1
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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; 16:1462-1472. [PMID: 38898213 PMCID: PMC11374673 DOI: 10.1038/s41557-024-01516-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [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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2
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Shen C, Song J, Hsieh CY, Cao D, Kang Y, Ye W, Wu Z, Wang J, Zhang O, Zhang X, Zeng H, Cai H, Chen Y, Chen L, Luo H, Zhao X, Jian T, Chen T, Jiang D, Wang M, Ye Q, Wu J, Du H, Shi H, Deng Y, Hou T. DrugFlow: An AI-Driven One-Stop Platform for Innovative Drug Discovery. J Chem Inf Model 2024; 64:5381-5391. [PMID: 38920405 DOI: 10.1021/acs.jcim.4c00621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2024]
Abstract
Artificial intelligence (AI)-aided drug design has demonstrated unprecedented effects on modern drug discovery, but there is still an urgent need for user-friendly interfaces that bridge the gap between these sophisticated tools and scientists, particularly those who are less computer savvy. Herein, we present DrugFlow, an AI-driven one-stop platform that offers a clean, convenient, and cloud-based interface to streamline early drug discovery workflows. By seamlessly integrating a range of innovative AI algorithms, covering molecular docking, quantitative structure-activity relationship modeling, molecular generation, ADMET (absorption, distribution, metabolism, excretion and toxicity) prediction, and virtual screening, DrugFlow can offer effective AI solutions for almost all crucial stages in early drug discovery, including hit identification and hit/lead optimization. We hope that the platform can provide sufficiently valuable guidance to aid real-word drug design and discovery. The platform is available at https://drugflow.com.
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Affiliation(s)
- Chao Shen
- Hangzhou Carbonsilicon AI Technology Co., Ltd., Hangzhou 310018, Zhejiang, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Jianfei Song
- Hangzhou Carbonsilicon AI Technology Co., Ltd., Hangzhou 310018, Zhejiang, China
| | - Chang-Yu Hsieh
- Hangzhou Carbonsilicon AI Technology Co., Ltd., Hangzhou 310018, Zhejiang, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Dongsheng Cao
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410004, Hunan, China
| | - Yu Kang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Wenling Ye
- Hangzhou Carbonsilicon AI Technology Co., Ltd., Hangzhou 310018, Zhejiang, China
| | - Zhenxing Wu
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Jike Wang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Odin Zhang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Xujun Zhang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Hao Zeng
- Hangzhou Carbonsilicon AI Technology Co., Ltd., Hangzhou 310018, Zhejiang, China
| | - Heng Cai
- Hangzhou Carbonsilicon AI Technology Co., Ltd., Hangzhou 310018, Zhejiang, China
| | - Yu Chen
- Hangzhou Carbonsilicon AI Technology Co., Ltd., Hangzhou 310018, Zhejiang, China
| | - Linkang Chen
- Hangzhou Carbonsilicon AI Technology Co., Ltd., Hangzhou 310018, Zhejiang, China
| | - Hao Luo
- Hangzhou Carbonsilicon AI Technology Co., Ltd., Hangzhou 310018, Zhejiang, China
| | - Xinda Zhao
- Hangzhou Carbonsilicon AI Technology Co., Ltd., Hangzhou 310018, Zhejiang, China
| | - Tianye Jian
- Hangzhou Carbonsilicon AI Technology Co., Ltd., Hangzhou 310018, Zhejiang, China
| | - Tong Chen
- Hangzhou Carbonsilicon AI Technology Co., Ltd., Hangzhou 310018, Zhejiang, China
| | - Dejun Jiang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Mingyang Wang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Qing Ye
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Jialu Wu
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Hongyan Du
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Hui Shi
- Hangzhou Carbonsilicon AI Technology Co., Ltd., Hangzhou 310018, Zhejiang, China
| | - Yafeng Deng
- Hangzhou Carbonsilicon AI Technology Co., Ltd., Hangzhou 310018, Zhejiang, China
- Department of Automation, Tsinghua University, Beijing 100084, China
| | - Tingjun Hou
- Hangzhou Carbonsilicon AI Technology Co., Ltd., Hangzhou 310018, Zhejiang, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
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3
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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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4
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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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5
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Cumming JG, Kreis L, Kühne H, Wermuth R, Vercruysse M, Cantrill C, Bissantz C, Qiu H, Kramer C, Andreotti D, Fossati G. Novel Indane-Containing NBTIs with Potent Anti-Gram-Negative Activity and Minimal hERG Inhibition. ACS Med Chem Lett 2023; 14:1791-1799. [PMID: 38116438 PMCID: PMC10726470 DOI: 10.1021/acsmedchemlett.3c00422] [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: 09/19/2023] [Revised: 11/02/2023] [Accepted: 11/07/2023] [Indexed: 12/21/2023] Open
Abstract
Novel bacterial topoisomerase inhibitors (NBTIs) make up a promising new class of antibiotics with the potential to combat the growing threat of antimicrobial resistance. Two key challenges in the development of NBTIs have been to obtain broad spectrum activity against multidrug-resistant Gram-negative bacteria and to diminish inhibition of the hERG cardiac ion channel. Here we report the optimization of a series of NBTIs bearing a novel indane DNA intercalating moiety. The addition of a basic, polar side chain connected to the indane by an ether or an N-linked secondary amide linkage together with a lipophilicity-lowering modification of the enzyme binding moiety led to compounds such as 2a and 2g which showed excellent broad spectrum potency and minimal hERG inhibition. Compound 2a demonstrated robust bactericidal in vivo activity in a mouse lung infection model with the strain P. aeruginosa ATCC 27853 which is resistant to several clinically relevant antibiotics. Rodent pharmacokinetic studies with 2a revealed an unusual profile characterized by rapid tissue distribution and a prolonged, flat terminal phase. This profile precluded further development of these compounds as potential new antibiotics.
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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
| | - Carina Cantrill
- Roche
Pharma Research & Early Development, F. Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland
| | - Caterina Bissantz
- Roche
Pharma Research & Early Development, F. Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland
| | - Hongxia Qiu
- China
Innovation Center of Roche, Roche R&D
Center (China) Ltd., Shanghai 201203, China
| | - Christian Kramer
- Roche
Pharma Research & Early Development, F. Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland
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6
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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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7
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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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8
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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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9
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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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10
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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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11
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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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12
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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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13
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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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14
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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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15
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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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16
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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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17
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Novel bacterial topoisomerase inhibitors derived from isomannide. Eur J Med Chem 2020; 199:112324. [PMID: 32402932 DOI: 10.1016/j.ejmech.2020.112324] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 04/03/2020] [Accepted: 04/07/2020] [Indexed: 11/20/2022]
Abstract
A series of Novel Bacterial Topoisomerase Inhibitors (NBTIs) employing a linker derived from isomannide were synthesized and evaluated. Reduced hERG inhibition was observed compared to structure-matched analogues with different linkers, and compound 6 showed minimal proarrhythmic potential using an in vitro panel of cardiac ion channels. Compound 6 also displayed excellent activity against fluoroquinolone-resistant MRSA (MIC90 = 2 μg/mL) and other Gram-positive pathogens.
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18
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Kolarič A, Anderluh M, Minovski N. Two Decades of Successful SAR-Grounded Stories of the Novel Bacterial Topoisomerase Inhibitors (NBTIs). J Med Chem 2020; 63:5664-5674. [PMID: 32027491 PMCID: PMC7307926 DOI: 10.1021/acs.jmedchem.9b01738] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The emergence of bacterial resistance against life-saving medicines has forced the scientific community and pharmaceutical industry to take actions in the quest for novel antibacterials. These should not only overcome the existing bacterial resistance but also provide at least interim effective protection against emerging bacterial infections. Research into DNA gyrase and topoisomerase IV inhibitors has become a particular focus, with the description of a new class of bacterial topoisomerase type II inhibitors known as "novel bacterial topoisomerase inhibitors", NBTIs. Elucidation of the key structural modifications incorporated into these inhibitors and the impact these can have on their general physicochemical properties are detailed in this review. This defines novel bacterial topoisomerase inhibitors with promising antibacterial activities and potencies, which thus represent one potential example of the future "drugs for bad bugs", as identified by the World Health Organization.
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Affiliation(s)
- Anja Kolarič
- Laboratory for Cheminformatics, Theory Department, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia.,Chair of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia
| | - Marko Anderluh
- Chair of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia
| | - Nikola Minovski
- Laboratory for Cheminformatics, Theory Department, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
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19
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Magarò G, Prati F, Garofalo B, Corso G, Furlotti G, Apicella C, Mangano G, D'Atanasio N, Robinson D, Di Giorgio FP, Ombrato R. Virtual Screening Approach and Investigation of Structure-Activity Relationships To Discover Novel Bacterial Topoisomerase Inhibitors Targeting Gram-Positive and Gram-Negative Pathogens. J Med Chem 2019; 62:7445-7472. [PMID: 31276392 DOI: 10.1021/acs.jmedchem.9b00394] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacterial resistance is increasing rapidly, requiring urgent identification of new antibacterial drugs that are effective against multidrug-resistant pathogens. Novel bacterial topoisomerase inhibitors (NBTIs) provide a new strategy for investigating the well-validated DNA gyrase and topoisomerase IV targets while preventing cross-resistance issues. On this basis, starting from a virtual screening campaign and subsequent structure-based hit optimization guided by X-ray studies, a novel class of piperazine-like NBTIs with outstanding enzymatic activity against Staphylococcus aureus and Escherichia coli DNA gyrase and topoisomerase IV was identified. Notably, compounds (±)-33, (±)-35, and (±)-36 with potent and balanced multitarget enzymatic profiles exhibited excellent efficacy against selected Gram-positive and Gram-negative pathogens, as well as clinically relevant resistant strains. Overall, the new NBTI chemotype described herein, owing to the broad-spectrum antibacterial activity and favorable in vitro safety profile, might serve as a basis for the development of novel treatments against serious infections.
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Affiliation(s)
- Gabriele Magarò
- Angelini RR&D (Research, Regulatory & Development) , Angelini S.p.A. , Piazzale della Stazione SNC, S. Palomba-Pomezia , Rome 00071 , Italy
| | - Federica Prati
- Angelini RR&D (Research, Regulatory & Development) , Angelini S.p.A. , Piazzale della Stazione SNC, S. Palomba-Pomezia , Rome 00071 , Italy
| | - Barbara Garofalo
- Angelini RR&D (Research, Regulatory & Development) , Angelini S.p.A. , Piazzale della Stazione SNC, S. Palomba-Pomezia , Rome 00071 , Italy
| | - Gaia Corso
- Angelini RR&D (Research, Regulatory & Development) , Angelini S.p.A. , Piazzale della Stazione SNC, S. Palomba-Pomezia , Rome 00071 , Italy
| | - Guido Furlotti
- Angelini RR&D (Research, Regulatory & Development) , Angelini S.p.A. , Piazzale della Stazione SNC, S. Palomba-Pomezia , Rome 00071 , Italy
| | - Claudia Apicella
- Angelini RR&D (Research, Regulatory & Development) , Angelini S.p.A. , Piazzale della Stazione SNC, S. Palomba-Pomezia , Rome 00071 , Italy
| | - Giorgina Mangano
- Angelini RR&D (Research, Regulatory & Development) , Angelini S.p.A. , Piazzale della Stazione SNC, S. Palomba-Pomezia , Rome 00071 , Italy
| | - Noemi D'Atanasio
- Angelini RR&D (Research, Regulatory & Development) , Angelini S.p.A. , Piazzale della Stazione SNC, S. Palomba-Pomezia , Rome 00071 , Italy
| | - Daniel Robinson
- Schrodinger , 120 West 45th Street , New York , New York 10036 , United States
| | - Francesco Paolo Di Giorgio
- Angelini RR&D (Research, Regulatory & Development) , Angelini S.p.A. , Piazzale della Stazione SNC, S. Palomba-Pomezia , Rome 00071 , Italy
| | - Rosella Ombrato
- Angelini RR&D (Research, Regulatory & Development) , Angelini S.p.A. , Piazzale della Stazione SNC, S. Palomba-Pomezia , Rome 00071 , Italy
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20
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Li L, Okumu AA, Nolan S, English A, Vibhute S, Lu Y, Hervert-Thomas K, Seffernick JT, Azap L, Cole SL, Shinabarger D, Koeth LM, Lindert S, Yalowich JC, Wozniak DJ, Mitton-Fry MJ. 1,3-Dioxane-Linked Bacterial Topoisomerase Inhibitors with Enhanced Antibacterial Activity and Reduced hERG Inhibition. ACS Infect Dis 2019; 5:1115-1128. [PMID: 31041863 DOI: 10.1021/acsinfecdis.8b00375] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The development of new therapies to treat methicillin-resistant Staphylococcus aureus (MRSA) is needed to counteract the significant threat that MRSA presents to human health. Novel inhibitors of DNA gyrase and topoisomerase IV (TopoIV) constitute one highly promising approach, but continued optimization is required to realize the full potential of this class of antibiotics. Herein, we report further studies on a series of dioxane-linked derivatives, demonstrating improved antistaphylococcal activity and reduced hERG inhibition. A subseries of analogues also possesses enhanced inhibition of the secondary target, TopoIV.
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Affiliation(s)
- Linsen Li
- Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, 500 West 12th Avenue, Columbus, Ohio 43210, United States
| | - Antony A. Okumu
- Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, 500 West 12th Avenue, Columbus, Ohio 43210, United States
| | - Sheri Nolan
- Microbial Infection and Immunity, The Ohio State University, 460 West 12th Avenue, Columbus, Ohio 43210, United States
| | - Anthony English
- Division of Pharmacology, The Ohio State University, 500 West 12th Avenue, Columbus, Ohio 43210, United States
| | - Sandip Vibhute
- Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, 500 West 12th Avenue, Columbus, Ohio 43210, United States
| | - Yanran Lu
- Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, 500 West 12th Avenue, Columbus, Ohio 43210, United States
| | - Katherine Hervert-Thomas
- Department of Chemistry, Ohio Wesleyan University, 61 South Sandusky Street, Delaware, Ohio 43015, United States
| | - Justin T. Seffernick
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Lovette Azap
- Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, 500 West 12th Avenue, Columbus, Ohio 43210, United States
| | - Serena L. Cole
- Micromyx, 4717 Campus Drive, Kalamazoo, Michigan 49008, United States
| | - D. Shinabarger
- Micromyx, 4717 Campus Drive, Kalamazoo, Michigan 49008, United States
| | - Laura M. Koeth
- Laboratory Specialists, Inc., 26214 Center Ridge Road, Westlake, Ohio 44145, United States
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Jack C. Yalowich
- Division of Pharmacology, The Ohio State University, 500 West 12th Avenue, Columbus, Ohio 43210, United States
| | - Daniel J. Wozniak
- Microbial Infection and Immunity, The Ohio State University, 460 West 12th Avenue, Columbus, Ohio 43210, United States
- Department of Microbiology, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210, United States
| | - Mark J. Mitton-Fry
- Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, 500 West 12th Avenue, Columbus, Ohio 43210, United States
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DNA Topoisomerase Inhibitors: Trapping a DNA-Cleaving Machine in Motion. J Mol Biol 2019; 431:3427-3449. [PMID: 31301408 PMCID: PMC6723622 DOI: 10.1016/j.jmb.2019.07.008] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 06/24/2019] [Accepted: 07/02/2019] [Indexed: 12/29/2022]
Abstract
Type II topoisomerases regulate DNA topology by making a double-stranded break in one DNA duplex, transporting another DNA segment through this break and then resealing it. Bacterial type IIA topoisomerase inhibitors, such as fluoroquinolones and novel bacterial topoisomerase inhibitors, can trap DNA cleavage complexes with double- or single-stranded cleaved DNA. To study the mode of action of such compounds, 21 crystal structures of a “gyraseCORE” fusion truncate of Staphyloccocus aureus DNA gyrase complexed with DNA and diverse inhibitors have been published, as well as 4 structures lacking inhibitors. These structures have the DNA in various cleavage states and appear to track trajectories along the catalytic paths of the DNA cleavage/religation steps. The various conformations sampled by these multiple “gyraseCORE” structures show rigid body movements of the catalytic GyrA WHD and GyrB TOPRIM domains across the dimer interface. Conformational changes common to all compound-bound structures suggest common mechanisms for DNA cleavage-stabilizing compounds. The structures suggest that S. aureus gyrase uses a single moving-metal ion for cleavage and that the central four base pairs need to be stretched between the two catalytic sites, in order for a scissile phosphate to attract a metal ion to the A-site to catalyze cleavage, after which it is “stored” in another coordination configuration (B-site) in the vicinity. We present a simplified model for the catalytic cycle in which capture of the transported DNA segment causes conformational changes in the ATPase domain that push the DNA gate open, resulting in stretching and cleaving the gate-DNA in two steps. Type II DNA topoisomerases, such as DNA gyrase, control the topological state of DNA in all cells. As these enzymes bind, cleave and re-ligate DNA, multiple binding pockets for small compounds appear. We discuss how crystal structures of gyrase, DNA and different compounds may be trapping different stages in the catalytic cycle of the enzyme. We propose a model for DNA strand cleavage involving a moving metal ion.
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