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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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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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Yahya Alqahtani F, Sfouq Aleanizy F, Alkahtani HM, El Tahir E, Akber Ansari S, Alharbi A, Al-Bdrawy A, Shakeel F, Haq N, Al-Rasheed LS, Alfaraj R, Alshememry AK, Alsarra IA. Chitosan loaded RNA polymerase inhibitor nanoparticles increased attenuation in toxin release from Streptococcus pneumonia. Saudi Pharm J 2023; 31:170-179. [PMID: 36685302 PMCID: PMC9845126 DOI: 10.1016/j.jsps.2022.11.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 11/20/2022] [Indexed: 11/27/2022] Open
Abstract
Background Multidrug-resistant (MDR) bacterial infections have become an emerging health concern around the world. Antibiotics resistance among S. pneumoniae strains increased recently contributing to increase in incidence of pneumococcal infection. This necessitates the discovery of novel antipnemococcal such as compound C3-005 which target the interaction between RNA polymerase and σ factors. Chitosan nanoparticles (CNPs) exhibited antibacterial activity including S. pneumonia. Therefore, the aims of the current investigation were to formulate CNPs loaded with C3-005 and characteristic their antimicrobial properties against S. pneumonia. Methods The CNPs and C3-005 loaded CNPs were produced utilizing ionic gelation method, and their physicochemical characteristics including particle size, zeta potential, polydispersity index (PDI), encapsulation efficiency (EE%), and in vitro release profile were studied. Both differential scanning calorimetry (DSC) and fourier transform infrared spectroscopy (FTIR) were used for chemical characterization. The synthesized NPs' minimum inhibitory concentration (MIC) was determined using killing assay and broth dilution method, and their impact on bacteria induced hemolysis were also studied. Results The NPs encapsulating C3-005 were successfully prepared with particle size of 343.5 nm ± 1.3, zeta potential of 29.8 ± 0.37, and PDI of 0.20 ± 0.03. 70 % of C3-005 were encapsulated in CNPs and sustained release pattern of C3-005 from CNPs was revealed by an in vitro release study. CNPs containing C3-005 exhibited higher antipnomcoccal activity with MIC50 of 30 µg/ml when compared with C3-005 and empty CNPs alone. The prepared C3-CNPs showed a reduction of bacterial hemolysis in a concentration-related (dependent) manner and was higher than C3-005 alone. Conclusions The findings of this study showed the potential for using C3-005 loaded CNPs to treat pneumococcal infection.
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Affiliation(s)
- Fulwah Yahya Alqahtani
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh 11495, Saudi Arabia
- Corresponding author.
| | - Fadilah Sfouq Aleanizy
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh 11495, Saudi Arabia
| | - Hamad M. Alkahtani
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Eram El Tahir
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh 11495, Saudi Arabia
| | - Siddique Akber Ansari
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Atheer Alharbi
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh 11495, Saudi Arabia
| | - Asmaa Al-Bdrawy
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh 11495, Saudi Arabia
| | - Faiyaz Shakeel
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh 11495, Saudi Arabia
| | - Nazrul Haq
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh 11495, Saudi Arabia
| | - Lamees S. Al-Rasheed
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Rihaf Alfaraj
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh 11495, Saudi Arabia
| | - Abdullah K. Alshememry
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh 11495, Saudi Arabia
| | - Ibrahim A. Alsarra
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh 11495, Saudi Arabia
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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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Lam LY, Chan KH, Ma C. Copper-Catalyzed Synthesis of Functionalized Aryl Sulfonamides from Sodium Sulfinates in Green Solvents. J Org Chem 2022; 87:8802-8810. [PMID: 35723444 DOI: 10.1021/acs.joc.2c00777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Functionalized aryl sulfonamides are important building blocks in the pharmaceutical industry. A one-step synthesis catalyzed by a copper salt was developed using stable solid commodity chemicals in sulfolane or, alternatively, in green solvents such as γ-valerolactone, iPrOAc, or nBuOAc with acetic acid. The method tolerated diverse functional groups commonly presented in current medicines and drug intermediates. The mechanistic study showed a radical coupling pathway between the sulfonyl and anilinium radicals through the use of K2S2O8 and copper catalyst, respectively.
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Affiliation(s)
- Long Yin Lam
- 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
| | - King Hong 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, 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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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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QSAR, Docking, and Molecular Dynamics Simulation Studies of Sigmacidins as Antimicrobials against Streptococci. Int J Mol Sci 2022; 23:ijms23084085. [PMID: 35456906 PMCID: PMC9025105 DOI: 10.3390/ijms23084085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/05/2022] [Accepted: 04/05/2022] [Indexed: 12/02/2022] Open
Abstract
Streptococci are a family of bacterial species significantly affecting human health. In addition, environmental Streptococci represent one of the major causes of diverse livestock diseases. Due to antimicrobial resistance, there is an urgent need for novel antimicrobial agent discovery against Streptococci. We discovered a class of benzoic acid derivatives named sigmacidins inhibiting the bacterial RNA polymerase-σ factor interaction and demonstrating excellent antimicrobial activity against Streptococci. In this work, a combinational computer approach was applied to gain insight into the structural basis and mechanism of action of sigmacidins as antimicrobials against Streptococcus pneumoniae. Both two- and three-dimensional quantitative structure-active relationships (2D and 3D QSAR) of sigmacidins displayed good predictive ability. Moreover, molecular docking and molecular dynamics simulation studies disclosed possible contacts between the inhibitors and the protein. The results obtained in this study provided understanding and new directions to the further optimizations of sigmacidins as novel antimicrobials.
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Lam LY, Ma C. Chan-Lam-Type C-S Coupling Reaction by Sodium Aryl Sulfinates and Organoboron Compounds. Org Lett 2021; 23:6164-6168. [PMID: 34292759 DOI: 10.1021/acs.orglett.1c02299] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A Chan-Lam-type C-S coupling reaction using sodium aryl sulfinates has been developed to provide diaryl thioethers in up to 92% yields in the presence of a copper catalyst and potassium sulfite. Both electron-rich and electron-poor sodium aryl sulfinates and diverse organoboron compounds were tolerated for the synthesis of aryl and heteroaryl thioethers and dithioethers. The mechanistic study suggested that potassium sulfite was involved in the deoxygenation of sulfinate through a radical process.
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Affiliation(s)
- Long Yin Lam
- 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
| | - 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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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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11
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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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Liu Y, Lam LY, Ye J, Blanchard N, Ma C. DABCO‐promoted Diaryl Thioether Formation by Metal‐catalyzed Coupling of Sodium Sulfinates and Aryl Iodides. Adv Synth Catal 2020. [DOI: 10.1002/adsc.202000221] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Yanpeng Liu
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical TechnologyThe Hong Kong Polytechnic University, Hung Hom, Kowloon Hong Kong SAR
| | - Long Yin Lam
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical TechnologyThe Hong Kong Polytechnic University, Hung Hom, Kowloon Hong Kong SAR
| | - Jiqing Ye
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical TechnologyThe Hong Kong Polytechnic University, Hung Hom, Kowloon Hong Kong SAR
| | - Nicolas Blanchard
- Laboratoire d'Innovation Moléculaire et Applications (LIMA), Université de Haute-AlsaceUniversité de Strasbourg, CNRS, UMR 7042 Mulhouse 68200 France
| | - Cong Ma
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical TechnologyThe Hong Kong Polytechnic University, Hung Hom, Kowloon Hong Kong SAR
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