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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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Collins J, Basarab GS, Chibale K, Osheroff N. Interactions between Zoliflodacin and Neisseria gonorrhoeae Gyrase and Topoisomerase IV: Enzymological Basis for Cellular Targeting. ACS Infect Dis 2024; 10:3071-3082. [PMID: 39082980 PMCID: PMC11320581 DOI: 10.1021/acsinfecdis.4c00438] [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: 05/28/2024] [Revised: 07/09/2024] [Accepted: 07/16/2024] [Indexed: 08/10/2024]
Abstract
Gyrase and topoisomerase IV are the cellular targets for fluoroquinolones, a critically important class of antibacterial agents used to treat a broad spectrum of human infections. Unfortunately, the clinical efficacy of the fluoroquinolones has been curtailed by the emergence of target-mediated resistance. This is especially true for Neisseria gonorrhoeae, the causative pathogen of the sexually transmitted infection gonorrhea. Spiropyrimidinetriones (SPTs), a new class of antibacterials, were developed to combat the growing antibacterial resistance crisis. Zoliflodacin is the most clinically advanced SPT and displays efficacy against uncomplicated urogenital gonorrhea in human trials. Like fluoroquinolones, the primary target of zoliflodacin in N. gonorrhoeae is gyrase, and topoisomerase IV is a secondary target. Because unbalanced gyrase/topoisomerase IV targeting has facilitated the evolution of fluoroquinolone-resistant bacteria, it is important to understand the underlying basis for the differential targeting of zoliflodacin in N. gonorrhoeae. Therefore, we assessed the effects of this SPT on the catalytic and DNA cleavage activities of N. gonorrhoeae gyrase and topoisomerase IV. In all reactions examined, zoliflodacin displayed higher potency against gyrase than topoisomerase IV. Moreover, zoliflodacin generated more DNA cleavage and formed more stable enzyme-cleaved DNA-SPT complexes with gyrase. The SPT also maintained higher activity against fluoroquinolone-resistant gyrase than topoisomerase IV. Finally, when compared to zoliflodacin, the novel SPT H3D-005722 induced more balanced double-stranded DNA cleavage with gyrase and topoisomerase IV from N. gonorrhoeae, Escherichia coli, and Bacillus anthracis. This finding suggests that further development of the SPT class could yield compounds with a more balanced targeting against clinically important bacterial infections.
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Affiliation(s)
- Jessica
A. Collins
- Department
of Biochemistry, Vanderbilt University School
of Medicine, Nashville, Tennessee 37232, United States
| | - Gregory S. Basarab
- Holistic
Drug Discovery and Development (H3D) Centre, University of Cape Town, Rondebosch 7701, South Africa
| | - Kelly Chibale
- Holistic
Drug Discovery and Development (H3D) Centre, and South African Medical
Research Council Drug Discovery and Development Research Unit, Department
of Chemistry and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch 7701, South Africa
| | - 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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3
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Germe TRM, Bush NG, Baskerville VM, Saman D, Benesch JLP, Maxwell A. Rapid, DNA-induced interface swapping by DNA gyrase. eLife 2024; 12:RP86722. [PMID: 38856655 PMCID: PMC11164529 DOI: 10.7554/elife.86722] [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] [Indexed: 06/11/2024] Open
Abstract
DNA gyrase, a ubiquitous bacterial enzyme, is a type IIA topoisomerase formed by heterotetramerisation of 2 GyrA subunits and 2 GyrB subunits, to form the active complex. DNA gyrase can loop DNA around the C-terminal domains (CTDs) of GyrA and pass one DNA duplex through a transient double-strand break (DSB) established in another duplex. This results in the conversion from a positive (+1) to a negative (-1) supercoil, thereby introducing negative supercoiling into the bacterial genome by steps of 2, an activity essential for DNA replication and transcription. The strong protein interface in the GyrA dimer must be broken to allow passage of the transported DNA segment and it is generally assumed that the interface is usually stable and only opens when DNA is transported, to prevent the introduction of deleterious DSBs in the genome. In this paper, we show that DNA gyrase can exchange its DNA-cleaving interfaces between two active heterotetramers. This so-called interface 'swapping' (IS) can occur within a few minutes in solution. We also show that bending of DNA by gyrase is essential for cleavage but not for DNA binding per se and favors IS. Interface swapping is also favored by DNA wrapping and an excess of GyrB. We suggest that proximity, promoted by GyrB oligomerization and binding and wrapping along a length of DNA, between two heterotetramers favors rapid interface swapping. This swapping does not require ATP, occurs in the presence of fluoroquinolones, and raises the possibility of non-homologous recombination solely through gyrase activity. The ability of gyrase to undergo interface swapping explains how gyrase heterodimers, containing a single active-site tyrosine, can carry out double-strand passage reactions and therefore suggests an alternative explanation to the recently proposed 'swivelling' mechanism for DNA gyrase (Gubaev et al., 2016).
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Affiliation(s)
- Thomas RM Germe
- Department Biochemistry & Metabolism, John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - Natassja G Bush
- Department Biochemistry & Metabolism, John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - Victoria M Baskerville
- Department Biochemistry & Metabolism, John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - Dominik Saman
- Department of Chemistry, Biochemistry Building, University of OxfordOxfordUnited Kingdom
| | - Justin LP Benesch
- Department of Chemistry, Biochemistry Building, University of OxfordOxfordUnited Kingdom
| | - Anthony Maxwell
- Department Biochemistry & Metabolism, John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
- Department of Molecular Microbiology, John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
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4
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French S, Guo ABY, Ellis MJ, Deisinger JP, Johnson JW, Rachwalski K, Piquette ZA, Lluka T, Zary M, Gamage S, Magolan J, Brown ED. A platform for predicting mechanism of action based on bacterial transcriptional responses identifies an unusual DNA gyrase inhibitor. Cell Rep 2024; 43:114053. [PMID: 38578824 DOI: 10.1016/j.celrep.2024.114053] [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: 04/26/2023] [Revised: 02/02/2024] [Accepted: 03/19/2024] [Indexed: 04/07/2024] Open
Abstract
In the search for much-needed new antibacterial chemical matter, a myriad of compounds have been reported in academic and pharmaceutical screening endeavors. Only a small fraction of these, however, are characterized with respect to mechanism of action (MOA). Here, we describe a pipeline that categorizes transcriptional responses to antibiotics and provides hypotheses for MOA. 3D-printed imaging hardware PFIboxes) profiles responses of Escherichia coli promoter-GFP fusions to more than 100 antibiotics. Notably, metergoline, a semi-synthetic ergot alkaloid, mimics a DNA replication inhibitor. In vitro supercoiling assays confirm this prediction, and a potent analog thereof (MLEB-1934) inhibits growth at 0.25 μg/mL and is highly active against quinolone-resistant strains of methicillin-resistant Staphylococcus aureus. Spontaneous suppressor mutants map to a seldom explored allosteric binding pocket, suggesting a mechanism distinct from DNA gyrase inhibitors used in the clinic. In all, the work highlights the potential of this platform to rapidly assess MOA of new antibacterial compounds.
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Affiliation(s)
- Shawn French
- McMaster University, Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON L8S 4L8, Canada
| | - Amelia Bing Ya Guo
- McMaster University, Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON L8S 4L8, Canada
| | - Michael J Ellis
- McMaster University, Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON L8S 4L8, Canada
| | - Julia P Deisinger
- McMaster University, Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON L8S 4L8, Canada
| | - Jarrod W Johnson
- McMaster University, Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON L8S 4L8, Canada
| | - Kenneth Rachwalski
- McMaster University, Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON L8S 4L8, Canada
| | - Zoë A Piquette
- McMaster University, Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON L8S 4L8, Canada
| | - Telmah Lluka
- McMaster University, Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON L8S 4L8, Canada
| | - Miranda Zary
- McMaster University, Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON L8S 4L8, Canada
| | - Sineli Gamage
- McMaster University, Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON L8S 4L8, Canada
| | - Jakob Magolan
- McMaster University, Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON L8S 4L8, Canada
| | - Eric D Brown
- McMaster University, Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON L8S 4L8, Canada.
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5
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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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6
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Eygeris Y, Gupta M, Kim J, Jozic A, Gautam M, Renner J, Nelson D, Bloom E, Tuttle A, Stoddard J, Reynaga R, Neuringer M, Lauer AK, Ryals RC, Sahay G. Thiophene-based lipids for mRNA delivery to pulmonary and retinal tissues. Proc Natl Acad Sci U S A 2024; 121:e2307813120. [PMID: 38437570 PMCID: PMC10945828 DOI: 10.1073/pnas.2307813120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 09/16/2023] [Indexed: 03/06/2024] Open
Abstract
Lipid nanoparticles (LNPs) largely rely on ionizable lipids to yield successful nucleic acid delivery via electrostatic disruption of the endosomal membrane. Here, we report the identification and evaluation of ionizable lipids containing a thiophene moiety (Thio-lipids). The Thio-lipids can be readily synthesized via the Gewald reaction, allowing for modular lipid design with functional constituents at various positions of the thiophene ring. Through the rational design of ionizable lipid structure, we prepared 47 Thio-lipids and identified some structural criteria required in Thio-lipids for efficient mRNA (messenger RNA) encapsulation and delivery in vitro and in vivo. Notably, none of the tested lipids have a pH-response profile like traditional ionizable lipids, potentially due to the electron delocalization in the thiophene core. Placement of the tails and localization of the ionizable headgroup in the thiophene core can endow the nanoparticles with the capability to reach various tissues. Using high-throughput formulation and barcoding techniques, we optimized the formulations to select two top lipids-20b and 29d-and investigated their biodistribution in mice. Lipid 20b enabled LNPs to transfect the liver and spleen, and 29d LNP transfected the lung and spleen. Unexpectedly, LNP with lipid 20b was especially potent in mRNA delivery to the retina with no acute toxicity, leading to the successful delivery to the photoreceptors and retinal pigment epithelium in non-human primates.
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Affiliation(s)
- Yulia Eygeris
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Portland, OR97201
- EnterX Biosciences, Inc., Portland, OR97214
| | - Mohit Gupta
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Portland, OR97201
| | - Jeonghwan Kim
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Portland, OR97201
- College of Pharmacy, Yeungnam University, Gyeongsan38541, Republic of Korea
| | - Antony Jozic
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Portland, OR97201
| | - Milan Gautam
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Portland, OR97201
| | - Jonas Renner
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Portland, OR97201
| | - Dylan Nelson
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Portland, OR97201
- EnterX Biosciences, Inc., Portland, OR97214
| | - Elissa Bloom
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Portland, OR97201
| | | | - Jonathan Stoddard
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR97006
| | - Rene Reynaga
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR97006
| | - Martha Neuringer
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR97006
- Department of Ophthalmology, Casey Eye Institute, Oregon Health and Science University, Portland, OR97239
| | - Andreas K. Lauer
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR97006
- Department of Ophthalmology, Casey Eye Institute, Oregon Health and Science University, Portland, OR97239
| | - Renee C. Ryals
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR97006
- Department of Ophthalmology, Casey Eye Institute, Oregon Health and Science University, Portland, OR97239
| | - Gaurav Sahay
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Portland, OR97201
- Department of Ophthalmology, Casey Eye Institute, Oregon Health and Science University, Portland, OR97239
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR97201
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7
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Ruan S, Tu CH, Bourne CR. Friend or Foe: Protein Inhibitors of DNA Gyrase. BIOLOGY 2024; 13:84. [PMID: 38392303 PMCID: PMC10886550 DOI: 10.3390/biology13020084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/20/2024] [Accepted: 01/26/2024] [Indexed: 02/24/2024]
Abstract
DNA gyrase is essential for the successful replication of circular chromosomes, such as those found in most bacterial species, by relieving topological stressors associated with unwinding the double-stranded genetic material. This critical central role makes gyrase a valued target for antibacterial approaches, as exemplified by the highly successful fluoroquinolone class of antibiotics. It is reasonable that the activity of gyrase could be intrinsically regulated within cells, thereby helping to coordinate DNA replication with doubling times. Numerous proteins have been identified to exert inhibitory effects on DNA gyrase, although at lower doses, it can appear readily reversible and therefore may have regulatory value. Some of these, such as the small protein toxins found in plasmid-borne addiction modules, can promote cell death by inducing damage to DNA, resulting in an analogous outcome as quinolone antibiotics. Others, however, appear to transiently impact gyrase in a readily reversible and non-damaging mechanism, such as the plasmid-derived Qnr family of DNA-mimetic proteins. The current review examines the origins and known activities of protein inhibitors of gyrase and highlights opportunities to further exert control over bacterial growth by targeting this validated antibacterial target with novel molecular mechanisms. Furthermore, we are gaining new insights into fundamental regulatory strategies of gyrase that may prove important for understanding diverse growth strategies among different bacteria.
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Affiliation(s)
- Shengfeng Ruan
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
| | - Chih-Han Tu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
| | - Christina R Bourne
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
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8
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Lee JC, Shirey RJ, Turner LD, Park H, Lairson LL, Janda KD. Discovery of PLD4 modulators by high-throughput screening and kinetic analysis. RESULTS IN CHEMISTRY 2024; 7:101349. [PMID: 38560090 PMCID: PMC10977906 DOI: 10.1016/j.rechem.2024.101349] [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] [Indexed: 04/04/2024] Open
Abstract
Phospholipase D3 (PLD3) and D4 (PLD4) are endolysosomal exonucleases of ssDNA and ssRNA that regulate innate immunity. Polymorphisms of these enzymes are correlated with numerous human diseases, including Alzheimer's, rheumatoid arthritis, and systemic sclerosis. Pharmacological modulation of these immunoregulatory proteins may yield novel immunotherapies and adjuvants. A previous study reported a high-throughput screen (N = 17,952) that discovered a PLD3-selective activator and inhibitor, as well as a nonselective inhibitor, but failed to identify selective modulators of PLD4. However, modulators selective for PLD4 are therapeutically pertinent, since recent reports have shown that regulating this protein has direct implications in cancer and autoimmune diseases. Furthermore, the high expression of PLD4 in dendritic and myeloid cells, in comparison to the broader expression of PLD3, presents the opportunity for a cell-targeted immunotherapy. Here, we describe screening of an expended diversity library (N = 45,760) with an improved platform and report the discovery of one inhibitor and three activators selective for PLD4. Furthermore, kinetic modeling and structural analysis suggest mechanistic differences in the modulation of these hits. These findings further establish the utility of this screening platform and provide a set of chemical scaffolds to guide future small-molecule development for this novel immunoregulator target.
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Affiliation(s)
- Jinny Claire Lee
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute for Research and Medicine (WIRM), The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Ryan J. Shirey
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute for Research and Medicine (WIRM), The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Lewis D. Turner
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute for Research and Medicine (WIRM), The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Hyeri Park
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute for Research and Medicine (WIRM), The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Luke L. Lairson
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute for Research and Medicine (WIRM), The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Kim D. Janda
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute for Research and Medicine (WIRM), The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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9
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Badshah G, Gomes CMB, Ali S, Luz EQ, Silvério GL, Santana FS, Seckler D, Paixão DB, Schneider PH, Rampon DS. Palladium-Catalyzed Direct Selanylation of Chalcogenophenes and Arenes Assisted by 2-(Methylthio)amide. J Org Chem 2023; 88:14033-14047. [PMID: 37712931 DOI: 10.1021/acs.joc.3c01577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/16/2023]
Abstract
The direct and selective conversion of a C-H bond into a C-Se bond remains a significant challenge, which is even more intricate with substrates having an innate regioselectivity under several reaction conditions, such as chalcogenophenes. We overrode their selectivity toward selanylation using palladium, copper, and the 2-(methylthio)amide directing group. This chelation-assisted direct selanylation was also suitable for mono and double ortho functionalization of arenes. The mechanistic studies indicate high-valent Pd(IV) species in the catalytic cycle, a reversible C-H activation step, and Cu(II) as a sequestering agent for organoselenide byproducts.
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Affiliation(s)
- Gul Badshah
- Laboratory of Polymers and Catalysis(LaPoCa),Department of Chemistry, Federal University of Paraná, P.O. Box 19061, Curitiba 81531-980, Paraná, Brazil
| | - Carla M B Gomes
- Laboratory of Polymers and Catalysis(LaPoCa),Department of Chemistry, Federal University of Paraná, P.O. Box 19061, Curitiba 81531-980, Paraná, Brazil
| | - Sher Ali
- Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga 13635-900, São Paulo, Brazil
| | - Eduardo Q Luz
- Laboratory of Polymers and Catalysis(LaPoCa),Department of Chemistry, Federal University of Paraná, P.O. Box 19061, Curitiba 81531-980, Paraná, Brazil
| | - Gabriel L Silvério
- Laboratory of Polymers and Catalysis(LaPoCa),Department of Chemistry, Federal University of Paraná, P.O. Box 19061, Curitiba 81531-980, Paraná, Brazil
| | - Francielli S Santana
- Department of Chemistry, Federal University of Paraná, P.O. Box 19061, Curitiba 81531-990, Paraná, Brazil
| | - Diego Seckler
- Laboratory of Polymers and Catalysis(LaPoCa),Department of Chemistry, Federal University of Paraná, P.O. Box 19061, Curitiba 81531-980, Paraná, Brazil
| | - Douglas B Paixão
- Instituto de Química, Departamento de Química Orgânica, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91501-970, Rio Grande do Sul, Brazil
| | - Paulo H Schneider
- Instituto de Química, Departamento de Química Orgânica, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91501-970, Rio Grande do Sul, Brazil
| | - Daniel S Rampon
- Laboratory of Polymers and Catalysis(LaPoCa),Department of Chemistry, Federal University of Paraná, P.O. Box 19061, Curitiba 81531-980, Paraná, Brazil
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10
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Wen Y, Lun S, Jiao Y, Zhang W, Liu T, Yang F, Tang J, Bishai WR, Yu LF. Structure-directed identification of pyridine-2-methylamine derivatives as MmpL3 inhibitors for use as antitubercular agents. Eur J Med Chem 2023; 255:115351. [PMID: 37116266 PMCID: PMC10239758 DOI: 10.1016/j.ejmech.2023.115351] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 04/30/2023]
Abstract
Mycobacterial membrane protein Large 3 (MmpL3), an inner membrane protein, plays a crucial role in the transport of mycolic acids that are essential for the viability of M. tuberculosis and has been a promising therapeutic target for new anti-TB agents. Herein, we report the discovery of pyridine-2-methylamine antitubercular compounds using a structure-based drug design strategy. Compound 62 stands out as the most potent compound with high activity against M. tb strain H37Rv (MIC = 0.016 μg/mL) as well as the clinically isolated strains of MDR/XDR-TB (MIC = 0.0039-0.0625 μg/mL), low Vero cell toxicity (IC50 ≥ 16 μg/mL), and moderate liver microsomal stability (CLint = 28 μL/min/mg). Furthermore, the resistant mutant of S288T due to single nucleotide polymorphism in mmpL3 was resistant to pyridine-2-methylamine 62, demonstrating compound 62 is likely target to MmpL3.
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Affiliation(s)
- Yu Wen
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China
| | - Shichun Lun
- Center for Tuberculosis Research, Department of Medicine, Division of Infectious Disease, Johns Hopkins School of Medicine, Baltimore, MD, 21231-1044, United States
| | - Yuxue Jiao
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China
| | - Wei Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China
| | - Ting Liu
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China
| | - Fan Yang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China.
| | - Jie Tang
- Shanghai Key Laboratory of Green Chemistry and Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China
| | - William R Bishai
- Center for Tuberculosis Research, Department of Medicine, Division of Infectious Disease, Johns Hopkins School of Medicine, Baltimore, MD, 21231-1044, United States.
| | - Li-Fang Yu
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China.
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11
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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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12
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A 2.8 Å Structure of Zoliflodacin in a DNA Cleavage Complex with Staphylococcus aureus DNA Gyrase. Int J Mol Sci 2023; 24:ijms24021634. [PMID: 36675148 PMCID: PMC9865888 DOI: 10.3390/ijms24021634] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/04/2023] [Accepted: 01/07/2023] [Indexed: 01/17/2023] Open
Abstract
Since 2000, some thirteen quinolones and fluoroquinolones have been developed and have come to market. The quinolones, one of the most successful classes of antibacterial drugs, stabilize DNA cleavage complexes with DNA gyrase and topoisomerase IV (topo IV), the two bacterial type IIA topoisomerases. The dual targeting of gyrase and topo IV helps decrease the likelihood of resistance developing. Here, we report on a 2.8 Å X-ray crystal structure, which shows that zoliflodacin, a spiropyrimidinetrione antibiotic, binds in the same DNA cleavage site(s) as quinolones, sterically blocking DNA religation. The structure shows that zoliflodacin interacts with highly conserved residues on GyrB (and does not use the quinolone water-metal ion bridge to GyrA), suggesting it may be more difficult for bacteria to develop target mediated resistance. We show that zoliflodacin has an MIC of 4 µg/mL against Acinetobacter baumannii (A. baumannii), an improvement of four-fold over its progenitor QPT-1. The current phase III clinical trial of zoliflodacin for gonorrhea is due to be read out in 2023. Zoliflodacin, together with the unrelated novel bacterial topoisomerase inhibitor gepotidacin, is likely to become the first entirely novel chemical entities approved against Gram-negative bacteria in the 21st century. Zoliflodacin may also become the progenitor of a new safer class of antibacterial drugs against other problematic Gram-negative bacteria.
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13
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Imai Y, Hauk G, Quigley J, Liang L, Son S, Ghiglieri M, Gates MF, Morrissette M, Shahsavari N, Niles S, Baldisseri D, Honrao C, Ma X, Guo JJ, Berger JM, Lewis K. Evybactin is a DNA gyrase inhibitor that selectively kills Mycobacterium tuberculosis. Nat Chem Biol 2022; 18:1236-1244. [PMID: 35996001 PMCID: PMC9844538 DOI: 10.1038/s41589-022-01102-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 06/30/2022] [Indexed: 01/19/2023]
Abstract
The antimicrobial resistance crisis requires the introduction of novel antibiotics. The use of conventional broad-spectrum compounds selects for resistance in off-target pathogens and harms the microbiome. This is especially true for Mycobacterium tuberculosis, where treatment requires a 6-month course of antibiotics. Here we show that a novel antimicrobial from Photorhabdus noenieputensis, which we named evybactin, is a potent and selective antibiotic acting against M. tuberculosis. Evybactin targets DNA gyrase and binds to a site overlapping with synthetic thiophene poisons. Given the conserved nature of DNA gyrase, the observed selectivity against M. tuberculosis is puzzling. We found that evybactin is smuggled into the cell by a promiscuous transporter of hydrophilic compounds, BacA. Evybactin is the first, but likely not the only, antimicrobial compound found to employ this unusual mechanism of selectivity.
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Affiliation(s)
- Yu Imai
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA.,Present address: Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, Nagano, Japan.,These authors contributed equally: Yu Imai, Glenn Hauk
| | - Glenn Hauk
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,These authors contributed equally: Yu Imai, Glenn Hauk
| | - Jeffrey Quigley
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA
| | - Libang Liang
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA
| | - Sangkeun Son
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA
| | - Meghan Ghiglieri
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA
| | - Michael F. Gates
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA
| | - Madeleine Morrissette
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA
| | - Negar Shahsavari
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA
| | - Samantha Niles
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA
| | | | - Chandrashekhar Honrao
- Center for Drug Discovery, Department of Pharmaceutical Sciences, Northeastern University, Boston, MA, USA
| | - Xiaoyu Ma
- Center for Drug Discovery, Department of Pharmaceutical Sciences, Northeastern University, Boston, MA, USA
| | - Jason J. Guo
- Center for Drug Discovery, Department of Pharmaceutical Sciences, Northeastern University, Boston, MA, USA.,Barnett Institute for Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - James M. Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Correspondence and requests for materials should be addressed to James M. Berger or Kim Lewis. ;
| | - Kim Lewis
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA.,Correspondence and requests for materials should be addressed to James M. Berger or Kim Lewis. ;
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14
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Salman M, Sharma P, Kumar M, Ethayathulla AS, Kaur P. Targeting novel sites in DNA gyrase for development of anti-microbials. Brief Funct Genomics 2022; 22:180-194. [PMID: 36064602 DOI: 10.1093/bfgp/elac029] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 07/28/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
Antimicrobial resistance in bacteria poses major challenges in selection of the therapeutic regime for managing the infectious disease. There is currently an upsurge in the appearance of multiple drug resistance in bacterial pathogens and a decline in the discovery of novel antibiotics. DNA gyrase is an attractive target used for antibiotic discovery due to its vital role in bacterial DNA replication and segregation in addition to its absence in mammalian organisms. Despite the presence of successful antibiotics targeting this enzyme, there is a need to bypass the resistance against this validated drug target. Hence, drug development in DNA gyrase is a highly active research area. In addition to the conventional binding sites for the novobiocin and fluoroquinolone antibiotics, several novel sites are being exploited for drug discovery. The binding sites for novel bacterial type II topoisomerase inhibitor (NBTI), simocyclinone, YacG, Thiophene and CcdB are structurally and biochemically validated active sites, which inhibit the supercoiling activity of topoisomerases. The novel chemical moieties with varied scaffolds have been identified to target DNA gyrase. Amongst them, the NBTI constitutes the most advanced DNA gyrase inhibitor which are in phase III trial of drug development. The present review aims to classify the novel binding sites other than the conventional novobiocin and quinolone binding pocket to bypass the resistance due to mutations in the DNA gyrase enzyme. These sites can be exploited for the identification of new scaffolds for the development of novel antibacterial compounds.
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Affiliation(s)
- Mohd Salman
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Priyanka Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Mukesh Kumar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - A S Ethayathulla
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Punit Kaur
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
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15
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Studies on the antibacterial activities and molecular mechanism of GyrB inhibitors by 3D-QSAR, molecular docking and molecular dynamics simulation. ARAB J CHEM 2022. [DOI: 10.1016/j.arabjc.2022.103872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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16
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Juliana Martins F, Savacini Sagrillo F, Josiane Vinturelle Medeiros R, Gonçalves de Souza A, Rodrigues Pinto Costa A, Silva Novais J, Alves Miceli L, R Campos V, Marie Sá Figueiredo A, Claudia Cunha A, Lidmar von Ranke N, Lamim Bello M, de A Abrahim-Vieira B, M T De Souza A, A Ratcliffe N, da Costa Santos Boechat F, Cecília Bastos Vieira de Souza M, Rangel Rodrigues C, Carla Castro H. Evaluation of biological activities of quinone-4-oxoquinoline derivatives against pathogens of clinical importance. Curr Top Med Chem 2022; 22:973-991. [PMID: 35524665 DOI: 10.2174/1568026622666220504124710] [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: 12/16/2021] [Revised: 03/02/2022] [Accepted: 03/17/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND Microbial resistance has become a worldwide public health problem, and may lead to morbidity and mortality in affected patients. OBJECTIVE Therefore, this work aimed to evaluate the antibacterial activity of quinone-4-oxoquinoline derivatives. METHOD These derivatives were evaluated against Gram-positive and Gram-negative bacteria by their antibacterial activity, anti-biofilm, and hemolytic activities and by in silico assays. RESULTS The quinone-4-oxoquinoline derivatives presented broad-spectrum antibacterial activities, and in some cases were more active than commercially available reference drugs. These compounds also inhibited bacterial adhesion and the assays revealed seven non-hemolytic derivatives. The derivatives seem to cause damage to the bacterial cell membrane and those containing the carboxyl group at the C-3 position of the 4-quinolonic nucleus were more active than those containing a carboxyethyl group. CONCLUSION The isoquinoline-5,8-dione nucleus also favored antimicrobial activity. The study showed that the target of the derivatives must be a non-conventional hydrophobic allosteric binding pocket on the DNA gyrase enzyme.
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Affiliation(s)
- Francislene Juliana Martins
- Federal Fluminense University, Biology Institute, Postgraduate Program in Science and Biotechnology, Niterói, Rio de Janeiro, Brazil
| | - Fernanda Savacini Sagrillo
- Federal Fluminense University, Chemistry Institute, Department of Organic Chemistry, Niterói, Rio de Janeiro, Brazil
| | | | - Alan Gonçalves de Souza
- Federal Fluminense University, Chemistry Institute, Department of Organic Chemistry, Niterói, Rio de Janeiro, Brazil
| | - Amanda Rodrigues Pinto Costa
- Federal Fluminense University, Chemistry Institute, Department of Organic Chemistry, Niterói, Rio de Janeiro, Brazil
| | - Juliana Silva Novais
- Federal Fluminense University, Medical School, Postgraduate in Pathology, Niterói, Rio de Janeiro, Brazil.,Universidade Estácio de Sá (UNESA), Faculdade de Farmácia, São Gonçalo, Rio de Janeiro, Brazil
| | - Leonardo Alves Miceli
- Federal University of Rio de Janeiro, Faculdade de Farmácia, Departamento de Fármacos e Medicamentos, Rio de Janeiro, Brazil
| | - Vinícius R Campos
- Federal Fluminense University, Chemistry Institute, Department of Organic Chemistry, Niterói, Rio de Janeiro, Brazil
| | - Agnes Marie Sá Figueiredo
- Federal University of Rio de Janeiro, Microbiology Institute Professor Paulo Goes, Department of Medical Microbiology, Rio de Janeiro, Brazil
| | - Anna Claudia Cunha
- Federal Fluminense University, Chemistry Institute, Department of Organic Chemistry, Niterói, Rio de Janeiro, Brazil
| | - Natalia Lidmar von Ranke
- Federal University of Rio de Janeiro, Faculdade de Farmácia, Departamento de Fármacos e Medicamentos, Rio de Janeiro, Brazil
| | - Murilo Lamim Bello
- Federal University of Rio de Janeiro, Faculdade de Farmácia, Departamento de Fármacos e Medicamentos, Rio de Janeiro, Brazil
| | - Bárbara de A Abrahim-Vieira
- Federal University of Rio de Janeiro, Faculdade de Farmácia, Departamento de Fármacos e Medicamentos, Rio de Janeiro, Brazil
| | - Alessandra M T De Souza
- Federal University of Rio de Janeiro, Faculdade de Farmácia, Departamento de Fármacos e Medicamentos, Rio de Janeiro, Brazil
| | - Norman A Ratcliffe
- Department of Biosciences, College of Science Swansea University, SA2 8PP. UK
| | | | | | - Carlos Rangel Rodrigues
- Federal University of Rio de Janeiro, Faculdade de Farmácia, Departamento de Fármacos e Medicamentos, Rio de Janeiro, Brazil
| | - Helena Carla Castro
- Federal Fluminense University, Biology Institute, Postgraduate Program in Science and Biotechnology, Niterói, Rio de Janeiro, Brazil
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17
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Roman G. Thiophene-containing compounds with antimicrobial activity. Arch Pharm (Weinheim) 2022; 355:e2100462. [PMID: 35289443 DOI: 10.1002/ardp.202100462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/08/2022] [Accepted: 02/10/2022] [Indexed: 12/19/2022]
Abstract
Thiophene, as a member of the group of five-membered heterocycles containing one heteroatom, is one of the simplest heterocyclic systems. Many synthetic strategies allow the accurate positioning of various functionalities onto the thiophene ring. This review provides a comprehensive, systematic and detailed account of the developments in the field of antimicrobial compounds featuring at least one thiophene ring in their structure, over the last decade.
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Affiliation(s)
- Gheorghe Roman
- Department of Inorganic Polymers, Petru Poni Institute of Macromolecular Chemistry, Iaşi, Romania
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18
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Exploitation of a novel allosteric binding region in DNA gyrase and its implications for antibacterial drug discovery. Future Med Chem 2021; 13:2125-2127. [PMID: 34605249 DOI: 10.4155/fmc-2021-0266] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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19
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EVREN AE, DAWBAA S, NUHA D, YAVUZ ŞA, GÜL ÜD, YURTTAŞ L. Design and synthesis of new 4-methylthiazole derivatives: In vitro and in silico studies of antimicrobial activity. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130692] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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20
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Messina C, Ottenwaelder X, Forgione P. Programmed Synthesis of Tetra-Aryl Thiophenes with Stepwise, Ester-Controlled Regioselectivity. Org Lett 2021; 23:7348-7352. [PMID: 34506149 DOI: 10.1021/acs.orglett.1c02447] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Herein, we report a modular synthetic route to access tetra-arylated thiophene compounds with four different substituents with programmed chemical control provided by an ester activating/directing group. This method enables the functionalization of individual positions of thiophene sequentially via regioselective halogenations and cross-coupling reactions. The reaction sequence described provides tetra-arylated thiophenes in higher yields than previous routes and employs practical reaction protocols, simple catalytic systems, and short reaction times.
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Affiliation(s)
- Cynthia Messina
- Department of Chemistry and Biochemistry, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - Xavier Ottenwaelder
- Department of Chemistry and Biochemistry, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - Pat Forgione
- Department of Chemistry and Biochemistry, Concordia University, Montreal, Quebec H4B 1R6, Canada
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21
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Abstract
Malaria persists as a major health problem due to the spread of drug resistance and the lack of effective vaccines. DNA gyrase is a well-validated and extremely effective therapeutic target in bacteria, and it is also known to be present in the apicoplast of malarial species, including Plasmodium falciparum. This raises the possibility that it could be a useful target for novel antimalarials. To date, characterization and screening of this gyrase have been hampered by difficulties in cloning and purification of the GyrA subunit, which is necessary together with GyrB for reconstitution of the holoenzyme. To overcome this, we employed a library of compounds with specificity for P. falciparum GyrB and assessed them in activity tests utilizing P. falciparum GyrB together with Escherichia coli GyrA to reconstitute a functional hybrid enzyme. Two inhibitory compounds were identified that preferentially inhibited the supercoiling activity of the hybrid enzyme over the E. coli enzyme. Of these, purpurogallin (PPG) was found to disrupt DNA binding to the hybrid gyrase complex and thus reduce the DNA-induced ATP hydrolysis of the enzyme. Binding studies indicated that PPG showed higher-affinity binding to P. falciparum GyrB than to the E. coli protein. We suggest that PPG achieves its inhibitory effect on gyrase through interaction with P. falciparum GyrB leading to disruption of DNA binding and, consequently, reduction of DNA-induced ATPase activity. The compound also showed an inhibitory effect against the malaria parasite in vitro and may be of interest for further development as an antimalarial agent.
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22
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Towards Conformation-Sensitive Inhibition of Gyrase: Implications of Mechanistic Insight for the Identification and Improvement of Inhibitors. Molecules 2021; 26:molecules26051234. [PMID: 33669078 PMCID: PMC7956263 DOI: 10.3390/molecules26051234] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 02/19/2021] [Accepted: 02/20/2021] [Indexed: 12/17/2022] Open
Abstract
Gyrase is a bacterial type IIA topoisomerase that catalyzes negative supercoiling of DNA. The enzyme is essential in bacteria and is a validated drug target in the treatment of bacterial infections. Inhibition of gyrase activity is achieved by competitive inhibitors that interfere with ATP- or DNA-binding, or by gyrase poisons that stabilize cleavage complexes of gyrase covalently bound to the DNA, leading to double-strand breaks and cell death. Many of the current inhibitors suffer from severe side effects, while others rapidly lose their antibiotic activity due to resistance mutations, generating an unmet medical need for novel, improved gyrase inhibitors. DNA supercoiling by gyrase is associated with a series of nucleotide- and DNA-induced conformational changes, yet the full potential of interfering with these conformational changes as a strategy to identify novel, improved gyrase inhibitors has not been explored so far. This review highlights recent insights into the mechanism of DNA supercoiling by gyrase and illustrates the implications for the identification and development of conformation-sensitive and allosteric inhibitors.
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23
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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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24
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2-Methoxy-5-(6-methoxypyridin-3-yl-imino-methyl)phenol and its transition metal complexes as potent antibacterial agents: Synthesis, characterization, theoretical investigations and biological evaluation. RESULTS IN CHEMISTRY 2021. [DOI: 10.1016/j.rechem.2021.100120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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25
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Bush NG, Diez-Santos I, Abbott LR, Maxwell A. Quinolones: Mechanism, Lethality and Their Contributions to Antibiotic Resistance. Molecules 2020; 25:E5662. [PMID: 33271787 PMCID: PMC7730664 DOI: 10.3390/molecules25235662] [Citation(s) in RCA: 125] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/27/2020] [Accepted: 11/28/2020] [Indexed: 12/05/2022] Open
Abstract
Fluoroquinolones (FQs) are arguably among the most successful antibiotics of recent times. They have enjoyed over 30 years of clinical usage and become essential tools in the armoury of clinical treatments. FQs target the bacterial enzymes DNA gyrase and DNA topoisomerase IV, where they stabilise a covalent enzyme-DNA complex in which the DNA is cleaved in both strands. This leads to cell death and turns out to be a very effective way of killing bacteria. However, resistance to FQs is increasingly problematic, and alternative compounds are urgently needed. Here, we review the mechanisms of action of FQs and discuss the potential pathways leading to cell death. We also discuss quinolone resistance and how quinolone treatment can lead to resistance to non-quinolone antibiotics.
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Affiliation(s)
| | | | | | - Anthony Maxwell
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK; (N.G.B.); (I.D.-S.); (L.R.A.)
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Recent advances in DNA gyrase-targeted antimicrobial agents. Eur J Med Chem 2020; 199:112326. [DOI: 10.1016/j.ejmech.2020.112326] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 04/07/2020] [Accepted: 04/08/2020] [Indexed: 12/16/2022]
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27
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Shetye GS, Franzblau SG, Cho S. New tuberculosis drug targets, their inhibitors, and potential therapeutic impact. Transl Res 2020; 220:68-97. [PMID: 32275897 DOI: 10.1016/j.trsl.2020.03.007] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 02/28/2020] [Accepted: 03/09/2020] [Indexed: 11/18/2022]
Abstract
The current tuberculosis (TB) predicament poses numerous challenges and therefore every incremental scientific work and all positive socio-political engagements, are steps taken in the right direction to eradicate TB. Progression of the late stage TB-drug pipeline into the clinics is an immediate deliverable of this global effort. At the same time, fueling basic research and pursuing early discovery work must be sustained to maintain a healthy TB-drug pipeline. This review encompasses a broad analysis of chemotherapeutic strategies that target the DNA replication, protein synthesis, cell wall biosynthesis, energy metabolism and proteolysis of Mycobacterium tuberculosis (Mtb). It includes a status check of the current TB-drug pipeline with a focus on the associated biology, emerging targets, and their promising chemical inhibitors. Potential synergies and/or gaps within or across different chemotherapeutic strategies are systematically reviewed as well.
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Affiliation(s)
- Gauri S Shetye
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois
| | - Scott G Franzblau
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois
| | - Sanghyun Cho
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois.
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Ghannam IA, Abd El-Meguid EA, Ali IH, Sheir DH, El Kerdawy AM. Novel 2-arylbenzothiazole DNA gyrase inhibitors: Synthesis, antimicrobial evaluation, QSAR and molecular docking studies. Bioorg Chem 2019; 93:103373. [DOI: 10.1016/j.bioorg.2019.103373] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 10/06/2019] [Accepted: 10/16/2019] [Indexed: 11/29/2022]
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Singer AC, Kirchhelle C, Roberts AP. (Inter)nationalising the antibiotic research and development pipeline. THE LANCET. INFECTIOUS DISEASES 2019; 20:e54-e62. [PMID: 31753765 DOI: 10.1016/s1473-3099(19)30552-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 08/28/2019] [Accepted: 09/11/2019] [Indexed: 01/03/2023]
Abstract
In this Personal View, we critically examine the wider context of international efforts to stimulate commercial antibiotic research and development via public-private initiatives. Despite these efforts, antibiotics remain a global resource without an international support structure that is commensurate to the risks from antibiotic-resistant infections and the long-term nature of required solutions. To protect this resource, we propose a two-pronged antibiotic research and development strategy based on a short-term strengthening of incentives (such as market entry rewards) to maximise the delivery of existing opportunities in the pipeline, and on a concurrent medium-term to long-term establishment of a global, publicly funded antibiotic research and development institute. Designed sustainably to deliver novel and first-in-class antibiotics targeting key human health gaps, the institute and its staff would become a global resource that, unlike the private pharmaceutical sector, would be managed as an open science platform. Our model of internationalised public research and development would maximise scientific synergy and cross-fertilisation, minimise replication of effort, acquire and preserve existing know-how, and ensure equitable and sustainable access to novel and effective antibiotics. Its genuinely global focus would also help counteract tendencies to equate donor with global health priorities. Our proposal is not radical. Historical precedent and developments in other research areas show that sustained international funding of publicly owned research can hasten the delivery of critically needed drugs and lower barriers to access.
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Affiliation(s)
| | - Claas Kirchhelle
- Oxford Martin School and Wellcome Unit for the History of Medicine, University of Oxford, Oxford, UK
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30
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Vanden Broeck A, Lotz C, Ortiz J, Lamour V. Cryo-EM structure of the complete E. coli DNA gyrase nucleoprotein complex. Nat Commun 2019; 10:4935. [PMID: 31666516 PMCID: PMC6821735 DOI: 10.1038/s41467-019-12914-y] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 10/07/2019] [Indexed: 12/12/2022] Open
Abstract
DNA gyrase is an essential enzyme involved in the homeostatic control of DNA supercoiling and the target of successful antibacterial compounds. Despite extensive studies, a detailed architecture of the full-length DNA gyrase from the model organism E. coli is still missing. Herein, we report the complete structure of the E. coli DNA gyrase nucleoprotein complex trapped by the antibiotic gepotidacin, using phase-plate single-particle cryo-electron microscopy. Our data unveil the structural and spatial organization of the functional domains, their connections and the position of the conserved GyrA-box motif. The deconvolution of two states of the DNA-binding/cleavage domain provides a better understanding of the allosteric movements of the enzyme complex. The local atomic resolution in the DNA-bound area reaching up to 3.0 Å enables the identification of the antibiotic density. Altogether, this study paves the way for the cryo-EM determination of gyrase complexes with antibiotics and opens perspectives for targeting conformational intermediates. Bacterial DNA gyrase is the only type II DNA topoisomerase capable of introducing negative supercoils into DNA and is of interest as a drug target. Here the authors present the cryo-EM structure of the complete E. coli DNA gyrase bound to a 180 bp double-stranded DNA and the antibiotic gepotidacin, which reveals the connections between the functional domains and their spatial organization.
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Affiliation(s)
- Arnaud Vanden Broeck
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1 Rue Laurent Fries, 67404, Illkirch Cedex, France.,Centre National de Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de Santé et de Recherche Médicale (INSERM) U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Christophe Lotz
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1 Rue Laurent Fries, 67404, Illkirch Cedex, France.,Centre National de Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de Santé et de Recherche Médicale (INSERM) U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Julio Ortiz
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1 Rue Laurent Fries, 67404, Illkirch Cedex, France.,Centre National de Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de Santé et de Recherche Médicale (INSERM) U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Valérie Lamour
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1 Rue Laurent Fries, 67404, Illkirch Cedex, France. .,Centre National de Recherche Scientifique (CNRS) UMR 7104, Illkirch, France. .,Institut National de Santé et de Recherche Médicale (INSERM) U1258, Illkirch, France. .,Université de Strasbourg, Illkirch, France. .,Hôpitaux Universitaires de Strasbourg, 1 Place de l'Hôpital, 67091, Strasbourg Cedex, France.
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31
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Discovery of a Novel DNA Gyrase-Targeting Antibiotic through the Chemical Perturbation of Streptomyces venezuelae Sporulation. Cell Chem Biol 2019; 26:1274-1282.e4. [PMID: 31279606 PMCID: PMC6856721 DOI: 10.1016/j.chembiol.2019.06.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 05/15/2019] [Accepted: 06/13/2019] [Indexed: 12/11/2022]
Abstract
Common approaches to antibiotic discovery include small-molecule screens for growth inhibition in target pathogens and screens for inhibitors of purified enzymes. These approaches have a shared intent of seeking to directly target a vital Achilles heel in a pathogen of interest. Here, we report the first screen against a sporulation pathway in a non-pathogenic bacterium as a means of discovering novel antibiotics—this effort has resulted in two important discoveries. First, we show that the sporulation program of Streptomyces venezuelae is exquisitely sensitive to numerous forms of DNA damage. Second, we have identified a DNA gyrase inhibitor. This molecule, EN-7, is active against pathogenic species that are resistant to ciprofloxacin and other clinically important antibiotics. We suggest that this strategy could be applied to other morphogenetic pathways in prokaryotes or eukaryotes as a means of identifying novel chemical matter having scientific and clinical utility. Streptomyces sporulation is sensitive to chemically induced DNA damage Screening 3,705 synthetic molecules uncovered novel sporulation inhibitors Lead molecule, EN-7, is an inhibitor of extensively resistant Gram-positive pathogens EN-7 targets DNA gyrase
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Rapid Evolution of Reduced Susceptibility against a Balanced Dual-Targeting Antibiotic through Stepping-Stone Mutations. Antimicrob Agents Chemother 2019; 63:AAC.00207-19. [PMID: 31235632 DOI: 10.1128/aac.00207-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 06/14/2019] [Indexed: 11/20/2022] Open
Abstract
Multitargeting antibiotics, i.e., single compounds capable of inhibiting two or more bacterial targets, are generally considered to be a promising therapeutic strategy against resistance evolution. The rationale for this theory is that multitargeting antibiotics demand the simultaneous acquisition of multiple mutations at their respective target genes to achieve significant resistance. The theory presumes that individual mutations provide little or no benefit to the bacterial host. Here, we propose that such individual stepping-stone mutations can be prevalent in clinical bacterial isolates, as they provide significant resistance to other antimicrobial agents. To test this possibility, we focused on gepotidacin, an antibiotic candidate that selectively inhibits both bacterial DNA gyrase and topoisomerase IV. In a susceptible organism, Klebsiella pneumoniae, a combination of two specific mutations in these target proteins provide an >2,000-fold reduction in susceptibility, while individually, none of these mutations affect resistance significantly. Alarmingly, strains with decreased susceptibility against gepotidacin are found to be as virulent as the wild-type Klebsiella pneumoniae strain in a murine model. Moreover, numerous pathogenic isolates carry mutations which could promote the evolution of clinically significant reduction of susceptibility against gepotidacin in the future. As might be expected, prolonged exposure to ciprofloxacin, a clinically widely employed gyrase inhibitor, coselected for reduced susceptibility against gepotidacin. We conclude that extensive antibiotic usage could select for mutations that serve as stepping-stones toward resistance against antimicrobial compounds still under development. Our research indicates that even balanced multitargeting antibiotics are prone to resistance evolution.
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33
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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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34
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Opportunities for Overcoming Mycobacterium tuberculosis Drug Resistance: Emerging Mycobacterial Targets and Host-Directed Therapy. Int J Mol Sci 2019; 20:ijms20122868. [PMID: 31212777 PMCID: PMC6627145 DOI: 10.3390/ijms20122868] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 05/31/2019] [Accepted: 06/06/2019] [Indexed: 02/08/2023] Open
Abstract
The ever-increasing incidence of drug-resistant Mycobacterium tuberculosis infections has invigorated the focus on the discovery and development of novel treatment options. The discovery and investigation of essential mycobacterial targets is of utmost importance. In addition to the discovery of novel targets, focusing on non-lethal pathways and the use of host-directed therapies has gained interest. These adjunctive treatment options could not only lead to increased antibiotic susceptibility of Mycobacterium tuberculosis, but also have the potential to avoid the emergence of drug resistance. Host-directed therapies, on the other hand, can also reduce the associated lung pathology and improve disease outcome. This review will provide an outline of recent opportunities.
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35
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Thalji RK, Raha K, Andreotti D, Checchia A, Cui H, Meneghelli G, Profeta R, Tonelli F, Tommasi S, Bakshi T, Donovan BT, Howells A, Jain S, Nixon C, Quinque G, McCloskey L, Bax BD, Neu M, Chan PF, Stavenger RA. Structure-guided design of antibacterials that allosterically inhibit DNA gyrase. Bioorg Med Chem Lett 2019; 29:1407-1412. [DOI: 10.1016/j.bmcl.2019.03.029] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/15/2019] [Accepted: 03/21/2019] [Indexed: 12/23/2022]
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36
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Gibson EG, Bax B, Chan PF, Osheroff N. Mechanistic and Structural Basis for the Actions of the Antibacterial Gepotidacin against Staphylococcus aureus Gyrase. ACS Infect Dis 2019; 5:570-581. [PMID: 30757898 DOI: 10.1021/acsinfecdis.8b00315] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Gepotidacin is a first-in-class triazaacenaphthylene novel bacterial topoisomerase inhibitor (NBTI). The compound has successfully completed phase II trials for the treatment of acute bacterial skin/skin structure infections and for the treatment of uncomplicated urogenital gonorrhea. It also displays robust in vitro activity against a range of wild-type and fluoroquinolone-resistant bacteria. Due to the clinical promise of gepotidacin, a detailed understanding of its interactions with its antibacterial targets is essential. Thus, we characterized the mechanism of action of gepotidacin against Staphylococcus aureus gyrase. Gepotidacin was a potent inhibitor of gyrase-catalyzed DNA supercoiling (IC50 ≈ 0.047 μM) and relaxation of positively supercoiled substrates (IC50 ≈ 0.6 μM). Unlike fluoroquinolones, which induce primarily double-stranded DNA breaks, gepotidacin induced high levels of gyrase-mediated single-stranded breaks. No double-stranded breaks were observed even at high gepotidacin concentration, long cleavage times, or in the presence of ATP. Moreover, gepotidacin suppressed the formation of double-stranded breaks. Gepotidacin formed gyrase-DNA cleavage complexes that were stable for >4 h. In vitro competition suggests that gyrase binding by gepotidacin and fluoroquinolones are mutually exclusive. Finally, we determined crystal structures of gepotidacin with the S. aureus gyrase core fusion truncate with nicked (2.31 Å resolution) or intact (uncleaved) DNA (2.37 Å resolution). In both cases, a single gepotidacin molecule was bound midway between the two scissile DNA bonds and in a pocket between the two GyrA subunits. A comparison of the two structures demonstrates conformational flexibility within the central linker of gepotidacin, which may contribute to the activity of the compound.
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Affiliation(s)
| | - Ben Bax
- Medicines Discovery Institute, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
| | - Pan F. Chan
- Infectious Diseases Discovery, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Neil Osheroff
- VA Tennessee Valley Healthcare System, 1310 24th Avenue S., Nashville, Tennessee 37212, United States
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37
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Opportunities in biotechnology. J Biotechnol 2018; 282:38-45. [DOI: 10.1016/j.jbiotec.2018.06.303] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 05/28/2018] [Accepted: 06/05/2018] [Indexed: 12/21/2022]
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38
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Gibson EG, Blower TR, Cacho M, Bax B, Berger JM, Osheroff N. Mechanism of Action of Mycobacterium tuberculosis Gyrase Inhibitors: A Novel Class of Gyrase Poisons. ACS Infect Dis 2018; 4:1211-1222. [PMID: 29746087 DOI: 10.1021/acsinfecdis.8b00035] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Tuberculosis is one of the leading causes of morbidity worldwide, and the incidences of drug resistance and intolerance are prevalent. Thus, there is a desperate need for the development of new antitubercular drugs. Mycobacterium tuberculosis gyrase inhibitors (MGIs) are napthyridone/aminopiperidine-based drugs that display activity against M. tuberculosis cells and tuberculosis in mouse models [Blanco, D., et al. (2015) Antimicrob. Agents Chemother. 59, 1868-1875]. Genetic and mutagenesis studies suggest that gyrase, which is the target for fluoroquinolone antibacterials, is also the target for MGIs. However, little is known regarding the interaction of these drugs with the bacterial type II enzyme. Therefore, we examined the effects of two MGIs, GSK000 and GSK325, on M. tuberculosis gyrase. MGIs greatly enhanced DNA cleavage mediated by the bacterial enzyme. In contrast to fluoroquinolones (which induce primarily double-stranded breaks), MGIs induced only single-stranded DNA breaks under a variety of conditions. MGIs work by stabilizing covalent gyrase-cleaved DNA complexes and appear to suppress the ability of the enzyme to induce double-stranded breaks. The drugs displayed little activity against type II topoisomerases from several other bacterial species, suggesting that these drugs display specificity for M. tuberculosis gyrase. Furthermore, MGIs maintained activity against M. tuberuclosis gyrase enzymes that contained the three most common fluoroquinolone resistance mutations seen in the clinic and displayed no activity against human topoisomerase IIα. These findings suggest that MGIs have potential as antitubercular drugs, especially in the case of fluoroquinolone-resistant disease.
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Affiliation(s)
| | - Tim R. Blower
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205-2185, United States
| | - Monica Cacho
- Department of Diseases of the Developing World, GlaxoSmithKline, Parque Tecnológico de Madrid, Calle de Severo Ochoa, 2, 28760 Tres Cantos, Madrid, Spain
| | - Ben Bax
- Medicines Discovery Institute, Cardiff University, Cardiff CF10 3AT, United Kingdom
| | - James M. Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205-2185, United States
| | - Neil Osheroff
- VA Tennessee Valley Healthcare System, Nashville, Tennessee 37212, United States
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New N-phenylpyrrolamide DNA gyrase B inhibitors: Optimization of efficacy and antibacterial activity. Eur J Med Chem 2018; 154:117-132. [PMID: 29778894 DOI: 10.1016/j.ejmech.2018.05.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 03/27/2018] [Accepted: 05/07/2018] [Indexed: 01/04/2023]
Abstract
The ATP binding site located on the subunit B of DNA gyrase is an attractive target for the development of new antibacterial agents. In recent decades, several small-molecule inhibitor classes have been discovered but none has so far reached the market. We present here the discovery of a promising new series of N-phenylpyrrolamides with low nanomolar IC50 values against DNA gyrase, and submicromolar IC50 values against topoisomerase IV from Escherichia coli and Staphylococcus aureus. The most potent compound in the series has an IC50 value of 13 nM against E. coli gyrase. Minimum inhibitory concentrations (MICs) against Gram-positive bacteria are in the low micromolar range. The oxadiazolone derivative 11a, with an IC50 value of 85 nM against E. coli DNA gyrase displays the most potent antibacterial activity, with MIC values of 1.56 μM against Enterococcus faecalis, and 3.13 μM against wild type S. aureus, methicillin-resistant S. aureus (MRSA) and vancomycin-resistant Enterococcus (VRE). The activity against wild type E. coli in the presence of efflux pump inhibitor phenylalanine-arginine β-naphthylamide (PAβN) is 4.6 μM.
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Germe T, Vörös J, Jeannot F, Taillier T, Stavenger RA, Bacqué E, Maxwell A, Bax BD. A new class of antibacterials, the imidazopyrazinones, reveal structural transitions involved in DNA gyrase poisoning and mechanisms of resistance. Nucleic Acids Res 2018; 46:4114-4128. [PMID: 29538767 PMCID: PMC5934680 DOI: 10.1093/nar/gky181] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 02/16/2018] [Accepted: 03/02/2018] [Indexed: 12/24/2022] Open
Abstract
Imidazopyrazinones (IPYs) are a new class of compounds that target bacterial topoisomerases as a basis for their antibacterial activity. We have characterized the mechanism of these compounds through structural/mechanistic studies showing they bind and stabilize a cleavage complex between DNA gyrase and DNA ('poisoning') in an analogous fashion to fluoroquinolones, but without the requirement for the water-metal-ion bridge. Biochemical experiments and structural studies of cleavage complexes of IPYs compared with an uncleaved gyrase-DNA complex, reveal conformational transitions coupled to DNA cleavage at the DNA gate. These involve movement at the GyrA interface and tilting of the TOPRIM domains toward the scissile phosphate coupled to capture of the catalytic metal ion. Our experiments show that these structural transitions are involved generally in poisoning of gyrase by therapeutic compounds and resemble those undergone by the enzyme during its adenosine triphosphate-coupled strand-passage cycle. In addition to resistance mutations affecting residues that directly interact with the compounds, we characterized a mutant (D82N) that inhibits formation of the cleavage complex by the unpoisoned enzyme. The D82N mutant appears to act by stabilizing the binary conformation of DNA gyrase with uncleaved DNA without direct interaction with the compounds. This provides general insight into the resistance mechanisms to antibiotics targeting bacterial type II topoisomerases.
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Affiliation(s)
- Thomas Germe
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Judit Vörös
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Frederic Jeannot
- Sanofi R&D, TSU Infectious Diseases, 1541 Avenue Marcel Mérieux, 69280 Marcy L’Etoile, France
| | - Thomas Taillier
- Sanofi R&D, TSU Infectious Diseases, 1541 Avenue Marcel Mérieux, 69280 Marcy L’Etoile, France
| | - Robert A Stavenger
- Antibacterial Discovery Performance Unit, Infectious Diseases Therapy Area Unit, GlaxoSmithKline, 1250 Collegeville Road, Collegeville, PA 19426, USA
| | - Eric Bacqué
- Sanofi R&D, TSU Infectious Diseases, 1541 Avenue Marcel Mérieux, 69280 Marcy L’Etoile, France
| | - Anthony Maxwell
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Benjamin D Bax
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
- Platform Technology and Science, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK
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Suppression of Reactive Oxygen Species Accumulation Accounts for Paradoxical Bacterial Survival at High Quinolone Concentration. Antimicrob Agents Chemother 2018; 62:AAC.01622-17. [PMID: 29229642 DOI: 10.1128/aac.01622-17] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 12/01/2017] [Indexed: 11/20/2022] Open
Abstract
When bacterial cells are exposed to increasing concentrations of quinolone-class antibacterials, survival drops, reaches a minimum, and then recovers, sometimes to 100%. Despite decades of study, events underlying this paradoxical high-concentration survival remain obscure. Since reactive oxygen species (ROS) have been implicated in antimicrobial lethality, conditions generating paradoxical survival were examined for diminished ROS accumulation. Escherichia coli cultures were treated with various concentrations of nalidixic acid, followed by measurements of survival, rate of protein synthesis, and ROS accumulation. The last measurement used a dye (carboxy-H2DCFDA) that fluoresces in the presence of ROS; fluorescence was assessed by microscopy (individual cells) and flow cytometry (batch cultures). High, nonlethal concentrations of nalidixic acid induced lower levels of ROS than moderate, lethal concentrations. Sublethal doses of exogenous hydrogen peroxide became lethal and eliminated the nalidixic acid-associated paradoxical survival. Thus, quinolone-mediated lesions needed for ROS-executed killing persist at high, nonlethal quinolone concentrations, thereby implicating ROS as a key factor in cell death. Chloramphenicol suppressed nalidixic acid-induced ROS accumulation and blocked lethality, further supporting a role for ROS in killing. Nalidixic acid also inhibited protein synthesis, with extensive inhibition at high concentrations correlating with lower ROS accumulation and paradoxical survival. A catalase deficiency, which elevated ROS levels, overcame the inhibitory effect of chloramphenicol on nalidixic acid-mediated killing, emphasizing the importance of ROS. The data collectively indicate that ROS play a dominant role in the lethal action of narrow-spectrum quinolone-class compounds; a drop in ROS levels accounted for the quinolone tolerance observed at very high concentrations.
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Franco-Ulloa S, La Sala G, Miscione GP, De Vivo M. Novel Bacterial Topoisomerase Inhibitors Exploit Asp83 and the Intrinsic Flexibility of the DNA Gyrase Binding Site. Int J Mol Sci 2018; 19:ijms19020453. [PMID: 29401640 PMCID: PMC5855675 DOI: 10.3390/ijms19020453] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 01/29/2018] [Accepted: 01/30/2018] [Indexed: 11/19/2022] Open
Abstract
DNA gyrases are enzymes that control the topology of DNA in bacteria cells. This is a vital function for bacteria. For this reason, DNA gyrases are targeted by widely used antibiotics such as quinolones. Recently, structural and biochemical investigations identified a new class of DNA gyrase inhibitors called NBTIs (i.e., novel bacterial topoisomerase inhibitors). NBTIs are particularly promising because they are active against multi-drug resistant bacteria, an alarming clinical issue. Structural data recently demonstrated that these NBTIs bind tightly to a newly identified pocket at the dimer interface of the DNA–protein complex. In the present study, we used molecular dynamics (MD) simulations and docking calculations to shed new light on the binding of NBTIs to this site. Interestingly, our MD simulations demonstrate the intrinsic flexibility of this binding site, which allows the pocket to adapt its conformation and form optimal interactions with the ligand. In particular, we examined two ligands, AM8085 and AM8191, which induced a repositioning of a key aspartate (Asp83B), whose side chain can rotate within the binding site. The conformational rearrangement of Asp83B allows the formation of a newly identified H-bond interaction with an NH on the bound NBTI, which seems important for the binding of NBTIs having such functionality. We validated these findings through docking calculations using an extended set of cognate oxabicyclooctane-linked NBTIs derivatives (~150, in total), screened against multiple target conformations. The newly identified H-bond interaction significantly improves the docking enrichment. These insights could be helpful for future virtual screening campaigns against DNA gyrase.
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Affiliation(s)
- Sebastian Franco-Ulloa
- COBO Computational Bio-Organic Chemistry Bogotá, Chemistry Department, Universidad de los Andes, Cra 1 No 18A-12, 111711 Bogotá, Colombia.
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy.
| | - Giuseppina La Sala
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy.
| | - Gian Pietro Miscione
- COBO Computational Bio-Organic Chemistry Bogotá, Chemistry Department, Universidad de los Andes, Cra 1 No 18A-12, 111711 Bogotá, Colombia.
| | - Marco De Vivo
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy.
- IAS-5/INM-9 Computational Biomedicine Forschungszentrum Jülich Wilhelm-Johnen-Straße, 52428 Jülich, Germany.
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Delgado JL, Hsieh CM, Chan NL, Hiasa H. Topoisomerases as anticancer targets. Biochem J 2018; 475:373-398. [PMID: 29363591 PMCID: PMC6110615 DOI: 10.1042/bcj20160583] [Citation(s) in RCA: 264] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 12/14/2017] [Accepted: 12/21/2017] [Indexed: 12/15/2022]
Abstract
Many cancer type-specific anticancer agents have been developed and significant advances have been made toward precision medicine in cancer treatment. However, traditional or nonspecific anticancer drugs are still important for the treatment of many cancer patients whose cancers either do not respond to or have developed resistance to cancer-specific anticancer agents. DNA topoisomerases, especially type IIA topoisomerases, are proved therapeutic targets of anticancer and antibacterial drugs. Clinically successful topoisomerase-targeting anticancer drugs act through topoisomerase poisoning, which leads to replication fork arrest and double-strand break formation. Unfortunately, this unique mode of action is associated with the development of secondary cancers and cardiotoxicity. Structures of topoisomerase-drug-DNA ternary complexes have revealed the exact binding sites and mechanisms of topoisomerase poisons. Recent advances in the field have suggested a possibility of designing isoform-specific human topoisomerase II poisons, which may be developed as safer anticancer drugs. It may also be possible to design catalytic inhibitors of topoisomerases by targeting certain inactive conformations of these enzymes. Furthermore, identification of various new bacterial topoisomerase inhibitors and regulatory proteins may inspire the discovery of novel human topoisomerase inhibitors. Thus, topoisomerases remain as important therapeutic targets of anticancer agents.
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Affiliation(s)
- Justine L Delgado
- Division of Medicinal and Natural Products Chemistry, Department of Pharmaceutical Sciences and Experimental Therapeutics, College of Pharmacy, University of Iowa, 115 S Grand Ave., S321 Pharmacy Building, Iowa City, IA 52242, U.S.A
| | - Chao-Ming Hsieh
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei City 100, Taiwan
| | - Nei-Li Chan
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei City 100, Taiwan
| | - Hiroshi Hiasa
- Department of Pharmacology, University of Minnesota Medical School, 6-120 Jackson Hall, 321 Church Street SE, Minneapolis, MN 55455, U.S.A.
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