1
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Desai J, Patel B, Panchal N, Gite A, Darji B, Viswanathan K, Trivedi J, Vyas P, Pawar V, Giri P, S S, Sharma R, Jain M, Iyer P, Kumar S. Discovery of aminopiperidine based potent & novel topoisomerase inhibitor with broad spectrum anti-bacterial activity. Bioorg Med Chem Lett 2024; 111:129911. [PMID: 39067715 DOI: 10.1016/j.bmcl.2024.129911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 07/13/2024] [Accepted: 07/24/2024] [Indexed: 07/30/2024]
Abstract
Bacterial DNA gyrase and topoisomerase IV inhibition has emerged as a promising strategy for the cure of infections caused by antibiotic-resistant bacteria. The Novel Bacterial Topoisomerase Inhibitors (NBTIs) bind to a different site from that of the quinolones with novel mechanism of action. This evades the existing target-mediated bacterial resistance associated with quinolones. This article presents our efforts to identify in vitro potent and broad-spectrum antibacterial agent 4l.
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Affiliation(s)
- Jigar Desai
- Zydus Research Centre, Sarkhej Bavla NH No 8A, Moraiya, Ahmedabad 382213, Gujarat, India.
| | - Bhaumin Patel
- Zydus Research Centre, Sarkhej Bavla NH No 8A, Moraiya, Ahmedabad 382213, Gujarat, India
| | - Nandini Panchal
- Zydus Research Centre, Sarkhej Bavla NH No 8A, Moraiya, Ahmedabad 382213, Gujarat, India
| | - Archana Gite
- Zydus Research Centre, Sarkhej Bavla NH No 8A, Moraiya, Ahmedabad 382213, Gujarat, India
| | - Brijesh Darji
- Zydus Research Centre, Sarkhej Bavla NH No 8A, Moraiya, Ahmedabad 382213, Gujarat, India
| | - Kasinath Viswanathan
- Zydus Research Centre, Sarkhej Bavla NH No 8A, Moraiya, Ahmedabad 382213, Gujarat, India
| | - Jinal Trivedi
- Zydus Research Centre, Sarkhej Bavla NH No 8A, Moraiya, Ahmedabad 382213, Gujarat, India
| | - Purvi Vyas
- Zydus Research Centre, Sarkhej Bavla NH No 8A, Moraiya, Ahmedabad 382213, Gujarat, India
| | - Vishwanath Pawar
- Zydus Research Centre, Sarkhej Bavla NH No 8A, Moraiya, Ahmedabad 382213, Gujarat, India
| | - Poonam Giri
- Zydus Research Centre, Sarkhej Bavla NH No 8A, Moraiya, Ahmedabad 382213, Gujarat, India
| | - Sachchidanand S
- Zydus Research Centre, Sarkhej Bavla NH No 8A, Moraiya, Ahmedabad 382213, Gujarat, India
| | - Rajiv Sharma
- Zydus Research Centre, Sarkhej Bavla NH No 8A, Moraiya, Ahmedabad 382213, Gujarat, India
| | - Mukul Jain
- Zydus Research Centre, Sarkhej Bavla NH No 8A, Moraiya, Ahmedabad 382213, Gujarat, India
| | - Pravin Iyer
- Zydus Research Centre, Sarkhej Bavla NH No 8A, Moraiya, Ahmedabad 382213, Gujarat, India
| | - Sanjay Kumar
- Zydus Research Centre, Sarkhej Bavla NH No 8A, Moraiya, Ahmedabad 382213, Gujarat, India
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2
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Powell J, Mann CA, Toth PD, Nolan S, Steinert A, Ove C, Seffernick JT, Wozniak DJ, Kebriaei R, Lindert S, Osheroff N, Yalowich JC, Mitton-Fry MJ. Development of Novel Bacterial Topoisomerase Inhibitors Assisted by Computational Screening. ACS Med Chem Lett 2024; 15:1287-1297. [PMID: 39140037 PMCID: PMC11318591 DOI: 10.1021/acsmedchemlett.4c00162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 06/16/2024] [Accepted: 06/20/2024] [Indexed: 08/15/2024] Open
Abstract
Multidrug-resistant bacterial infections pose an ever-evolving threat to public health. Since the outset of the antibacterial age, bacteria have developed a multitude of diverse resistance mechanisms that suppress the effectiveness of current therapies. New drug entities, such as Novel Bacterial Topoisomerase Inhibitors (NBTIs), can circumvent this major issue. A computational docking model was employed to predict the binding to DNA gyrase of atypical NBTIs with novel pharmacophores. Synthesis of NBTIs based on computational docking and subsequent antibacterial evaluation against both Gram-positive and Gram-negative bacteria yielded congeners with outstanding anti-staphylococcal activity and varying activity against select Gram-negative pathogens.
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Affiliation(s)
- Joshua
W. Powell
- Division
of Medicinal Chemistry and Pharmacognosy, Department of Chemistry and Biochemistry, Microbial Infection
and Immunity, Division of Outcomes and Translational Sciences, Department of Microbiology, and Division of Pharmaceutics
and Pharmacology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Chelsea A. Mann
- Division
of Medicinal Chemistry and Pharmacognosy, Department of Chemistry and Biochemistry, Microbial Infection
and Immunity, Division of Outcomes and Translational Sciences, Department of Microbiology, and Division of Pharmaceutics
and Pharmacology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Paul D. Toth
- Division
of Medicinal Chemistry and Pharmacognosy, Department of Chemistry and Biochemistry, Microbial Infection
and Immunity, Division of Outcomes and Translational Sciences, Department of Microbiology, and Division of Pharmaceutics
and Pharmacology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Sheri Nolan
- Division
of Medicinal Chemistry and Pharmacognosy, Department of Chemistry and Biochemistry, Microbial Infection
and Immunity, Division of Outcomes and Translational Sciences, Department of Microbiology, and Division of Pharmaceutics
and Pharmacology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Anja Steinert
- Division
of Medicinal Chemistry and Pharmacognosy, Department of Chemistry and Biochemistry, Microbial Infection
and Immunity, Division of Outcomes and Translational Sciences, Department of Microbiology, and Division of Pharmaceutics
and Pharmacology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Clarissa Ove
- Division
of Medicinal Chemistry and Pharmacognosy, Department of Chemistry and Biochemistry, Microbial Infection
and Immunity, Division of Outcomes and Translational Sciences, Department of Microbiology, and Division of Pharmaceutics
and Pharmacology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Justin T. Seffernick
- Division
of Medicinal Chemistry and Pharmacognosy, Department of Chemistry and Biochemistry, Microbial Infection
and Immunity, Division of Outcomes and Translational Sciences, Department of Microbiology, and Division of Pharmaceutics
and Pharmacology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Daniel J. Wozniak
- Division
of Medicinal Chemistry and Pharmacognosy, Department of Chemistry and Biochemistry, Microbial Infection
and Immunity, Division of Outcomes and Translational Sciences, Department of Microbiology, and Division of Pharmaceutics
and Pharmacology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Razieh Kebriaei
- Division
of Medicinal Chemistry and Pharmacognosy, Department of Chemistry and Biochemistry, Microbial Infection
and Immunity, Division of Outcomes and Translational Sciences, Department of Microbiology, and Division of Pharmaceutics
and Pharmacology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Steffen Lindert
- Division
of Medicinal Chemistry and Pharmacognosy, Department of Chemistry and Biochemistry, Microbial Infection
and Immunity, Division of Outcomes and Translational Sciences, Department of Microbiology, and Division of Pharmaceutics
and Pharmacology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Neil Osheroff
- Department of Biochemistry and Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
| | - Jack C. Yalowich
- Division
of Medicinal Chemistry and Pharmacognosy, Department of Chemistry and Biochemistry, Microbial Infection
and Immunity, Division of Outcomes and Translational Sciences, Department of Microbiology, and Division of Pharmaceutics
and Pharmacology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Mark J. Mitton-Fry
- Division
of Medicinal Chemistry and Pharmacognosy, Department of Chemistry and Biochemistry, Microbial Infection
and Immunity, Division of Outcomes and Translational Sciences, Department of Microbiology, and Division of Pharmaceutics
and Pharmacology, The Ohio State University, Columbus, Ohio 43210, United States
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3
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Kherroubi L, Bacon J, Rahman KM. Navigating fluoroquinolone resistance in Gram-negative bacteria: a comprehensive evaluation. JAC Antimicrob Resist 2024; 6:dlae127. [PMID: 39144447 PMCID: PMC11323783 DOI: 10.1093/jacamr/dlae127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 07/04/2024] [Indexed: 08/16/2024] Open
Abstract
Since the introduction of quinolone and fluoroquinolone antibiotics to treat bacterial infections in the 1960s, there has been a pronounced increase in the number of bacterial species that have developed resistance to fluoroquinolone treatment. In 2017, the World Health Organization established a priority list of the most critical Gram-negative resistant pathogens. These included Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Escherichia coli. In the last three decades, investigations into the mechanisms of fluoroquinolone resistance have revealed that mutations in the target enzymes of fluoroquinolones, DNA gyrase or topoisomerase IV, are the most prevalent mechanism conferring high levels of resistance. Alterations to porins and efflux pumps that facilitate fluoroquinolone permeation and extrusion across the bacterial cell membrane also contribute to the development of resistance. However, there is a growing observation of novel mutants with newer generations of fluoroquinolones, highlighting the need for novel treatments. Currently, steady progress has been made in the development of novel antimicrobial agents that target DNA gyrase or topoisomerase IV through different avenues than current fluoroquinolones to prevent target-mediated resistance. Therefore, an updated review of the current understanding of fluoroquinolone resistance within the literature is imperative to aid in future investigations.
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Affiliation(s)
- Linda Kherroubi
- School of Cancer and Pharmaceutical Science, King’s College London, London SE1 9NH, UK
| | - Joanna Bacon
- Discovery Group, Vaccine Development and Evaluation Centre, UK Health Security Agency, Porton Down, Salisbury SP4 0JG, UK
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4
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Bakker AT, Kotsogianni I, Avalos M, Punt JM, Liu B, Piermarini D, Gagestein B, Slingerland CJ, Zhang L, Willemse JJ, Ghimire LB, van den Berg RJHBN, Janssen APA, Ottenhoff THM, van Boeckel CAA, van Wezel GP, Ghilarov D, Martin NI, van der Stelt M. Discovery of isoquinoline sulfonamides as allosteric gyrase inhibitors with activity against fluoroquinolone-resistant bacteria. Nat Chem 2024:10.1038/s41557-024-01516-x. [PMID: 38898213 DOI: 10.1038/s41557-024-01516-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 03/22/2024] [Indexed: 06/21/2024]
Abstract
Bacteria have evolved resistance to nearly all known antibacterials, emphasizing the need to identify antibiotics that operate via novel mechanisms. Here we report a class of allosteric inhibitors of DNA gyrase with antibacterial activity against fluoroquinolone-resistant clinical isolates of Escherichia coli. Screening of a small-molecule library revealed an initial isoquinoline sulfonamide hit, which was optimized via medicinal chemistry efforts to afford the more potent antibacterial LEI-800. Target identification studies, including whole-genome sequencing of in vitro selected mutants with resistance to isoquinoline sulfonamides, unanimously pointed to the DNA gyrase complex, an essential bacterial topoisomerase and an established antibacterial target. Using single-particle cryogenic electron microscopy, we determined the structure of the gyrase-LEI-800-DNA complex. The compound occupies an allosteric, hydrophobic pocket in the GyrA subunit and has a mode of action that is distinct from the clinically used fluoroquinolones or any other gyrase inhibitor reported to date. LEI-800 provides a chemotype suitable for development to counter the increasingly widespread bacterial resistance to fluoroquinolones.
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Affiliation(s)
- Alexander T Bakker
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Ioli Kotsogianni
- Biological Chemistry Group, Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Mariana Avalos
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Jeroen M Punt
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Bing Liu
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Diana Piermarini
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Berend Gagestein
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Cornelis J Slingerland
- Biological Chemistry Group, Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Le Zhang
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Joost J Willemse
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Leela B Ghimire
- Department of Molecular Microbiology, John Innes Centre, Norwich, UK
| | | | - Antonius P A Janssen
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Tom H M Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands
| | - Constant A A van Boeckel
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Gilles P van Wezel
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Dmitry Ghilarov
- Department of Molecular Microbiology, John Innes Centre, Norwich, UK.
| | - Nathaniel I Martin
- Biological Chemistry Group, Institute of Biology, Leiden University, Leiden, the Netherlands.
| | - Mario van der Stelt
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands.
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5
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Dobričić V, Marodi M, Marković B, Tomašič T, Durcik M, Zidar N, Mašič LP, Ilaš J, Kikelj D, Čudina O. Estimation of passive gastrointestinal absorption of new dual DNA gyrase and topoisomerase IV inhibitors using PAMPA and biopartitioning micellar chromatography and quantitative structure-retention relationship analysis. J Chromatogr B Analyt Technol Biomed Life Sci 2024; 1240:124158. [PMID: 38776787 DOI: 10.1016/j.jchromb.2024.124158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 04/09/2024] [Accepted: 05/16/2024] [Indexed: 05/25/2024]
Abstract
DNA gyrase and topoisomerase IV play significant role in maintaining the correct structure of DNA during replication and they have been identified as validated targets in antibacterial drug discovery. Inadequate pharmacokinetic properties are responsible for many failures during drug discovery and their estimation in the early phase of this process maximizes the chance of getting useful drug candidates. Passive gastrointestinal absorption of a selected group of thirteen dual DNA gyrase and topoisomerase IV inhibitors was estimated using two in vitro tests - parallel artificial membrane permeability assay (PAMPA) and biopartitioning micellar chromatography (BMC). Due to good correlation between obtained results, passive gastrointestinal absorption of remaining ten compounds was estimated using only BMC. With this experimental setup, it was possible to identify compounds with high values of retention factors (k) and highest expected passive gastrointestinal absorption, and compounds with low values of k for which low passive gastrointestinal absorption is predicted. Quantitative structure-retention relationship (QSRR) modelling was performed by creating multiple linear regression (MLR), partial least squares (PLS) and support vector machines (SVM) models. Descriptors with the highest influence on retention factor were identified and their interpretation can be used for the design of new compounds with improved passive gastrointestinal absorption.
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Affiliation(s)
- Vladimir Dobričić
- Department of Pharmaceutical Chemistry, University of Belgrade - Faculty of Pharmacy, Vojvode Stepe 450, 11000 Belgrade, Serbia.
| | - Marko Marodi
- Department of Pharmaceutical Chemistry, University of Belgrade - Faculty of Pharmacy, Vojvode Stepe 450, 11000 Belgrade, Serbia
| | - Bojan Marković
- Department of Pharmaceutical Chemistry, University of Belgrade - Faculty of Pharmacy, Vojvode Stepe 450, 11000 Belgrade, Serbia
| | - Tihomir Tomašič
- University of Ljubljana, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Martina Durcik
- University of Ljubljana, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Nace Zidar
- University of Ljubljana, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Lucija Peterlin Mašič
- University of Ljubljana, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Janez Ilaš
- University of Ljubljana, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Danijel Kikelj
- University of Ljubljana, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Olivera Čudina
- Department of Pharmaceutical Chemistry, University of Belgrade - Faculty of Pharmacy, Vojvode Stepe 450, 11000 Belgrade, Serbia
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6
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Kokot M, Minovski N. Dynamic Profiling and Binding Affinity Prediction of NBTI Antibacterials against DNA Gyrase Enzyme by Multidimensional Machine Learning and Molecular Dynamics Simulations. ACS OMEGA 2024; 9:18278-18295. [PMID: 38680300 PMCID: PMC11044241 DOI: 10.1021/acsomega.4c00036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 03/25/2024] [Accepted: 03/29/2024] [Indexed: 05/01/2024]
Abstract
Bacterial type II topoisomerases are well-characterized and clinically important targets for antibacterial chemotherapy. Novel bacterial topoisomerase inhibitors (NBTIs) are a newly disclosed class of antibacterials. Prediction of their binding affinity to these enzymes would be beneficial for de novo design/optimization of new NBTIs. Utilizing in vitro NBTI experimental data, we constructed two comprehensive multidimensional DNA gyrase surrogate models for Staphylococcus aureus (q2 = 0.791) and Escherichia coli (q2 = 0.806). Both models accurately predicted the IC50s of 26 NBTIs from our recent studies. To investigate the NBTI's dynamic profile and binding to both targets, 10 selected NBTIs underwent molecular dynamics (MD) simulations. The analysis of MD production trajectories confirmed key hydrogen-bonding and hydrophobic contacts that NBTIs establish in both enzymes. Moreover, the binding free energies of selected NBTIs were computed by the linear interaction energy (LIE) method employing an in-house derived set of fitting parameters (α = 0.16, β = 0.029, γ = 0.0, and intercept = -1.72), which are successfully applicable to DNA gyrase of Gram-positive/Gram-negative pathogens. Both methods offer accurate predictions of the binding free energies of NBTIs against S. aureus and E. coli DNA gyrase. We are confident that this integrated modeling approach could be valuable in the de novo design and optimization of efficient NBTIs for combating resistant bacterial pathogens.
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Affiliation(s)
- Maja Kokot
- Laboratory
for Cheminformatics, Theory Department, National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia
- The
Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Nikola Minovski
- Laboratory
for Cheminformatics, Theory Department, National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia
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7
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Collins J, Osheroff N. Gyrase and Topoisomerase IV: Recycling Old Targets for New Antibacterials to Combat Fluoroquinolone Resistance. ACS Infect Dis 2024; 10:1097-1115. [PMID: 38564341 PMCID: PMC11019561 DOI: 10.1021/acsinfecdis.4c00128] [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: 02/16/2024] [Revised: 03/14/2024] [Accepted: 03/18/2024] [Indexed: 04/04/2024]
Abstract
Beyond their requisite functions in many critical DNA processes, the bacterial type II topoisomerases, gyrase and topoisomerase IV, are the targets of fluoroquinolone antibacterials. These drugs act by stabilizing gyrase/topoisomerase IV-generated DNA strand breaks and by robbing the cell of the catalytic activities of these essential enzymes. Since their clinical approval in the mid-1980s, fluoroquinolones have been used to treat a broad spectrum of infectious diseases and are listed among the five "highest priority" critically important antimicrobial classes by the World Health Organization. Unfortunately, the widespread use of fluoroquinolones has been accompanied by a rise in target-mediated resistance caused by specific mutations in gyrase and topoisomerase IV, which has curtailed the medical efficacy of this drug class. As a result, efforts are underway to identify novel antibacterials that target the bacterial type II topoisomerases. Several new classes of gyrase/topoisomerase IV-targeted antibacterials have emerged, including novel bacterial topoisomerase inhibitors, Mycobacterium tuberculosis gyrase inhibitors, triazaacenaphthylenes, spiropyrimidinetriones, and thiophenes. Phase III clinical trials that utilized two members of these classes, gepotidacin (triazaacenaphthylene) and zoliflodacin (spiropyrimidinetrione), have been completed with positive outcomes, underscoring the potential of these compounds to become the first new classes of antibacterials introduced into the clinic in decades. Because gyrase and topoisomerase IV are validated targets for established and emerging antibacterials, this review will describe the catalytic mechanism and cellular activities of the bacterial type II topoisomerases, their interactions with fluoroquinolones, the mechanism of target-mediated fluoroquinolone resistance, and the actions of novel antibacterials against wild-type and fluoroquinolone-resistant gyrase and topoisomerase IV.
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Affiliation(s)
- Jessica
A. Collins
- Department
of Biochemistry, Vanderbilt University School
of Medicine, Nashville, Tennessee 37232, United States
| | - Neil Osheroff
- Department
of Biochemistry, Vanderbilt University School
of Medicine, Nashville, Tennessee 37232, United States
- Department
of Medicine (Hematology/Oncology), Vanderbilt
University School of Medicine, Nashville, Tennessee 37232, United States
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8
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Yang H, Yao Z, Yang K, Wang C, Li M, Zhang Y, Yan J, Lv R, Wang Y, Huang A, Zhang D, Li W, Wu Y, Miao Z. Synthesis and antibacterial evaluation of novel psoralen derivatives against methicillin-resistant Staphylococcus aureus (MRSA). Chem Biodivers 2024:e202302048. [PMID: 38263380 DOI: 10.1002/cbdv.202302048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/21/2024] [Accepted: 01/23/2024] [Indexed: 01/25/2024]
Abstract
Today, the bacterial infections caused by multidrug-resistant pathogens seriously threaten human health. Thereby, there is an urgent need to discover antibacterial drugs with novel mechanism. Here, novel psoralen derivatives had been designed and synthesized by a scaffold hopping strategy. Among these targeted twenty-five compounds, compound ZM631 showed the best antibacterial activity against methicillin-resistant S. aureus (MRSA) with the low MIC of 1 μg/mL which is 2-fold more active than that of the positive drug gepotidacin. Molecular docking study revealed that compound ZM631 fitted well in the active pockets of bacterial S. aureus DNA gyrase and formed a key hydrogen bond binding with the residue ASP-1083. These findings demonstrated that the psoralen scaffold could serve as an antibacterial lead compound for further drug development against multidrug-resistant bacterial infections.
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Affiliation(s)
- Hang Yang
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, 100 Haiquan Road, Shanghai, 201418, the People's Republic of China
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai, 200433, the People's Republic of China
| | - Zheng Yao
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, 100 Haiquan Road, Shanghai, 201418, the People's Republic of China
| | - Keli Yang
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, 100 Haiquan Road, Shanghai, 201418, the People's Republic of China
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai, 200433, the People's Republic of China
| | - Chuanhao Wang
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei Road, Nanjing, 210094, the People's Republic of China
- School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, the People's Republic of China
| | - Mochenxuan Li
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai, 200433, the People's Republic of China
- School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, the People's Republic of China
| | - Yanming Zhang
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai, 200433, the People's Republic of China
| | - Jianyu Yan
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai, 200433, the People's Republic of China
| | - Rongxue Lv
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, 100 Haiquan Road, Shanghai, 201418, the People's Republic of China
| | - Yongchuang Wang
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, 100 Haiquan Road, Shanghai, 201418, the People's Republic of China
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai, 200433, the People's Republic of China
| | - Anhua Huang
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, 100 Haiquan Road, Shanghai, 201418, the People's Republic of China
| | - Daozuan Zhang
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, 100 Haiquan Road, Shanghai, 201418, the People's Republic of China
| | - Wei Li
- School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, the People's Republic of China
| | - Yuelin Wu
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, 100 Haiquan Road, Shanghai, 201418, the People's Republic of China
| | - Zhenyuan Miao
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai, 200433, the People's Republic of China
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9
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Durcik M, Cruz CD, Scorciapino MA, Ilaš J, Tammela P, Ceccarelli M, Mašič LP, Tomašič T. Benzothiazole DNA gyrase inhibitors and their conjugates with siderophore mimics: design, synthesis and evaluation. RSC Adv 2024; 14:2905-2917. [PMID: 38239435 PMCID: PMC10794952 DOI: 10.1039/d3ra08337c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 01/11/2024] [Indexed: 01/22/2024] Open
Abstract
Benzothiazole-based bacterial DNA gyrase and topoisomerase IV inhibitors are promising new antibacterial agents with potent activity against Gram-positive and Gram-negative bacterial strains. The aim of this study was to improve the uptake of these inhibitors into the cytoplasm of Gram-negative bacteria by conjugating them to the small siderophore mimics. The best conjugate 18b displayed potent Escherichia coli DNA gyrase and topoisomerase IV inhibition. The interaction analysis of molecular dynamics simulation trajectory showed the important contribution of the siderophore mimic moiety to binding affinity. By NMR spectroscopy, we demonstrated that the hydroxypyridinone moiety alone was responsible for the chelation of iron(iii). Moreover, 18b showed an enhancement of antibacterial activity against E. coli JW5503 in an iron-depleted medium, clearly indicating an increased uptake of 18b in this bacterial strain.
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Affiliation(s)
- Martina Durcik
- University of Ljubljana, Faculty of Pharmacy Aškerčeva cesta 7 1000 Ljubljana Slovenia
| | - Cristina D Cruz
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki P. O. Box 56 (Viikinkaari 5 E) FI-00014 Helsinki Finland
| | - Mariano Andrea Scorciapino
- Department of Chemical and Geological Sciences, University of Cagliari, Cittadella Universitaria di Monserrato - S. P. 8 km 0.700 09042 - Monserrato (CA) Italy
| | - Janez Ilaš
- University of Ljubljana, Faculty of Pharmacy Aškerčeva cesta 7 1000 Ljubljana Slovenia
| | - Päivi Tammela
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki P. O. Box 56 (Viikinkaari 5 E) FI-00014 Helsinki Finland
| | - Matteo Ceccarelli
- Department of Physics and IOM/CNR, Sezione di Cagliari, University of Cagliari, Cittadella Universitaria di Monserrato - S. P. 8 km 0700 09042 - Monserrato (CA) Italy
| | - Lucija Peterlin Mašič
- University of Ljubljana, Faculty of Pharmacy Aškerčeva cesta 7 1000 Ljubljana Slovenia
| | - Tihomir Tomašič
- University of Ljubljana, Faculty of Pharmacy Aškerčeva cesta 7 1000 Ljubljana Slovenia
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10
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Zorman M, Hrast Rambaher M, Kokot M, Minovski N, Anderluh M. The overview of development of novel bacterial topoisomerase inhibitors effective against multidrug-resistant bacteria in an academic environment: From early hits to in vivo active antibacterials. Eur J Pharm Sci 2024; 192:106632. [PMID: 37949194 DOI: 10.1016/j.ejps.2023.106632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 09/29/2023] [Accepted: 11/06/2023] [Indexed: 11/12/2023]
Abstract
Antimicrobial resistance caused by the excessive and inappropriate use of antibacterial drugs is a global health concern. Currently, we are walking a fine line between the fact that most bacterial infections can still be cured with the antibiotics known so far, and the emergence of infections with bacteria resistant to several drugs at the same time, against which we no longer have an effective drug. Therefore, new antibacterial drugs are urgently needed to curb the hard-to-treat infections. Our group has developed new antibacterials from the class of novel bacterial topoisomerase inhibitors (NBTIs) that exhibit broad-spectrum antibacterial activity. This article reviews our efforts in developing highly potent NBTIs over the past decade. Following the discovery of an initial hit with potent enzyme inhibitory and broad-spectrum antibacterial activity, an extensive hit-to-lead campaign was conducted with the goal of optimizing physicochemical properties, reducing hERG inhibition, and maintaining antibacterial activity against both Gram-positive and Gram-negative bacteria, with a focus on methicillin-resistant Staphylococcus aureus (MRSA). This optimization strategy resulted in an amide-containing, focused NBTI library with compounds exhibiting potent antibacterial activity against Gram-positive bacteria, reduced hERG inhibition, no cardiotoxicity in in vivo zebrafish model, and favorable in vivo efficacy in a neutropenic murine thigh infection model for MRSA infections.
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Affiliation(s)
- Maša Zorman
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, Ljubljana 1000, Slovenia; Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, Hajdrihova 19, Ljubljana 1001, Slovenia
| | - Martina Hrast Rambaher
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, Ljubljana 1000, Slovenia
| | - Maja Kokot
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, Ljubljana 1000, Slovenia; Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, Hajdrihova 19, Ljubljana 1001, Slovenia
| | - Nikola Minovski
- Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, Hajdrihova 19, Ljubljana 1001, Slovenia.
| | - Marko Anderluh
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, Ljubljana 1000, Slovenia.
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11
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Mann CA, Carvajal Moreno JJ, Lu Y, Dellos-Nolan S, Wozniak DJ, Yalowich JC, Mitton-Fry MJ. Novel bacterial topoisomerase inhibitors: unique targeting activities of amide enzyme-binding motifs for tricyclic analogs. Antimicrob Agents Chemother 2023; 67:e0048223. [PMID: 37724886 PMCID: PMC10583662 DOI: 10.1128/aac.00482-23] [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: 04/13/2023] [Accepted: 07/14/2023] [Indexed: 09/21/2023] Open
Abstract
Antimicrobial resistance has made a sizeable impact on public health and continues to threaten the effectiveness of antibacterial therapies. Novel bacterial topoisomerase inhibitors (NBTIs) are a promising class of antibacterial agents with a unique binding mode and distinct pharmacology that enables them to evade existing resistance mechanisms. The clinical development of NBTIs has been plagued by several issues, including cardiovascular safety. Herein, we report a sub-series of tricyclic NBTIs bearing an amide linkage that displays promising antibacterial activity, potent dual-target inhibition of DNA gyrase and topoisomerase IV (TopoIV), as well as improved cardiovascular safety and metabolic profiles. These amide NBTIs induced both single- and double-strand breaks in pBR322 DNA mediated by Staphylococcus aureus DNA gyrase, in contrast to prototypical NBTIs that cause only single-strand breaks. Unexpectedly, amides 1a and 1b targeted human topoisomerase IIα (TOP2α) causing both single- and double-strand breaks in pBR322 DNA, and induced DNA strand breaks in intact human leukemia K562 cells. In addition, anticancer drug-resistant K/VP.5 cells containing decreased levels of TOP2α were cross-resistant to amides 1a and 1b. Together, these results demonstrate broad spectrum antibacterial properties of selected tricyclic NBTIs, desirable safety profiles, an unusual ability to induce DNA double-stranded breaks, and activity against human TOP2α. Future work will be directed toward optimization and development of tricyclic NBTIs with potent and selective activity against bacteria. Finally, the current results may provide an additional avenue for development of selective anticancer agents.
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Affiliation(s)
- Chelsea A. Mann
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio, USA
| | - Jessika J. Carvajal Moreno
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio, USA
| | - Yanran Lu
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio, USA
| | - Sheri Dellos-Nolan
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Daniel J. Wozniak
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Jack C. Yalowich
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio, USA
| | - Mark J. Mitton-Fry
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio, USA
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12
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Dias M, Chapagain T, Leng F. A Fluorescence-Based, T5 Exonuclease-Amplified DNA Cleavage Assay for Discovering Bacterial DNA Gyrase Poisons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.16.562555. [PMID: 37904923 PMCID: PMC10614890 DOI: 10.1101/2023.10.16.562555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
Fluoroquinolones (FQs) are potent antibiotics of clinical significance, known for their unique mechanism of action as gyrase poisons, which stabilize gyrase-DNA cleavage complexes and convert gyrase into a DNA-damaging machinery. Unfortunately, FQ resistance has emerged, and these antibiotics can cause severe side effects. Therefore, discovering novel gyrase poisons with different chemical scaffolds is essential. The challenge lies in efficiently identifying them from compound libraries containing thousands or millions of drug-like compounds, as high-throughput screening (HTS) assays are currently unavailable. Here we report a novel fluorescence-based, T5 exonuclease-amplified DNA cleavage assay for gyrase poison discovery. This assay capitalizes on recent findings showing that multiple gyrase molecules can simultaneously bind to a plasmid DNA molecule, forming multiple gyrase-DNA cleavage complexes on the same plasmid. These gyrase-DNA cleavage complexes, stabilized by a gyrase poison, can be captured using sarkosyl. Proteinase K digestion results in producing small DNA fragments. T5 exonuclease, selectively digesting linear and nicked DNA, can fully digest the fragmented linear DNA molecules and, thus, "amplify" the decrease in fluorescence signal of the DNA cleavage products after SYBR Green staining. This fluorescence-based, T5 exonuclease-amplified DNA cleavage HTS assay is validated using a 50-compound library, making it suitable for screening large compound libraries.
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13
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Phelps HA, Kuhn M, Lu Y, Vibhute S, Watts JL, Mitton-Fry MJ. Antibacterial activity of novel bacterial topoisomerase inhibitors against key veterinary pathogens. Vet Microbiol 2023; 284:109840. [PMID: 37531840 DOI: 10.1016/j.vetmic.2023.109840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 07/07/2023] [Accepted: 07/28/2023] [Indexed: 08/04/2023]
Abstract
Multidrug-resistant bacteria infect companion animals and livestock in addition to their devastating impact on human health. Novel Bacterial Topoisomerase Inhibitors (NBTIs) with excellent activity against Gram-positive bacteria have previously been identified as promising new antibacterial agents. Herein, we evaluate the antibacterial activity of these NBTIs against a variety of important veterinary pathogens and demonstrate outstanding in vitro activity, especially against staphylococci.
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Affiliation(s)
- Hilary A Phelps
- Global Therapeutics, Anti-Infectives Research, Zoetis, 333 Portage Street, Kalamazoo, MI 49007, United States
| | - Michael Kuhn
- Global Therapeutics, Anti-Infectives Research, Zoetis, 333 Portage Street, Kalamazoo, MI 49007, United States
| | - Yanran Lu
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, 500 West 12th Avenue, Columbus, OH 43210, United States
| | - Sandip Vibhute
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, 500 West 12th Avenue, Columbus, OH 43210, United States
| | - Jeffrey L Watts
- Global Therapeutics, Anti-Infectives Research, Zoetis, 333 Portage Street, Kalamazoo, MI 49007, United States
| | - Mark J Mitton-Fry
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, 500 West 12th Avenue, Columbus, OH 43210, United States.
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14
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Cumming JG, Kreis L, Kühne H, Wermuth R, Vercruysse M, Kramer C, Rudolph MG, Xu Z. Discovery of a Series of Indane-Containing NBTIs with Activity against Multidrug-Resistant Gram-Negative Pathogens. ACS Med Chem Lett 2023; 14:993-998. [PMID: 37465290 PMCID: PMC10350941 DOI: 10.1021/acsmedchemlett.3c00187] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 06/20/2023] [Indexed: 07/20/2023] Open
Abstract
The rise of multidrug-resistant (MDR) Gram-negative bacteria is a major global health problem necessitating the discovery of new classes of antibiotics. Novel bacterial topoisomerase inhibitors (NBTIs) target the clinically validated bacterial type II topoisomerases with a distinct binding site and mechanism of action to fluoroquinolone antibiotics, thus avoiding cross-resistance to this drug class. Here we report the discovery of a series of NBTIs incorporating a novel indane DNA binding moiety. X-ray cocrystal structures of compounds 2 and 17a bound to Staphylococcus aureus DNA gyrase-DNA were determined, revealing specific interactions with the enzyme binding pocket at the GyrA dimer interface and a long-range electrostatic interaction between the basic amine in the linker and the carboxylate of Asp83. Exploration of the structure-activity relationship within the series led to the identification of lead compound 18c, which showed potent broad-spectrum activity against a panel of MDR Gram-negative bacteria.
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Affiliation(s)
- John G. Cumming
- Roche
Pharma Research & Early Development, F. Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland
| | - Lukas Kreis
- Roche
Pharma Research & Early Development, F. Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland
| | - Holger Kühne
- Roche
Pharma Research & Early Development, F. Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland
| | - Roger Wermuth
- Roche
Pharma Research & Early Development, F. Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland
| | - Maarten Vercruysse
- Roche
Pharma Research & Early Development, F. Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland
| | - Christian Kramer
- Roche
Pharma Research & Early Development, F. Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland
| | - Markus G. Rudolph
- Roche
Pharma Research & Early Development, F. Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland
| | - Zhiheng Xu
- China
Innovation Center of Roche, Roche R&D
Center (China) Ltd., Shanghai 201203, China
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15
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Whelan AO, Cooper I, Ooi N, Orr D, Blades K, Kirkham J, Lyons A, Barnes KB, Richards MI, Salisbury AM, Craighead M, Harding SV. In Vitro Activity of Novel Topoisomerase Inhibitors against Francisella tularensis and Burkholderia pseudomallei. Antibiotics (Basel) 2023; 12:983. [PMID: 37370302 DOI: 10.3390/antibiotics12060983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/03/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
Antimicrobial resistance is a global issue, and the investigation of alternative therapies that are not traditional antibiotics are warranted. Novel bacterial type II topoisomerase inhibitors (NBTIs) have recently emerged as a novel class of antibiotics with reduced potential for cross-resistance to fluoroquinolones due to their novel mechanism of action. This study investigated the in vitro activity of a series of cyclohexyl-oxazolidinone bacterial topoisomerase inhibitors against type strains of Francisella tularensis and Burkholderia pseudomallei. Broth microdilution, time-kill, and cell infection assays were performed to determine activity against these biothreat pathogens. Two candidates were identified that demonstrated in vitro activity in multiple assays that in some instances was equivalent to ciprofloxacin and doxycycline. These data warrant the further evaluation of these novel NBTIs and future iterations in vitro and in vivo.
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Affiliation(s)
- Adam O Whelan
- Defence Science and Technology Laboratory, Porton Down, Salisbury SP4 0JQ, UK
| | - Ian Cooper
- Infex Therapeutics Ltd., Mereside, Alderley Park, Macclesfield SK10 4TG, UK
| | - Nicola Ooi
- Infex Therapeutics Ltd., Mereside, Alderley Park, Macclesfield SK10 4TG, UK
| | - David Orr
- Infex Therapeutics Ltd., Mereside, Alderley Park, Macclesfield SK10 4TG, UK
| | - Kevin Blades
- Infex Therapeutics Ltd., Mereside, Alderley Park, Macclesfield SK10 4TG, UK
| | - James Kirkham
- Infex Therapeutics Ltd., Mereside, Alderley Park, Macclesfield SK10 4TG, UK
| | - Amanda Lyons
- Redx Anti-Infectives Ltd., Alderley Park, Macclesfield SK10 4TG, UK
| | - Kay B Barnes
- Defence Science and Technology Laboratory, Porton Down, Salisbury SP4 0JQ, UK
| | - Mark I Richards
- Defence Science and Technology Laboratory, Porton Down, Salisbury SP4 0JQ, UK
| | | | - Mark Craighead
- Redx Anti-Infectives Ltd., Alderley Park, Macclesfield SK10 4TG, UK
| | - Sarah V Harding
- Defence Science and Technology Laboratory, Porton Down, Salisbury SP4 0JQ, UK
- School of Respiratory Sciences, University of Leicester, Leicester LE1 7RH, UK
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16
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Kokot M, Weiss M, Zdovc I, Senerovic L, Radakovic N, Anderluh M, Minovski N, Hrast M. Amide containing NBTI antibacterials with reduced hERG inhibition, retained antimicrobial activity against gram-positive bacteria and in vivo efficacy. Eur J Med Chem 2023; 250:115160. [PMID: 36753879 DOI: 10.1016/j.ejmech.2023.115160] [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: 11/07/2022] [Revised: 01/23/2023] [Accepted: 01/24/2023] [Indexed: 02/05/2023]
Abstract
Novel bacterial topoisomerase inhibitors (NBTIs) are new promising antimicrobials for the treatment of multidrug-resistant bacterial infections. In recent years, many new NBTIs have been discovered, however most of them struggle with the same issue - the balance between antibacterial activity and hERG-related toxicity. We started a new campaign by optimizing the previous series of NBTIs, followed by the design and synthesis of a new, amide-containing focused NBTI library to reduce hERG inhibition and maintain antibacterial activity against Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus (MRSA). This optimization strategy yielded the lead compound 12 that exhibits potent antibacterial activity against Gram-positive bacteria, reduced hERG inhibition, no cardiotoxicity in zebrafish model, and a favorable in vivo efficacy in a neutropenic murine thigh infection model of MRSA infection.
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Affiliation(s)
- Maja Kokot
- Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, 1000, Ljubljana, Slovenia
| | - Matjaž Weiss
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, 1000, Ljubljana, Slovenia
| | - Irena Zdovc
- Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1000, Ljubljana, Slovenia
| | - Lidija Senerovic
- Laboratory for Microbial Molecular Genetics and Ecology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11 042, Belgrade, Serbia
| | - Natasa Radakovic
- Laboratory for Microbial Molecular Genetics and Ecology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11 042, Belgrade, Serbia
| | - Marko Anderluh
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, 1000, Ljubljana, Slovenia
| | - Nikola Minovski
- Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia.
| | - Martina Hrast
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, 1000, Ljubljana, Slovenia.
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17
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Grossman S, Fishwick CWG, McPhillie MJ. Developments in Non-Intercalating Bacterial Topoisomerase Inhibitors: Allosteric and ATPase Inhibitors of DNA Gyrase and Topoisomerase IV. Pharmaceuticals (Basel) 2023; 16:261. [PMID: 37259406 PMCID: PMC9964621 DOI: 10.3390/ph16020261] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 10/15/2023] Open
Abstract
Increases in antibiotic usage and antimicrobial resistance occurrence have caused a dramatic reduction in the effectiveness of many frontline antimicrobial treatments. Topoisomerase inhibitors including fluoroquinolones are broad-spectrum antibiotics used to treat a range of infections, which stabilise a topoisomerase-DNA cleavage complex via intercalation of the bound DNA. However, these are subject to bacterial resistance, predominantly in the form of single-nucleotide polymorphisms in the active site. Significant research has been undertaken searching for novel bioactive molecules capable of inhibiting bacterial topoisomerases at sites distal to the fluoroquinolone binding site. Notably, researchers have undertaken searches for anti-infective agents that can inhibit topoisomerases through alternate mechanisms. This review summarises work looking at the inhibition of topoisomerases predominantly through non-intercalating agents, including those acting at a novel allosteric site, ATPase domain inhibitors, and those offering unique binding modes and mechanisms of action.
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Affiliation(s)
- Scott Grossman
- School of Chemistry, University of Leeds, Leeds LS2 9JT, UK
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18
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Essential Paralogous Proteins as Potential Antibiotic Multitargets in Escherichia coli. Microbiol Spectr 2022; 10:e0204322. [PMID: 36445138 PMCID: PMC9769728 DOI: 10.1128/spectrum.02043-22] [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] [Indexed: 11/30/2022] Open
Abstract
Antimicrobial resistance threatens our current standards of care for the treatment and prevention of infectious disease. Antibiotics that have multiple targets have a lower propensity for the development of antibiotic resistance than those that have single targets and therefore represent an important tool in the fight against antimicrobial resistance. In this work, groups of essential paralogous proteins were identified in the important Gram-negative pathogen Escherichia coli that could represent novel targets for multitargeting antibiotics. These groups include targets from a broad range of essential macromolecular and biosynthetic pathways, including cell wall synthesis, membrane biogenesis, transcription, translation, DNA replication, fatty acid biosynthesis, and riboflavin and isoprenoid biosynthesis. Importantly, three groups of clinically validated antibiotic multitargets were identified using this method: the two subunits of the essential topoisomerases, DNA gyrase and topoisomerase IV, and one pair of penicillin-binding proteins. An additional eighteen protein groups represent potentially novel multitargets that could be explored in drug discovery efforts aimed at developing compounds having multiple targets in E. coli and other bacterial pathogens. IMPORTANCE Many types of bacteria have gained resistance to existing antibiotics used in medicine today. Therefore, new antibiotics with novel mechanisms must continue to be developed. One tool to prevent the development of antibiotic resistance is for a single drug to target multiple processes in a bacterium so that more than one change must arise for resistance to develop. The work described here provides a comprehensive search for proteins in the bacterium Escherichia coli that could be targets for such multitargeting antibiotics. Several groups of proteins that are already targets of clinically used antibiotics were identified, indicating that this approach can uncover clinically relevant antibiotic targets. In addition, eighteen currently unexploited groups of proteins were identified, representing new multitargets that could be explored in antibiotic research and development.
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19
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Chen A, Dellos-Nolan S, Lu Y, West JS, Wozniak DJ, Mitton-Fry MJ. Dioxane-Linked Novel Bacterial Topoisomerase Inhibitors Exhibit Bactericidal Activity against Planktonic and Biofilm Staphylococcus aureus In Vitro. Microbiol Spectr 2022; 10:e0205622. [PMID: 36250857 PMCID: PMC9769912 DOI: 10.1128/spectrum.02056-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 09/28/2022] [Indexed: 01/06/2023] Open
Abstract
The development of novel treatments for Staphylococcus aureus infections remains a high priority worldwide. We previously reported compounds 0147 and 0186, novel bacterial topoisomerase inhibitors (NBTIs) with potent antibacterial activity against S. aureus, including methicillin-resistant S. aureus. Here, we further investigated the in vitro activity of 0147 and 0186 against S. aureus ATCC 29213. Both compounds demonstrated bactericidal activity against planktonic and biofilm S. aureus, which then translated into significant inhibition of biofilm formation. Combinations of NBTIs and glycopeptides yielded indifferent interactions against planktonic S. aureus, but several had synergistic effects against S. aureus biofilms. This work reinforces the potential of NBTIs as future therapeutics for S. aureus infections. IMPORTANCE The pathogen Staphylococcus aureus contributes substantially to infection-related mortality. Biofilms render bacteria more recalcitrant to antibacterial therapy. The manuscript describes the potent activity of a new class of antibacterial agents against both planktonic and biofilm populations of Staphylococcus aureus.
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Affiliation(s)
- Anna Chen
- Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Sheri Dellos-Nolan
- Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Yanran Lu
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio, USA
| | - Jason S. West
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio, USA
| | - Daniel J. Wozniak
- Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, Ohio, USA
- Department of Microbiology, College of Arts and Sciences, The Ohio State University, Columbus, Ohio, USA
| | - Mark J. Mitton-Fry
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio, USA
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20
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Novikov A, Sayfutdinova A, Botchkova E, Kopitsyn D, Fakhrullin R. Antibiotic Susceptibility Testing with Raman Biosensing. Antibiotics (Basel) 2022; 11:antibiotics11121812. [PMID: 36551469 PMCID: PMC9774239 DOI: 10.3390/antibiotics11121812] [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: 10/20/2022] [Revised: 11/29/2022] [Accepted: 12/02/2022] [Indexed: 12/15/2022] Open
Abstract
Antibiotics guard us against bacterial infections and are among the most commonly used medicines. The immediate consequence of their large-scale production and prescription is the development of antibiotic resistance. Therefore, rapid detection of antibiotic susceptibility is required for efficient antimicrobial therapy. One of the promising methods for rapid antibiotic susceptibility testing is Raman spectroscopy. Raman spectroscopy combines fast and contactless acquisition of spectra with good selectivity towards bacterial cells. The antibiotic-induced changes in bacterial cell physiology are detected as distinct features in Raman spectra and can be associated with antibiotic susceptibility. Therefore, the Raman-based approach may be beneficial in designing therapy against multidrug-resistant infections. The surface-enhanced Raman spectroscopy (SERS) and resonance Raman spectroscopy (RRS) additionally provide excellent sensitivity. In this review, we present an analysis of the Raman spectroscopy-based optical biosensing approaches aimed at antibiotic susceptibility testing.
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Affiliation(s)
- Andrei Novikov
- Department of Physical and Colloid Chemistry, Gubkin University, 65/1 Leninsky Prospect, 119991 Moscow, Russia
- Correspondence: (A.N.); (R.F.)
| | - Adeliya Sayfutdinova
- Department of Physical and Colloid Chemistry, Gubkin University, 65/1 Leninsky Prospect, 119991 Moscow, Russia
| | - Ekaterina Botchkova
- Department of Physical and Colloid Chemistry, Gubkin University, 65/1 Leninsky Prospect, 119991 Moscow, Russia
| | - Dmitry Kopitsyn
- Department of Physical and Colloid Chemistry, Gubkin University, 65/1 Leninsky Prospect, 119991 Moscow, Russia
| | - Rawil Fakhrullin
- Department of Physical and Colloid Chemistry, Gubkin University, 65/1 Leninsky Prospect, 119991 Moscow, Russia
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Republic of Tatarstan, Russia
- Correspondence: (A.N.); (R.F.)
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21
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Singh SB, Tan CM, Kaelin D, Meinke PT, Miesel L, Olsen DB, Fukuda H, Kishii R, Takei M, Ohata K, Takeuchi T, Shibue T, Takano H, Nishimura A, Fukuda Y. Structure activity relationship of N-1 substituted 1,5-naphthyrid-2-one analogs of oxabicyclooctane-linked novel bacterial topoisomerase inhibitors as broad-spectrum antibacterial agents (Part-9). Bioorg Med Chem Lett 2022; 75:128808. [PMID: 35609741 DOI: 10.1016/j.bmcl.2022.128808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 05/13/2022] [Accepted: 05/17/2022] [Indexed: 11/02/2022]
Abstract
Novel bacterial topoisomerase inhibitors (NBTIs) are the newest members of gyrase inhibitor broad-spectrum antibacterial agents, represented by the most advanced member, gepotidacin, a 4-amino-piperidine linked NBTI, which is undergoing phase III clinical trials for treatment of urinary tract infections (UTI). We have extensively reported studies on oxabicyclooctane linked NBTIs, including AM-8722. The present study summarizes structure activity relationship (SAR) of AM-8722 leading to identification of 7-fluoro-1-cyanomethyl-1,5-naphthyridin-2-one based NBTI (16, AM-8888) with improved potency and spectrum (MIC values of 0.016-4 μg/mL), with Pseudomonas aeruginosa being the least sensitive strain (MIC 4 μg/mL).
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Affiliation(s)
| | | | | | | | - Lynn Miesel
- Merck & Co., Inc., Kenilworth, NJ 07033, USA
| | | | - Hideyuki Fukuda
- Kyorin Pharmaceutical Co., Ltd., 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Ryuta Kishii
- Kyorin Pharmaceutical Co., Ltd., 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Masaya Takei
- Kyorin Pharmaceutical Co., Ltd., 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Kohei Ohata
- Kyorin Pharmaceutical Co., Ltd., 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Tomoko Takeuchi
- Kyorin Pharmaceutical Co., Ltd., 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Taku Shibue
- Kyorin Pharmaceutical Co., Ltd., 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Hisashi Takano
- Kyorin Pharmaceutical Co., Ltd., 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Akinori Nishimura
- Kyorin Pharmaceutical Co., Ltd., 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Yasumichi Fukuda
- Kyorin Pharmaceutical Co., Ltd., 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan.
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22
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Alfonso EE, Deng Z, Boaretto D, Hood BL, Vasile S, Smith LH, Chambers JW, Chapagain P, Leng F. Novel and Structurally Diversified Bacterial DNA Gyrase Inhibitors Discovered through a Fluorescence-Based High-Throughput Screening Assay. ACS Pharmacol Transl Sci 2022; 5:932-944. [PMID: 36268121 PMCID: PMC9578135 DOI: 10.1021/acsptsci.2c00113] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Indexed: 12/25/2022]
Abstract
Bacterial DNA gyrase, a type IIA DNA topoisomerase that plays an essential role in bacterial DNA replication and transcription, is a clinically validated target for discovering and developing new antibiotics. In this article, based on a supercoiling-dependent fluorescence quenching (SDFQ) method, we developed a high-throughput screening (HTS) assay to identify inhibitors targeting bacterial DNA gyrase and screened the National Institutes of Health's Molecular Libraries Small Molecule Repository library containing 370,620 compounds in which 2891 potential gyrase inhibitors have been identified. According to these screening results, we acquired 235 compounds to analyze their inhibition activities against bacterial DNA gyrase using gel- and SDFQ-based DNA gyrase inhibition assays and discovered 155 new bacterial DNA gyrase inhibitors with a wide structural diversity. Several of them have potent antibacterial activities. These newly discovered gyrase inhibitors include several DNA gyrase poisons that stabilize the gyrase-DNA cleavage complexes and provide new chemical scaffolds for the design and synthesis of bacterial DNA gyrase inhibitors that may be used to combat multidrug-resistant bacterial pathogens. Additionally, this HTS assay can be applied to screen inhibitors against other DNA topoisomerases.
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Affiliation(s)
- Eddy E. Alfonso
- Biomolecular
Sciences Institute, Florida International
University, Miami, Florida 33199, United States
- Department
of Chemistry and Biochemistry, Florida International
University, Miami, Florida 33199, United
States
| | - Zifang Deng
- Biomolecular
Sciences Institute, Florida International
University, Miami, Florida 33199, United States
- Department
of Chemistry and Biochemistry, Florida International
University, Miami, Florida 33199, United
States
| | - Daniel Boaretto
- Biomolecular
Sciences Institute, Florida International
University, Miami, Florida 33199, United States
- Department
of Chemistry and Biochemistry, Florida International
University, Miami, Florida 33199, United
States
| | - Becky L. Hood
- Conrad
Prebys Center for Chemical Genomics, Sanford
Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - Stefan Vasile
- Conrad
Prebys Center for Chemical Genomics, Sanford
Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - Layton H. Smith
- Conrad
Prebys Center for Chemical Genomics, Sanford
Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - Jeremy W. Chambers
- Biomolecular
Sciences Institute, Florida International
University, Miami, Florida 33199, United States
- Department
of Environmental Health Sciences, Florida
International University, Miami, Florida 33199, United States
| | - Prem Chapagain
- Biomolecular
Sciences Institute, Florida International
University, Miami, Florida 33199, United States
- Department
of Physics, Florida International University, Miami, Florida 33199, United States
| | - Fenfei Leng
- Biomolecular
Sciences Institute, Florida International
University, Miami, Florida 33199, United States
- Department
of Chemistry and Biochemistry, Florida International
University, Miami, Florida 33199, United
States
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23
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Janin YL. On drug discovery against infectious diseases and academic medicinal chemistry contributions. Beilstein J Org Chem 2022; 18:1355-1378. [PMID: 36247982 PMCID: PMC9531561 DOI: 10.3762/bjoc.18.141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 09/21/2022] [Indexed: 11/23/2022] Open
Abstract
This perspective is an attempt to document the problems that medicinal chemists are facing in drug discovery. It is also trying to identify relevant/possible, research areas in which academics can have an impact and should thus be the subject of grant calls. Accordingly, it describes how hit discovery happens, how compounds to be screened are selected from available chemicals and the possible reasons for the recurrent paucity of useful/exploitable results reported. This is followed by the successful hit to lead stories leading to recent and original antibacterials which are, or about to be, used in human medicine. Then, illustrated considerations and suggestions are made on the possible inputs of academic medicinal chemists. This starts with the observation that discovering a “good” hit in the course of a screening campaign still rely on a lot of luck – which is within the reach of academics –, that the hit to lead process requires a lot of chemistry and that if public–private partnerships can be important throughout these stages, they are absolute requirements for clinical trials. Concerning suggestions to improve the current hit success rate, one academic input in organic chemistry would be to identify new and pertinent chemical space, design synthetic accesses to reach these and prepare the corresponding chemical libraries. Concerning hit to lead programs on a given target, if no new hits are available, previously reported leads along with new structural data can be pertinent starting points to design, prepare and assay original analogues. In conclusion, this text is an actual plea illustrating that, in many countries, academic research in medicinal chemistry should be more funded, especially in the therapeutic area neglected by the industry. At the least, such funds would provide the intensive to secure series of hopefully relevant chemical entities which appears to often lack when considering the results of academic as well as industrial screening campaigns.
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Affiliation(s)
- Yves L Janin
- Structure et Instabilité des Génomes (StrInG), Muséum National d'Histoire Naturelle, INSERM, CNRS, Alliance Sorbonne Université, 75005 Paris, France
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24
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Kokot M, Weiss M, Zdovc I, Anderluh M, Hrast M, Minovski N. Diminishing hERG inhibitory activity of aminopiperidine-naphthyridine linked NBTI antibacterials by structural and physicochemical optimizations. Bioorg Chem 2022; 128:106087. [PMID: 35970069 DOI: 10.1016/j.bioorg.2022.106087] [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: 05/20/2022] [Revised: 08/05/2022] [Accepted: 08/05/2022] [Indexed: 11/02/2022]
Abstract
Novel bacterial topoisomerase inhibitors (NBTIs) are an important new class of antibacterials targeting bacterial type II topoisomerases (DNA gyrase and topoisomerase IV). Notwithstanding their potent antibacterial activity, they suffer from a detrimental class-related hERG blockage. In this study, we designed and synthesized an optimized library of NBTIs comprising different linker moieties that exhibit reduced hERG inhibition and retain inhibitory potencies on DNA gyrase and topoisomerase IV of Staphylococcus aureus and Escherichia coli, respectively, as well as potent antibacterial activities. Substitution of the linker's tertiary amine with polar groups outcome in diminished hERG inhibition. Compound 17 expresses nanomolar enzyme inhibitory potency and antibacterial activity against both Gram-positive and Gram-negative bacteria as well as reduced hERG inhibition relative to our previously published NBTI analogs. Here, we point to some important NBTI's structural features that influence their hERG inhibitory activity.
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Affiliation(s)
- Maja Kokot
- Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia; The Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Matjaž Weiss
- The Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Irena Zdovc
- Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1000 Ljubljana, Slovenia
| | - Marko Anderluh
- The Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Martina Hrast
- The Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia.
| | - Nikola Minovski
- Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia.
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25
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Lu Y, Mann CA, Nolan S, Collins JA, Parker E, Papa J, Vibhute S, Jahanbakhsh S, Thwaites M, Hufnagel D, Hazbón MH, Moreno J, Stedman TT, Wittum T, Wozniak DJ, Osheroff N, Yalowich JC, Mitton-Fry MJ. 1,3-Dioxane-Linked Novel Bacterial Topoisomerase Inhibitors: Expanding Structural Diversity and the Antibacterial Spectrum. ACS Med Chem Lett 2022; 13:955-963. [PMID: 35707162 PMCID: PMC9189870 DOI: 10.1021/acsmedchemlett.2c00111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 05/05/2022] [Indexed: 11/29/2022] Open
Abstract
Antibacterial resistance continues its devastation of available therapies. Novel bacterial topoisomerase inhibitors (NBTIs) offer one solution to this critical issue. Two series of amine NBTIs bearing tricyclic DNA-binding moieties as well as amide NBTIs with a bicyclic DNA-binding moiety were synthesized and evaluated against methicillin-resistant Staphylococcus aureus (MRSA). Additionally, these compounds and a series of bicyclic amine analogues displayed high activity against susceptible and drug-resistant Neisseria gonorrhoeae, expanding the spectrum of these dioxane-linked NBTIs.
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Affiliation(s)
- Yanran Lu
- Division
of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Chelsea A. Mann
- Division
of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Sheri Nolan
- Microbial
Infection and Immunity, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jessica A. Collins
- Department
of Biochemistry, Vanderbilt University School
of Medicine, Nashville, Tennessee 37232, United States
| | - Elizabeth Parker
- Department
of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jonathan Papa
- Division
of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Sandip Vibhute
- Division
of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | | | | | | | | | - Jane Moreno
- ATCC, Manassas, Virginia 20110, United States
| | | | - Thomas Wittum
- Department
of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Daniel J. Wozniak
- Microbial
Infection and Immunity, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
- Department
of Microbiology, College of Arts and Sciences, The Ohio State University, Columbus, Ohio 43210, United States
| | - Neil Osheroff
- Department
of Biochemistry, Vanderbilt University School
of Medicine, Nashville, Tennessee 37232, United States
- Department
of Medicine (Hematology/Oncology), Vanderbilt
University School of Medicine, Nashville, Tennessee 37232, United States
- VA Tennessee Valley Healthcare System, Nashville, Tennessee 37212, United States
| | - Jack C. Yalowich
- Division
of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Mark J. Mitton-Fry
- Division
of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
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26
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Lyons A, Kirkham J, Blades K, Orr D, Dauncey E, Smith O, Dick E, Walker R, Matthews T, Bunt A, Finlayson J, Morrison I, Savage VJ, Moyo E, Butler HS, Newman R, Ooi N, Smith A, Charrier C, Ratcliffe AJ, Stokes NR, Best S, Salisbury AM, Craighead M, Cooper IR. Discovery and structure-activity relationships of a novel oxazolidinone class of bacterial type II topoisomerase inhibitors. Bioorg Med Chem Lett 2022; 65:128648. [PMID: 35231579 DOI: 10.1016/j.bmcl.2022.128648] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 11/02/2022]
Abstract
There is an increasingly urgent and unmet medical need for novel antibiotic drugs that tackle infections caused by multidrug-resistant (MDR) pathogens. Novel bacterial type II topoisomerase inhibitors (NBTIs) are of high interest due to limited cross-resistance with fluoroquinolones, however analogues with Gram-negative activity often suffer from hERG channel inhibition. A novel series of bicyclic-oxazolidinone inhibitors of bacterial type II topoisomerase were identified which display potent broad-spectrum anti-bacterial activity, including against MDR strains, along with an encouraging in vitro safety profile. In vivo proof of concept was achieved in a A. baumannii mouse thigh infection model.
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Affiliation(s)
- Amanda Lyons
- Redx Anti-Infectives Ltd, Alderley Park, Cheshire SK10 4TG, UK
| | - James Kirkham
- Infex Therapeutics Ltd, Mereside, Alderley Park, Macclesfield SK10 4TG,UK
| | - Kevin Blades
- Infex Therapeutics Ltd, Mereside, Alderley Park, Macclesfield SK10 4TG,UK
| | - David Orr
- Infex Therapeutics Ltd, Mereside, Alderley Park, Macclesfield SK10 4TG,UK
| | | | - Oliver Smith
- Infex Therapeutics Ltd, Mereside, Alderley Park, Macclesfield SK10 4TG,UK
| | - Emma Dick
- Redx Anti-Infectives Ltd, Alderley Park, Cheshire SK10 4TG, UK
| | - Rolf Walker
- Redx Anti-Infectives Ltd, Alderley Park, Cheshire SK10 4TG, UK
| | - Teresa Matthews
- Redx Anti-Infectives Ltd, Alderley Park, Cheshire SK10 4TG, UK
| | - Adam Bunt
- Infex Therapeutics Ltd, Mereside, Alderley Park, Macclesfield SK10 4TG,UK
| | | | - Ian Morrison
- Redx Anti-Infectives Ltd, Alderley Park, Cheshire SK10 4TG, UK
| | - Victoria J Savage
- Infex Therapeutics Ltd, Mereside, Alderley Park, Macclesfield SK10 4TG,UK
| | - Emmanuel Moyo
- Infex Therapeutics Ltd, Mereside, Alderley Park, Macclesfield SK10 4TG,UK
| | - Hayley S Butler
- Redx Anti-Infectives Ltd, Alderley Park, Cheshire SK10 4TG, UK
| | - Rebecca Newman
- Infex Therapeutics Ltd, Mereside, Alderley Park, Macclesfield SK10 4TG,UK
| | - Nicola Ooi
- Infex Therapeutics Ltd, Mereside, Alderley Park, Macclesfield SK10 4TG,UK
| | - Andrew Smith
- Redx Anti-Infectives Ltd, Alderley Park, Cheshire SK10 4TG, UK
| | - Cédric Charrier
- Redx Anti-Infectives Ltd, Alderley Park, Cheshire SK10 4TG, UK
| | | | - Neil R Stokes
- Redx Anti-Infectives Ltd, Alderley Park, Cheshire SK10 4TG, UK
| | - Stuart Best
- Redx Anti-Infectives Ltd, Alderley Park, Cheshire SK10 4TG, UK
| | | | - Mark Craighead
- Redx Anti-Infectives Ltd, Alderley Park, Cheshire SK10 4TG, UK
| | - Ian R Cooper
- Infex Therapeutics Ltd, Mereside, Alderley Park, Macclesfield SK10 4TG,UK.
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27
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Kokot M, Anderluh M, Hrast M, Minovski N. The Structural Features of Novel Bacterial Topoisomerase Inhibitors That Define Their Activity on Topoisomerase IV. J Med Chem 2022; 65:6431-6440. [PMID: 35503563 PMCID: PMC9109137 DOI: 10.1021/acs.jmedchem.2c00039] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
![]()
The continued emergence
of bacterial resistance has created an
urgent need for new and effective antibacterial agents. Bacterial
type II topoisomerases, such as DNA gyrase and topoisomerase IV (topoIV),
are well-validated targets for antibacterial chemotherapy. The novel
bacterial topoisomerase inhibitors (NBTIs) represent one of the new
promising classes of antibacterial agents. They can inhibit both of
these bacterial targets; however, their potencies differ on the targets
among species, making topoIV probably a primary target of NBTIs in
Gram-negative bacteria. Therefore, it is important to gain an insight
into the NBTIs key structural features that govern the topoIV inhibition.
However, in Gram-positive bacteria, topoIV is also a significant target
for achieving dual-targeting, which in turn contributes to avoiding
bacterial resistance caused by single-target mutations. In this perspective,
we address the structure–activity relationship guidelines for
NBTIs that target the topoIV enzyme in Gram-positive and Gram-negative
bacteria.
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Affiliation(s)
- Maja Kokot
- Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, SI-1000 Ljubljana, Slovenia
| | - Marko Anderluh
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, SI-1000 Ljubljana, Slovenia
| | - Martina Hrast
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, SI-1000 Ljubljana, Slovenia
| | - Nikola Minovski
- Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
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28
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Beuchel A, Robaa D, Negatu DA, Madani A, Alvarez N, Zimmerman MD, Richter A, Mann L, Hoenke S, Csuk R, Dick T, Imming P. Structure-Activity Relationship of Anti- Mycobacterium abscessus Piperidine-4-carboxamides, a New Class of NBTI DNA Gyrase Inhibitors. ACS Med Chem Lett 2022; 13:417-427. [PMID: 35300094 PMCID: PMC8919391 DOI: 10.1021/acsmedchemlett.1c00549] [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: 10/19/2021] [Accepted: 02/24/2022] [Indexed: 11/28/2022] Open
Abstract
Mycobacterium abscessus causes difficult-to-cure pulmonary infections. The bacterium is resistant to most anti-infective agents, including first line antituberculosis (anti-TB) drugs. MMV688844 (844) is a piperidine-4-carboxamide (P4C) with bactericidal properties against M. abscessus. We recently identified DNA gyrase as the molecular target of 844. Here, we present in silico docking and genetic evidence suggesting that P4Cs display a similar binding mode to DNA gyrase as gepotidacin. Gepotidacin is a member of the Novel Bacterial Topoisomerase Inhibitors (NBTIs), a new class of nonfluoroquinolone DNA gyrase poisons. Thus, our work suggests that P4Cs present a novel structural subclass of NBTI. We describe structure-activity relationship studies of 844 leading to analogues showing increased antibacterial activity. Selected derivatives were tested for their inhibitory activity against recombinant M. abscessus DNA gyrase. Further optimization of the lead structures led to improved stability in mouse plasma and increased oral bioavailability.
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Affiliation(s)
- Andreas Beuchel
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany, Kurt-Mothes-Str. 3, 06120 Halle (Saale), Germany
| | - Dina Robaa
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany, Kurt-Mothes-Str. 3, 06120 Halle (Saale), Germany
| | - Dereje A Negatu
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey 07110, United States.,Center for Innovative Drug Development and Therapeutic Trials for Africa (CDT-Africa), Addis Ababa University, Addis Ababa 1000, Ethiopia
| | - Abdeldjalil Madani
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey 07110, United States
| | - Nadine Alvarez
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey 07110, United States
| | - Matthew D Zimmerman
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey 07110, United States
| | - Adrian Richter
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany, Kurt-Mothes-Str. 3, 06120 Halle (Saale), Germany
| | - Lea Mann
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany, Kurt-Mothes-Str. 3, 06120 Halle (Saale), Germany
| | - Sophie Hoenke
- Institut für Chemie, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 2, 06120 Halle (Saale), Germany
| | - René Csuk
- Institut für Chemie, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 2, 06120 Halle (Saale), Germany
| | - Thomas Dick
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey 07110, United States.,Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, New Jersey 07110, United States.,Department of Microbiology and Immunology, Georgetown University, Washington, D.C. 20057, United States
| | - Peter Imming
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany, Kurt-Mothes-Str. 3, 06120 Halle (Saale), Germany
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29
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Hammoud MM, Nageeb AS, Morsi MA, Gomaa EA, Elmaaty AA, Al-Karmalawy AA. Design, synthesis, biological evaluation, and SAR studies of novel cyclopentaquinoline derivatives as DNA intercalators, topoisomerase II inhibitors, and apoptotic inducers. NEW J CHEM 2022. [DOI: 10.1039/d2nj01646j] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Novel cyclopentaquinoline derivatives as promising DNA intercalators, topoisomerase II inhibitors, and apoptotic inducers.
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Affiliation(s)
- Mohamed M. Hammoud
- Department of Chemistry, College of Science and Humanities in Al-Kharj, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
- Department of Chemistry, Faculty of Science, Mansoura University, Mansoura 35516, Egypt
| | - Alaa S. Nageeb
- Department of Chemistry, Faculty of Science, Mansoura University, Mansoura 35516, Egypt
| | - M. A. Morsi
- Department of Chemistry, Faculty of Science, Mansoura University, Mansoura 35516, Egypt
| | - Esam A. Gomaa
- Department of Chemistry, Faculty of Science, Mansoura University, Mansoura 35516, Egypt
| | - Ayman Abo Elmaaty
- Department of Medicinal Chemistry, Faculty of Pharmacy, Port Said University, Port Said 42526, Egypt
| | - Ahmed A. Al-Karmalawy
- Department of Pharmaceutical Medicinal Chemistry, Faculty of Pharmacy, Horus University-Egypt, New Damietta 34518, Egypt
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30
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Flagstad T, Pedersen MT, Jakobsen TH, Felding J, Tolker-Nielsen T, Givskov M, Qvortrup K, Nielsen TE. Solid-phase synthesis and biological evaluation of piperazine-based novel bacterial topoisomerase inhibitors. Bioorg Med Chem Lett 2021; 57:128499. [PMID: 34906671 DOI: 10.1016/j.bmcl.2021.128499] [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: 10/05/2021] [Revised: 12/05/2021] [Accepted: 12/06/2021] [Indexed: 11/28/2022]
Abstract
There is an emerging global need for new and more effective antibiotics against multi-resistant bacteria. This situation has led to massive industrial investigations on novel bacterial topoisomerase inhibitors (NBTIs) that target the vital bacterial enzymes DNA gyrase and topoisomerase IV. However, several of the NBTI compound classes have been associated with inhibition of the hERG potassium channel, an undesired cause of cardiac arrhythmia, which challenges medicinal chemistry efforts through lengthy synthetic routes. We herein present a solid-phase strategy that rapidly facilitates the chemical synthesis of a promising new class of NBTIs. A proof-of-concept library was synthesized with the ability to modulate both hERG affinity and antibacterial activity through scaffold substitutions.
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Affiliation(s)
- Thomas Flagstad
- Department of Chemistry, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Mette T Pedersen
- Department of Chemistry, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Tim H Jakobsen
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | | | - Tim Tolker-Nielsen
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Michael Givskov
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark; Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore
| | - Katrine Qvortrup
- Department of Chemistry, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
| | - Thomas E Nielsen
- Department of Chemistry, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark; Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark; Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore.
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31
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Lu Y, Vibhute S, Li L, Okumu A, Ratigan SC, Nolan S, Papa JL, Mann CA, English A, Chen A, Seffernick JT, Koci B, Duncan LR, Roth B, Cummings JE, Slayden RA, Lindert S, McElroy CA, Wozniak DJ, Yalowich J, Mitton-Fry MJ. Optimization of TopoIV Potency, ADMET Properties, and hERG Inhibition of 5-Amino-1,3-dioxane-Linked Novel Bacterial Topoisomerase Inhibitors: Identification of a Lead with In Vivo Efficacy against MRSA. J Med Chem 2021; 64:15214-15249. [PMID: 34614347 DOI: 10.1021/acs.jmedchem.1c01250] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Novel bacterial topoisomerase inhibitors (NBTIs) are among the most promising new antibiotics in preclinical/clinical development. We previously reported dioxane-linked NBTIs with potent antistaphylococcal activity and reduced hERG inhibition, a key safety liability. Herein, polarity-focused optimization enabled the delineation of clear structure-property relationships for both microsomal metabolic stability and hERG inhibition, resulting in the identification of lead compound 79. This molecule demonstrates potent antibacterial activity against diverse Gram-positive pathogens, inhibition of both DNA gyrase and topoisomerase IV, a low frequency of resistance, a favorable in vitro cardiovascular safety profile, and in vivo efficacy in a murine model of methicillin-resistant Staphylococcus aureus infection.
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Affiliation(s)
- Yanran Lu
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Sandip Vibhute
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Linsen Li
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Antony Okumu
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Steven C Ratigan
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Sheri Nolan
- Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jonathan L Papa
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Chelsea A Mann
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Anthony English
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Anna Chen
- Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Justin T Seffernick
- Department of Chemistry and Biochemistry, College of Arts and Sciences, The Ohio State University, Columbus, Ohio 43210, United States
| | - Bryan Koci
- Eurofins Panlabs, St. Charles, Missouri 63304, United States
| | | | - Brieanna Roth
- JMI Laboratories, North Liberty, Iowa 52317, United States
| | - Jason E Cummings
- Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Richard A Slayden
- Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, College of Arts and Sciences, The Ohio State University, Columbus, Ohio 43210, United States
| | - Craig A McElroy
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Daniel J Wozniak
- Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States.,Department of Microbiology, College of Arts and Sciences, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jack Yalowich
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Mark J Mitton-Fry
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
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32
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Kokot M, Weiss M, Zdovc I, Hrast M, Anderluh M, Minovski N. Structurally Optimized Potent Dual-Targeting NBTI Antibacterials with an Enhanced Bifurcated Halogen-Bonding Propensity. ACS Med Chem Lett 2021; 12:1478-1485. [PMID: 34527181 PMCID: PMC8436411 DOI: 10.1021/acsmedchemlett.1c00345] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 08/12/2021] [Indexed: 11/30/2022] Open
Abstract
![]()
We designed and synthesized
an optimized library of novel bacterial
topoisomerase inhibitors with p-halogenated phenyl
right-hand side fragments and significantly enhanced and balanced
dual-targeted DNA gyrase and topoisomerase IV activities of Staphylococcus aureus and Escherichia coli. By increasing the electron-withdrawing properties of the p-halogenated phenyl right-hand side fragment and maintaining
a similar lipophilicity and size, an increased potency was achieved,
indicating that the antibacterial activities of this series of novel
bacterial topoisomerase inhibitors against all target enzymes are
determined by halogen-bonding rather than van der Waals interactions.
They show nanomolar enzyme inhibitory and whole-cell antibacterial
activities against S. aureus and methicillin-resistant S. aureus (MRSA) strains. However, due to the relatively
high substrate specificity for the bacterial efflux pumps, they tend
to be less potent against E. coli and other Gram-negative
pathogens.
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Affiliation(s)
- Maja Kokot
- Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
- The Chair of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, SI-1000 Ljubljana, Slovenia
| | - Matjaž Weiss
- The Chair of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, SI-1000 Ljubljana, Slovenia
| | - Irena Zdovc
- Veterinary Faculty, Institute of Microbiology and Parasitology, University of Ljubljana, Gerbičeva 60, SI-1000 Ljubljana, Slovenia
| | - Martina Hrast
- The Chair of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, SI-1000 Ljubljana, Slovenia
| | - Marko Anderluh
- The Chair of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, SI-1000 Ljubljana, Slovenia
| | - Nikola Minovski
- Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
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33
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Santos D, Gomes HF, Ribeiro L, Farias AB, Romeiro NC, da Fonseca RN, Nepomuceno-Silva JL, Moraes J. Inhibition of Aedes aegypti DNA topoisomerase II by etoposide: Impact on survival and morphology of larvae and pupae. Comp Biochem Physiol C Toxicol Pharmacol 2021; 247:109066. [PMID: 33930525 DOI: 10.1016/j.cbpc.2021.109066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 04/18/2021] [Accepted: 04/21/2021] [Indexed: 10/01/2022]
Abstract
DNA topoisomerase II enzymes maintain DNA stability during vital processes, such as genome replication, transcription and chromosomal segregation during mitosis and meiosis. In the present work, we analyzed functional aspects of the DNA topoisomerase II (AeTopII) enzyme of the mosquito Aedes aegypti. Here, we show that AeTopII mRNA is expressed at all stages of mosquito development. By in situ hybridization, we found that the AeTopII mRNA is concentrated along the ovarian follicular cells as well as in the region of the follicles. The observed expression profiles likely reflect increased topoisomerase II cellular requirements due to the intense ovarian growth and egg production following blood feeding in Ae. aegypti females. The drug etoposide, a classic inhibitor of topoisomerase II, was used for in vivo testing with 2nd stage larvae, in order to investigate the functional importance of this enzyme in Ae. aegypti survival and development. Inhibition of topoisomerase II activity with etoposide concentrations ranging from 10 to 200 μM did not leads to the immediate death of larvae. However, after 10 days of observation, etoposide treatments resulted in 30-40% decrease in survival, in a dose dependent manner, with persisting larvae and pupae presenting incomplete development, as well as morphological abnormalities. Also, approximately 50% of the treated larvae did not reach the pupal stage. Thus, we conclude that AeTopII is a vital enzyme in the development of Ae. aegypti and its sensitivity to inhibitors should be explored for potential chemical agents to be used in vector control.
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Affiliation(s)
- Daniele Santos
- Laboratório Integrado de Bioquímica Hatisaburo Masuda, NUPEM, Instituto de Biodiversidade e Sustentabilidade, Universidade Federal do Rio de Janeiro, Avenida São José Barreto, N° 764, Bairro, São José do Barreto, Macaé, RJ CEP: 27.965-045, Brazil
| | - Helga F Gomes
- Laboratório Integrado de Bioquímica Hatisaburo Masuda, NUPEM, Instituto de Biodiversidade e Sustentabilidade, Universidade Federal do Rio de Janeiro, Avenida São José Barreto, N° 764, Bairro, São José do Barreto, Macaé, RJ CEP: 27.965-045, Brazil
| | - Lupis Ribeiro
- Laboratório Integrado Ciências Morfofuncionais, NUPEM, Instituto de Biodiversidade e Sustentabilidade, Universidade Federal do Rio de Janeiro, Avenida São José Barreto, N° 764, Bairro, São José do Barreto, Macaé, RJ CEP: 27.965-045, Brazil
| | - André B Farias
- Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro CEP: 21941-909, Brazil; Laboratório Integrado de Computação Científica, Universidade Federal do Rio de Janeiro, Campus Macaé Professor Aloísio Teixeira, Avenida Aluízio da Silva Gomes, 50, CEP 27930-560, Granja dos Cavaleiros, Macaé, RJ, Brazil
| | - Nelilma C Romeiro
- Laboratório Integrado de Computação Científica, Universidade Federal do Rio de Janeiro, Campus Macaé Professor Aloísio Teixeira, Avenida Aluízio da Silva Gomes, 50, CEP 27930-560, Granja dos Cavaleiros, Macaé, RJ, Brazil
| | - Rodrigo Nunes da Fonseca
- Laboratório Integrado Ciências Morfofuncionais, NUPEM, Instituto de Biodiversidade e Sustentabilidade, Universidade Federal do Rio de Janeiro, Avenida São José Barreto, N° 764, Bairro, São José do Barreto, Macaé, RJ CEP: 27.965-045, Brazil
| | - José L Nepomuceno-Silva
- Laboratório Integrado de Bioquímica Hatisaburo Masuda, NUPEM, Instituto de Biodiversidade e Sustentabilidade, Universidade Federal do Rio de Janeiro, Avenida São José Barreto, N° 764, Bairro, São José do Barreto, Macaé, RJ CEP: 27.965-045, Brazil
| | - Jorge Moraes
- Laboratório Integrado de Bioquímica Hatisaburo Masuda, NUPEM, Instituto de Biodiversidade e Sustentabilidade, Universidade Federal do Rio de Janeiro, Avenida São José Barreto, N° 764, Bairro, São José do Barreto, Macaé, RJ CEP: 27.965-045, Brazil.
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34
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A Fine-Tuned Lipophilicity/Hydrophilicity Ratio Governs Antibacterial Potency and Selectivity of Bifurcated Halogen Bond-Forming NBTIs. Antibiotics (Basel) 2021; 10:antibiotics10070862. [PMID: 34356782 PMCID: PMC8300687 DOI: 10.3390/antibiotics10070862] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/12/2021] [Accepted: 07/12/2021] [Indexed: 12/15/2022] Open
Abstract
Herein, we report the design of a focused library of novel bacterial topoisomerase inhibitors (NBTIs) based on innovative mainly monocyclic right-hand side fragments active against DNA gyrase and Topo IV. They exhibit a very potent and wide range of antibacterial activity, even against some of the most concerning hard-to-treat pathogens for which new antibacterials are urgently needed, as reported by the WHO and CDC. NBTIs enzyme activity and whole cell potency seems to depend on the fine-tuned lipophilicity/hydrophilicity ratio that governs the permeability of those compounds through the bacterial membranes. Lipophilicity of NBTIs is apparently optimal for passing through the membrane of Gram-positive bacteria, but the higher, although not excessive lipophilicity and suitable hydrophilicity seems to determine the passage through Gram-negative bacterial membranes. However, due to the considerable hERG inhibition, which is still at least two orders of magnitude away from MICs, continued optimization is required to realize their full potential.
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35
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Ibrahim TS, Almalki AJ, Moustafa AH, Allam RM, Abuo-Rahma GEDA, El Subbagh HI, Mohamed MFA. Novel 1,2,4-oxadiazole-chalcone/oxime hybrids as potential antibacterial DNA gyrase inhibitors: Design, synthesis, ADMET prediction and molecular docking study. Bioorg Chem 2021; 111:104885. [PMID: 33838559 DOI: 10.1016/j.bioorg.2021.104885] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/26/2021] [Accepted: 03/28/2021] [Indexed: 01/19/2023]
Abstract
New antibacterial drugs are urgently needed to tackle the rapid rise in multi-drug resistant bacteria. DNA gyrase is a validated target for the development of new antibacterial drugs. Thus, in the present investigation, a novel series of 1,2,4-oxadiazole-chalcone/oxime (6a-f) and (7a-f) were synthesized and characterized by IR, NMR (1H and 13C) and elemental analyses. The title compounds were evaluated for their in-vitro antimicrobial activity by the modified agar diffusion method as well as their E. coli DNA gyrase inhibitory activity. The minimum inhibitory concentration (MIC) and the structure activity relationships (SARs) were evaluated. Among all, compounds 6a, 6c-e, 7b and 7e were the most potent and proved to possess broad spectrum activity against the tested Gram-positive and Gram-negative organisms. Additionally, compounds 6a (against S. aureus), 6c (against B. subtilis and E. hirae), 6e (against E. hirae), 6f, 7a and 7c (against E. coli) and 7d (against B. subtilis), with MIC value of 3.12 μM were two-fold more potent than the standard ciprofloxacin (MIC = 6.25 μM). Mechanistically, compounds 6c, 7c, 7e and 7b had good inhibitory activity against E. coli gyrase with IC50 values of 17.05, 13.4, 16.9, and 19.6 µM, respectively, in comparison with novobiocin (IC50 = 12.3 µM) and ciprofloxacin (IC50 = 10.5 µM). The molecular docking results at DNA gyrase active site revealed that the most potent compounds 6c and 7c have binding mode and docking scores comparable to that of ciprofloxacin and novobiocin suggesting their antibacterial activity via inhibition of DNA gyrase. Finally, the predicted parameters of Lipinski's rule of five and ADMET analysis showed that 6c and 7c had good drug-likeness and acceptable physicochemical properties. Therefore, the hybridization of the chalcone and oxadiazole moieties could be promising lead as antibacterial candidate which merit further future structural optimizations.
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Affiliation(s)
- Tarek S Ibrahim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt.
| | - Ahmad J Almalki
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Amr H Moustafa
- Department of Chemistry, Faculty of Science, Sohag University, Sohag 82524, Egypt
| | - Rasha M Allam
- Pharmacology Department, National Research Centre, Cairo 12622 (ID: 60014618), Egypt
| | - Gamal El-Din A Abuo-Rahma
- Department of Medicinal Chemistry, Faculty of Pharmacy, Minia University, Minia 61519, Egypt; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Deraya University, New Minia, Minia, Egypt
| | - Hussein I El Subbagh
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, 35516 Mansoura, Egypt
| | - Mamdouh F A Mohamed
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Sohag University, 82524 Sohag, Egypt.
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36
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Sabnis RW. Novel Oxopyrido[1,2- a]pyrimidine Compounds for Treating Bacterial Infection. ACS Med Chem Lett 2021; 12:324-325. [PMID: 33738054 DOI: 10.1021/acsmedchemlett.1c00077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Indexed: 11/29/2022] Open
Affiliation(s)
- Ram W. Sabnis
- Smith, Gambrell & Russell LLP, 1230 Peachtree Street NE, Suite 3100, Atlanta, Georgia 30309, United States
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37
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Padilla-Montaño N, de León Guerra L, Moujir L. Antimicrobial Activity and Mode of Action of Celastrol, a Nortriterpen Quinone Isolated from Natural Sources. Foods 2021; 10:foods10030591. [PMID: 33799720 PMCID: PMC7998816 DOI: 10.3390/foods10030591] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/05/2021] [Accepted: 03/05/2021] [Indexed: 01/07/2023] Open
Abstract
Species of the Celastraceae family are traditionally consumed in different world regions for their stimulating properties. Celastrol, a triterpene methylene quinone isolated from plants of celastraceas, specifically activates satiety centers in the brain that play an important role in controlling body weight. In this work, the antimicrobial activity and mechanism of action of celastrol and a natural derivative, pristimerin, were investigated in Bacillus subtilis. Celastrol showed a higher antimicrobial activity compared with pristimerin, being active against Gram-positive bacteria with minimum inhibitory concentrations (MICs) that ranged between 0.16 and 2.5 µg/mL. Killing curves displayed a bactericidal effect that was dependent on the inoculum size. Monitoring of macromolecular synthesis in bacterial populations treated with these compounds revealed inhibition in the incorporation of all radiolabeled precursors, but not simultaneously. Celastrol at 3 µg/mL and pristimerin at 10 µg/mL affected DNA and RNA synthesis first, followed by protein synthesis, although the inhibitory action on the uptake of radiolabeled precursors was more dramatic with celastrol. This compound also caused cytoplasmic membrane disruption observed by potassium leakage and formation of mesosome-like structures. The inhibition of oxygen consumption of whole and disrupted cells after treatments with both quinones indicates damage in the cellular structure, suggesting the cytoplasmic membrane as a potential target. These findings indicate that celastrol could be considered as an interesting alternative to control outbreaks caused by spore-forming bacteria.
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38
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Xu X, Ai Y, Wang R, Liu L, Yang J, Li F. Ruthenium-catalyzed acceptorless dehydrogenative coupling of o-aminobenzyl alcohols with ketones to quinolines in the presence of carbonate salt. J Catal 2021. [DOI: 10.1016/j.jcat.2020.12.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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39
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Kong Q, Yang Y. Recent advances in antibacterial agents. Bioorg Med Chem Lett 2021; 35:127799. [PMID: 33476772 DOI: 10.1016/j.bmcl.2021.127799] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/10/2021] [Accepted: 01/11/2021] [Indexed: 12/12/2022]
Abstract
Antimicrobial resistance is a global challenge and the effectiveness of old antibiotics is decreasing. Discovery and development of antibacterial agents have been accelerated to replenish the arsenal of antibiotics which is limited and shrinking. In recent years, significant advances have achieved in the antibacterial area, including new compounds of known classes and new compounds with new mechanisms. This review summarizes these advances and provides perspective on future directions of antibacterial agents.
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Affiliation(s)
- Qidi Kong
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Beijing 100049, China
| | - Yushe Yang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Beijing 100049, China.
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40
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Kolarič A, Germe T, Hrast M, Stevenson CEM, Lawson DM, Burton NP, Vörös J, Maxwell A, Minovski N, Anderluh M. Potent DNA gyrase inhibitors bind asymmetrically to their target using symmetrical bifurcated halogen bonds. Nat Commun 2021; 12:150. [PMID: 33420011 PMCID: PMC7794245 DOI: 10.1038/s41467-020-20405-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 11/25/2020] [Indexed: 12/13/2022] Open
Abstract
Novel bacterial type II topoisomerase inhibitors (NBTIs) stabilize single-strand DNA cleavage breaks by DNA gyrase but their exact mechanism of action has remained hypothetical until now. We have designed a small library of NBTIs with an improved DNA gyrase-binding moiety resulting in low nanomolar inhibition and very potent antibacterial activity. They stabilize single-stranded cleavage complexes and, importantly, we have obtained the crystal structure where an NBTI binds gyrase–DNA in a single conformation lacking apparent static disorder. This directly proves the previously postulated NBTI mechanism of action and shows that they stabilize single-strand cleavage through asymmetric intercalation with a shift of the scissile phosphate. This crystal stucture shows that the chlorine forms a halogen bond with the backbone carbonyls of the two symmetry-related Ala68 residues. To the best of our knowledge, such a so-called symmetrical bifurcated halogen bond has not been identified in a biological system until now. The mechanism of DNA gyrase inhibitor stabilization of single-strand DNA cleavage breaks by DNA gyrase has been hypothetical. Here, the authors show experimental evidence of the mechanism using a library of inhibitors with improved binding and employ crystal analysis to show bifurcated halogen bonding.
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Affiliation(s)
- Anja Kolarič
- Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000, Ljubljana, Slovenia
| | - Thomas Germe
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Martina Hrast
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000, Ljubljana, Slovenia
| | - Clare E M Stevenson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - David M Lawson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Nicolas P Burton
- Inspiralis Ltd., Innovation Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7GJ, UK
| | - Judit Vörös
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Anthony Maxwell
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Nikola Minovski
- Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia.
| | - Marko Anderluh
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000, Ljubljana, Slovenia.
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41
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Cools F, Delputte P, Cos P. The search for novel treatment strategies for Streptococcus pneumoniae infections. FEMS Microbiol Rev 2021; 45:6064299. [PMID: 33399826 PMCID: PMC8371276 DOI: 10.1093/femsre/fuaa072] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 01/01/2021] [Indexed: 12/13/2022] Open
Abstract
This review provides an overview of the most important novel treatment strategies against Streptococcus pneumoniae infections published over the past 10 years. The pneumococcus causes the majority of community-acquired bacterial pneumonia cases, and it is one of the prime pathogens in bacterial meningitis. Over the last 10 years, extensive research has been conducted to prevent severe pneumococcal infections, with a major focus on (i) boosting the host immune system and (ii) discovering novel antibacterials. Boosting the immune system can be done in two ways, either by actively modulating host immunity, mostly through administration of selective antibodies, or by interfering with pneumococcal virulence factors, thereby supporting the host immune system to effectively overcome an infection. While several of such experimental therapies are promising, few have evolved to clinical trials. The discovery of novel antibacterials is hampered by the high research and development costs versus the relatively low revenues for the pharmaceutical industry. Nevertheless, novel enzymatic assays and target-based drug design, allow the identification of targets and the development of novel molecules to effectively treat this life-threatening pathogen.
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Affiliation(s)
- F Cools
- Laboratory for Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - P Delputte
- Laboratory for Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - P Cos
- Laboratory for Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
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42
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Lu Y, Papa JL, Nolan S, English A, Seffernick JT, Shkolnikov N, Powell J, Lindert S, Wozniak DJ, Yalowich J, Mitton-Fry MJ. Dioxane-Linked Amide Derivatives as Novel Bacterial Topoisomerase Inhibitors against Gram-Positive Staphylococcus aureus. ACS Med Chem Lett 2020; 11:2446-2454. [PMID: 33335666 DOI: 10.1021/acsmedchemlett.0c00428] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/14/2020] [Indexed: 12/19/2022] Open
Abstract
In recent years, novel bacterial topoisomerase inhibitors (NBTIs) have been developed as future antibacterials for treating multidrug-resistant bacterial infections. A series of dioxane-linked NBTIs with an amide moiety has been synthesized and evaluated. Compound 3 inhibits DNA gyrase, induces the formation of single strand breaks to bacterial DNA, and achieves potent antibacterial activity against a variety of Gram-positive pathogens, including methicillin-resistant Staphylococcus aureus (MRSA). Optimization of this series of analogues led to the discovery of a subseries of compounds (22-25) with more potent anti-MRSA activity, dual inhibition of DNA gyrase and topoisomerase IV, and the ability to induce double strand breaks through inhibition of S. aureus DNA gyrase.
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