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Chen S, Mao Q, Cheng H, Tai W. RNA-Binding Small Molecules in Drug Discovery and Delivery: An Overview from Fundamentals. J Med Chem 2024; 67:16002-16017. [PMID: 39287926 DOI: 10.1021/acs.jmedchem.4c01330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2024]
Abstract
RNA molecules, similar to proteins, fold into complex structures to confer diverse functions in cells. The intertwining of functions with RNA structures offers a new therapeutic opportunity for small molecules to bind and manipulate disease-relevant RNA pathways, thus creating a therapeutic realm of RNA-binding small molecules. The ongoing interest in RNA targeting and subsequent screening campaigns have led to the identification of numerous compounds that can regulate RNAs from splicing, degradation to malfunctions, with therapeutic benefits for a variety of diseases. Moreover, along with the rise of RNA-based therapeutics, RNA-binding small molecules have expanded their application to the modification, regulation, and delivery of RNA drugs, leading to the burgeoning interest in this field. This Perspective overviews the emerging roles of RNA-binding small molecules in drug discovery and delivery, covering aspects from their action fundamentals to therapeutic applications, which may inspire researchers to advance the field.
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Affiliation(s)
- Siyi Chen
- Department of Pharmaceutical Engineering, School of Pharmaceutical Sciences, Wuhan University, Wuhan, Hubei 430071, China
- Department of Pharmacy, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
| | - Qi Mao
- Department of Pharmaceutical Engineering, School of Pharmaceutical Sciences, Wuhan University, Wuhan, Hubei 430071, China
- Department of Pharmacy, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
| | - Hong Cheng
- Department of Pharmaceutical Engineering, School of Pharmaceutical Sciences, Wuhan University, Wuhan, Hubei 430071, China
- Department of Pharmacy, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
| | - Wanyi Tai
- Department of Pharmaceutical Engineering, School of Pharmaceutical Sciences, Wuhan University, Wuhan, Hubei 430071, China
- Department of Pharmacy, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
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2
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Yildirim O, Barman D, Chung M, Stone S, Geißen R, Boby ML, Sherborne BS, Tan DS. Design and synthesis of a library of C8-substituted sulfamidoadenosines to probe bacterial permeability. Bioorg Med Chem Lett 2024; 110:129844. [PMID: 38851357 PMCID: PMC11361631 DOI: 10.1016/j.bmcl.2024.129844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 05/30/2024] [Accepted: 06/05/2024] [Indexed: 06/10/2024]
Abstract
Gram-negative bacteria pose a major challenge in antibiotic drug discovery because their cell envelope presents a permeability barrier that affords high intrinsic resistance to small-molecule drugs. The identification of correlations between chemical structure and Gram-negative permeability would thus enable development of predictive tools to facilitate antibiotic discovery. Toward this end, have advanced a library design paradigm in which various chemical scaffolds are functionalized at different regioisomeric positions using a uniform reagent set. This design enables decoupling of scaffold, regiochemistry, and substituent effects upon Gram-negative permeability of these molecules. Building upon our recent synthesis of a library of C2-substituted sulfamidoadenosines, we have now developed an efficient synthetic route to an analogous library of regioisomeric C8-substituted congeners. The C8 library samples a region of antibiotic-relevant chemical space that is similar to that addressed by the C2 library, but distinct from that sampled by a library of analogously substituted oxazolidinones. Selected molecules were tested for accumulation in Escherichia coli in a pilot analysis, setting the stage for full comparative evaluation of these libraries in the future.
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Affiliation(s)
- Okan Yildirim
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Dipti Barman
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Mia Chung
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Samantha Stone
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Raphael Geißen
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA; Doctoral Program, Faculty of Biology, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg im Breisgau, Germany
| | - Melissa L Boby
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA; Pharmacology Graduate Program, Weill Cornell Graduate School, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | | | - Derek S Tan
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA; Pharmacology Graduate Program, Weill Cornell Graduate School, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA; Tri-Institutional Research Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA.
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3
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Liu Y, Chen Y, Zhao YJ, Zhang GQ, Zheng Y, Yu P, Chen P, Jia ZJ. Iron-Catalyzed Primary Amination of C(sp 3)-H Bonds. J Am Chem Soc 2024; 146:24863-24870. [PMID: 39192496 DOI: 10.1021/jacs.4c05407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2024]
Abstract
Primary amines are privileged molecules in drug development. Yet, there is a noticeable scarcity of methods for directly introducing a primary amine group into the ubiquitous C(sp3)-H bonds within organic compounds. Here, we report an iron-based catalytic system that enables direct primary amination of C(sp3)-H bonds under aqueous conditions and air. Various types of C(sp3)-H bonds, including benzylic, allylic, and aliphatic ones, can be readily functionalized with high selectivity and efficiency. The broad utility of this method has been further verified by late-stage amination of 11 complex bioactive molecules. Mechanistic studies unveil a protonated iron-nitrene complex as the key intermediate for the C-H bond activation. This work extends the toolbox for direct C(sp3)-H functionalizations, opening up new opportunities for late-stage modifications of organic molecules.
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Affiliation(s)
- Ye Liu
- Department of Biopharmaceutics, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Children's Medicine Key Laboratory of Sichuan Province, Department of Pharmacy/Evidence-Based Pharmacy Center, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Yu Chen
- Department of Chemistry and Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yu-Jie Zhao
- Department of Biopharmaceutics, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Children's Medicine Key Laboratory of Sichuan Province, Department of Pharmacy/Evidence-Based Pharmacy Center, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Guo-Qing Zhang
- Department of Biopharmaceutics, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Children's Medicine Key Laboratory of Sichuan Province, Department of Pharmacy/Evidence-Based Pharmacy Center, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Yongxiang Zheng
- Department of Biopharmaceutics, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Children's Medicine Key Laboratory of Sichuan Province, Department of Pharmacy/Evidence-Based Pharmacy Center, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Peiyuan Yu
- Department of Chemistry and Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen 518055, China
| | - Peng Chen
- Department of Biopharmaceutics, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Children's Medicine Key Laboratory of Sichuan Province, Department of Pharmacy/Evidence-Based Pharmacy Center, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Zhi-Jun Jia
- Department of Biopharmaceutics, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Children's Medicine Key Laboratory of Sichuan Province, Department of Pharmacy/Evidence-Based Pharmacy Center, West China Second University Hospital, Sichuan University, Chengdu 610041, China
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4
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Schum D, Elsen FAV, Ruddell S, Schorpp K, Junca H, Müsken M, Chen SY, Fiedler MK, Pickl T, Pieper DH, Hadian K, Zacharias M, Sieber SA. Screening Privileged Alkyl Guanidinium Motifs under Host-Mimicking Conditions Reveals a Novel Antibiotic with an Unconventional Mode of Action. JACS AU 2024; 4:3125-3134. [PMID: 39211621 PMCID: PMC11350587 DOI: 10.1021/jacsau.4c00449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 06/20/2024] [Accepted: 06/24/2024] [Indexed: 09/04/2024]
Abstract
Screening large molecule libraries against pathogenic bacteria is often challenged by a low hit rate due to limited uptake, underrepresentation of antibiotic structural motifs, and assays that do not resemble the infection conditions. To address these limitations, we present a screen of a focused library of alkyl guanidinium compounds, a structural motif associated with antibiotic activity and enhanced uptake, under host-mimicking infection conditions against a panel of disease-associated bacteria. Several hit molecules were identified with activities against Gram-positive and Gram-negative bacteria, highlighting the fidelity of the general concept. We selected one compound (L15) for in-depth mode of action studies that exhibited bactericidal activity against methicillin-resistant Staphylococcus aureus USA300 with a minimum inhibitory concentration of 1.5 μM. Structure-activity relationship studies confirmed the necessity of the guanidinium motif for antibiotic activity. The mode of action was investigated using affinity-based protein profiling with an L15 probe and identified the signal peptidase IB (SpsB) as the most promising hit. Validation by activity assays, binding site identification, docking, and molecular dynamics simulations demonstrated SpsB activation by L15, a recently described mechanism leading to the dysregulation of protein secretion and cell death. Overall, this study highlights the need for unconventional screening strategies to identify novel antibiotics.
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Affiliation(s)
- Dominik Schum
- TUM
School of Natural Sciences, Department of Bioscience, Chair of Organic Chemistry II, Center for Functional Protein Assemblies
(CPA), Technical University of Munich (TUM), Ernst-Otto-Fischer Str. 8, Garching 85748, Germany
| | - Franziska A. V. Elsen
- TUM
School of Natural Sciences, Department of Bioscience, Chair of Organic Chemistry II, Center for Functional Protein Assemblies
(CPA), Technical University of Munich (TUM), Ernst-Otto-Fischer Str. 8, Garching 85748, Germany
| | - Stuart Ruddell
- TUM
School of Natural Sciences, Department of Bioscience, Chair of Organic Chemistry II, Center for Functional Protein Assemblies
(CPA), Technical University of Munich (TUM), Ernst-Otto-Fischer Str. 8, Garching 85748, Germany
| | - Kenji Schorpp
- Helmholtz
Zentrum München, Research Unit Signaling and Translation, Ingolstädter Landstraße
1, Neuherberg, Munich 85764, Germany
| | - Howard Junca
- Helmholtz
Centre for Infection Research, Microbial Interactions and Processes, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Mathias Müsken
- Helmholtz
Centre for Infection Research, Central Facility for Microscopy, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Shu-Yu Chen
- TUM
School of Natural Sciences, Department of Bioscience, Theoretical Biophysics (T38), Center for Functional Protein Assemblies
(CPA), Technical University of Munich (TUM), Ernst-Otto-Fischer Str. 8, Garching 85748, Germany
| | - Michaela K. Fiedler
- TUM
School of Natural Sciences, Department of Bioscience, Chair of Organic Chemistry II, Center for Functional Protein Assemblies
(CPA), Technical University of Munich (TUM), Ernst-Otto-Fischer Str. 8, Garching 85748, Germany
| | - Thomas Pickl
- TUM School
of Natural Sciences, Department of Chemistry, Catalysis Research Center (CRC), Technical University of Munich (TUM), Ernst-Otto-Fischer Str. 1, Garching 85748, Germany
| | - Dietmar H. Pieper
- Helmholtz
Centre for Infection Research, Microbial Interactions and Processes, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Kamyar Hadian
- Helmholtz
Zentrum München, Research Unit Signaling and Translation, Ingolstädter Landstraße
1, Neuherberg, Munich 85764, Germany
| | - Martin Zacharias
- TUM
School of Natural Sciences, Department of Bioscience, Theoretical Biophysics (T38), Center for Functional Protein Assemblies
(CPA), Technical University of Munich (TUM), Ernst-Otto-Fischer Str. 8, Garching 85748, Germany
| | - Stephan A. Sieber
- TUM
School of Natural Sciences, Department of Bioscience, Chair of Organic Chemistry II, Center for Functional Protein Assemblies
(CPA), Technical University of Munich (TUM), Ernst-Otto-Fischer Str. 8, Garching 85748, Germany
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5
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Godek J, Sivinski J, Watson ER, Lebario F, Xu W, Stevens M, Zerio CJ, Ambrose AJ, Zhu X, Trindl CA, Zhang DD, Johnson SM, Lander GC, Chapman E. Bis-sulfonamido-2-phenylbenzoxazoles Validate the GroES/EL Chaperone System as a Viable Antibiotic Target. J Am Chem Soc 2024; 146:20845-20856. [PMID: 39041457 DOI: 10.1021/jacs.4c05057] [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] [Indexed: 07/24/2024]
Abstract
We recently reported on small-molecule inhibitors of the GroES/GroEL chaperone system as potential antibiotics against Escherichia coli and the ESKAPE pathogens but were unable to establish GroES/GroEL as the cellular target, leading to cell death. In this study, using two of our most potent bis-sulfonamido-2-phenylbenzoxazoles (PBZs), we established the binding site of the PBZ molecules using cryo-EM and found that GroEL was the cellular target responsible for the mode of action. Cryo-EM revealed that PBZ1587 binds at the GroEL ring-ring interface (RRI). A cellular reporter assay confirmed that PBZ1587 engaged GroEL in cells, but cellular rescue experiments showed potential off-target effects. This prompted us to explore a closely related analogue, PBZ1038, which is also bound to the RRI. Biochemical characterization showed potent inhibition of Gram-negative chaperonins but much lower potency of chaperonin from a Gram-positive organism, Enterococcus faecium. A cellular reporter assay showed that PBZ1038 also engaged GroEL in cells and that the cytotoxic phenotype could be rescued by a chromosomal copy of E. faecium GroEL/GroES or by expressing a recalcitrant RRI mutant. These data argue that PBZ1038's antimicrobial action is exerted through inhibition of GroES/GroEL, validating this chaperone system as an antibiotic target.
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Affiliation(s)
- Jack Godek
- College of Medicine, Department of Pharmacology and Therapeutics, Center for Inflammation Science and Systems Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, University of Florida, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Jared Sivinski
- College of Pharmacy, Department of Pharmacology and Toxicology, The University of Arizona, 1703 E. Mabel Street, P.O. Box 210207, Tucson, Arizona 85721, United States
| | - Edmond R Watson
- Department of Integrative Structural and Computational Biology, Scripps Research, 10550 N. Torrey Pines Road, La Jolla, California 92037, United States
| | - Felicidad Lebario
- College of Medicine, Department of Pharmacology and Therapeutics, Center for Inflammation Science and Systems Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, University of Florida, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Wenli Xu
- College of Pharmacy, Department of Pharmacology and Toxicology, The University of Arizona, 1703 E. Mabel Street, P.O. Box 210207, Tucson, Arizona 85721, United States
| | - Mckayla Stevens
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Dr., Indianapolis, Indiana 46202, United States
| | - Christopher J Zerio
- College of Pharmacy, Department of Pharmacology and Toxicology, The University of Arizona, 1703 E. Mabel Street, P.O. Box 210207, Tucson, Arizona 85721, United States
| | - Andrew J Ambrose
- College of Pharmacy, Department of Pharmacology and Toxicology, The University of Arizona, 1703 E. Mabel Street, P.O. Box 210207, Tucson, Arizona 85721, United States
| | - Xiaoyi Zhu
- College of Medicine, Department of Pharmacology and Therapeutics, Center for Inflammation Science and Systems Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, University of Florida, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Carlee A Trindl
- College of Medicine, Department of Pharmacology and Therapeutics, Center for Inflammation Science and Systems Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, University of Florida, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Donna D Zhang
- The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Center for Inflammation Science and Systems Medicine, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Steven M Johnson
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Dr., Indianapolis, Indiana 46202, United States
| | - Gabriel C Lander
- Department of Integrative Structural and Computational Biology, Scripps Research, 10550 N. Torrey Pines Road, La Jolla, California 92037, United States
| | - Eli Chapman
- College of Medicine, Department of Pharmacology and Therapeutics, Center for Inflammation Science and Systems Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, University of Florida, 130 Scripps Way, Jupiter, Florida 33458, United States
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6
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Butler MS, Vollmer W, Goodall ECA, Capon RJ, Henderson IR, Blaskovich MAT. A Review of Antibacterial Candidates with New Modes of Action. ACS Infect Dis 2024. [PMID: 39018341 DOI: 10.1021/acsinfecdis.4c00218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/19/2024]
Abstract
There is a lack of new antibiotics to combat drug-resistant bacterial infections that increasingly threaten global health. The current pipeline of clinical-stage antimicrobials is primarily populated by "new and improved" versions of existing antibiotic classes, supplemented by several novel chemical scaffolds that act on traditional targets. The lack of fresh chemotypes acting on previously unexploited targets (the "holy grail" for new antimicrobials due to their scarcity) is particularly unfortunate as these offer the greatest opportunity for innovative breakthroughs to overcome existing resistance. In recognition of their potential, this review focuses on this subset of high value antibiotics, providing chemical structures where available. This review focuses on candidates that have progressed to clinical trials, as well as selected examples of promising pioneering approaches in advanced stages of development, in order to stimulate additional research aimed at combating drug-resistant infections.
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Affiliation(s)
- Mark S Butler
- Centre for Superbug Solutions and ARC Training Centre for Environmental and Agricultural Solutions to Antimicrobial Resistance, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Waldemar Vollmer
- Centre for Superbug Solutions and ARC Training Centre for Environmental and Agricultural Solutions to Antimicrobial Resistance, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Emily C A Goodall
- Centre for Superbug Solutions and ARC Training Centre for Environmental and Agricultural Solutions to Antimicrobial Resistance, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Robert J Capon
- Centre for Superbug Solutions and ARC Training Centre for Environmental and Agricultural Solutions to Antimicrobial Resistance, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Ian R Henderson
- Centre for Superbug Solutions and ARC Training Centre for Environmental and Agricultural Solutions to Antimicrobial Resistance, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Mark A T Blaskovich
- Centre for Superbug Solutions and ARC Training Centre for Environmental and Agricultural Solutions to Antimicrobial Resistance, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
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7
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Chen Y, Jiang H, Sun Z, Liu F, Su M. Hydantoin derivative dimers as broad-spectrum antimicrobial agents against ESKAPE pathogens with enhanced killing rate and stability. RSC Med Chem 2024; 15:2340-2350. [PMID: 39026634 PMCID: PMC11253853 DOI: 10.1039/d4md00374h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 05/29/2024] [Indexed: 07/20/2024] Open
Abstract
A new series of hydantoin derivative dimers as potential broad-spectrum antibiotic agents is designed and synthesized to combat ESKAPE pathogens. As membrane-active antimicrobial agents, in addition to cationic charged and hydrophobic groups that mimic AMPs (antimicrobial peptides), hydantoin backbones and aromatic linkers increased the rigidity and lipophilicity of the designed compounds, thus improving the stability and bactericidal killing rate. After whole cell phenotypic screening against eight bacterial strains, including MRSA (methicillin-resistant S. aureus), compound 18 was chosen as the lead compound with overall excellent broad-spectrum antibacterial activity (GM = 7.32 μg mL-1) and good selectivity. Kill-kinetic studies of compound 18 showed that the bacterial growth of both Gram-positive and Gram-negative was completely inhibited within one hour, which demonstrated excellent sterilization efficiency of 18. Furthermore, drug resistance and mechanism studies showed that compound 18 exhibited a steady antibacterial performance during 25 passages and could disrupt bacterial cell membrane integrity and cause cell death. Along with the facile synthesis procedures in solution, this series of hydantoin derivative dimer compounds could be an appealing next generation of antibiotic agents to combat emergent drug resistance.
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Affiliation(s)
- Yating Chen
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Department of Medicinal Chemistry, College of Pharmaceutical Sciences, Soochow University 199 Ren-Ai Road Suzhou Jiangsu 215123 China
- Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University 199 Ren-Ai Road Suzhou Jiangsu 215123 People's Republic of China
| | - Huiqin Jiang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Department of Medicinal Chemistry, College of Pharmaceutical Sciences, Soochow University 199 Ren-Ai Road Suzhou Jiangsu 215123 China
- Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University 199 Ren-Ai Road Suzhou Jiangsu 215123 People's Republic of China
| | - Zibin Sun
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Department of Medicinal Chemistry, College of Pharmaceutical Sciences, Soochow University 199 Ren-Ai Road Suzhou Jiangsu 215123 China
- Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University 199 Ren-Ai Road Suzhou Jiangsu 215123 People's Republic of China
| | - Feng Liu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Department of Medicinal Chemistry, College of Pharmaceutical Sciences, Soochow University 199 Ren-Ai Road Suzhou Jiangsu 215123 China
- Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University 199 Ren-Ai Road Suzhou Jiangsu 215123 People's Republic of China
| | - Ma Su
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Department of Medicinal Chemistry, College of Pharmaceutical Sciences, Soochow University 199 Ren-Ai Road Suzhou Jiangsu 215123 China
- Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University 199 Ren-Ai Road Suzhou Jiangsu 215123 People's Republic of China
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8
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Muñoz KA, Ulrich RJ, Vasan AK, Sinclair M, Wen PC, Holmes JR, Lee HY, Hung CC, Fields CJ, Tajkhorshid E, Lau GW, Hergenrother PJ. A Gram-negative-selective antibiotic that spares the gut microbiome. Nature 2024; 630:429-436. [PMID: 38811738 DOI: 10.1038/s41586-024-07502-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 05/01/2024] [Indexed: 05/31/2024]
Abstract
Infections caused by Gram-negative pathogens are increasingly prevalent and are typically treated with broad-spectrum antibiotics, resulting in disruption of the gut microbiome and susceptibility to secondary infections1-3. There is a critical need for antibiotics that are selective both for Gram-negative bacteria over Gram-positive bacteria, as well as for pathogenic bacteria over commensal bacteria. Here we report the design and discovery of lolamicin, a Gram-negative-specific antibiotic targeting the lipoprotein transport system. Lolamicin has activity against a panel of more than 130 multidrug-resistant clinical isolates, shows efficacy in multiple mouse models of acute pneumonia and septicaemia infection, and spares the gut microbiome in mice, preventing secondary infection with Clostridioides difficile. The selective killing of pathogenic Gram-negative bacteria by lolamicin is a consequence of low sequence homology for the target in pathogenic bacteria versus commensals; this doubly selective strategy can be a blueprint for the development of other microbiome-sparing antibiotics.
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Affiliation(s)
- Kristen A Muñoz
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Rebecca J Ulrich
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Archit K Vasan
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Matt Sinclair
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Po-Chao Wen
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jessica R Holmes
- High-Performance Computing in Biology, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Hyang Yeon Lee
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Chien-Che Hung
- Veterinary Diagnostic Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Christopher J Fields
- High-Performance Computing in Biology, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Emad Tajkhorshid
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Gee W Lau
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Paul J Hergenrother
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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9
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Berida TI, Adekunle YA, Dada-Adegbola H, Kdimy A, Roy S, Sarker SD. Plant antibacterials: The challenges and opportunities. Heliyon 2024; 10:e31145. [PMID: 38803958 PMCID: PMC11128932 DOI: 10.1016/j.heliyon.2024.e31145] [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: 11/30/2023] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 05/29/2024] Open
Abstract
Nature possesses an inexhaustible reservoir of agents that could serve as alternatives to combat the growing threat of antimicrobial resistance (AMR). While some of the most effective drugs for treating bacterial infections originate from natural sources, they have predominantly been derived from fungal and bacterial species. However, a substantial body of literature is available on the promising antibacterial properties of plant-derived compounds. In this comprehensive review, we address the major challenges associated with the discovery and development of plant-derived antimicrobial compounds, which have acted as obstacles preventing their clinical use. These challenges encompass limited sourcing, the risk of agent rediscovery, suboptimal drug metabolism, and pharmacokinetics (DMPK) properties, as well as a lack of knowledge regarding molecular targets and mechanisms of action, among other pertinent issues. Our review underscores the significance of these challenges and their implications in the quest for the discovery and development of effective plant-derived antimicrobial agents. Through a critical examination of the current state of research, we give valuable insights that will advance our understanding of these classes of compounds, offering potential solutions to the global crisis of AMR. © 2017 Elsevier Inc. All rights reserved.
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Affiliation(s)
- Tomayo I. Berida
- Department of BioMolecular Sciences, Division of Pharmacognosy, University of Mississippi, University, MS, 38677, USA
| | - Yemi A. Adekunle
- Department of Pharmaceutical and Medicinal Chemistry, College of Pharmacy, Afe Babalola University, Ado-Ekiti, Nigeria
- Centre for Natural Products Discovery (CNPD), School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, Byrom Street, Liverpool, L3 3AF, United Kingdom
| | - Hannah Dada-Adegbola
- Department of Medical Microbiology and Parasitology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Ayoub Kdimy
- LS3MN2E, CERNE2D, Faculty of Science, Mohammed V University in Rabat, Rabat, 10056, Morocco
| | - Sudeshna Roy
- Department of BioMolecular Sciences, Division of Pharmacognosy, University of Mississippi, University, MS, 38677, USA
| | - Satyajit D. Sarker
- Centre for Natural Products Discovery (CNPD), School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, Byrom Street, Liverpool, L3 3AF, United Kingdom
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10
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Barbieri F, Carlen V, Martina MG, Sannio F, Cancade S, Perini C, Restori M, Crespan E, Maga G, Docquier JD, Cagno V, Radi M. 4-Trifluoromethyl bithiazoles as broad-spectrum antimicrobial agents for virus-related bacterial infections or co-infections. RSC Med Chem 2024; 15:1589-1600. [PMID: 38784463 PMCID: PMC11110737 DOI: 10.1039/d3md00686g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 03/07/2024] [Indexed: 05/25/2024] Open
Abstract
Respiratory tract infections involving a variety of microorganisms such as viruses, bacteria, and fungi are a prominent cause of morbidity and mortality globally, exacerbating various pre-existing respiratory and non-respiratory conditions. Moreover, the ability of bacteria and viruses to coexist might impact the development and severity of lung infections, promoting bacterial colonization and subsequent disease exacerbation. Secondary bacterial infections following viral infections represent a complex challenge to be overcome from a therapeutic point of view. We report herein our efforts in the development of new bithiazole derivatives showing broad-spectrum antimicrobial activity against both viruses and bacteria. A series of 4-trifluoromethyl bithiazole analogues was synthesized and screened against selected viruses (hRVA16, EVD68, and ZIKV) and a panel of Gram-positive and Gram-negative bacteria. Among them, two promising broad-spectrum antimicrobial compounds (8a and 8j) have been identified: both compounds showed low micromolar activity against all tested viruses, 8a showed synergistic activity against E. coli and A. baumannii in the presence of a subinhibitory concentration of colistin, while 8j showed a broader spectrum of activity against Gram-positive and Gram-negative bacteria. Activity against antibiotic-resistant clinical isolates is also reported. Given the ever-increasing need to adequately address viral and bacterial infections or co-infections, this study paves the way for the development of new agents with broad antimicrobial properties and synergistic activity with common antivirals and antibacterials.
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Affiliation(s)
- Francesca Barbieri
- Dipartimento di Scienze degli Alimenti e del Farmaco (DipALIFAR), Università degli Studi di Parma Viale delle Scienze, 27/A 43124 Parma Italy
| | - Vincent Carlen
- Institute of Microbiology, University Hospital of Lausanne, University of Lausanne 1011 Lausanne Switzerland
| | - Maria Grazia Martina
- Dipartimento di Scienze degli Alimenti e del Farmaco (DipALIFAR), Università degli Studi di Parma Viale delle Scienze, 27/A 43124 Parma Italy
| | - Filomena Sannio
- Dipartimento di Biotecnologie Mediche, Università degli Studi di Siena Viale Bracci 16 53100 Siena Italy
| | - Sacha Cancade
- Dipartimento di Biotecnologie Mediche, Università degli Studi di Siena Viale Bracci 16 53100 Siena Italy
| | - Cecilia Perini
- Institute of Molecular Genetics IGM-CNR "Luigi Luca Cavalli-Sforza" Via Abbiategrasso 207 I-27100 Pavia Italy
| | - Margherita Restori
- Dipartimento di Scienze degli Alimenti e del Farmaco (DipALIFAR), Università degli Studi di Parma Viale delle Scienze, 27/A 43124 Parma Italy
| | - Emmanuele Crespan
- Institute of Molecular Genetics IGM-CNR "Luigi Luca Cavalli-Sforza" Via Abbiategrasso 207 I-27100 Pavia Italy
| | - Giovanni Maga
- Institute of Molecular Genetics IGM-CNR "Luigi Luca Cavalli-Sforza" Via Abbiategrasso 207 I-27100 Pavia Italy
| | - Jean-Denis Docquier
- Dipartimento di Biotecnologie Mediche, Università degli Studi di Siena Viale Bracci 16 53100 Siena Italy
| | - Valeria Cagno
- Institute of Microbiology, University Hospital of Lausanne, University of Lausanne 1011 Lausanne Switzerland
| | - Marco Radi
- Dipartimento di Scienze degli Alimenti e del Farmaco (DipALIFAR), Università degli Studi di Parma Viale delle Scienze, 27/A 43124 Parma Italy
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11
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Said G, Ali A, Ahmad L. Design, semi-synthesis of soft coral-derived Aspergillus sp. secondary metabolite geodin derivatives and their antibacterial activities. Nat Prod Res 2024:1-9. [PMID: 38462767 DOI: 10.1080/14786419.2024.2326990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 02/27/2024] [Indexed: 03/12/2024]
Abstract
A series of novel ester derivatives 2 - 7, of natural product geodin 1, isolated from the soft coral-derived fungus Aspergillus sp., were designed and semi-synthesised through one step reaction with high yield. Compound 5 showed strong antifouling inhibitory activities with MIC of 4.80 μM while compound 4 showed selective inhibitory activities with MICs values 8.59 μM against Aeromonas salmonicida and Pseudomonas aeruginosa (Sea-Nine 211, MIC = 0.27 μM). Compounds 3, 4 and 6 showed potent anti-pathogenic inhibitory activities with MICs of 2.29 μM, 4.29 μM and 4.56 μM respectively against Staphylococcus aureus (Ciprofloxacin, MIC = 0.156 μM). Compound 2 showed weak inhibitory activity against A. salmonicida with MIC 18.75 μM (Sea-Nine 211, MIC = 0.27 μM) and with MICs 9.38 μM against S. aureus (ciprofloxacin, MIC = 0.156 μM). However, compound 7 showed very low antibacterial activities with MIC = >20 μM. The preliminary structure-activity relationships of compounds 2 - 7 further prove that the modification of 4-OH group of natural product geodin 1 improves the antibacterial activities such as antifouling and anti-pathogenic activities.
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Affiliation(s)
- Gulab Said
- Department of Chemistry, Women University Swabi, Swabi, Pakistan
| | - Amjad Ali
- Center of Excellence in Marine Biology, University of Karachi, Karachi, Pakistan
| | - Latif Ahmad
- Department of Botany, Women University Swabi, Swabi, Pakistan
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12
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Shen T, Guo J, Han Z, Zhang G, Liu Q, Si X, Wang D, Wu S, Xia J. AutoMolDesigner for Antibiotic Discovery: An AI-Based Open-Source Software for Automated Design of Small-Molecule Antibiotics. J Chem Inf Model 2024; 64:575-583. [PMID: 38265916 DOI: 10.1021/acs.jcim.3c01562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
Discovery of small-molecule antibiotics with novel chemotypes serves as one of the essential strategies to address antibiotic resistance. Although a considerable number of computational tools committed to molecular design have been reported, there is a deficit in holistic and efficient tools specifically developed for small-molecule antibiotic discovery. To address this issue, we report AutoMolDesigner, a computational modeling software dedicated to small-molecule antibiotic design. It is a generalized framework comprising two functional modules, i.e., generative-deep-learning-enabled molecular generation and automated machine-learning-based antibacterial activity/property prediction, wherein individually trained models and curated datasets are out-of-the-box for whole-cell-based antibiotic screening and design. It is open-source, thus allowing for the incorporation of new features for flexible use. Unlike most software programs based on Linux and command lines, this application equipped with a Qt-based graphical user interface can be run on personal computers with multiple operating systems, making it much easier to use for experimental scientists. The software and related materials are freely available at GitHub (https://github.com/taoshen99/AutoMolDesigner) and Zenodo (https://zenodo.org/record/10097899).
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Affiliation(s)
- Tao Shen
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Jiale Guo
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Zunsheng Han
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Gao Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Qingxin Liu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- School of Pharmacy, Jiangsu Ocean University, Lianyungang, Jiangsu 222005, China
| | - Xinxin Si
- School of Pharmacy, Jiangsu Ocean University, Lianyungang, Jiangsu 222005, China
| | - Dongmei Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Song Wu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Jie Xia
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
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13
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Santos AL, Liu D, van Venrooy A, Beckham JL, Oliver A, Tegos GP, Tour JM. Nonlethal Molecular Nanomachines Potentiate Antibiotic Activity Against Gram-Negative Bacteria by Increasing Cell Permeability and Attenuating Efflux. ACS NANO 2024; 18:3023-3042. [PMID: 38241477 DOI: 10.1021/acsnano.3c08041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2024]
Abstract
Antibiotic resistance is a pressing public health threat. Despite rising resistance, antibiotic development, especially for Gram-negative bacteria, has stagnated. As the traditional antibiotic research and development pipeline struggles to address this growing concern, alternative solutions become imperative. Synthetic molecular nanomachines (MNMs) are molecular structures that rotate unidirectionally in a controlled manner in response to a stimulus, such as light, resulting in a mechanical action that can propel molecules to drill into cell membranes, causing rapid cell death. Due to their broad destructive capabilities, clinical translation of MNMs remains challenging. Hence, here, we explore the ability of nonlethal visible-light-activated MNMs to potentiate conventional antibiotics against Gram-negative bacteria. Nonlethal MNMs enhanced the antibacterial activity of various classes of conventional antibiotics against Gram-negative bacteria, including those typically effective only against Gram-positive strains, reducing the antibiotic concentration required for bactericidal action. Our study also revealed that MNMs bind to the negatively charged phospholipids of the bacterial inner membrane, leading to permeabilization of the cell envelope and impairment of efflux pump activity following light activation of MNMs. The combined effects of MNMs on membrane permeability and efflux pumps resulted in increased antibiotic accumulation inside the cell, reversing antibiotic resistance and attenuating its development. These results identify nonlethal MNMs as pleiotropic antibiotic enhancers or adjuvants. The combination of MNMs with traditional antibiotics is a promising strategy against multidrug-resistant Gram-negative infections. This approach can reduce the amount of antibiotics needed and slow down antibiotic resistance development, thereby preserving the effectiveness of our current antibiotics.
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Affiliation(s)
- Ana L Santos
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
- IdISBA - Fundación de Investigación Sanitaria de las Islas Baleares, 07120 Palma, Spain
| | - Dongdong Liu
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Alexis van Venrooy
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Jacob L Beckham
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Antonio Oliver
- IdISBA - Fundación de Investigación Sanitaria de las Islas Baleares, 07120 Palma, Spain
- Servicio de Microbiologia, Hospital Universitari Son Espases, 07120 Palma, Spain
- Centro de Investigación Biomédica en Red, Enfermedades Infecciosas (CIBERINFEC), Av. Monforte de Lemos 3-5, 28029 Madrid, Spain
| | - George P Tegos
- Office of Research, Faxton St. Luke's Healthcare, Mohawk Valley Health System, 1676 Sunset Avenue, Utica, New York 13502, United States
| | - James M Tour
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
- Smalley-Curl Institute, Rice University, Houston, Texas 77005, United States
- Department of Materials Science and NanoEngineering, Rice University, Houston, Texas 77005, United States
- NanoCarbon Center and Rice Advanced Materials Institute, Rice University, Houston, Texas 77005, United States
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14
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Zhao S, Maceren J, Chung M, Stone S, Geißen R, Boby ML, Sherborne BS, Tan DS. Design and synthesis of a library of C2-substituted sulfamidoadenosines to probe bacterial permeability. Bioorg Med Chem Lett 2024; 97:129486. [PMID: 37734424 PMCID: PMC10842738 DOI: 10.1016/j.bmcl.2023.129486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/18/2023] [Accepted: 09/18/2023] [Indexed: 09/23/2023]
Abstract
Antibiotic resistance is a major threat to public health, and Gram-negative bacteria pose a particular challenge due to their combination of a low permeability cell envelope and efflux pumps. Our limited understanding of the chemical rules for overcoming these barriers represents a major obstacle in antibacterial drug discovery. Several recent efforts to address this problem have involved screening compound libraries for accumulation in bacteria in order to understand the structural properties required for Gram-negative permeability. Toward this end, we used cheminformatic analysis to design a library of sulfamidoadenosines (AMSN) having diverse substituents at the adenine C2 position. An efficient synthetic route was developed with installation of a uniform cross-coupling reagent set using Sonogashira and Suzuki reactions of a C2-iodide. The potential utility of these compounds was demonstrated by pilot analysis of selected analogues for accumulation in Escherichia coli.
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Affiliation(s)
- Shibin Zhao
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA
| | - Julian Maceren
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA
| | - Mia Chung
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA
| | - Samantha Stone
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA
| | - Raphael Geißen
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA; Doctoral Program, Faculty of Biology, Albert-Ludwigs-Universität Freiburg,79104 Freiburg im Breisgau, Germany
| | - Melissa L Boby
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA; Pharmacology Graduate Program, Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA
| | | | - Derek S Tan
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA; Pharmacology Graduate Program, Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA; Tri-Institutional Research Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA.
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15
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Theuretzbacher U, Blasco B, Duffey M, Piddock LJV. Unrealized targets in the discovery of antibiotics for Gram-negative bacterial infections. Nat Rev Drug Discov 2023; 22:957-975. [PMID: 37833553 DOI: 10.1038/s41573-023-00791-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2023] [Indexed: 10/15/2023]
Abstract
Advances in areas that include genomics, systems biology, protein structure determination and artificial intelligence provide new opportunities for target-based antibacterial drug discovery. The selection of a 'good' new target for direct-acting antibacterial compounds is the first decision, for which multiple criteria must be explored, integrated and re-evaluated as drug discovery programmes progress. Criteria include essentiality of the target for bacterial survival, its conservation across different strains of the same species, bacterial species and growth conditions (which determines the spectrum of activity of a potential antibiotic) and the level of homology with human genes (which influences the potential for selective inhibition). Additionally, a bacterial target should have the potential to bind to drug-like molecules, and its subcellular location will govern the need for inhibitors to penetrate one or two bacterial membranes, which is a key challenge in targeting Gram-negative bacteria. The risk of the emergence of target-based drug resistance for drugs with single targets also requires consideration. This Review describes promising but as-yet-unrealized targets for antibacterial drugs against Gram-negative bacteria and examples of cognate inhibitors, and highlights lessons learned from past drug discovery programmes.
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Affiliation(s)
| | - Benjamin Blasco
- Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland
| | - Maëlle Duffey
- Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland
| | - Laura J V Piddock
- Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland.
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16
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Slingerland CJ, Lysenko V, Chaudhuri S, Wesseling CMJ, Barnes D, Masereeuw R, Martin NI. Semisynthetic polymyxins with potent antibacterial activity and reduced kidney cell toxicity. RSC Med Chem 2023; 14:2417-2425. [PMID: 37974968 PMCID: PMC10650952 DOI: 10.1039/d3md00456b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/06/2023] [Indexed: 11/19/2023] Open
Abstract
The growing incidence of infections caused by multi-drug resistant Gram-negative bacteria has led to an increased use of last-resort antibiotics such as the polymyxins. Polymyxin therapy is limited by toxicity concerns, most notably nephrotoxicity. Recently we reported the development of a novel class of semisynthetic polymyxins with reduced toxicity wherein the N-terminal lipid and diaminobutyric acid residue are replaced by a cysteine-linked lipid featuring a reductively labile disulfide bond. In the present study we further explored the potential of this approach by also varying the amino acid residue directly adjacent to the polymyxin macrocycle. This led to the identification of new semisynthetic polymyxins that maintain the potent antibacterial activity of the clinically used polymyxin B while exhibiting a further reduction in toxicity toward human proximal tubule epithelial cells. Furthermore, these new polymyxins were found to effectively synergize with novobiocin, rifampicin, and erythromycin against mcr-positive, polymyxin resistant E. coli.
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Affiliation(s)
- Cornelis J Slingerland
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University Sylviusweg 72 2333 BE Leiden The Netherlands
| | - Vladyslav Lysenko
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University Sylviusweg 72 2333 BE Leiden The Netherlands
| | - Samhita Chaudhuri
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University Sylviusweg 72 2333 BE Leiden The Netherlands
| | - Charlotte M J Wesseling
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University Sylviusweg 72 2333 BE Leiden The Netherlands
| | - Devon Barnes
- Division of Pharmacology, Utrecht Institute of Pharmaceutical Sciences, Utrecht University 3584 CG Utrecht The Netherlands
| | - Rosalinde Masereeuw
- Division of Pharmacology, Utrecht Institute of Pharmaceutical Sciences, Utrecht University 3584 CG Utrecht The Netherlands
| | - Nathaniel I Martin
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University Sylviusweg 72 2333 BE Leiden The Netherlands
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17
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Lembke HK, Carlson EE. Activity-based probes in pathogenic bacteria: Investigating drug targets and molecule specificity. Curr Opin Chem Biol 2023; 76:102359. [PMID: 37406424 PMCID: PMC10526982 DOI: 10.1016/j.cbpa.2023.102359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/01/2023] [Accepted: 06/05/2023] [Indexed: 07/07/2023]
Abstract
Bacteria comprise complex communities within our bodies and largely have beneficial roles, however a small percentage are pathogenic. While all pathogens are important to public health, immediate action is necessary to combat bacterial strains developing pan- and multi-resistance to antibiotics. As present therapeutics fail to tackle this problem, novel strategies are required to address this threat. Activity-based probes (ABPs) are one method to investigate proteins of interest in pathogens. These probes can serve multiple purposes to better our understanding of bacterial pathogenicity. Herein, we highlight recent studies that used ABPs to identify new drug targets or visualize antibiotic resistance- or bacterial virulence-associated proteins, and introduce strategies to determine the specificity of ABPs within a targeted enzyme class.
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Affiliation(s)
- Hannah K Lembke
- Department of Chemistry, University of Minnesota, Minneapolis, MN, United States
| | - Erin E Carlson
- Department of Chemistry, University of Minnesota, Minneapolis, MN, United States; Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, United States; Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, United States; Department of Pharmacology, University of Minnesota, Minneapolis, MN, United States.
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18
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Lembke HK, Espinasse A, Hanson MG, Grimme CJ, Tan Z, Reineke TM, Carlson EE. Cationic Polymers Enable Internalization of Negatively Charged Chemical Probes into Bacteria. ACS Chem Biol 2023; 18:2063-2072. [PMID: 37671702 PMCID: PMC10947785 DOI: 10.1021/acschembio.3c00351] [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] [Indexed: 09/07/2023]
Abstract
The bacterial cell envelope provides a protective barrier that is challenging for small molecules and biomolecules to cross. Given the anionic nature of both Gram-positive and Gram-negative bacterial cell envelopes, negatively charged molecules are particularly difficult to deliver into these organisms. Many strategies have been employed to penetrate bacteria, ranging from reagents such as cell-penetrating peptides, enzymes, and metal-chelating compounds to physical perturbations. While cationic polymers are known antimicrobial agents, polymers that promote the permeabilization of bacterial cells without causing high levels of toxicity and cell lysis have not yet been described. Here, we investigate four polymers that display a cationic poly(2-(dimethylamino)ethyl methacrylate (D) block for the internalization of an anionic adenosine triphosphate (ATP)-based chemical probe into Escherichia coli and Bacillus subtilis. We evaluated two polymer architectures, linear and micellar, to determine how shape and hydrophobicity affect internalization efficiency. We found that, in addition to these reagents successfully promoting probe internalization, the probe-labeled cells were able to continue to grow and divide. The micellar structures in particular were highly effective for the delivery of the negatively charged chemical probe. Finally, we demonstrated that these cationic polymers could act as general permeabilization reagents, promoting the entry of other molecules, such as antibiotics.
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Affiliation(s)
- Hannah K Lembke
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Adeline Espinasse
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Mckenna G Hanson
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Christian J Grimme
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Zhe Tan
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Theresa M Reineke
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Erin E Carlson
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Department of Pharmacology, University of Minnesota, Minneapolis, Minnesota 55455, United States
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19
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Datta S. The conundrum of bacteria-specific antibiotics. J Antimicrob Chemother 2023; 78:1354-1358. [PMID: 37144577 DOI: 10.1093/jac/dkad130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023] Open
Abstract
There is a continual debate on the pros and cons of broad-spectrum versus pathogen-specific antibiotics. The unmet need for a solution for antimicrobial resistance (AMR) has put this argument into sharper focus. A shortage of clinically differentiated antibiotics in late-stage clinical development coupled with the global unmet need in the face of the AMR onslaught has exacerbated the treatment options of drug-resistant bacterial infections. An added dimension to this problem is the current understanding of dysbiosis caused by antibiotics, often leading to negative fallout in immunocompromised patients. We attempt to deconstruct the nuances of this debate from an antibiotics discovery and a clinical standpoint.
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Affiliation(s)
- Santanu Datta
- Bugworks Research India Pvt Ltd, C-CAMP, NCBS, Bellary Road, Bangalore 560065, India
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20
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Sadeeshkumar H, Balaji A, Sutherland AG, Mootien S, Anthony KG, Breaker RR. Screening for small molecule inhibitors of SAH nucleosidase using an SAH riboswitch. Anal Biochem 2023; 666:115047. [PMID: 36682579 PMCID: PMC11149561 DOI: 10.1016/j.ab.2023.115047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/30/2022] [Accepted: 01/09/2023] [Indexed: 01/21/2023]
Abstract
Due to the emergence of multidrug resistant pathogens, it is imperative to identify new targets for antibiotic drug discovery. The S-adenosylhomocysteine (SAH) nucleosidase enzyme is a promising target for antimicrobial drug development due to its critical functions in multiple bacterial processes including recycling of toxic byproducts of S-adenosylmethionine (SAM)-mediated reactions and producing the precursor of the universal quorum sensing signal, autoinducer-2 (AI-2). Riboswitches are structured RNA elements typically used by bacteria to precisely monitor and respond to changes in essential bacterial processes, including metabolism. Natural riboswitches fused to a reporter gene can be exploited to detect changes in metabolism or in physiological signaling. We performed a high-throughput screen (HTS) using an SAH-riboswitch controlled β-galactosidase reporter gene in Escherichia coli to discover small molecules that inhibit SAH recycling. We demonstrate that the assay strategy using SAH riboswitches to detect the effects of SAH nucleosidase inhibitors can quickly identify compounds that penetrate the barriers of Gram-negative bacterial cells and perturb pathways involving SAH.
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Affiliation(s)
- Harini Sadeeshkumar
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, 06520-8103, USA
| | - Aparaajita Balaji
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, 06520-8103, USA
| | | | | | - Karen G Anthony
- L2 Diagnostics, LLC, 300 George Street, New Haven, CT, 06511, USA
| | - Ronald R Breaker
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, 06520-8103, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520-8103, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT, 06520-8103, USA.
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21
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Maingot M, Bourotte M, Vetter AC, Schellhorn B, Antraygues K, Scherer H, Gitzinger M, Kemmer C, Dale GE, Defert O, Lociuro S, Brönstrup M, Willand N, Trebosc V. Structure-activity relationships of actively FhuE transported rifabutin derivatives with potent activity against Acinetobacter baumannii. Eur J Med Chem 2023; 252:115257. [PMID: 36948128 DOI: 10.1016/j.ejmech.2023.115257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/22/2023] [Accepted: 03/07/2023] [Indexed: 03/17/2023]
Abstract
Hospital-acquired infections are on the rise and represent both, a clinical and financial burden. With resistance emerging and an ever-dwindling armamentarium at hand, infections caused by Acinetobacter baumannii are particularly problematic, since these bacteria have a high level of resistance and resilience to traditional and even last-resort antibiotics. The antibiotic rifabutin was recently found to show potent in vitro and in vivo activity against extensively drug resistant A. baumannii. Building on this discovery, we report on the synthesis and activity of rifabutin analogs, with a focus on N-functionalization of the piperidine ring. The antimicrobial testing uncovered structure activity relationships (SAR) for A. baumannii that were not reflected in Staphylococcus aureus. The cellular activity did not correlate with cell-free transcription inhibition, but with bacterial intracellular compound accumulation. Mass spectrometry-based accumulation studies confirmed the involvement of the siderophore receptor FhuE in active compound translocation at low concentrations, and they showed a strong impact of the culture medium on the accumulation of rifabutin. Overall, the study underlines the structural feature required for strong accumulation of rifabutin in A. baumannii and identifies analogs as or more potent than rifabutin against A. baumannii.
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Affiliation(s)
- M Maingot
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, 59000, Lille, France
| | - M Bourotte
- BioVersys SAS, 1 rue du Professeur Calmette, 59000, Lille, France
| | - A C Vetter
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124, Braunschweig, Germany
| | - B Schellhorn
- BioVersys AG, 60C Hochbergerstrasse, 4057, Basel, Switzerland
| | - K Antraygues
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, 59000, Lille, France
| | - H Scherer
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, 59000, Lille, France
| | - M Gitzinger
- BioVersys AG, 60C Hochbergerstrasse, 4057, Basel, Switzerland
| | - C Kemmer
- BioVersys AG, 60C Hochbergerstrasse, 4057, Basel, Switzerland
| | - G E Dale
- BioVersys AG, 60C Hochbergerstrasse, 4057, Basel, Switzerland
| | - O Defert
- BioVersys SAS, 1 rue du Professeur Calmette, 59000, Lille, France
| | - S Lociuro
- BioVersys AG, 60C Hochbergerstrasse, 4057, Basel, Switzerland
| | - M Brönstrup
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124, Braunschweig, Germany
| | - N Willand
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, 59000, Lille, France.
| | - V Trebosc
- BioVersys AG, 60C Hochbergerstrasse, 4057, Basel, Switzerland.
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22
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Smitten K, Southam HM, Fairbanks S, Graf A, Chauvet A, Thomas JA. Clearing an ESKAPE Pathogen in a Model Organism; A Polypyridyl Ruthenium(II) Complex Theranostic that Treats a Resistant Acinetobacter baumannii Infection in Galleria mellonella. Chemistry 2023; 29:e202203555. [PMID: 36420820 PMCID: PMC10946903 DOI: 10.1002/chem.202203555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 11/22/2022] [Accepted: 11/24/2022] [Indexed: 11/27/2022]
Abstract
In previous studies we have described the therapeutic action of luminescent dinuclear ruthenium(II) complexes based on the tetrapyridylphenazine, tpphz, bridging ligand on pathogenic strains of Escherichia coli and Enterococcus faecalis. Herein, the antimicrobial activity of the complex against pernicious Gram-negative ESKAPE pathogenic strains of Acinetobacter baumannii (AB12, AB16, AB184 and AB210) and Pseudomonas aeruginosa (PA2017, PA_ 007_ IMP and PA_ 004_ CRCN) are reported. Estimated minimum inhibitory concentrations and minimum bactericidal concentrations for the complexes revealed the complex shows potent activity against all A. baumannii strains, in both glucose defined minimal media and standard nutrient rich Mueller-Hinton-II. Although the activity was lower in P. aureginosa, a moderately high potency was observed and retained in carbapenem-resistant strains. Optical microscopy showed that the compound is rapidly internalized by A. baumannii. As previous reports had revealed the complex exhibited no toxicity in Galleria Mellonella up to concentrations of 80 mg/kg, the ability to clear pathogenic infection within this model was explored. The pathogenic concentrations to the larvae for each bacterium were determined to be≥105 for AB184 and≥103 CFU/mL for PA2017. It was found a single dose of the compound totally cleared a pathogenic A. baumannii infection from all treated G. mellonella within 96 h. Uniquely, in these conditions thanks to the imaging properties of the complex the clearance of the bacteria within the hemolymph of G. mellonella could be directly visualized through both optical and transmission electron microscopy.
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Affiliation(s)
- Kirsty Smitten
- Department of ChemistryUniversity of SheffieldSheffieldS3 7HFUK
| | | | - Simon Fairbanks
- Department of ChemistryUniversity of SheffieldSheffieldS3 7HFUK
| | - Arthur Graf
- Department of ChemistryUniversity of SheffieldSheffieldS3 7HFUK
| | - Adrien Chauvet
- Department of ChemistryUniversity of SheffieldSheffieldS3 7HFUK
| | - Jim A Thomas
- Department of ChemistryUniversity of SheffieldSheffieldS3 7HFUK
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23
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Plant-Derived Xanthones against Clostridial Enteric Infections. Antibiotics (Basel) 2023; 12:antibiotics12020232. [PMID: 36830143 PMCID: PMC9952316 DOI: 10.3390/antibiotics12020232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/13/2023] [Accepted: 01/17/2023] [Indexed: 01/26/2023] Open
Abstract
Intestinal bacterial infections are a major threat to human and animal health. In this study, we found plant-derived antibacterial xanthones, particularly α-mangostin (AMG) from the mangosteen peel, exhibiting extraordinary activities against Clostridium perfringens. Structure-activity relationship analysis showed that prenylation modulated the activity of xanthones. The efficacy of AMG (4, 8, 20 mg/kg body weight) was also demonstrated in the broiler chicken necrotic enteritis model infected with Clostridium perfringens. In the models (n = 6 per group), feed supplementation of AMG maintained the homeostasis of the gut microbiome by reducing the colonization of clostridia and promoting the integrity of intestinal barriers via the upregulation of mucin expression. These results suggest that plant-derived xanthones may be a potential alternative to antibiotics for treating clostridial enteric infections in the clinic.
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24
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Ruparel FJ, Shah SK, Patel JH, Thakkar NR, Gajera GN, Kothari VO. Network analysis for identifying potential anti-virulence targets from whole transcriptome of Pseudomonas aeruginosa and Staphylococcus aureus exposed to certain anti-pathogenic polyherbal formulations. Drug Target Insights 2023; 17:58-69. [PMID: 37275512 PMCID: PMC10238913 DOI: 10.33393/dti.2022.2595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 05/10/2023] [Indexed: 06/07/2023] Open
Abstract
Introduction Antimicrobial resistance (AMR) is a serious global threat. Identification of novel antibacterial targets is urgently warranted to help antimicrobial drug discovery programs. This study attempted identification of potential targets in two important pathogens Pseudomonas aeruginosa and Staphylococcus aureus. Methods Transcriptomes of P. aeruginosa and S. aureus exposed to two different quorum-modulatory polyherbal formulations were subjected to network analysis to identify the most highly networked differentially expressed genes (hubs) as potential anti-virulence targets. Results Genes associated with denitrification and sulfur metabolism emerged as the most important targets in P. aeruginosa. Increased buildup of nitrite (NO2) in P. aeruginosa culture exposed to the polyherbal formulation Panchvalkal was confirmed through in vitro assay too. Generation of nitrosative stress and inducing sulfur starvation seemed to be effective anti-pathogenic strategies against this notorious gram-negative pathogen. Important targets identified in S. aureus were the transcriptional regulator sarA, immunoglobulin-binding protein Sbi, serine protease SplA, the saeR/S response regulator system, and gamma-hemolysin components hlgB and hlgC. Conclusion Further validation of the potential targets identified in this study is warranted through appropriate in vitro and in vivo assays in model hosts. Such validated targets can prove vital to many antibacterial drug discovery programs globally.
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Affiliation(s)
- Feny J Ruparel
- Institute of Science, Nirma University, Ahmedabad - India
- FJR, NRT, and GNG contributed equally
| | - Siddhi K Shah
- Institute of Science, Nirma University, Ahmedabad - India
- FJR, NRT, and GNG contributed equally
| | - Jhanvi H Patel
- Institute of Science, Nirma University, Ahmedabad - India
- FJR, NRT, and GNG contributed equally
| | - Nidhi R Thakkar
- Institute of Science, Nirma University, Ahmedabad - India
- FJR, NRT, and GNG contributed equally
| | - Gemini N Gajera
- Institute of Science, Nirma University, Ahmedabad - India
- FJR, NRT, and GNG contributed equally
| | - Vijay O Kothari
- Institute of Science, Nirma University, Ahmedabad - India
- FJR, NRT, and GNG contributed equally
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25
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Ruparel FJ, Shah SK, Patel JH, Thakkar NR, Gajera GN, Kothari VO. Network analysis for identifying potential anti-virulence targets from whole transcriptome of Pseudomonas aeruginosa and Staphylococcus aureus exposed to certain anti-pathogenic polyherbal formulations. Drug Target Insights 2023; 17:58-69. [PMID: 37275512 PMCID: PMC10238913 DOI: 10.33393/dti.2023.2595] [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: 04/29/2023] [Accepted: 05/10/2023] [Indexed: 03/07/2024] Open
Abstract
Introduction Antimicrobial resistance (AMR) is a serious global threat. Identification of novel antibacterial targets is urgently warranted to help antimicrobial drug discovery programs. This study attempted identification of potential targets in two important pathogens Pseudomonas aeruginosa and Staphylococcus aureus. Methods Transcriptomes of P. aeruginosa and S. aureus exposed to two different quorum-modulatory polyherbal formulations were subjected to network analysis to identify the most highly networked differentially expressed genes (hubs) as potential anti-virulence targets. Results Genes associated with denitrification and sulfur metabolism emerged as the most important targets in P. aeruginosa. Increased buildup of nitrite (NO2) in P. aeruginosa culture exposed to the polyherbal formulation Panchvalkal was confirmed through in vitro assay too. Generation of nitrosative stress and inducing sulfur starvation seemed to be effective anti-pathogenic strategies against this notorious gram-negative pathogen. Important targets identified in S. aureus were the transcriptional regulator sarA, immunoglobulin-binding protein Sbi, serine protease SplA, the saeR/S response regulator system, and gamma-hemolysin components hlgB and hlgC. Conclusion Further validation of the potential targets identified in this study is warranted through appropriate in vitro and in vivo assays in model hosts. Such validated targets can prove vital to many antibacterial drug discovery programs globally.
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Affiliation(s)
- Feny J Ruparel
- Institute of Science, Nirma University, Ahmedabad - India
- FJR, NRT, and GNG contributed equally
| | - Siddhi K Shah
- Institute of Science, Nirma University, Ahmedabad - India
- FJR, NRT, and GNG contributed equally
| | - Jhanvi H Patel
- Institute of Science, Nirma University, Ahmedabad - India
- FJR, NRT, and GNG contributed equally
| | - Nidhi R Thakkar
- Institute of Science, Nirma University, Ahmedabad - India
- FJR, NRT, and GNG contributed equally
| | - Gemini N Gajera
- Institute of Science, Nirma University, Ahmedabad - India
- FJR, NRT, and GNG contributed equally
| | - Vijay O Kothari
- Institute of Science, Nirma University, Ahmedabad - India
- FJR, NRT, and GNG contributed equally
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26
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Walesch S, Birkelbach J, Jézéquel G, Haeckl FPJ, Hegemann JD, Hesterkamp T, Hirsch AKH, Hammann P, Müller R. Fighting antibiotic resistance-strategies and (pre)clinical developments to find new antibacterials. EMBO Rep 2022; 24:e56033. [PMID: 36533629 PMCID: PMC9827564 DOI: 10.15252/embr.202256033] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 12/23/2022] Open
Abstract
Antibacterial resistance is one of the greatest threats to human health. The development of new therapeutics against bacterial pathogens has slowed drastically since the approvals of the first antibiotics in the early and mid-20th century. Most of the currently investigated drug leads are modifications of approved antibacterials, many of which are derived from natural products. In this review, we highlight the challenges, advancements and current standing of the clinical and preclinical antibacterial research pipeline. Additionally, we present novel strategies for rejuvenating the discovery process and advocate for renewed and enthusiastic investment in the antibacterial discovery pipeline.
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Affiliation(s)
- Sebastian Walesch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)SaarbrückenGermany,Department of PharmacySaarland UniversitySaarbrückenGermany,Helmholtz Centre for Infection research (HZI)BraunschweigGermany,German Center for infection research (DZIF)BraunschweigGermany
| | - Joy Birkelbach
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)SaarbrückenGermany,Department of PharmacySaarland UniversitySaarbrückenGermany,Helmholtz Centre for Infection research (HZI)BraunschweigGermany,German Center for infection research (DZIF)BraunschweigGermany
| | - Gwenaëlle Jézéquel
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)SaarbrückenGermany,Helmholtz Centre for Infection research (HZI)BraunschweigGermany
| | - F P Jake Haeckl
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)SaarbrückenGermany,Department of PharmacySaarland UniversitySaarbrückenGermany,Helmholtz Centre for Infection research (HZI)BraunschweigGermany,German Center for infection research (DZIF)BraunschweigGermany
| | - Julian D Hegemann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)SaarbrückenGermany,Department of PharmacySaarland UniversitySaarbrückenGermany,Helmholtz Centre for Infection research (HZI)BraunschweigGermany,German Center for infection research (DZIF)BraunschweigGermany
| | - Thomas Hesterkamp
- Helmholtz Centre for Infection research (HZI)BraunschweigGermany,German Center for infection research (DZIF)BraunschweigGermany
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)SaarbrückenGermany,Department of PharmacySaarland UniversitySaarbrückenGermany,Helmholtz Centre for Infection research (HZI)BraunschweigGermany,German Center for infection research (DZIF)BraunschweigGermany,Helmholtz International Lab for Anti‐InfectivesSaarbrückenGermany
| | - Peter Hammann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)SaarbrückenGermany,Department of PharmacySaarland UniversitySaarbrückenGermany,Helmholtz Centre for Infection research (HZI)BraunschweigGermany,German Center for infection research (DZIF)BraunschweigGermany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)SaarbrückenGermany,Department of PharmacySaarland UniversitySaarbrückenGermany,Helmholtz Centre for Infection research (HZI)BraunschweigGermany,German Center for infection research (DZIF)BraunschweigGermany,Helmholtz International Lab for Anti‐InfectivesSaarbrückenGermany
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27
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Zhou Y, Huang W, Lei E, Yang A, Li Y, Wen K, Wang M, Li L, Chen Z, Zhou C, Bai S, Han J, Song W, Ren X, Zeng X, Pu H, Wan M, Feng X. Cooperative Membrane Damage as a Mechanism for Pentamidine-Antibiotic Mutual Sensitization. ACS Chem Biol 2022; 17:3178-3190. [PMID: 36269311 DOI: 10.1021/acschembio.2c00613] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Most Gram-positive-selective antibiotics have low activity against Gram-negative bacteria due to the presence of an outer membrane barrier. There is, therefore, interest in developing combination therapies that can penetrate the outer membrane (OM) with known antibiotics coupled with membrane-active sensitizing adjuvants. However, two unanswered questions hinder the development of such combination therapies: the sensitization spectrum of the sensitizer and the mechanism of antibiotic-sensitizer mutual potentiation. Here, with pentamidine as an example, we screened a library of 170 FDA-approved antibiotics in combination with pentamidine, a compound known to disturb the OM of Gram-negative bacteria. We found that four antibiotics, minocycline, linezolid, valnemulin, and nadifloxacin, displaced enhanced activity in combination with pentamidine against several multidrug-resistant Gram-negative bacteria. Through a descriptor-based structural-activity analysis and multiple cell-based biochemical assays, we found that hydrophobicity, partial charge, rigidity, and surface rugosity were key factors that affected sensitization via a cooperative membrane damage mechanism in which lipopolysaccharides and phospholipids were identified as sites of synergy. Finally, in vitro experiments showed that the linezolid-pentamidine combination slowed the generation of drug resistance, and there was also potent activity in in vivo experiments. Overall, our results highlight the importance of the physicochemical properties of antibiotics and cooperative membrane damage for synergistic pentamidine-antibiotic drug combinations.
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Affiliation(s)
- Yu Zhou
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Wei Huang
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - E Lei
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Anming Yang
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Youzhi Li
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Kang Wen
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Min Wang
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Lanxin Li
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Zheng Chen
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Cailing Zhou
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.,College of Biology, Hunan University, Changsha, Hunan 410082, China
| | - Silei Bai
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Jingyu Han
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Wenwen Song
- Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, Hunan 410082, China.,College of Biology, Hunan University, Changsha, Hunan 410082, China
| | - Xuanbai Ren
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Xiangxiang Zeng
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Huangsheng Pu
- College of Advanced Interdisciplinary Studies, National University of Defense Technology, Changsha, Hunan 410073, China
| | - Muyang Wan
- Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, Hunan 410082, China.,College of Biology, Hunan University, Changsha, Hunan 410082, China
| | - Xinxin Feng
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
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28
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Meir O, Zaknoon F, Mor A. An efflux-susceptible antibiotic-adjuvant with systemic efficacy against mouse infections. Sci Rep 2022; 12:17673. [PMID: 36271103 PMCID: PMC9586926 DOI: 10.1038/s41598-022-21526-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 09/28/2022] [Indexed: 01/18/2023] Open
Abstract
Scarcity of effective treatments against sepsis is daunting, especially under the contemporary standpoints on antibiotics resistance, entailing the development of alternative treatment strategies. Here, we describe the design and antibiotic adjuvant properties of a new lipopeptide-like pentamer, decanoyl-bis.diaminobutyrate-aminododecanoyl-diaminobutyrate-amide (C10BBc12B), whose sub-maximal tolerated doses combinations with inefficient antibiotics demonstrated systemic efficacies in murine models of peritonitis-sepsis and urinary-tract infections. Attempts to shed light into the mechanism of action using membrane-active fluorescent probes, suggest outer-membrane interactions to dominate the pentamer's adjuvant properties, which were not associated with typical inner-membrane damages or with delayed bacterial growth. Yet, checkerboard titrations with low micromolar concentrations of C10BBc12B exhibited unprecedented capacities in potentiation of hydrophobic antibiotics towards Gram-negative ESKAPE pathogens, with an apparent low propensity for prompting resistance to the antibiotics. Assessment of the pentamer's potentiating activities upon efflux inhibition incites submission of a hitherto unreported, probable action mechanism implicating the pentamer's de-facto capacity to hijack bacterial efflux pumps for boosting its adjuvant activity through repetitive steps including outer-membrane adhesion, translocation and subsequent expulsion.
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Affiliation(s)
- Ohad Meir
- grid.6451.60000000121102151Faculty of Biotechnology and Food Engineering, Technion – Israel Institute of Technology, 3200003 Haifa, Israel
| | - Fadia Zaknoon
- grid.6451.60000000121102151Faculty of Biotechnology and Food Engineering, Technion – Israel Institute of Technology, 3200003 Haifa, Israel
| | - Amram Mor
- grid.6451.60000000121102151Faculty of Biotechnology and Food Engineering, Technion – Israel Institute of Technology, 3200003 Haifa, Israel
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29
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30
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Wang Y, Kong J, Zhang X, Liu Y, Huang Z, Yuan L, Zhang Y, Cao J, Chen L, Liu Y, Zhou T. Plumbagin resurrect colistin susceptible against colistin-resistant Pseudomonas aeruginosa in vitro and in vivo. Front Microbiol 2022; 13:1020652. [PMID: 36274701 PMCID: PMC9579824 DOI: 10.3389/fmicb.2022.1020652] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/08/2022] [Indexed: 11/22/2022] Open
Abstract
The global emergence and spread of multi-drug resistant (MDR) strains is becoming increasingly worrisome due to the overuse of broad-spectrum antibiotics. Colistin, the last resort for treating MDR strains infections, has once again returned to the clinician’s choice. However, with the widespread use of colistin, colistin-resistant gram-negative bacteria (GNB) have subsequently emerged, including colistin-resistant Pseudomonas aeruginosa (COL-R PA). Therefore, available solutions are urgently needed to respond to this situation. Here, we inspiringly found that the combination of plumbagin and colistin had an efficiently inhibitory effect for colistin-resistant P. aeruginosa in vitro through checkerboard assay and time-kill assay. The combinatorial inhibition of biofilm formation was clearly demonstrated by crystal violet staining and scanning electron microscopy (SEM), and this combination can not only inhibited biofilm formation but also eradicated the mature biofilm. Erythrocytes hemolysis test showed that plumbagin has negligible hemolysis ability. In addition, the increased survival rate of Galleria mellonella (G. mellonella) larva confirmed this combination as same as effective in vivo. As for the mechanism of this combination, propidium iodide (PI) staining showed colistin combined with plumbagin could significantly change the membrane permeability, thus exerting synergistic antibacterial activity. In conclusion, the combination of plumbagin and colistin shows a prominently synergistic antibacterial effect in vitro and in vivo, providing a promising option for the therapy of COL-R PA infection.
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Affiliation(s)
- Yue Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jingchun Kong
- Department of Medical Lab Science, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xiaodong Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yan Liu
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Zeyu Huang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Lu Yuan
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, China
| | - Ying Zhang
- Department of Medical Lab Science, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jianming Cao
- Department of Medical Lab Science, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Lijiang Chen
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yong Liu
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, China
- Yong Liu,
| | - Tieli Zhou
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
- *Correspondence: Tieli Zhou,
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31
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Dan W, Gao J, Qi X, Wang J, Dai J. Antibacterial quaternary ammonium agents: Chemical diversity and biological mechanism. Eur J Med Chem 2022; 243:114765. [PMID: 36116235 DOI: 10.1016/j.ejmech.2022.114765] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 09/04/2022] [Accepted: 09/07/2022] [Indexed: 01/04/2023]
Abstract
Bacterial infections have seriously threatened public health especially with the increasing resistance and the cliff-like decline of the number of newly approved antibacterial agents. Quaternary ammonium compounds (QACs) possess potent medicinal properties with 95 successfully marketed drugs, which also have a long history as antibacterial agents. In this review, we summarize the chemical diversity of antibacterial QACs, divided into chain-like and aromatic ring, reported over the past decade (2012 to mid-2022). Additionally, the structure-activity relationships, mainly covering hydrophobicity, charges and skeleton features, are discussed. In the cases where sufficient information is available, antibacterial mechanisms including biofilm, cell membrane, and intracellular targets are presented. It is hoped that this review will provide sufficient information for medicinal chemists to discover the new generation of antibacterial agents based on QACs.
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Affiliation(s)
- Wenjia Dan
- School of Life Science and Technology, Weifang Medical University, Shandong, China
| | - Jixiang Gao
- School of Life Science and Technology, Weifang Medical University, Shandong, China
| | - Xiaohui Qi
- School of Life Science and Technology, Weifang Medical University, Shandong, China
| | - Junru Wang
- College of Chemistry & Pharmacy, Northwest A&F University, Shaanxi, China.
| | - Jiangkun Dai
- School of Life Science and Technology, Weifang Medical University, Shandong, China.
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32
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Parker E, Cain BN, Hajian B, Ulrich RJ, Geddes EJ, Barkho S, Lee HY, Williams JD, Raynor M, Caridha D, Zaino A, Shekhar M, Muñoz KA, Rzasa KM, Temple ER, Hunt D, Jin X, Vuong C, Pannone K, Kelly AM, Mulligan MP, Lee KK, Lau GW, Hung DT, Hergenrother PJ. An Iterative Approach Guides Discovery of the FabI Inhibitor Fabimycin, a Late-Stage Antibiotic Candidate with In Vivo Efficacy against Drug-Resistant Gram-Negative Infections. ACS CENTRAL SCIENCE 2022; 8:1145-1158. [PMID: 36032774 PMCID: PMC9413440 DOI: 10.1021/acscentsci.2c00598] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Indexed: 05/13/2023]
Abstract
Genomic studies and experiments with permeability-deficient strains have revealed a variety of biological targets that can be engaged to kill Gram-negative bacteria. However, the formidable outer membrane and promiscuous efflux pumps of these pathogens prevent many candidate antibiotics from reaching these targets. One such promising target is the enzyme FabI, which catalyzes the rate-determining step in bacterial fatty acid biosynthesis. Notably, FabI inhibitors have advanced to clinical trials for Staphylococcus aureus infections but not for infections caused by Gram-negative bacteria. Here, we synthesize a suite of FabI inhibitors whose structures fit permeation rules for Gram-negative bacteria and leverage activity against a challenging panel of Gram-negative clinical isolates as a filter for advancement. The compound to emerge, called fabimycin, has impressive activity against >200 clinical isolates of Escherichia coli, Klebsiella pneumoniae, and Acinetobacter baumannii, and does not kill commensal bacteria. X-ray structures of fabimycin in complex with FabI provide molecular insights into the inhibition. Fabimycin demonstrates activity in multiple mouse models of infection caused by Gram-negative bacteria, including a challenging urinary tract infection model. Fabimycin has translational promise, and its discovery provides additional evidence that antibiotics can be systematically modified to accumulate in Gram-negative bacteria and kill these problematic pathogens.
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Affiliation(s)
- Erica
N. Parker
- Department
of Chemistry and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Brett N. Cain
- Department
of Chemistry and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Behnoush Hajian
- Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Rebecca J. Ulrich
- Department
of Chemistry and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Emily J. Geddes
- Department
of Chemistry and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Sulyman Barkho
- Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Hyang Yeon Lee
- Department
of Chemistry and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - John D. Williams
- Walter
Reed Army Institute of Research, Silver Spring, Maryland 20910 United States
| | - Malik Raynor
- Walter
Reed Army Institute of Research, Silver Spring, Maryland 20910 United States
| | - Diana Caridha
- Walter
Reed Army Institute of Research, Silver Spring, Maryland 20910 United States
| | - Angela Zaino
- Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Mrinal Shekhar
- Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Kristen A. Muñoz
- Department
of Chemistry and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Kara M. Rzasa
- Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Emily R. Temple
- Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Diana Hunt
- Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department
of Molecular Biology and Center for Computational and Integrative
Biology, Massachusetts General Hospital, Boston, Massachusetts 02115, United States
| | - Xiannu Jin
- Walter
Reed Army Institute of Research, Silver Spring, Maryland 20910 United States
| | - Chau Vuong
- Walter
Reed Army Institute of Research, Silver Spring, Maryland 20910 United States
| | - Kristina Pannone
- Walter
Reed Army Institute of Research, Silver Spring, Maryland 20910 United States
| | - Aya M. Kelly
- Department
of Chemistry and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Michael P. Mulligan
- Department
of Chemistry and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Katie K. Lee
- Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Gee W. Lau
- Department
of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Deborah T. Hung
- Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department
of Molecular Biology and Center for Computational and Integrative
Biology, Massachusetts General Hospital, Boston, Massachusetts 02115, United States
| | - Paul J. Hergenrother
- Department
of Chemistry and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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33
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Corti MB, Campagno LP, Romero VL, Gutierrez S, Alovero FL. Cationic polymer contributes to broaden the spectrum of vancomycin activity achieving eradication of Pseudomonas aeruginosa. Arch Microbiol 2022; 204:507. [PMID: 35859215 DOI: 10.1007/s00203-022-03117-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 06/27/2022] [Accepted: 06/30/2022] [Indexed: 01/24/2023]
Abstract
Vancomycin (VAN) is unable to penetrate the outer membrane of Gram-negative bacteria and reach the target site. One approach to overcome this limitation is to associate it with compounds with permeabilizing or antimicrobial properties. Eudragit E100® (Eu) is a cationic polymer insufficiently characterized for its potential antimicrobial action. Eu-VAN combinations were characterized, the antimicrobial efficacy against Pseudomonas aeruginosa was evaluated and previous studies on the effects of Eu on bacterial envelopes were extended. Time-kill assays showed eradication of P. aeruginosa within 3-6 h exposure to Eu-VAN, whilst VAN was ineffective. Eu showed regrowth in 24 h and delayed colony pigmentation. Although permeabilization of bacterial envelopes or morphological alterations observed by TEM and flow cytometry after exposure to Eu were insufficient to cause bacterial death, they allowed access of VAN to the target site, since Eu-VAN/Van-FL-treated cultures showed fluorescent staining in all bacterial cells, indicating Van-FL internalization. Consequently, Eu potentiated the activity of an otherwise inactive antibiotic against P. aeruginosa. Moreover, Eu-VAN combinations exhibited improved physicochemical properties and could be used in the development of therapeutic alternatives in the treatment of bacterial keratitis.
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Affiliation(s)
- Melisa B Corti
- Departamento de Ciencias Farmacéuticas, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba and Unidad de Investigación y Desarrollo en Tecnología Farmacéutica (UNITEFA), CONICET, Medina Allende y Haya de la Torre, Edificio Ciencias II, X5000HUA, Ciudad Universitaria, Córdoba, Argentina
| | - Luciana P Campagno
- Departamento de Ciencias Farmacéuticas, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba and Unidad de Investigación y Desarrollo en Tecnología Farmacéutica (UNITEFA), CONICET, Medina Allende y Haya de la Torre, Edificio Ciencias II, X5000HUA, Ciudad Universitaria, Córdoba, Argentina
| | - Verónica L Romero
- Departamento de Ciencias Farmacéuticas, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba and Unidad de Investigación y Desarrollo en Tecnología Farmacéutica (UNITEFA), CONICET, Medina Allende y Haya de la Torre, Edificio Ciencias II, X5000HUA, Ciudad Universitaria, Córdoba, Argentina
- Instituto de Farmacología Experimental de Córdoba (IFEC), CONICET and Departamento de Farmacología, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Silvina Gutierrez
- Centro de Microscopia Electrónica, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Fabiana L Alovero
- Departamento de Ciencias Farmacéuticas, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba and Unidad de Investigación y Desarrollo en Tecnología Farmacéutica (UNITEFA), CONICET, Medina Allende y Haya de la Torre, Edificio Ciencias II, X5000HUA, Ciudad Universitaria, Córdoba, Argentina.
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34
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Lei E, Tao H, Jiao S, Yang A, Zhou Y, Wang M, Wen K, Wang Y, Chen Z, Chen X, Song J, Zhou C, Huang W, Xu L, Guan D, Tan C, Liu H, Cai Q, Zhou K, Modica J, Huang SY, Huang W, Feng X. Potentiation of Vancomycin: Creating Cooperative Membrane Lysis through a "Derivatization-for-Sensitization" Approach. J Am Chem Soc 2022; 144:10622-10639. [PMID: 35657057 DOI: 10.1021/jacs.2c03784] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Gram-negative bacteria, especially the ones with multidrug resistance, post dire challenges to antibiotic treatments due to the presence of the outer membrane (OM), which blocks the entry of many antibiotics. Current solutions for such permeability issues, namely lipophilic-cationic derivatization of antibiotics and sensitization with membrane-active agents, cannot effectively potentiate the large, globular, and hydrophilic antibiotics such as vancomycin, due to ineffective disruption of the OM. Here, we present our solution for high-degree OM binding of vancomycin via a hybrid "derivatization-for-sensitization" approach, which features a combination of LPS-targeting lipo-cationic modifications on vancomycin and OM disruption activity from a sensitizing adjuvant. 106- to 107-fold potentiation of vancomycin and 20-fold increase of the sensitizer's effectiveness were achieved with a combination of a vancomycin derivative and its sensitizer. Such potentiation is the result of direct membrane lysis through cooperative membrane binding for the sensitizer-antibiotic complex, which strongly promotes the uptake of vancomycin and adds to the extensive antiresistance effectiveness. The potential of such derivatization-for-sensitization approach was also supported by the combination's potent in vivo antimicrobial efficacy in mouse model studies, and the expanded application of such strategy on other antibiotics and sensitizer structures.
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Affiliation(s)
- E Lei
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Huanyu Tao
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Shang Jiao
- CAS Key Laboratory of Receptor Research, CAS Center for Excellence in Molecular Cell Science, Center for Biotherapeutics Discovery Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Anming Yang
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Yu Zhou
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Min Wang
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Kang Wen
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Yi Wang
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.,School of Biology, Hunan University, Changsha, Hunan, 410082, China, Hunan University, Changsha, Hunan 410082, China
| | - Zhiyong Chen
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Xianhui Chen
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Junfeng Song
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Cailing Zhou
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.,School of Biology, Hunan University, Changsha, Hunan, 410082, China, Hunan University, Changsha, Hunan 410082, China
| | - Wei Huang
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Lili Xu
- CAS Key Laboratory of Receptor Research, CAS Center for Excellence in Molecular Cell Science, Center for Biotherapeutics Discovery Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Dongliang Guan
- CAS Key Laboratory of Receptor Research, CAS Center for Excellence in Molecular Cell Science, Center for Biotherapeutics Discovery Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Cuiyan Tan
- Department of Pulmonary and Critical Care Medicine, Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai, Guangdong 519000, China
| | - Haoran Liu
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Qingyun Cai
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Kai Zhou
- Shenzhen Institute of Respiratory Diseases, The First Affiliated Hospital of Southern University of Science and Technology (Shenzhen People's Hospital), Shenzhen, Guangdong 518020, China
| | - Justin Modica
- Departments of Chemistry and Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Sheng-You Huang
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Wei Huang
- CAS Key Laboratory of Receptor Research, CAS Center for Excellence in Molecular Cell Science, Center for Biotherapeutics Discovery Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xinxin Feng
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
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35
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Sinha S, Dhanabal VB, Sperandeo P, Polissi A, Bhattacharjya S. Linking dual mode of action of host defense antimicrobial peptide thanatin: Structures, lipopolysaccharide and LptA m binding of designed analogs. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183839. [PMID: 34915021 DOI: 10.1016/j.bbamem.2021.183839] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 12/02/2021] [Accepted: 12/06/2021] [Indexed: 06/14/2023]
Abstract
At present, antibiotics options to cure infections caused by drug resistant Gram-negative pathogens are highly inadequate. LPS outer membrane, proteins involved in LPS transport and biosynthesis pathways are vital targets. Thanatin, an insect derived 21-residue long antimicrobial peptide may be exploited for the development of effective antibiotics against Gram-negative bacteria. As a mode of bacterial cell killing, thanatin disrupts LPS outer membrane and inhibits LPS transport by binding to the periplasmic protein LptAm. Here, we report structure-activity correlation of thanatin and analogs for the purpose of rational design. These analogs of thanatin are investigated, by NMR, ITC and fluorescence, to correlate structure, antibacterial activity and binding with LPS and LptAm, a truncated monomeric variant. Our results demonstrate that an analog thanatin M21F exhibits superior antibacterial activity. In LPS interaction analyses, thanatin M21F demonstrate high affinity binding to outer membrane LPS. The atomic resolution structure of thanatin M21F in LPS micelle reveals four stranded β-sheet structure in a dimeric topology whereby the sidechain of aromatic residues Y10, F21 sustained mutual packing at the interface. Strikingly, LptAm binding affinity of thanatin M21F has been significantly increased with an estimated Kd ~ 0.73 nM vs 13 nM for thanatin. Further, atomic resolution structures and interactions of Ala based thanatin analogs define plausible correlations with antibacterial activity and LPS, LptAm interactions. Taken together, the current work provides a frame-work for the designing of thanatin based potent antimicrobial peptides for the treatment of drug resistance Gram-negative bacteria.
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Affiliation(s)
- Sheetal Sinha
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore; Interdisciplinary Graduate School, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore; Advanced Environmental Biotechnology Centre, Nanyang Environment and Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, Singapore 637141, Singapore
| | - Vidhya Bharathi Dhanabal
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Paola Sperandeo
- Dept. of Pharmacological and Biomolecular Sciences, University of Milano, Via Balzaretti 9, 20133 Milano, Italy
| | - Alessandra Polissi
- Dept. of Pharmacological and Biomolecular Sciences, University of Milano, Via Balzaretti 9, 20133 Milano, Italy
| | - Surajit Bhattacharjya
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
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36
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Dharuman S, Wallace MJ, Reeve SM, Bulitta JB, Lee RE. Synthesis and Structure–Activity Relationship of Thioacetamide-Triazoles against Escherichia coli. Molecules 2022; 27:molecules27051518. [PMID: 35268619 PMCID: PMC8911640 DOI: 10.3390/molecules27051518] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/21/2022] [Accepted: 02/21/2022] [Indexed: 02/04/2023] Open
Abstract
Infections due to Gram-negative bacteria are increasingly dangerous due to the spread of multi-drug resistant strains, emphasizing the urgent need for new antibiotics with alternative modes of action. We have previously identified a novel class of antibacterial agents, thioacetamide-triazoles, using an antifolate targeted screen and determined their mode of action which is dependent on activation by cysteine synthase A. Herein, we report a detailed examination of the anti-E. coli structure–activity relationship of the thioacetamide-triazoles. Analogs of the initial hit compounds were synthesized to study the contribution of the aryl, thioacetamide, and triazole sections. A clear structure–activity relationship was observed generating compounds with excellent inhibition values. Substitutions to the aryl ring were generally best tolerated, including the introduction of thiazole and pyridine heteroaryl systems. Substitutions to the central thioacetamide linker section were more nuanced; the introduction of a methyl branch to the thioacetamide linker substantially decreased antibacterial activity, but the isomeric propionamide and N-benzamide systems retained activity. Changes to the triazole portion of the molecule dramatically decreased the antibacterial activity, further indicating that 1,2,3-triazole is critical for potency. From these studies, we have identified new lead compounds with desirable in-vitro ADME properties and in-vivo pharmacokinetic properties.
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Affiliation(s)
- Suresh Dharuman
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (S.D.); (M.J.W.); (S.M.R.)
| | - Miranda J. Wallace
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (S.D.); (M.J.W.); (S.M.R.)
- Department of Pathology & Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Stephanie M. Reeve
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (S.D.); (M.J.W.); (S.M.R.)
| | - Jürgen B. Bulitta
- Departments of Pharmaceutics and Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, FL 31836, USA;
| | - Richard E. Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (S.D.); (M.J.W.); (S.M.R.)
- Correspondence:
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37
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Schumacher CE, Rausch M, Greven T, Neudörfl JM, Schneider T, Schmalz HG. Total Synthesis and Antibiotic Properties of Amino‐Functionalized Aromatic Terpenoids Related to Erogorgiaene and the Pseudopterosins. European J Org Chem 2022. [DOI: 10.1002/ejoc.202200058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | - Marvin Rausch
- University of Bonn: Rheinische Friedrich-Wilhelms-Universitat Bonn Pharmaceutical Microbiology GERMANY
| | - Tobias Greven
- University of Cologne: Universitat zu Koln Chemistry GERMANY
| | | | - Tanja Schneider
- University of Bonn: Rheinische Friedrich-Wilhelms-Universitat Bonn Pharmaceutical Biology GERMANY
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Orritt KM, Feng L, Newell JF, Sutton JN, Grossman S, Germe T, Abbott LR, Jackson HL, Bury BKL, Maxwell A, McPhillie MJ, Fishwick CWG. De novo design of type II topoisomerase inhibitors as potential antimicrobial agents targeting a novel binding region. RSC Med Chem 2022; 13:831-839. [PMID: 35919336 PMCID: PMC9298182 DOI: 10.1039/d2md00049k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/30/2022] [Indexed: 11/21/2022] Open
Abstract
By 2050, it is predicted that antimicrobial resistance will be responsible for 10 million global deaths annually, more deaths than cancer, costing the world economy $100 trillion. Clearly, strategies to address this problem are essential as bacterial evolution is rendering our current antibiotics ineffective. The discovery of an allosteric binding site on the established antibacterial target DNA gyrase offers a new medicinal chemistry strategy. As this site is distinct from the fluoroquinolone binding site, resistance is not yet documented. Using in silico molecular design methods, we have designed and synthesised a novel series of biphenyl-based inhibitors inspired by a published thiophene-based allosteric inhibitor. This series was evaluated in vitro against Escherichia coli DNA gyrase and E. coli topoisomerase IV with the most potent compounds exhibiting IC50 values towards the low micromolar range for DNA gyrase and only ∼2-fold less active against topoisomerase IV. The structure–activity relationships reported herein suggest insights to further exploit this allosteric site, offering a pathway to overcome developing fluoroquinolone resistance. A computational design, make and test strategy was used to identify antibacterial inhibitors of bacterial DNA gyrase and topoisomerase IV, proposed to bind at a novel allosteric site.![]()
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Affiliation(s)
- Kyle M. Orritt
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK
| | - Lipeng Feng
- Dept. Biochemistry & Metabolism, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | | | - Jack N. Sutton
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK
| | - Scott Grossman
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK
| | - Thomas Germe
- Dept. Biochemistry & Metabolism, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Lauren R. Abbott
- Dept. Biochemistry & Metabolism, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | | | | | - Anthony Maxwell
- Dept. Biochemistry & Metabolism, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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King A, Blackledge MS. Evaluation of small molecule kinase inhibitors as novel antimicrobial and antibiofilm agents. Chem Biol Drug Des 2021; 98:1038-1064. [PMID: 34581492 PMCID: PMC8616828 DOI: 10.1111/cbdd.13962] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 08/24/2021] [Accepted: 09/15/2021] [Indexed: 12/25/2022]
Abstract
Antibiotic resistance is a global and pressing concern. Our current therapeutic arsenal is increasingly limited as bacteria are developing resistance at a rate that far outpaces our ability to create new treatments. Novel approaches to treating and curing bacterial infections are urgently needed. Bacterial kinases have been increasingly explored as novel drug targets and are poised for development into novel therapeutic agents to combat bacterial infections. This review describes several general classes of bacterial kinases that play important roles in bacterial growth, antibiotic resistance, and biofilm formation. General features of these kinase classes are discussed and areas of particular interest for the development of inhibitors will be highlighted. Small molecule kinase inhibitors are described and organized by phenotypic effect, spotlighting particularly interesting inhibitors with novel functions and potential therapeutic benefit. Finally, we provide our perspective on the future of bacterial kinase inhibition as a viable strategy to combat bacterial infections and overcome the pressures of increasing antibiotic resistance.
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Affiliation(s)
- Ashley King
- Department of Chemistry, High Point University, One University Parkway, High Point, NC 27268
| | - Meghan S. Blackledge
- Department of Chemistry, High Point University, One University Parkway, High Point, NC 27268
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Zheng M, Zheng M, Epstein S, Harnagel AP, Kim H, Lupoli TJ. Chemical Biology Tools for Modulating and Visualizing Gram-Negative Bacterial Surface Polysaccharides. ACS Chem Biol 2021; 16:1841-1865. [PMID: 34569792 DOI: 10.1021/acschembio.1c00341] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Bacterial cells present a wide diversity of saccharides that decorate the cell surface and help mediate interactions with the environment. Many Gram-negative cells express O-antigens, which are long sugar polymers that makeup the distal portion of lipopolysaccharide (LPS) that constitutes the surface of the outer membrane. This review highlights chemical biology tools that have been developed in recent years to facilitate the modulation of O-antigen synthesis and composition, as well as related bacterial polysaccharide pathways, and the detection of unique glycan sequences. Advances in the biochemistry and structural biology of O-antigen biosynthetic machinery are also described, which provide guidance for the design of novel chemical and biomolecular probes. Many of the tools noted here have not yet been utilized in biological systems and offer researchers the opportunity to investigate the complex sugar architecture of Gram-negative cells.
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Affiliation(s)
- Meng Zheng
- Department of Chemistry, New York University, New York, 10003 New York, United States
| | - Maggie Zheng
- Department of Chemistry, New York University, New York, 10003 New York, United States
| | - Samuel Epstein
- Department of Chemistry, New York University, New York, 10003 New York, United States
| | - Alexa P. Harnagel
- Department of Chemistry, New York University, New York, 10003 New York, United States
| | - Hanee Kim
- Department of Chemistry, New York University, New York, 10003 New York, United States
| | - Tania J. Lupoli
- Department of Chemistry, New York University, New York, 10003 New York, United States
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41
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Geddes EJ, Li Z, Hergenrother PJ. An LC-MS/MS assay and complementary web-based tool to quantify and predict compound accumulation in E. coli. Nat Protoc 2021; 16:4833-4854. [PMID: 34480129 PMCID: PMC8715754 DOI: 10.1038/s41596-021-00598-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 06/25/2021] [Indexed: 02/08/2023]
Abstract
Novel classes of broad-spectrum antibiotics have been extremely difficult to discover, largely due to the impermeability of the Gram-negative membranes coupled with a poor understanding of the physicochemical properties a compound should possess to promote its accumulation inside the cell. To address this challenge, numerous methodologies for assessing intracellular compound accumulation in Gram-negative bacteria have been established, including classic radiometric and fluorescence-based methods. The recent development of accumulation assays that utilize liquid chromatography-tandem mass spectrometry (LC-MS/MS) have circumvented the requirement for labeled compounds, enabling assessment of a substantially broader range of small molecules. Our unbiased study of accumulation trends in Escherichia coli using an LC-MS/MS-based assay led to the development of the eNTRy rules, which stipulate that a compound is most likely to accumulate in E. coli if it has an ionizable Nitrogen, has low Three-dimensionality and is relatively Rigid. To aid in the implementation of the eNTRy rules, we developed a complementary web tool, eNTRyway, which calculates relevant properties and predicts compound accumulation. Here we provide a comprehensive protocol for analysis and prediction of intracellular accumulation of small molecules in E. coli using an LC-MS/MS-based assay (which takes ~2 d) and eNTRyway, a workflow that is readily adoptable by any microbiology, biochemistry or chemical biology laboratory.
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Affiliation(s)
- Emily J Geddes
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
| | - Zhong Li
- Metabolomics Lab, Roy J. Carver Biotechnology Center, University of Illinois, Urbana, IL, USA
| | - Paul J Hergenrother
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA.
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42
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Kell DB. The Transporter-Mediated Cellular Uptake and Efflux of Pharmaceutical Drugs and Biotechnology Products: How and Why Phospholipid Bilayer Transport Is Negligible in Real Biomembranes. Molecules 2021; 26:5629. [PMID: 34577099 PMCID: PMC8470029 DOI: 10.3390/molecules26185629] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/03/2021] [Accepted: 09/14/2021] [Indexed: 12/12/2022] Open
Abstract
Over the years, my colleagues and I have come to realise that the likelihood of pharmaceutical drugs being able to diffuse through whatever unhindered phospholipid bilayer may exist in intact biological membranes in vivo is vanishingly low. This is because (i) most real biomembranes are mostly protein, not lipid, (ii) unlike purely lipid bilayers that can form transient aqueous channels, the high concentrations of proteins serve to stop such activity, (iii) natural evolution long ago selected against transport methods that just let any undesirable products enter a cell, (iv) transporters have now been identified for all kinds of molecules (even water) that were once thought not to require them, (v) many experiments show a massive variation in the uptake of drugs between different cells, tissues, and organisms, that cannot be explained if lipid bilayer transport is significant or if efflux were the only differentiator, and (vi) many experiments that manipulate the expression level of individual transporters as an independent variable demonstrate their role in drug and nutrient uptake (including in cytotoxicity or adverse drug reactions). This makes such transporters valuable both as a means of targeting drugs (not least anti-infectives) to selected cells or tissues and also as drug targets. The same considerations apply to the exploitation of substrate uptake and product efflux transporters in biotechnology. We are also beginning to recognise that transporters are more promiscuous, and antiporter activity is much more widespread, than had been realised, and that such processes are adaptive (i.e., were selected by natural evolution). The purpose of the present review is to summarise the above, and to rehearse and update readers on recent developments. These developments lead us to retain and indeed to strengthen our contention that for transmembrane pharmaceutical drug transport "phospholipid bilayer transport is negligible".
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Affiliation(s)
- Douglas B. Kell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown St, Liverpool L69 7ZB, UK;
- Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs Lyngby, Denmark
- Mellizyme Biotechnology Ltd., IC1, Liverpool Science Park, Mount Pleasant, Liverpool L3 5TF, UK
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Fihn CA, Carlson EE. Targeting a highly conserved domain in bacterial histidine kinases to generate inhibitors with broad spectrum activity. Curr Opin Microbiol 2021; 61:107-114. [PMID: 33932730 PMCID: PMC8189720 DOI: 10.1016/j.mib.2021.03.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/22/2021] [Accepted: 03/25/2021] [Indexed: 11/30/2022]
Abstract
With the rise in antimicrobial resistance and the dearth of effective strategies to combat this threat, the development of novel therapies is of utmost importance. Targeting of bacterial signaling through their the two-component systems (TCSs) may be a viable strategy. TCSs are comprised of a sensory histidine kinase (HK), of which a bacterium can have up to 160 distinct proteins, and a cognate response regulator (RR). The TCSs are generally non-essential for life, but control many virulence and antibiotic-resistance mechanisms. This, along with their absence in animals makes the TCSs an attractive target for antimicrobial therapy, whether as a stand-alone treatments or adjuvants for existing therapies. This review focuses on progress in the development of inhibitors that target the HK ATP-binding domain. Because this domain is highly conserved, it may be feasible to disrupt multiple TCSs within a single organism to increase effectiveness and reduce pressure for the evolution of resistance.
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Affiliation(s)
- Conrad A Fihn
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, MN 55454, United States
| | - Erin E Carlson
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, MN 55454, United States; Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455, United States; Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church St SE, Minneapolis, MN 55454, United States; Department of Pharmacology, University of Minnesota, 321 Church St SE, Minneapolis, MN 55454, United States.
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