Accepted: 05/06/2022] [Indexed: 11/25/2022]
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5
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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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6
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Kahan R, Worm DJ, de Castro GV, Ng S, Barnard A. Modulators of protein-protein interactions as antimicrobial agents. RSC Chem Biol 2021; 2:387-409. [PMID: 34458791 PMCID: PMC8341153 DOI: 10.1039/d0cb00205d] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/27/2021] [Indexed: 12/12/2022] Open
Abstract
Protein-Protein interactions (PPIs) are involved in a myriad of cellular processes in all living organisms and the modulation of PPIs is already under investigation for the development of new drugs targeting cancers, autoimmune diseases and viruses. PPIs are also involved in the regulation of vital functions in bacteria and, therefore, targeting bacterial PPIs offers an attractive strategy for the development of antibiotics with novel modes of action. The latter are urgently needed to tackle multidrug-resistant and multidrug-tolerant bacteria. In this review, we describe recent developments in the modulation of PPIs in pathogenic bacteria for antibiotic development, including advanced small molecule and peptide inhibitors acting on bacterial PPIs involved in division, replication and transcription, outer membrane protein biogenesis, with an additional focus on toxin-antitoxin systems as upcoming drug targets.
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Affiliation(s)
- Rashi Kahan
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 82 Wood Lane London W12 0BZ UK
| | - Dennis J Worm
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 82 Wood Lane London W12 0BZ UK
| | - Guilherme V de Castro
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 82 Wood Lane London W12 0BZ UK
| | - Simon Ng
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 82 Wood Lane London W12 0BZ UK
| | - Anna Barnard
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 82 Wood Lane London W12 0BZ UK
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Ye J, Chu AJ, Lin L, Chan ST, Harper R, Xiao M, Artsimovitch I, Zuo Z, Ma C, Yang X. Benzyl and benzoyl benzoic acid inhibitors of bacterial RNA polymerase-sigma factor interaction. Eur J Med Chem 2020; 208:112671. [PMID: 32920341 PMCID: PMC7680358 DOI: 10.1016/j.ejmech.2020.112671] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/26/2020] [Accepted: 07/13/2020] [Indexed: 02/08/2023]
Abstract
Transcription is an essential biological process in bacteria requiring a core enzyme, RNA polymerase (RNAP). Bacterial RNAP is catalytically active but requires sigma (σ) factors for transcription of natural DNA templates. σ factor binds to RNAP to form a holoenzyme which specifically recognizes a promoter, melts the DNA duplex, and commences RNA synthesis. Inhibiting the binding of σ to RNAP is expected to inhibit bacterial transcription and growth. We previously identified a triaryl hit compound that mimics σ at its major binding site of RNAP, thereby inhibiting the RNAP holoenzyme formation. In this study, we modified this scaffold to provide a series of benzyl and benzoyl benzoic acid derivatives possessing improved antimicrobial activity. A representative compound demonstrated excellent activity against Staphylococcus epidermidis with minimum inhibitory concentrations reduced to 0.5 μg/mL, matching that of vancomycin. The molecular mechanism of inhibition was confirmed using biochemical and cellular assays. Low cytotoxicity and metabolic stability of compounds demonstrated the potential for further studies.
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Affiliation(s)
- Jiqing Ye
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
| | - Adrian Jun Chu
- Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - Lin Lin
- Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - Shu Ting Chan
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
| | - Rachel Harper
- Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - Min Xiao
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Irina Artsimovitch
- Department of Microbiology and the Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA
| | - Zhong Zuo
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Cong Ma
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China.
| | - Xiao Yang
- Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China.
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8
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Chu AJ, Qiu Y, Harper R, Lin L, Ma C, Yang X. Nusbiarylins Inhibit Transcription and Target Virulence Factors in Bacterial Pathogen Staphylococcus aureus. Int J Mol Sci 2020; 21:ijms21165772. [PMID: 32796751 PMCID: PMC7461214 DOI: 10.3390/ijms21165772] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/02/2020] [Accepted: 08/07/2020] [Indexed: 12/29/2022] Open
Abstract
The emergence of multidrug resistance in the clinically significant pathogen Staphylococcus aureus is a global health burden, compounded by a diminishing drug development pipeline, and a lack of approved novel antimicrobials. Our previously reported first-in-class bacterial transcription inhibitors “nusbiarylins” presented a promising prospect towards the discovery of novel antimicrobial agents with a novel mechanism. Here we investigated and characterised the lead nusbiarylin compound, MC4, and several of its chemical derivatives in both methicillin-resistant S. aureus (MRSA) and the S. aureus type strains, demonstrating their capacity for the arrest of growth and cellular respiration, impairment of RNA and intracellular protein levels at subinhibitory concentrations. In some instances, derivatives of MC4 were also shown to attenuate the production of staphylococcal virulence factors in vitro, such as the exoproteins α-toxin and Panton–Valentine Leukocidin (PVL). Trends observed from quantitative PCR assays suggested that nusbiarylins elicited these effects possibly by acting via but not limited to the modulation of global regulatory pathways, such as the agr regulon, which coordinates the expression of S. aureus genes associated with virulence. Our findings encourage the continued development of more potent compounds within this novel family of bacterial transcription inhibitors.
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Affiliation(s)
- Adrian Jun Chu
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong; (A.J.C.); (R.H.); (L.L.)
| | - Yangyi Qiu
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Hong Kong;
| | - Rachel Harper
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong; (A.J.C.); (R.H.); (L.L.)
| | - Lin Lin
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong; (A.J.C.); (R.H.); (L.L.)
| | - Cong Ma
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Hong Kong;
- Correspondence: (C.M.); (X.Y.)
| | - Xiao Yang
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong; (A.J.C.); (R.H.); (L.L.)
- Correspondence: (C.M.); (X.Y.)
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9
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Ye J, Chu AJ, Harper R, Chan ST, Shek TL, Zhang Y, Ip M, Sambir M, Artsimovitch I, Zuo Z, Yang X, Ma C. Discovery of Antibacterials That Inhibit Bacterial RNA Polymerase Interactions with Sigma Factors. J Med Chem 2020; 63:7695-7720. [PMID: 32633513 DOI: 10.1021/acs.jmedchem.0c00520] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Formation of a bacterial RNA polymerase (RNAP) holoenzyme by a catalytic core RNAP and a sigma (σ) initiation factor is essential for bacterial viability. As the primary binding site for the housekeeping σ factors, the RNAP clamp helix domain represents an attractive target for novel antimicrobial agent discovery. Previously, we designed a pharmacophore model based on the essential amino acids of the clamp helix, such as R278, R281, and I291 (Escherichia coli numbering), and identified hit compounds with antimicrobial activity that interfered with the core-σ interactions. In this work, we rationally designed and synthesized a class of triaryl derivatives of one hit compound and succeeded in drastically improving the antimicrobial activity against Streptococcus pneumoniae, with the minimum inhibitory concentration reduced from 256 to 1 μg/mL. Additional characterization of antimicrobial activity, inhibition of transcription, in vitro pharmacological properties, and cytotoxicity of the optimized compounds demonstrated their potential for further development.
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Affiliation(s)
- Jiqing Ye
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, People's Republic of China
| | - Adrian Jun Chu
- Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, People's Republic of China
| | - Rachel Harper
- Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, People's Republic of China
| | - Shu Ting Chan
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, People's Republic of China
| | - Tsun Lam Shek
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, People's Republic of China
| | - Yufeng Zhang
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, People's Republic of China
| | - Margaret Ip
- Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, People's Republic of China
| | - Mariya Sambir
- Department of Microbiology and the Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Irina Artsimovitch
- Department of Microbiology and the Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Zhong Zuo
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, People's Republic of China
| | - Xiao Yang
- Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, People's Republic of China
| | - Cong Ma
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, People's Republic of China
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10
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Qiu Y, Ma C. HPLC, quantitative NMR and HRMS spectroscopic data of nusbiarylins as a new class of antimicrobial agents. Data Brief 2020; 29:105313. [PMID: 32154348 PMCID: PMC7056622 DOI: 10.1016/j.dib.2020.105313] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 02/10/2020] [Accepted: 02/13/2020] [Indexed: 01/22/2023] Open
Abstract
Bacterial transcription is a valid but underutilized target for antimicrobial agent discovery [1]. Nusbiarylins are the first-in-class bacterial ribosomal RNA synthesis inhibitors that possess potent activity against various types of multidrug-resistant bacteria with a novel mode of action by targeting the interaction of bacterial transcription factors NusB and NusE [2]. To facilitate the characterization of nusbiarylin derivatives produced by other researchers, high-performance liquid chromatography (HPLC) profiles, quantitative nuclear magnetic resonance (qNMR) and high-resolution mass spectrometry (HRMS) spectroscopic data were presented for the quick determination of purity and characterization of 95 nusbiarylin compounds. The data presented in this article supplement the 1H and 13C NMR data provided previously [3,4], and assist the reproduction of nusbiarylins for chemical, biological and drug discovery research.
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Affiliation(s)
- Yangyi Qiu
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong Special Administrative Region
| | - Cong Ma
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong Special Administrative Region
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11
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Nusbiarylins, a new class of antimicrobial agents: Rational design of bacterial transcription inhibitors targeting the interaction between the NusB and NusE proteins. Bioorg Chem 2019; 92:103203. [PMID: 31446238 DOI: 10.1016/j.bioorg.2019.103203] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/15/2019] [Accepted: 08/14/2019] [Indexed: 01/03/2023]
Abstract
Discovery of antibiotics of a novel mode of action is highly required in the fierce battlefield with multi-drug resistant bacterial infections. Previously we have validated the protein-protein interaction between bacterial NusB and NusE proteins as an unprecedented antimicrobial target and reported the identification of a first-in-class inhibitor of bacterial ribosomal RNA synthesis with antimicrobial activities. In this paper, derivatives of the hit compound were rationally designed based on the pharmacophore model for chemical synthesis, followed by biological evaluations. Some of the derivatives demonstrated the improved antimicrobial activity with the minimum inhibitory concentration (MIC) at 1-2 μg/mL against clinically significant bacterial pathogens. Time-kill kinetics, confocal microscope, ATP production, cytotoxicity, hemolytic property and cell permeability using Caco-2 cells of a representative compound were also measured. This series of compounds were named "nusbiarylins" based on their target protein NusB and the biaryl structure and were expected to be further developed towards novel antimicrobial drug candidates in the near future.
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12
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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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Design, synthesis and biological evaluation of antimicrobial diarylimine and -amine compounds targeting the interaction between the bacterial NusB and NusE proteins. Eur J Med Chem 2019; 178:214-231. [PMID: 31185412 DOI: 10.1016/j.ejmech.2019.05.090] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 05/30/2019] [Accepted: 05/31/2019] [Indexed: 01/05/2023]
Abstract
Discovery of antimicrobial agents with a novel model of action is in urgent need for the clinical management of multidrug-resistant bacterial infections. Recently, we reported the identification of a first-in-class bacterial ribosomal RNA synthesis inhibitor, which interrupted the interaction between the bacterial transcription factor NusB and NusE. In this study, a series of diaryl derivatives were rationally designed and synthesized based on the previously established pharmacophore model. Inhibitory activity against the NusB-NusE binding, circular dichroism of compound treated NusB, antimicrobial activity, cytotoxicity, hemolytic property and cell permeability using Caco-2 cells were measured. Structure-activity relationship and quantitative structure-activity relationship were also concluded and discussed. Some of the derivatives demonstrated improved antimicrobial activity than the hit compound against a panel of clinically important pathogens, lowering the minimum inhibition concentration to 1-2 μg/mL against Staphylococcus aureus, including clinical strains of methicillin-resistant Staphylococcus aureus at a level comparable to some of the marketed antibiotics. Given the improved antimicrobial activity, specific inhibition of target protein-protein interaction and promising pharmacokinetic properties without significant cytotoxicity, this series of diaryl compounds have high potentials and deserve for further studies towards a new class of antimicrobial agents in the future.
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Tsang TF, Qiu Y, Lin L, Ye J, Ma C, Yang X. Simple Method for Studying in Vitro Protein-Protein Interactions Based on Protein Complementation and Its Application in Drug Screening Targeting Bacterial Transcription. ACS Infect Dis 2019; 5:521-527. [PMID: 30834747 DOI: 10.1021/acsinfecdis.9b00020] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Protein-protein interactions (PPIs) underpin essential cellular processes of all organisms and are increasingly considered as drug targets. A number of techniques have been established to study PPIs; however, development of a simple and cost-effective method for in vitro high throughput screening of PPI inhibitors is still in demand or desirable. We report herein a simple method based on protein complementation for the in vitro study of PPIs, as well as screening of inhibitors against the PPI of interest. We have validated this system utilizing bacterial transcription factors NusB and NusE. Three derivatives of an inhibitor targeting the NusB-NusE interaction were synthesized and characterized with the system, which showed specific inhibition and antimicrobial activities. We have further confirmed the system with the RNA polymerase-σ interaction and an inhibitor. This system is expected to be suitable for more extensive high throughput screening of large chemical libraries. Additionally, our vector system can be easily adapted to study other PPI pairs, followed by inhibitor screening for hit identification in the application of early stage drug discovery.
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Affiliation(s)
- Tsz Fung Tsang
- Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, 30-32 Ngan Shing Street, Shatin, Hong Kong
| | - Yangyi Qiu
- The Hong Kong Polytechnic University Shenzhen Research Institute, 18 Yue Xing 1st Road, Nanshan, Shenzhen, Guangdong 518057, China
- State Key Laboratory of Chemical Biology and Drug Discovery and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, 11 Yuk Choi Road, Kowloon, Hong Kong
| | - Lin Lin
- Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, 30-32 Ngan Shing Street, Shatin, Hong Kong
| | - Jiqing Ye
- The Hong Kong Polytechnic University Shenzhen Research Institute, 18 Yue Xing 1st Road, Nanshan, Shenzhen, Guangdong 518057, China
- State Key Laboratory of Chemical Biology and Drug Discovery and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, 11 Yuk Choi Road, Kowloon, Hong Kong
| | - Cong Ma
- The Hong Kong Polytechnic University Shenzhen Research Institute, 18 Yue Xing 1st Road, Nanshan, Shenzhen, Guangdong 518057, China
- State Key Laboratory of Chemical Biology and Drug Discovery and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, 11 Yuk Choi Road, Kowloon, Hong Kong
| | - Xiao Yang
- Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, 30-32 Ngan Shing Street, Shatin, Hong Kong
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15
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Carro L. Protein-protein interactions in bacteria: a promising and challenging avenue towards the discovery of new antibiotics. Beilstein J Org Chem 2018; 14:2881-2896. [PMID: 30546472 PMCID: PMC6278769 DOI: 10.3762/bjoc.14.267] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 11/02/2018] [Indexed: 12/11/2022] Open
Abstract
Antibiotics are potent pharmacological weapons against bacterial infections; however, the growing antibiotic resistance of microorganisms is compromising the efficacy of the currently available pharmacotherapies. Even though antimicrobial resistance is not a new problem, antibiotic development has failed to match the growth of resistant pathogens and hence, it is highly critical to discover new anti-infective drugs with novel mechanisms of action which will help reducing the burden of multidrug-resistant microorganisms. Protein–protein interactions (PPIs) are involved in a myriad of vital cellular processes and have become an attractive target to treat diseases. Therefore, targeting PPI networks in bacteria may offer a new and unconventional point of intervention to develop novel anti-infective drugs which can combat the ever-increasing rate of multidrug-resistant bacteria. This review describes the progress achieved towards the discovery of molecules that disrupt PPI systems in bacteria for which inhibitors have been identified and whose targets could represent an alternative lead discovery strategy to obtain new anti-infective molecules.
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Affiliation(s)
- Laura Carro
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
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16
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Protein‐protein interactions as antibiotic targets: A medicinal chemistry perspective. Med Res Rev 2018; 40:469-494. [DOI: 10.1002/med.21519] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 05/28/2018] [Accepted: 06/03/2018] [Indexed: 12/27/2022]
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17
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Wang Z, Li T, Ni H, Wang G, Liu X, Cao Y, Li W, Meng F. Transgenic soybean plants expressing Spb18S dsRNA exhibit enhanced resistance to the soybean pod borer Leguminivora glycinivorella (Lepidoptera: Olethreutidae). ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2018; 98:e21461. [PMID: 29600519 DOI: 10.1002/arch.21461] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The soybean pod borer [SPB; Leguminivora glycinivorella (Mats.) Obraztsov] is a major soybean pest in northeastern Asia. A useful method for addressing this problem is the generation of transgenic plants producing double-stranded RNA (dsRNA) that target essential insect genes. In this study, we confirmed that 18S ribosomal RNA is critical for SPB development. Downregulated Spb18S expression induced by dsRNA injection increased larval mortality rates and resulted in early pupation. We also assessed whether Spb18S is silenced in SPB larvae fed on transgenic soybean expressing Spb18S dsRNA. Transgenic plants downregulated Spb18S expression levels and second-instar larval survival rates. Moreover, such plants were less damaged by SPB larvae than control plants under field conditions.
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Affiliation(s)
- Zhanchun Wang
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Tianyu Li
- Division of Soybean Breeding and Seed, Soybean Research & Development Center, CARS (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China, Ministry of Agriculture), Northeast Agricultural University, Harbin, China
| | - Hejia Ni
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Guoyue Wang
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Xinxin Liu
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Yingxue Cao
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Wenbin Li
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, China
- Division of Soybean Breeding and Seed, Soybean Research & Development Center, CARS (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China, Ministry of Agriculture), Northeast Agricultural University, Harbin, China
| | - Fanli Meng
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, China
- Division of Soybean Breeding and Seed, Soybean Research & Development Center, CARS (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China, Ministry of Agriculture), Northeast Agricultural University, Harbin, China
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