1
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Kokot M, Minovski N. Dynamic Profiling and Binding Affinity Prediction of NBTI Antibacterials against DNA Gyrase Enzyme by Multidimensional Machine Learning and Molecular Dynamics Simulations. ACS OMEGA 2024; 9:18278-18295. [PMID: 38680300 PMCID: PMC11044241 DOI: 10.1021/acsomega.4c00036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 03/25/2024] [Accepted: 03/29/2024] [Indexed: 05/01/2024]
Abstract
Bacterial type II topoisomerases are well-characterized and clinically important targets for antibacterial chemotherapy. Novel bacterial topoisomerase inhibitors (NBTIs) are a newly disclosed class of antibacterials. Prediction of their binding affinity to these enzymes would be beneficial for de novo design/optimization of new NBTIs. Utilizing in vitro NBTI experimental data, we constructed two comprehensive multidimensional DNA gyrase surrogate models for Staphylococcus aureus (q2 = 0.791) and Escherichia coli (q2 = 0.806). Both models accurately predicted the IC50s of 26 NBTIs from our recent studies. To investigate the NBTI's dynamic profile and binding to both targets, 10 selected NBTIs underwent molecular dynamics (MD) simulations. The analysis of MD production trajectories confirmed key hydrogen-bonding and hydrophobic contacts that NBTIs establish in both enzymes. Moreover, the binding free energies of selected NBTIs were computed by the linear interaction energy (LIE) method employing an in-house derived set of fitting parameters (α = 0.16, β = 0.029, γ = 0.0, and intercept = -1.72), which are successfully applicable to DNA gyrase of Gram-positive/Gram-negative pathogens. Both methods offer accurate predictions of the binding free energies of NBTIs against S. aureus and E. coli DNA gyrase. We are confident that this integrated modeling approach could be valuable in the de novo design and optimization of efficient NBTIs for combating resistant bacterial pathogens.
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Affiliation(s)
- Maja Kokot
- Laboratory
for Cheminformatics, Theory Department, National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia
- The
Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Nikola Minovski
- Laboratory
for Cheminformatics, Theory Department, National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia
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2
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Oviatt A, Gibson EG, Huang J, Mattern K, Neuman KC, Chan PF, Osheroff N. Interactions between Gepotidacin and Escherichia coli Gyrase and Topoisomerase IV: Genetic and Biochemical Evidence for Well-Balanced Dual-Targeting. ACS Infect Dis 2024; 10:1137-1151. [PMID: 38606465 PMCID: PMC11015057 DOI: 10.1021/acsinfecdis.3c00346] [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: 07/19/2023] [Revised: 02/07/2024] [Accepted: 02/13/2024] [Indexed: 04/13/2024]
Abstract
Antimicrobial resistance is a global threat to human health. Therefore, efforts have been made to develop new antibacterial agents that address this critical medical issue. Gepotidacin is a novel, bactericidal, first-in-class triazaacenaphthylene antibacterial in clinical development. Recently, phase III clinical trials for gepotidacin treatment of uncomplicated urinary tract infections caused by uropathogens, including Escherichia coli, were stopped for demonstrated efficacy. Because of the clinical promise of gepotidacin, it is important to understand how the compound interacts with its cellular targets, gyrase and topoisomerase IV, from E. coli. Consequently, we determined how gyrase and topoisomerase IV mutations in amino acid residues that are involved in gepotidacin interactions affect the susceptibility of E. coli cells to the compound and characterized the effects of gepotidacin on the activities of purified wild-type and mutant gyrase and topoisomerase IV. Gepotidacin displayed well-balanced dual-targeting of gyrase and topoisomerase IV in E. coli cells, which was reflected in a similar inhibition of the catalytic activities of these enzymes by the compound. Gepotidacin induced gyrase/topoisomerase IV-mediated single-stranded, but not double-stranded, DNA breaks. Mutations in GyrA and ParC amino acid residues that interact with gepotidacin altered the activity of the compound against the enzymes and, when present in both gyrase and topoisomerase IV, reduced the antibacterial activity of gepotidacin against this mutant strain. Our studies provide insights regarding the well-balanced dual-targeting of gyrase and topoisomerase IV by gepotidacin in E. coli.
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Affiliation(s)
- Alexandria
A. Oviatt
- Department
of Biochemistry, Vanderbilt University School
of Medicine, Nashville, Tennessee 37232, United States
| | - Elizabeth G. Gibson
- Department
of Biochemistry, Vanderbilt University School
of Medicine, Nashville, Tennessee 37232, United States
- Department
of Pharmacology, Vanderbilt University School
of Medicine, Nashville, Tennessee 37232, United States
| | - Jianzhong Huang
- Infectious
Diseases Research Unit, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Karen Mattern
- Infectious
Diseases Research Unit, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Keir C. Neuman
- Laboratory
of Single Molecule Biophysics, National
Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20982, United States
| | - Pan F. Chan
- Infectious
Diseases Research Unit, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Neil Osheroff
- Department
of Biochemistry, Vanderbilt University School
of Medicine, Nashville, Tennessee 37232, United States
- Department
of Medicine (Hematology/Oncology), Vanderbilt
University School of Medicine, Nashville, Tennessee 37232, United States
- VA
Tennessee
Valley Healthcare System, Nashville, Tennessee 37212, United States
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3
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Dauda SE, Collins JA, Byl JAW, Lu Y, Yalowich JC, Mitton-Fry MJ, Osheroff N. Actions of a Novel Bacterial Topoisomerase Inhibitor against Neisseria gonorrhoeae Gyrase and Topoisomerase IV: Enhancement of Double-Stranded DNA Breaks. Int J Mol Sci 2023; 24:12107. [PMID: 37569485 PMCID: PMC10419083 DOI: 10.3390/ijms241512107] [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: 06/28/2023] [Revised: 07/18/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
Novel bacterial topoisomerase inhibitors (NBTIs) are an emerging class of antibacterials that target gyrase and topoisomerase IV. A hallmark of NBTIs is their ability to induce gyrase/topoisomerase IV-mediated single-stranded DNA breaks and suppress the generation of double-stranded breaks. However, a previous study reported that some dioxane-linked amide NBTIs induced double-stranded DNA breaks mediated by Staphylococcus aureus gyrase. To further explore the ability of this NBTI subclass to increase double-stranded DNA breaks, we examined the effects of OSUAB-185 on DNA cleavage mediated by Neisseria gonorrhoeae gyrase and topoisomerase IV. OSUAB-185 induced single-stranded and suppressed double-stranded DNA breaks mediated by N. gonorrhoeae gyrase. However, the compound stabilized both single- and double-stranded DNA breaks mediated by topoisomerase IV. The induction of double-stranded breaks does not appear to correlate with the binding of a second OSUAB-185 molecule and extends to fluoroquinolone-resistant N. gonorrhoeae topoisomerase IV, as well as type II enzymes from other bacteria and humans. The double-stranded DNA cleavage activity of OSUAB-185 and other dioxane-linked NBTIs represents a paradigm shift in a hallmark characteristic of NBTIs and suggests that some members of this subclass may have alternative binding motifs in the cleavage complex.
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Affiliation(s)
- Soziema E. Dauda
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Jessica A. Collins
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Jo Ann W. Byl
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Yanran Lu
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Jack C. Yalowich
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 42310, USA
| | - Mark J. Mitton-Fry
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Neil Osheroff
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Department of Medicine (Hematology/Oncology), Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- VA Tennessee Valley Healthcare System, Nashville, TN 37212, USA
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4
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Synthesis, antibacterial evaluation, and in silico investigations of novel 3-amino-1,2-dihydroisoquinoline derivatives. Struct Chem 2022. [DOI: 10.1007/s11224-022-02116-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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5
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Lu Y, Mann CA, Nolan S, Collins JA, Parker E, Papa J, Vibhute S, Jahanbakhsh S, Thwaites M, Hufnagel D, Hazbón MH, Moreno J, Stedman TT, Wittum T, Wozniak DJ, Osheroff N, Yalowich JC, Mitton-Fry MJ. 1,3-Dioxane-Linked Novel Bacterial Topoisomerase Inhibitors: Expanding Structural Diversity and the Antibacterial Spectrum. ACS Med Chem Lett 2022; 13:955-963. [PMID: 35707162 PMCID: PMC9189870 DOI: 10.1021/acsmedchemlett.2c00111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 05/05/2022] [Indexed: 11/29/2022] Open
Abstract
Antibacterial resistance continues its devastation of available therapies. Novel bacterial topoisomerase inhibitors (NBTIs) offer one solution to this critical issue. Two series of amine NBTIs bearing tricyclic DNA-binding moieties as well as amide NBTIs with a bicyclic DNA-binding moiety were synthesized and evaluated against methicillin-resistant Staphylococcus aureus (MRSA). Additionally, these compounds and a series of bicyclic amine analogues displayed high activity against susceptible and drug-resistant Neisseria gonorrhoeae, expanding the spectrum of these dioxane-linked NBTIs.
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Affiliation(s)
- Yanran Lu
- Division
of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Chelsea A. Mann
- Division
of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Sheri Nolan
- Microbial
Infection and Immunity, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jessica A. Collins
- Department
of Biochemistry, Vanderbilt University School
of Medicine, Nashville, Tennessee 37232, United States
| | - Elizabeth Parker
- Department
of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jonathan Papa
- Division
of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Sandip Vibhute
- Division
of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | | | | | | | | | - Jane Moreno
- ATCC, Manassas, Virginia 20110, United States
| | | | - Thomas Wittum
- Department
of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Daniel J. Wozniak
- Microbial
Infection and Immunity, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
- Department
of Microbiology, College of Arts and Sciences, The Ohio State University, Columbus, Ohio 43210, United States
| | - Neil Osheroff
- Department
of Biochemistry, Vanderbilt University School
of Medicine, Nashville, Tennessee 37232, United States
- Department
of Medicine (Hematology/Oncology), Vanderbilt
University School of Medicine, Nashville, Tennessee 37232, United States
- VA Tennessee Valley Healthcare System, Nashville, Tennessee 37212, United States
| | - Jack C. Yalowich
- Division
of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Mark J. Mitton-Fry
- Division
of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
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6
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Kokot M, Anderluh M, Hrast M, Minovski N. The Structural Features of Novel Bacterial Topoisomerase Inhibitors That Define Their Activity on Topoisomerase IV. J Med Chem 2022; 65:6431-6440. [PMID: 35503563 PMCID: PMC9109137 DOI: 10.1021/acs.jmedchem.2c00039] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
![]()
The continued emergence
of bacterial resistance has created an
urgent need for new and effective antibacterial agents. Bacterial
type II topoisomerases, such as DNA gyrase and topoisomerase IV (topoIV),
are well-validated targets for antibacterial chemotherapy. The novel
bacterial topoisomerase inhibitors (NBTIs) represent one of the new
promising classes of antibacterial agents. They can inhibit both of
these bacterial targets; however, their potencies differ on the targets
among species, making topoIV probably a primary target of NBTIs in
Gram-negative bacteria. Therefore, it is important to gain an insight
into the NBTIs key structural features that govern the topoIV inhibition.
However, in Gram-positive bacteria, topoIV is also a significant target
for achieving dual-targeting, which in turn contributes to avoiding
bacterial resistance caused by single-target mutations. In this perspective,
we address the structure–activity relationship guidelines for
NBTIs that target the topoIV enzyme in Gram-positive and Gram-negative
bacteria.
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Affiliation(s)
- Maja Kokot
- Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, SI-1000 Ljubljana, Slovenia
| | - Marko Anderluh
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, SI-1000 Ljubljana, Slovenia
| | - Martina Hrast
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, SI-1000 Ljubljana, Slovenia
| | - Nikola Minovski
- Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
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7
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Fluorine-containing 2,3-diaryl quinolines as potent inhibitors of methicillin and vancomycin-resistant Staphylococcus aureus: Synthesis, antibacterial activity and molecular docking studies. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130924] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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8
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Lu Y, Vibhute S, Li L, Okumu A, Ratigan SC, Nolan S, Papa JL, Mann CA, English A, Chen A, Seffernick JT, Koci B, Duncan LR, Roth B, Cummings JE, Slayden RA, Lindert S, McElroy CA, Wozniak DJ, Yalowich J, Mitton-Fry MJ. Optimization of TopoIV Potency, ADMET Properties, and hERG Inhibition of 5-Amino-1,3-dioxane-Linked Novel Bacterial Topoisomerase Inhibitors: Identification of a Lead with In Vivo Efficacy against MRSA. J Med Chem 2021; 64:15214-15249. [PMID: 34614347 DOI: 10.1021/acs.jmedchem.1c01250] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Novel bacterial topoisomerase inhibitors (NBTIs) are among the most promising new antibiotics in preclinical/clinical development. We previously reported dioxane-linked NBTIs with potent antistaphylococcal activity and reduced hERG inhibition, a key safety liability. Herein, polarity-focused optimization enabled the delineation of clear structure-property relationships for both microsomal metabolic stability and hERG inhibition, resulting in the identification of lead compound 79. This molecule demonstrates potent antibacterial activity against diverse Gram-positive pathogens, inhibition of both DNA gyrase and topoisomerase IV, a low frequency of resistance, a favorable in vitro cardiovascular safety profile, and in vivo efficacy in a murine model of methicillin-resistant Staphylococcus aureus infection.
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Affiliation(s)
- Yanran Lu
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Sandip Vibhute
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Linsen Li
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Antony Okumu
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Steven C Ratigan
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Sheri Nolan
- Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jonathan L Papa
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Chelsea A Mann
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Anthony English
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Anna Chen
- Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Justin T Seffernick
- Department of Chemistry and Biochemistry, College of Arts and Sciences, The Ohio State University, Columbus, Ohio 43210, United States
| | - Bryan Koci
- Eurofins Panlabs, St. Charles, Missouri 63304, United States
| | | | - Brieanna Roth
- JMI Laboratories, North Liberty, Iowa 52317, United States
| | - Jason E Cummings
- Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Richard A Slayden
- Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, College of Arts and Sciences, The Ohio State University, Columbus, Ohio 43210, United States
| | - Craig A McElroy
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Daniel J Wozniak
- Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States.,Department of Microbiology, College of Arts and Sciences, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jack Yalowich
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Mark J Mitton-Fry
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
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9
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Fatima GN, Paliwal SK, Saraf SK. Synthesis and Antimicrobial Activity of Some Novel 7-Chloro-4-aminoquinoline Derivatives. RUSS J GEN CHEM+ 2021. [DOI: 10.1134/s1070363221020171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Cools F, Delputte P, Cos P. The search for novel treatment strategies for Streptococcus pneumoniae infections. FEMS Microbiol Rev 2021; 45:6064299. [PMID: 33399826 PMCID: PMC8371276 DOI: 10.1093/femsre/fuaa072] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 01/01/2021] [Indexed: 12/13/2022] Open
Abstract
This review provides an overview of the most important novel treatment strategies against Streptococcus pneumoniae infections published over the past 10 years. The pneumococcus causes the majority of community-acquired bacterial pneumonia cases, and it is one of the prime pathogens in bacterial meningitis. Over the last 10 years, extensive research has been conducted to prevent severe pneumococcal infections, with a major focus on (i) boosting the host immune system and (ii) discovering novel antibacterials. Boosting the immune system can be done in two ways, either by actively modulating host immunity, mostly through administration of selective antibodies, or by interfering with pneumococcal virulence factors, thereby supporting the host immune system to effectively overcome an infection. While several of such experimental therapies are promising, few have evolved to clinical trials. The discovery of novel antibacterials is hampered by the high research and development costs versus the relatively low revenues for the pharmaceutical industry. Nevertheless, novel enzymatic assays and target-based drug design, allow the identification of targets and the development of novel molecules to effectively treat this life-threatening pathogen.
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Affiliation(s)
- F Cools
- Laboratory for Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - P Delputte
- Laboratory for Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - P Cos
- Laboratory for Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
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11
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A computational study on hydroxychloroquine binding to target proteins related to SARS-COV-2 infection. INFORMATICS IN MEDICINE UNLOCKED 2021; 26:100714. [PMID: 34458558 PMCID: PMC8381687 DOI: 10.1016/j.imu.2021.100714] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/19/2021] [Accepted: 08/19/2021] [Indexed: 02/07/2023] Open
Abstract
COVID-19 disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has posed a global health emergency. Repurposing of existing drugs can be a rapid and effective strategy to fight the infection. Clinical trials have reported reduction or elimination of viral load when patients were treated with the anti-malarial drug Hydroxychloroquine (HCQ). To understand the molecular mechanism of action for effective repurposing of this drug we have carried out in silico docking and dynamics studies on complexes between HCQ and target proteins, which were identified through both literature survey and structural similarity searches in databases of small molecule - protein complexes. The proteins identified as binding HCQ are: Angiotensin Converting Enzyme 2 (ACE2), α7 nicotinic AcetylCholine Receptor (α7 nAChR), α1D-adrenergic receptor (α1D-AR), Histamine N- Methyl Transferase (HNMT) and DNA gyrase/Topoisomerase III β (Top3β). The majority of these proteins are novel and have not been used before, in docking studies. Our docking and simulation results support action of HCQ both at the entry and post-entry stages of SARS-CoV2 infection. The mechanism of action at the entry stage is through blocking the virus-binding sites on the two receptors, ACE2 & α7 nAChR, by binding directly at those sites. Our computational studies also show that the action of HCQ at the post-entry stage is to prevent both viral replication and generation of 'cytokine storm' by inhibiting host Top3β enzyme and α1D-AR, respectively. Binding of HCQ to HNMT is not a desired binding, and therefore this should be reduced during repurposing of HCQ.
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12
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Lu Y, Papa JL, Nolan S, English A, Seffernick JT, Shkolnikov N, Powell J, Lindert S, Wozniak DJ, Yalowich J, Mitton-Fry MJ. Dioxane-Linked Amide Derivatives as Novel Bacterial Topoisomerase Inhibitors against Gram-Positive Staphylococcus aureus. ACS Med Chem Lett 2020; 11:2446-2454. [PMID: 33335666 DOI: 10.1021/acsmedchemlett.0c00428] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/14/2020] [Indexed: 12/19/2022] Open
Abstract
In recent years, novel bacterial topoisomerase inhibitors (NBTIs) have been developed as future antibacterials for treating multidrug-resistant bacterial infections. A series of dioxane-linked NBTIs with an amide moiety has been synthesized and evaluated. Compound 3 inhibits DNA gyrase, induces the formation of single strand breaks to bacterial DNA, and achieves potent antibacterial activity against a variety of Gram-positive pathogens, including methicillin-resistant Staphylococcus aureus (MRSA). Optimization of this series of analogues led to the discovery of a subseries of compounds (22-25) with more potent anti-MRSA activity, dual inhibition of DNA gyrase and topoisomerase IV, and the ability to induce double strand breaks through inhibition of S. aureus DNA gyrase.
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13
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Jaswal S, Nehra B, Kumar S, Monga V. Recent advancements in the medicinal chemistry of bacterial type II topoisomerase inhibitors. Bioorg Chem 2020; 104:104266. [PMID: 33142421 DOI: 10.1016/j.bioorg.2020.104266] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/14/2020] [Accepted: 08/31/2020] [Indexed: 02/06/2023]
Abstract
Replication proteins are sought as a potential targets for antimicrobial agents. Despite their promising target characteristics, only topoisomerase II inhibitors targeting DNA gyrase and/or topoisomerase IV have reached clinical use. Topoisomerases are the enzymes that are essential for cellular functions and various biological activities. A wide range of natural and synthetic compounds have been identified as potential topoisomerase inhibitors but the resistance is most commonly found in these drugs. The emergence of FQ resistance has increased the need for the development of novel topoisomerase inhibitors with efficacy and high potency against FQ-resistant strains. Besides structural modifications of existing FQ scaffolds, novel non-quinolone topoisomerase II inhibitors, known as novel bacterial topoisomerase inhibitors, have been developed which showed remarkable inhibitory activity against DNA gyrase/topoisomerase IV or both with an improved spectrum of antibacterial potency including drug-resistant strains. This review aims to summarize various recent advancements in the medicinal chemistry of topoisomerase inhibitors with the following objectives: (1) To represent inclusive data on types of topoisomerases and various marketed topoisomerase inhibitors as drugs; (2) To discuss the recent advances in the medicinal chemistry of various topoisomerase inhibitors (DNA gyrase and topo IV) belonging to different structural classes as potential antibacterial agents; (3) To summarizes the structure activity relationship (SAR) including in silico and mechanistic studies to afford ideas and to provide focused direction for the development of new chemical entities which are effective against drug-resistant bacterial pathogens and biofilms.
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Affiliation(s)
- Shalini Jaswal
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, GT Road, Ghal Kalan, Moga 142001, Punjab, India
| | - Bhupender Nehra
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, GT Road, Ghal Kalan, Moga 142001, Punjab, India
| | - Shubham Kumar
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, GT Road, Ghal Kalan, Moga 142001, Punjab, India
| | - Vikramdeep Monga
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, GT Road, Ghal Kalan, Moga 142001, Punjab, India.
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14
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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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15
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Novel bacterial topoisomerase inhibitors derived from isomannide. Eur J Med Chem 2020; 199:112324. [PMID: 32402932 DOI: 10.1016/j.ejmech.2020.112324] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 04/03/2020] [Accepted: 04/07/2020] [Indexed: 11/20/2022]
Abstract
A series of Novel Bacterial Topoisomerase Inhibitors (NBTIs) employing a linker derived from isomannide were synthesized and evaluated. Reduced hERG inhibition was observed compared to structure-matched analogues with different linkers, and compound 6 showed minimal proarrhythmic potential using an in vitro panel of cardiac ion channels. Compound 6 also displayed excellent activity against fluoroquinolone-resistant MRSA (MIC90 = 2 μg/mL) and other Gram-positive pathogens.
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16
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Kolarič A, Anderluh M, Minovski N. Two Decades of Successful SAR-Grounded Stories of the Novel Bacterial Topoisomerase Inhibitors (NBTIs). J Med Chem 2020; 63:5664-5674. [PMID: 32027491 PMCID: PMC7307926 DOI: 10.1021/acs.jmedchem.9b01738] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The emergence of bacterial resistance against life-saving medicines has forced the scientific community and pharmaceutical industry to take actions in the quest for novel antibacterials. These should not only overcome the existing bacterial resistance but also provide at least interim effective protection against emerging bacterial infections. Research into DNA gyrase and topoisomerase IV inhibitors has become a particular focus, with the description of a new class of bacterial topoisomerase type II inhibitors known as "novel bacterial topoisomerase inhibitors", NBTIs. Elucidation of the key structural modifications incorporated into these inhibitors and the impact these can have on their general physicochemical properties are detailed in this review. This defines novel bacterial topoisomerase inhibitors with promising antibacterial activities and potencies, which thus represent one potential example of the future "drugs for bad bugs", as identified by the World Health Organization.
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Affiliation(s)
- Anja Kolarič
- Laboratory for Cheminformatics, Theory Department, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia.,Chair of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia
| | - Marko Anderluh
- Chair of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia
| | - Nikola Minovski
- Laboratory for Cheminformatics, Theory Department, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
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17
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Magarò G, Prati F, Garofalo B, Corso G, Furlotti G, Apicella C, Mangano G, D'Atanasio N, Robinson D, Di Giorgio FP, Ombrato R. Virtual Screening Approach and Investigation of Structure-Activity Relationships To Discover Novel Bacterial Topoisomerase Inhibitors Targeting Gram-Positive and Gram-Negative Pathogens. J Med Chem 2019; 62:7445-7472. [PMID: 31276392 DOI: 10.1021/acs.jmedchem.9b00394] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacterial resistance is increasing rapidly, requiring urgent identification of new antibacterial drugs that are effective against multidrug-resistant pathogens. Novel bacterial topoisomerase inhibitors (NBTIs) provide a new strategy for investigating the well-validated DNA gyrase and topoisomerase IV targets while preventing cross-resistance issues. On this basis, starting from a virtual screening campaign and subsequent structure-based hit optimization guided by X-ray studies, a novel class of piperazine-like NBTIs with outstanding enzymatic activity against Staphylococcus aureus and Escherichia coli DNA gyrase and topoisomerase IV was identified. Notably, compounds (±)-33, (±)-35, and (±)-36 with potent and balanced multitarget enzymatic profiles exhibited excellent efficacy against selected Gram-positive and Gram-negative pathogens, as well as clinically relevant resistant strains. Overall, the new NBTI chemotype described herein, owing to the broad-spectrum antibacterial activity and favorable in vitro safety profile, might serve as a basis for the development of novel treatments against serious infections.
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Affiliation(s)
- Gabriele Magarò
- Angelini RR&D (Research, Regulatory & Development) , Angelini S.p.A. , Piazzale della Stazione SNC, S. Palomba-Pomezia , Rome 00071 , Italy
| | - Federica Prati
- Angelini RR&D (Research, Regulatory & Development) , Angelini S.p.A. , Piazzale della Stazione SNC, S. Palomba-Pomezia , Rome 00071 , Italy
| | - Barbara Garofalo
- Angelini RR&D (Research, Regulatory & Development) , Angelini S.p.A. , Piazzale della Stazione SNC, S. Palomba-Pomezia , Rome 00071 , Italy
| | - Gaia Corso
- Angelini RR&D (Research, Regulatory & Development) , Angelini S.p.A. , Piazzale della Stazione SNC, S. Palomba-Pomezia , Rome 00071 , Italy
| | - Guido Furlotti
- Angelini RR&D (Research, Regulatory & Development) , Angelini S.p.A. , Piazzale della Stazione SNC, S. Palomba-Pomezia , Rome 00071 , Italy
| | - Claudia Apicella
- Angelini RR&D (Research, Regulatory & Development) , Angelini S.p.A. , Piazzale della Stazione SNC, S. Palomba-Pomezia , Rome 00071 , Italy
| | - Giorgina Mangano
- Angelini RR&D (Research, Regulatory & Development) , Angelini S.p.A. , Piazzale della Stazione SNC, S. Palomba-Pomezia , Rome 00071 , Italy
| | - Noemi D'Atanasio
- Angelini RR&D (Research, Regulatory & Development) , Angelini S.p.A. , Piazzale della Stazione SNC, S. Palomba-Pomezia , Rome 00071 , Italy
| | - Daniel Robinson
- Schrodinger , 120 West 45th Street , New York , New York 10036 , United States
| | - Francesco Paolo Di Giorgio
- Angelini RR&D (Research, Regulatory & Development) , Angelini S.p.A. , Piazzale della Stazione SNC, S. Palomba-Pomezia , Rome 00071 , Italy
| | - Rosella Ombrato
- Angelini RR&D (Research, Regulatory & Development) , Angelini S.p.A. , Piazzale della Stazione SNC, S. Palomba-Pomezia , Rome 00071 , Italy
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18
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Li L, Okumu AA, Nolan S, English A, Vibhute S, Lu Y, Hervert-Thomas K, Seffernick JT, Azap L, Cole SL, Shinabarger D, Koeth LM, Lindert S, Yalowich JC, Wozniak DJ, Mitton-Fry MJ. 1,3-Dioxane-Linked Bacterial Topoisomerase Inhibitors with Enhanced Antibacterial Activity and Reduced hERG Inhibition. ACS Infect Dis 2019; 5:1115-1128. [PMID: 31041863 DOI: 10.1021/acsinfecdis.8b00375] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The development of new therapies to treat methicillin-resistant Staphylococcus aureus (MRSA) is needed to counteract the significant threat that MRSA presents to human health. Novel inhibitors of DNA gyrase and topoisomerase IV (TopoIV) constitute one highly promising approach, but continued optimization is required to realize the full potential of this class of antibiotics. Herein, we report further studies on a series of dioxane-linked derivatives, demonstrating improved antistaphylococcal activity and reduced hERG inhibition. A subseries of analogues also possesses enhanced inhibition of the secondary target, TopoIV.
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Affiliation(s)
- Linsen Li
- Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, 500 West 12th Avenue, Columbus, Ohio 43210, United States
| | - Antony A. Okumu
- Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, 500 West 12th Avenue, Columbus, Ohio 43210, United States
| | - Sheri Nolan
- Microbial Infection and Immunity, The Ohio State University, 460 West 12th Avenue, Columbus, Ohio 43210, United States
| | - Anthony English
- Division of Pharmacology, The Ohio State University, 500 West 12th Avenue, Columbus, Ohio 43210, United States
| | - Sandip Vibhute
- Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, 500 West 12th Avenue, Columbus, Ohio 43210, United States
| | - Yanran Lu
- Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, 500 West 12th Avenue, Columbus, Ohio 43210, United States
| | - Katherine Hervert-Thomas
- Department of Chemistry, Ohio Wesleyan University, 61 South Sandusky Street, Delaware, Ohio 43015, United States
| | - Justin T. Seffernick
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Lovette Azap
- Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, 500 West 12th Avenue, Columbus, Ohio 43210, United States
| | - Serena L. Cole
- Micromyx, 4717 Campus Drive, Kalamazoo, Michigan 49008, United States
| | - D. Shinabarger
- Micromyx, 4717 Campus Drive, Kalamazoo, Michigan 49008, United States
| | - Laura M. Koeth
- Laboratory Specialists, Inc., 26214 Center Ridge Road, Westlake, Ohio 44145, United States
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Jack C. Yalowich
- Division of Pharmacology, The Ohio State University, 500 West 12th Avenue, Columbus, Ohio 43210, United States
| | - Daniel J. Wozniak
- Microbial Infection and Immunity, The Ohio State University, 460 West 12th Avenue, Columbus, Ohio 43210, United States
- Department of Microbiology, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210, United States
| | - Mark J. Mitton-Fry
- Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, 500 West 12th Avenue, Columbus, Ohio 43210, United States
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19
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Khan SA, Asiri AM, Basisi HM, Asad M, Zayed ME, Sharma K, Wani MY. Synthesis and evaluation of Quinoline-3-carbonitrile derivatives as potential antibacterial agents. Bioorg Chem 2019; 88:102968. [DOI: 10.1016/j.bioorg.2019.102968] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 03/26/2019] [Accepted: 04/29/2019] [Indexed: 12/24/2022]
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20
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Cyclohexyl amide-based novel bacterial topoisomerase inhibitors with prospective GyrA-binding fragments. Future Med Chem 2019; 11:935-945. [PMID: 31140866 DOI: 10.4155/fmc-2018-0472] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Aim: Novel bacterial topoisomerase inhibitors (NBTIs) are a promising class of bacterial topoisomerase II inhibitors that are gaining more and more importance mainly because of their excellent antibacterial activity, as well as their lack of cross-resistance to quinolones. Results: Described here is the synthesis and biological evaluation of a tiny series of new virtually assembled NBTIs containing synthetically feasible right-hand side fragments capable of binding the GyrA subunit of the bacterial DNA gyrase-DNA complex. Conclusion: NBTI variants with incorporated 1-phenylpyrazole right-hand side moiety show suitable antibacterial activity against Gram-positive Staphylococcus aureus, with confirmed selectivity over the human topoisomerase IIα enzyme.
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21
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Novel bacterial topoisomerase inhibitors: challenges and perspectives in reducing hERG toxicity. Future Med Chem 2018; 10:2241-2244. [PMID: 30215281 DOI: 10.4155/fmc-2018-0272] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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22
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Synthesis and anti-staphylococcal activity of novel bacterial topoisomerase inhibitors with a 5-amino-1,3-dioxane linker moiety. Bioorg Med Chem Lett 2018; 28:2477-2480. [DOI: 10.1016/j.bmcl.2018.06.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 05/14/2018] [Accepted: 06/01/2018] [Indexed: 12/30/2022]
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23
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Liu CW, Lin YC, Hung CM, Liu BL, Kuo SC, Ho CT, Way TD, Hung CH. CHM-1, a novel microtubule-destabilizing agent exhibits antitumor activity via inducing the expression of SIRT2 in human breast cancer cells. Chem Biol Interact 2018; 289:98-108. [PMID: 29679549 DOI: 10.1016/j.cbi.2018.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 03/05/2018] [Accepted: 04/05/2018] [Indexed: 11/28/2022]
Abstract
Breast cancer is a major public health problem throughout the world. In this report, we investigated whether CHM-1, a novel synthetic antimitotic agent could be developed into a potent antitumor agent for treating human breast cancer. CHM-1 induced growth inhibition in MDA-MB-231, MDA-MB-453 and MCF-7 cells in a concentration-dependent manner. Importantly, CHM-1 is less toxic to normal breast (HBL-100) cells. CHM-1 interacted with tubulin, markedly inhibited tubulin polymerization, and disrupted microtubule organization. Proteins from control and CHM-1-treated animal tumor specimens were analyzed by two-dimensional electrophoresis and MALDI-TOF mass spectrometry. Our results indicated that CHM-1 increased the expression of SIRT2 protein, an NAD-dependent tubulin deacetylase. A prodrug strategy was also investigated to address the problem of low aqueous solubility and low bioavailability of the antitumor agent CHM-1. The water-soluble prodrug of CHM-1 (CHM-1-P) was synthesized. After oral and intravenous administration, CHM-1-P induced a dose-dependent inhibition of tumor growth. The aforementioned excellent anti-tumor activity profiles of CHM-1 and its prodrug CHM-1-P, suggests that CHM-1-P deserves to further develop as a clinical trial candidate for treating human breast carcinoma.
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Affiliation(s)
- Chin-Wei Liu
- Department of Chemical Engineering and Institute of Biotechnology and Chemical Engineering, I-Shou University, Kaohsiung, Taiwan
| | - Ying-Chao Lin
- Division of Neurosurgery, Buddhist Tzu Chi General Hospital, Taichung Branch, Taiwan; School of Medicine, Tzu Chi University, Hualien, Taiwan; Department of Medical Imaging and Radiological Science, Central Taiwan University of Science and Technology, Taichung, Taiwan
| | - Chao-Ming Hung
- Department of General Surgery, E-Da Hospital, I-Shou University, Kaohsiung, Taiwan; School of Medicine, I-Shou University, Kaohsiung, Taiwan
| | - Bing-Lan Liu
- Department of Applied Chemistry, Chaoyang University of Technology, Taichung, Taiwan
| | - Sheng-Chu Kuo
- School of Pharmacy, College of Pharmacy, China Medical University, Taichung, Taiwan
| | - Chi-Tang Ho
- Department of Food Science, Rutgers University, New Brunswick, NJ, USA
| | - Tzong-Der Way
- Department of Biological Science and Technology, College of Biopharmaceutical and Food Sciences, China Medical University, Taichung, Taiwan; Department of Health and Nutrition Biotechnology, Asia University, Taichung, Taiwan.
| | - Chih-Hsin Hung
- Department of Chemical Engineering and Institute of Biotechnology and Chemical Engineering, I-Shou University, Kaohsiung, Taiwan.
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24
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Zampieri M, Szappanos B, Buchieri MV, Trauner A, Piazza I, Picotti P, Gagneux S, Borrell S, Gicquel B, Lelievre J, Papp B, Sauer U. High-throughput metabolomic analysis predicts mode of action of uncharacterized antimicrobial compounds. Sci Transl Med 2018; 10:eaal3973. [PMID: 29467300 PMCID: PMC6544516 DOI: 10.1126/scitranslmed.aal3973] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 04/11/2017] [Accepted: 09/27/2017] [Indexed: 12/19/2022]
Abstract
Rapidly spreading antibiotic resistance and the low discovery rate of new antimicrobial compounds demand more effective strategies for early drug discovery. One bottleneck in the drug discovery pipeline is the identification of the modes of action (MoAs) of new compounds. We have developed a rapid systematic metabolome profiling strategy to classify the MoAs of bioactive compounds. The method predicted MoA-specific metabolic responses in the nonpathogenic bacterium Mycobacterium smegmatis after treatment with 62 reference compounds with known MoAs and different metabolic and nonmetabolic targets. We then analyzed a library of 212 new antimycobacterial compounds with unknown MoAs from a drug discovery effort by the pharmaceutical company GlaxoSmithKline (GSK). More than 70% of these new compounds induced metabolic responses in M. smegmatis indicative of known MoAs, seven of which were experimentally validated. Only 8% (16) of the compounds appeared to target unconventional cellular processes, illustrating the difficulty in discovering new antibiotics with different MoAs among compounds used as monotherapies. For six of the GSK compounds with potentially new MoAs, the metabolome profiles suggested their ability to interfere with trehalose and lipid metabolism. This was supported by whole-genome sequencing of spontaneous drug-resistant mutants of the pathogen Mycobacterium tuberculosis and in vitro compound-proteome interaction analysis for one of these compounds. Our compendium of drug-metabolome profiles can be used to rapidly query the MoAs of uncharacterized antimicrobial compounds and should be a useful resource for the drug discovery community.
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Affiliation(s)
- Mattia Zampieri
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland.
| | - Balazs Szappanos
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Maria Virginia Buchieri
- Mycobacterial Genetics Unit, Institut Pasteur, 25-28 Rue du Docteur Roux, 75015 Paris, France
| | - Andrej Trauner
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Ilaria Piazza
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Paola Picotti
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Sébastien Gagneux
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Sonia Borrell
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Brigitte Gicquel
- Mycobacterial Genetics Unit, Institut Pasteur, 25-28 Rue du Docteur Roux, 75015 Paris, France
| | - Joel Lelievre
- Disease of the Developing World, GlaxoSmithKline, Severo Ochoa, Tres Cantos, Madrid 28760, Spain
| | - Balazs Papp
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
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25
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Bispo MLF, Lima CHS, Cardoso LNF, Candéa ALP, Bezerra FAFM, Lourenço MCS, Henriques MGMO, Alencastro RB, Kaiser CR, Souza MVN, Albuquerque MG. Anti-Mycobacterial Evaluation of 7-Chloro-4-Aminoquinolines and Hologram Quantitative Structure-Activity Relationship (HQSAR) Modeling of Amino-Imino Tautomers. Pharmaceuticals (Basel) 2017; 10:ph10020052. [PMID: 28598408 PMCID: PMC5490409 DOI: 10.3390/ph10020052] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 06/05/2017] [Accepted: 06/06/2017] [Indexed: 11/16/2022] Open
Abstract
In an ongoing research program for the development of new anti-tuberculosis drugs, we synthesized three series (A, B, and C) of 7-chloro-4-aminoquinolines, which were evaluated in vitro against Mycobacterium tuberculosis (MTB). Now, we report the anti-MTB and cytotoxicity evaluations of a new series, D (D01–D21). Considering the active compounds of series A (A01–A13), B (B01–B13), C (C01–C07), and D (D01–D09), we compose a data set of 42 compounds and carried out hologram quantitative structure–activity relationship (HQSAR) analysis. The amino–imino tautomerism of the 4-aminoquinoline moiety was considered using both amino (I) and imino (II) forms as independent datasets. The best HQSAR model from each dataset was internally validated and both models showed significant statistical indexes. Tautomer I model: leave-one-out (LOO) cross-validated correlation coefficient (q2) = 0.80, squared correlation coefficient (r2) = 0.97, standard error (SE) = 0.12, cross-validated standard error (SEcv) = 0.32. Tautomer II model: q2 = 0.77, r2 = 0.98, SE = 0.10, SEcv = 0.35. Both models were externally validated by predicting the activity values of the corresponding test set, and the tautomer II model, which showed the best external prediction performance, was used to predict the biological activity responses of the compounds that were not evaluated in the anti-MTB trials due to poor solubility, pointing out D21 for further solubility studies to attempt to determine its actual biological activity.
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Affiliation(s)
- Marcelle L F Bispo
- Departamento de Química, Universidade Estadual de Londrina (UEL), Londrina 86057-970, Brazil.
- Programa de Pós-Graduação em Química (PGQu), Instituto de Química (IQ), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21949-900, Brazil.
- Fundação Oswaldo Cruz (FioCruz), Instituto de Tecnologia em Fármacos (Far-Manguinhos), Rio de Janeiro 21041-250, Brazil.
| | - Camilo H S Lima
- Faculdade de Farmácia, Laboratório de Química Medicinal (LQMed), Programa de Pós-Graduação em Ciências Aplicadas a Produtos para Saúde, Universidade Federal Fluminense (UFF), Niterói 24241-000, Brazil.
- Programa de Pós-Graduação em Química (PGQu), Instituto de Química (IQ), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21949-900, Brazil.
- Fundação Oswaldo Cruz (FioCruz), Instituto de Tecnologia em Fármacos (Far-Manguinhos), Rio de Janeiro 21041-250, Brazil.
| | - Laura N F Cardoso
- Programa de Pós-Graduação em Química (PGQu), Instituto de Química (IQ), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21949-900, Brazil.
- Fundação Oswaldo Cruz (FioCruz), Instituto de Tecnologia em Fármacos (Far-Manguinhos), Rio de Janeiro 21041-250, Brazil.
| | - André L P Candéa
- Fundação Oswaldo Cruz (FioCruz), Instituto de Tecnologia em Fármacos (Far-Manguinhos), Rio de Janeiro 21041-250, Brazil.
| | - Flávio A F M Bezerra
- Fundação Oswaldo Cruz (FioCruz), Instituto de Pesquisas Clínicas Evandro Chagas (IPEC), Rio de Janeiro 21040-360, Brazil.
| | - Maria C S Lourenço
- Fundação Oswaldo Cruz (FioCruz), Instituto de Pesquisas Clínicas Evandro Chagas (IPEC), Rio de Janeiro 21040-360, Brazil.
| | - Maria G M O Henriques
- Fundação Oswaldo Cruz (FioCruz), Instituto de Tecnologia em Fármacos (Far-Manguinhos), Rio de Janeiro 21041-250, Brazil.
| | - Ricardo B Alencastro
- Programa de Pós-Graduação em Química (PGQu), Instituto de Química (IQ), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21949-900, Brazil.
| | - Carlos R Kaiser
- Programa de Pós-Graduação em Química (PGQu), Instituto de Química (IQ), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21949-900, Brazil.
| | - Marcus V N Souza
- Programa de Pós-Graduação em Química (PGQu), Instituto de Química (IQ), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21949-900, Brazil.
- Fundação Oswaldo Cruz (FioCruz), Instituto de Tecnologia em Fármacos (Far-Manguinhos), Rio de Janeiro 21041-250, Brazil.
| | - Magaly G Albuquerque
- Programa de Pós-Graduação em Química (PGQu), Instituto de Química (IQ), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21949-900, Brazil.
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26
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Mitton-Fry MJ, Brickner SJ, Hamel JC, Barham R, Brennan L, Casavant JM, Ding X, Finegan S, Hardink J, Hoang T, Huband MD, Maloney M, Marfat A, McCurdy SP, McLeod D, Subramanyam C, Plotkin M, Reilly U, Schafer J, Stone GG, Uccello DP, Wisialowski T, Yoon K, Zaniewski R, Zook C. Novel 3-fluoro-6-methoxyquinoline derivatives as inhibitors of bacterial DNA gyrase and topoisomerase IV. Bioorg Med Chem Lett 2017; 27:3353-3358. [PMID: 28610977 DOI: 10.1016/j.bmcl.2017.06.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 05/31/2017] [Accepted: 06/02/2017] [Indexed: 10/19/2022]
Abstract
Novel (non-fluoroquinolone) inhibitors of bacterial type II topoisomerases (NBTIs) are an emerging class of antibacterial agents. We report an optimized series of cyclobutylaryl-substituted NBTIs. Compound 14 demonstrated excellent activity both in vitro (S. aureus MIC90=0.125μg/mL) and in vivo (systemic and tissue infections). Enhanced inhibition of Topoisomerase IV correlated with improved activity in S. aureus strains with mutations conferring resistance to NBTIs. Compound 14 also displayed an improved hERG IC50 of 85.9μM and a favorable profile in the anesthetized guinea pig model.
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Affiliation(s)
| | | | - Judith C Hamel
- Pfizer Worldwide Research and Development, Groton, CT 06340, USA
| | - Rose Barham
- Pfizer Worldwide Research and Development, Groton, CT 06340, USA
| | - Lori Brennan
- Pfizer Worldwide Research and Development, Groton, CT 06340, USA
| | | | - Xiaoyuan Ding
- Pfizer Worldwide Research and Development, Groton, CT 06340, USA
| | - Steven Finegan
- Pfizer Worldwide Research and Development, Groton, CT 06340, USA
| | - Joel Hardink
- Pfizer Worldwide Research and Development, Groton, CT 06340, USA
| | - Thuy Hoang
- Pfizer Worldwide Research and Development, Groton, CT 06340, USA
| | - Michael D Huband
- Pfizer Worldwide Research and Development, Groton, CT 06340, USA
| | - Meghan Maloney
- Pfizer Worldwide Research and Development, Groton, CT 06340, USA
| | - Anthony Marfat
- Pfizer Worldwide Research and Development, Groton, CT 06340, USA
| | - Sandra P McCurdy
- Pfizer Worldwide Research and Development, Groton, CT 06340, USA
| | - Dale McLeod
- Pfizer Worldwide Research and Development, Groton, CT 06340, USA
| | | | - Michael Plotkin
- Pfizer Worldwide Research and Development, Groton, CT 06340, USA
| | - Usa Reilly
- Pfizer Worldwide Research and Development, Groton, CT 06340, USA
| | - John Schafer
- Pfizer Worldwide Research and Development, Groton, CT 06340, USA
| | - Gregory G Stone
- Pfizer Worldwide Research and Development, Groton, CT 06340, USA
| | - Daniel P Uccello
- Pfizer Worldwide Research and Development, Groton, CT 06340, USA
| | - Todd Wisialowski
- Pfizer Worldwide Research and Development, Groton, CT 06340, USA
| | - Kwansik Yoon
- Pfizer Worldwide Research and Development, Groton, CT 06340, USA
| | | | - Christopher Zook
- Pfizer Worldwide Research and Development, Groton, CT 06340, USA
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27
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N-Heterocyclic choline analogues based on 1,2,3,4-tetrahydro(iso)quinoline scaffold with anticancer and anti-infective dual action. Pharmacol Rep 2017; 69:575-581. [PMID: 31994086 DOI: 10.1016/j.pharep.2017.01.028] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 12/29/2016] [Accepted: 01/27/2017] [Indexed: 01/12/2023]
Abstract
BACKGROUND Pharmacological effects of biologically active "small molecules" can be improved by their targeted modification, which affects drug delivery and interaction with tumor cells and microorganisms. We aimed to evaluate anticancer and antimicrobial activity of lipid-like choline derivatives modified via simultaneous introduction of tetrahydro(iso)quinoline based pharmacophore system at nitrogen atom and long chain alkyl substituent at oxygen atom. METHODS Target compounds were synthesized under phase-transfer catalysis conditions followed by quaternization, and evaluated for cytotoxicity and NO-generation ability on HT-1080 and MG-22A tumor cell lines and NIH 3T3 normal mouse fibroblasts, and screened for antimicrobial activity against gram-positive (Staphylococcus aureus and Bacillus cereus) and gram-negative bacteria (Escherichia coli, Pseudomonas aeruginosa and Proteus mirabilis) and fungi (Candida albicans and Aspergillus niger). Inhibitory action of active compounds towards E. coli DNA gyrase was investigated. RESULTS Target compounds exhibit high selective cytotoxicity (LC50 < 1 μg/mL) and NO-induction ability, and reveal strong antimicrobial activity with MIC and MBC/MFC values of 0.5-32 μg/mL, predominantly vs. gram-positive bacteria and fungi. Tested substances displayed inhibitory effect towards E. coli DNA gyrase, though less than ciprofloxacin. Tetrahydroisoquinoline derivatives and compounds possessing substituents with chain length of 10 and 11 carbon atoms have highest indices of activities. CONCLUSIONS Lipid-like N-heterocyclic choline analogues based on 1,2,3,4-tetrahydro(iso)quinoline scaffold, possessing very high cytotoxicity with attendant strong antimicrobial activity are the leads for developing effective dual action therapeutics.
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28
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Jarolim K, Del Favero G, Ellmer D, Stark TD, Hofmann T, Sulyok M, Humpf HU, Marko D. Dual effectiveness of Alternaria but not Fusarium mycotoxins against human topoisomerase II and bacterial gyrase. Arch Toxicol 2016; 91:2007-2016. [PMID: 27682608 PMCID: PMC5364253 DOI: 10.1007/s00204-016-1855-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 09/15/2016] [Indexed: 11/28/2022]
Abstract
Type II DNA-topoisomerases (topo II) play a crucial role in the maintenance of DNA topology. Previously, fungi of the Alternaria genus were found to produce mycotoxins that target human topo II. These results implied the question why a fungus should produce secondary metabolites that target a human enzyme. In the current work, the homology between human topo II and its bacterial equivalent, gyrase, served as basis to study a potential dual inhibition of both enzymes by mycotoxins. A total of 15 secondary metabolites produced by fungi of the genera Alternaria and Fusarium were assessed for their impact on topo II of human and bacterial origin in the decatenation and the supercoiling assay, respectively. In line with the theory of dual topo II inhibition, six of the tested Alternaria mycotoxins were active against both enzymes, the dibenzo-α-pyrones alternariol (AOH) and alternariol monomethyl ether (AME), as well as the perylene-quinones altertoxin I (ATX I) and II (ATX II), alterperylenol (ALP) and stemphyltoxin III (STTX III). The Alternaria metabolites altersetin (ALN), macrosporin (MAC), altenusine (ALS) and pyrenophorol (PYR) impaired the function of human topo II, but did not show any effect on gyrase. The potency to inhibit topo II activity declined in the row STTX III (initial inhibitory concentration 10 µM) > AOH (25 µM) = AME (25 µM) = ALS (25 µM) = ATX II (25 µM) > ALN (50 µM) = ATX I (50 µM) > ALP (75 µM) = PYR (75 µM) > MAC (150 µM). Inhibition of gyrase activity was most pronounced for AOH and AME (initial inhibitory concentration 10 µM) followed by ATX II (25 µM) > ATX I = ALP = STTX III (50 µM). In contrast, none of the investigated Fusarium mycotoxins deoxynivalenol (DON), fumonisin B1, fusarin C and moniliformin, as well as the Alternaria metabolite tentoxin, had any impact on the activity of neither human nor bacterial topo II.
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Affiliation(s)
- Katharina Jarolim
- Department of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, 1090, Vienna, Austria
| | - Giorgia Del Favero
- Department of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, 1090, Vienna, Austria
| | - Doris Ellmer
- Chair of Food Chemistry and Molecular Sensory Science, Technical University of Munich, 85354, Freising, Germany
| | - Timo D Stark
- Chair of Food Chemistry and Molecular Sensory Science, Technical University of Munich, 85354, Freising, Germany
| | - Thomas Hofmann
- Chair of Food Chemistry and Molecular Sensory Science, Technical University of Munich, 85354, Freising, Germany
| | - Michael Sulyok
- Department IFA-Tulln, University of Natural Resources and Life Sciences Vienna (BOKU), 3430, Tulln, Austria
| | - Hans-Ulrich Humpf
- Institute of Food Chemistry, Westfälische Wilhelms-Universität Münster, 48149, Münster, Germany
| | - Doris Marko
- Department of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, 1090, Vienna, Austria.
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29
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In Vitro and In Vivo Characterization of the Novel Oxabicyclooctane-Linked Bacterial Topoisomerase Inhibitor AM-8722, a Selective, Potent Inhibitor of Bacterial DNA Gyrase. Antimicrob Agents Chemother 2016; 60:4830-9. [PMID: 27246784 DOI: 10.1128/aac.00619-16] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 05/25/2016] [Indexed: 01/08/2023] Open
Abstract
Oxabicyclooctane-linked novel bacterial topoisomerase inhibitors (NBTIs) represent a new class of recently described antibacterial agents with broad-spectrum activity. NBTIs dually inhibit the clinically validated bacterial targets DNA gyrase and topoisomerase IV and have been shown to bind distinctly from known classes of antibacterial agents directed against these targets. Herein we report the molecular, cellular, and in vivo characterization of AM-8722 as a representative N-alkylated-1,5-naphthyridone left-hand-side-substituted NBTI. Consistent with its mode of action, macromolecular labeling studies revealed a specific effect of AM-8722 to dose dependently inhibit bacterial DNA synthesis. AM-8722 displayed greater intrinsic enzymatic potency than levofloxacin versus both DNA gyrase and topoisomerase IV from Staphylococcus aureus and Escherichia coli and displayed selectivity against human topoisomerase II. AM-8722 was rapidly bactericidal and exhibited whole-cell activity versus a range of Gram-negative and Gram-positive organisms, with no whole-cell potency shift due to the presence of DNA or human serum. Frequency-of-resistance studies demonstrated an acceptable rate of resistance emergence in vitro at concentrations 16- to 32-fold the MIC. AM-8722 displayed acceptable pharmacokinetic properties and was shown to be efficacious in mouse models of bacterial septicemia. Overall, AM-8722 is a selective and potent NBTI that displays broad-spectrum antimicrobial activity in vitro and in vivo.
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30
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Miles TJ, Hennessy AJ, Bax B, Brooks G, Brown BS, Brown P, Cailleau N, Chen D, Dabbs S, Davies DT, Esken JM, Giordano I, Hoover JL, Jones GE, Kusalakumari Sukmar SK, Markwell RE, Minthorn EA, Rittenhouse S, Gwynn MN, Pearson ND. Novel tricyclics (e.g., GSK945237) as potent inhibitors of bacterial type IIA topoisomerases. Bioorg Med Chem Lett 2016; 26:2464-2469. [PMID: 27055939 DOI: 10.1016/j.bmcl.2016.03.106] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 03/28/2016] [Accepted: 03/29/2016] [Indexed: 01/06/2023]
Abstract
During the course of our research on the lead optimisation of the NBTI (Novel Bacterial Type II Topoisomerase Inhibitors) class of antibacterials, we discovered a series of tricyclic compounds that showed good Gram-positive and Gram-negative potency. Herein we will discuss the various subunits that were investigated in this series and report advanced studies on compound 1 (GSK945237) which demonstrates good PK and in vivo efficacy properties.
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Affiliation(s)
- Timothy J Miles
- Diseases of the Developing World CEDD, GlaxoSmithKline, Calle Severo Ochoa, 2, 28760 Tres Cantos, Madrid, Spain.
| | - Alan J Hennessy
- Infectious Diseases CEDD, GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - Ben Bax
- Platform Technology & Science, GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - Gerald Brooks
- Infectious Diseases CEDD, GlaxoSmithKline, Third Avenue, Harlow CM19 5AW, UK
| | - Barry S Brown
- Infectious Diseases CEDD, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, USA
| | - Pamela Brown
- Infectious Diseases CEDD, GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - Nathalie Cailleau
- Infectious Diseases CEDD, GlaxoSmithKline, Third Avenue, Harlow CM19 5AW, UK
| | - Dongzhao Chen
- Infectious Diseases CEDD, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, USA
| | - Steven Dabbs
- Infectious Diseases CEDD, GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - David T Davies
- Infectious Diseases CEDD, GlaxoSmithKline, Third Avenue, Harlow CM19 5AW, UK
| | - Joel M Esken
- Infectious Diseases CEDD, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, USA
| | - Ilaria Giordano
- Diseases of the Developing World CEDD, GlaxoSmithKline, Calle Severo Ochoa, 2, 28760 Tres Cantos, Madrid, Spain
| | - Jennifer L Hoover
- Infectious Diseases CEDD, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, USA
| | - Graham E Jones
- Infectious Diseases CEDD, GlaxoSmithKline, Third Avenue, Harlow CM19 5AW, UK
| | | | - Roger E Markwell
- Infectious Diseases CEDD, GlaxoSmithKline, Third Avenue, Harlow CM19 5AW, UK
| | - Elisabeth A Minthorn
- Oncology TA, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, USA
| | - Steve Rittenhouse
- Infectious Diseases CEDD, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, USA
| | - Michael N Gwynn
- Infectious Diseases CEDD, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, USA
| | - Neil D Pearson
- Infectious Diseases CEDD, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, USA
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31
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Li Y, Wong YX, Poh ZY, Wong YL, Lee MY, Ng HQ, Liu B, Hung AW, Cherian J, Hill J, Keller TH, Kang C. NMR structural characterization of the N-terminal active domain of the gyrase B subunit from Pseudomonas aeruginosa and its complex with an inhibitor. FEBS Lett 2015; 589:2683-9. [PMID: 26272827 DOI: 10.1016/j.febslet.2015.07.044] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 07/08/2015] [Accepted: 07/26/2015] [Indexed: 01/18/2023]
Abstract
The N-terminal ATP binding domain of the DNA gyrase B subunit is a validated drug target for antibacterial drug discovery. Structural information for this domain (pGyrB) from Pseudomonas aeruginosa is still missing. In this study, the interaction between pGyrB and a bis-pyridylurea inhibitor was characterized using several biophysical methods. We further carried out structural analysis of pGyrB using NMR spectroscopy. The secondary structures of free and inhibitor bound pGyrB were obtained based on backbone chemical shift assignment. Chemical shift perturbation and NOE experiments demonstrated that the inhibitor binds to the ATP binding pocket. The results of this study will be helpful for drug development targeting P. aeruginosa.
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Affiliation(s)
- Yan Li
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore
| | - Yun Xuan Wong
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore
| | - Zhi Ying Poh
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore
| | - Ying Lei Wong
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore
| | - Michelle Yueqi Lee
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore
| | - Hui Qi Ng
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore
| | - Boping Liu
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore
| | - Alvin W Hung
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore
| | - Joseph Cherian
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore
| | - Jeffrey Hill
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore
| | - Thomas H Keller
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore
| | - CongBao Kang
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore.
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32
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Azam MA, Thathan J, Jubie S. Dual targeting DNA gyrase B (GyrB) and topoisomerse IV (ParE) inhibitors: A review. Bioorg Chem 2015; 62:41-63. [PMID: 26232660 DOI: 10.1016/j.bioorg.2015.07.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 07/19/2015] [Accepted: 07/20/2015] [Indexed: 01/03/2023]
Abstract
GyrB and ParE are type IIA topoisomerases and found in most bacteria. Its function is vital for DNA replication, repair and decatenation. The highly conserved ATP-binding subunits of DNA GyrB and ParE are structurally related and have been recognized as prime candidates for the development of dual-targeting antibacterial agents with broad-spectrum potential. However, no natural product or small molecule inhibitors targeting ATPase catalytic domain of both GyrB and ParE enzymes have succeeded in the clinic. Moreover, no inhibitors of these enzymes with broad-spectrum antibacterial activity against Gram-negative pathogens have been reported. Availability of high resolution crystal structures of GyrB and ParE made it possible for the design of many different classes of inhibitors with dual mechanism of action. Among them benzimidazoles, benzothiazoles, thiazolopyridines, imidiazopyridazoles, pyridines, indazoles, pyrazoles, imidazopyridines, triazolopyridines, pyrrolopyrimidines, pyrimidoindoles as well as related structures are disclosed in literatures. Unfortunately most of these inhibitors are found to be active against Gram-positive pathogens. In the present review we discuss about studies on novel dual targeting ATPase inhibitors.
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Affiliation(s)
- Mohammed Afzal Azam
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy (A Constituent College of JSS University, Mysore), Udhagamandalam 643001, Tamil Nadu, India.
| | - Janarthanan Thathan
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy (A Constituent College of JSS University, Mysore), Udhagamandalam 643001, Tamil Nadu, India
| | - Selvaraj Jubie
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy (A Constituent College of JSS University, Mysore), Udhagamandalam 643001, Tamil Nadu, India
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33
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Hameed P S, Manjrekar P, Raichurkar A, Shinde V, Puttur J, Shanbhag G, Chinnapattu M, Patil V, Rudrapatana S, Sharma S, Kumar CNN, Nandishaiah R, Madhavapeddi P, Sriram D, Solapure S, Sambandamurthy VK. Left-Hand Side Exploration of Novel Bacterial Topoisomerase Inhibitors to Improve Selectivity against hERG Binding. ACS Med Chem Lett 2015; 6:741-6. [PMID: 26191359 DOI: 10.1021/ml500531p] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 05/22/2015] [Indexed: 02/07/2023] Open
Abstract
Structure-activity relationship (SAR) exploration on the left-hand side (LHS) of a novel class of bacterial topoisomerase inhibitors led to a significant improvement in the selectivity against hERG cardiac channel binding with concomitant potent antimycobacterial activity. Bulky polar substituents at the C-7 position of the naphthyridone ring did not disturb its positioning between two base pairs of DNA. Further optimization of the polar substituents on the LHS of the naphthyridone ring led to potent antimycobacterial activity (Mtb MIC = 0.06 μM) against Mycobacterium tuberculosis (Mtb). Additionally, this knowledge provided a robust SAR understanding to mitigate the hERG risk. This compound class inhibits Mtb DNA gyrase and retains its antimycobacterial activity against moxifloxacin-resistant strains of Mtb. Finally, we demonstrate in vivo proof of concept in an acute mouse model of TB following oral administration of compound 19.
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Affiliation(s)
- Shahul Hameed P
- AstraZeneca India Pvt. Ltd, Avishkar, Bellary Road, Bangalore-560024, India
| | - Praveena Manjrekar
- AstraZeneca India Pvt. Ltd, Avishkar, Bellary Road, Bangalore-560024, India
| | | | - Vikas Shinde
- AstraZeneca India Pvt. Ltd, Avishkar, Bellary Road, Bangalore-560024, India
| | - Jayashree Puttur
- AstraZeneca India Pvt. Ltd, Avishkar, Bellary Road, Bangalore-560024, India
| | - Gajanan Shanbhag
- AstraZeneca India Pvt. Ltd, Avishkar, Bellary Road, Bangalore-560024, India
| | | | - Vikas Patil
- AstraZeneca India Pvt. Ltd, Avishkar, Bellary Road, Bangalore-560024, India
| | - Suresh Rudrapatana
- AstraZeneca India Pvt. Ltd, Avishkar, Bellary Road, Bangalore-560024, India
| | - Sreevalli Sharma
- AstraZeneca India Pvt. Ltd, Avishkar, Bellary Road, Bangalore-560024, India
| | - C. N. Naveen Kumar
- AstraZeneca India Pvt. Ltd, Avishkar, Bellary Road, Bangalore-560024, India
| | - Radha Nandishaiah
- AstraZeneca India Pvt. Ltd, Avishkar, Bellary Road, Bangalore-560024, India
| | | | - D. Sriram
- AstraZeneca India Pvt. Ltd, Avishkar, Bellary Road, Bangalore-560024, India
| | - Suresh Solapure
- AstraZeneca India Pvt. Ltd, Avishkar, Bellary Road, Bangalore-560024, India
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34
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Singh SB, Kaelin DE, Meinke PT, Wu J, Miesel L, Tan CM, Olsen DB, Lagrutta A, Fukuda H, Kishii R, Takei M, Takeuchi T, Takano H, Ohata K, Kurasaki H, Nishimura A, Shibata T, Fukuda Y. Structure activity relationship of C-2 ether substituted 1,5-naphthyridine analogs of oxabicyclooctane-linked novel bacterial topoisomerase inhibitors as broad-spectrum antibacterial agents (Part-5). Bioorg Med Chem Lett 2015; 25:3630-5. [PMID: 26152426 DOI: 10.1016/j.bmcl.2015.06.061] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 06/12/2015] [Accepted: 06/15/2015] [Indexed: 02/02/2023]
Abstract
Oxabicyclooctane linked novel bacterial topoisomerase inhibitors (NBTIs) are new class of recently reported broad-spectrum antibacterial agents. They target bacterial DNA gyrase and topoisomerase IV and bind to a site different than quinolones. They show no cross-resistance to known antibiotics and provide opportunity to combat drug-resistant bacteria. A structure activity relationship of the C-2 substituted ether analogs of 1,5-naphthyridine oxabicyclooctane-linked NBTIs are described. Synthesis and antibacterial activities of a total of 63 analogs have been summarized representing alkyl, cyclo alkyl, fluoro alkyl, hydroxy alkyl, amino alkyl, and carboxyl alkyl ethers. All compounds were tested against three key strains each of Gram-positive and Gram-negative bacteria as well as for hERG binding activities. Many key compounds were also tested for the functional hERG activity. Six compounds were evaluated for efficacy in a murine bacteremia model of Staphylococcus aureus infection. Significant tolerance for the ether substitution (including polar groups such as amino and carboxyl) at C-2 was observed for S. aureus activity however the same was not true for Enterococcus faecium and Gram-negative strains. Reduced clogD generally showed reduced hERG activity and improved in vivo efficacy but was generally associated with decreased overall potency. One of the best compounds was hydroxy propyl ether (16), which mainly retained the potency, spectrum and in vivo efficacy of AM8085 associated with the decreased hERG activity and improved physical property.
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Affiliation(s)
- Sheo B Singh
- Merck Research Laboratories, Kenilworth, NJ 07033, United States.
| | - David E Kaelin
- Merck Research Laboratories, Kenilworth, NJ 07033, United States
| | - Peter T Meinke
- Merck Research Laboratories, Kenilworth, NJ 07033, United States
| | - Jin Wu
- Merck Research Laboratories, Kenilworth, NJ 07033, United States
| | - Lynn Miesel
- Merck Research Laboratories, Kenilworth, NJ 07033, United States
| | | | - David B Olsen
- Merck Research Laboratories, West Point, PA 19486, United States
| | - Armando Lagrutta
- Merck Research Laboratories, West Point, PA 19486, United States
| | - Hideyuki Fukuda
- Kyorin Pharmaceutical Co., Ltd, 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Ryuta Kishii
- Kyorin Pharmaceutical Co., Ltd, 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Masaya Takei
- Kyorin Pharmaceutical Co., Ltd, 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Tomoko Takeuchi
- Kyorin Pharmaceutical Co., Ltd, 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Hisashi Takano
- Kyorin Pharmaceutical Co., Ltd, 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Kohei Ohata
- Kyorin Pharmaceutical Co., Ltd, 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Haruaki Kurasaki
- Kyorin Pharmaceutical Co., Ltd, 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Akinori Nishimura
- Kyorin Pharmaceutical Co., Ltd, 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Takeshi Shibata
- Kyorin Pharmaceutical Co., Ltd, 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Yasumichi Fukuda
- Kyorin Pharmaceutical Co., Ltd, 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan.
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35
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Singh SB, Kaelin DE, Wu J, Miesel L, Tan CM, Meinke PT, Olsen DB, Lagrutta A, Wei C, Liao Y, Peng X, Wang X, Fukuda H, Kishii R, Takei M, Yajima M, Shibue T, Shibata T, Ohata K, Nishimura A, Fukuda Y. Structure activity relationship of pyridoxazinone substituted RHS analogs of oxabicyclooctane-linked 1,5-naphthyridinyl novel bacterial topoisomerase inhibitors as broad-spectrum antibacterial agents (Part-6). Bioorg Med Chem Lett 2015; 25:3636-43. [PMID: 26141771 DOI: 10.1016/j.bmcl.2015.06.057] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 06/12/2015] [Accepted: 06/15/2015] [Indexed: 12/30/2022]
Abstract
Oxabicyclooctane linked 1,5-naphthyridinyl-pyridoxazinones are novel broad-spectrum bacterial topoisomerase inhibitors (NBTIs) targeting bacterial DNA gyrase and topoisomerase IV at a site different than quinolones. Due to lack of cross-resistance to known antibiotics they present excellent opportunity to combat drug-resistant bacteria. A structure activity relationship of the pyridoxazinone moiety is described in this Letter. Chemical synthesis and activities of NBTIs with substitutions at C-3, C-4 and C-7 of the pyridoxazinone moiety with halogens, alkyl groups and methoxy group has been described. In addition, substitutions of the linker NH proton and its transformation into amide analogs of AM-8085 and AM-8191 have been reported. Fluoro, chloro, and methyl groups at C-3 of the pyridoxazinone moiety retained the potency and spectrum. In addition, a C-3 fluoro analog showed 4-fold better oral efficacy (ED50 3.9 mg/kg) as compared to the parent AM-8085 in a murine bacteremia model of infection of Staphylococcus aureus. Even modest polarity (e.g., methoxy) is not tolerated at C-3 of the pyridoxazinone unit. The basicity and NH group of the linker is important for the activity when CH2 is at the linker position-8. However, amides (with linker position-8 ketone) with a position-7 NH or N-methyl group retained potency and spectrum suggesting that neither basicity nor hydrogen-donor properties of the linker amide NH is essential for the activity. This would suggest likely an altered binding mode of the linker position-7,8 amide containing compounds. The amides showed highly improved hERG (functional IC50 >30 μM) profile.
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Affiliation(s)
- Sheo B Singh
- Merck Research Laboratories, Kenilworth, NJ 07033, United States.
| | - David E Kaelin
- Merck Research Laboratories, Kenilworth, NJ 07033, United States
| | - Jin Wu
- Merck Research Laboratories, Kenilworth, NJ 07033, United States
| | - Lynn Miesel
- Merck Research Laboratories, Kenilworth, NJ 07033, United States
| | | | - Peter T Meinke
- Merck Research Laboratories, Kenilworth, NJ 07033, United States
| | - David B Olsen
- Merck Research Laboratories, West Point, PA 19486, United States
| | - Armando Lagrutta
- Merck Research Laboratories, West Point, PA 19486, United States
| | | | | | - Xuanjia Peng
- WuXi AppTec, Shanghai, People's Republic of China
| | - Xiu Wang
- WuXi AppTec, Shanghai, People's Republic of China
| | - Hideyuki Fukuda
- Kyorin Pharmaceutical Co., Ltd, 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Ryuta Kishii
- Kyorin Pharmaceutical Co., Ltd, 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Masaya Takei
- Kyorin Pharmaceutical Co., Ltd, 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Masanobu Yajima
- Kyorin Pharmaceutical Co., Ltd, 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Taku Shibue
- Kyorin Pharmaceutical Co., Ltd, 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Takeshi Shibata
- Kyorin Pharmaceutical Co., Ltd, 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Kohei Ohata
- Kyorin Pharmaceutical Co., Ltd, 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Akinori Nishimura
- Kyorin Pharmaceutical Co., Ltd, 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Yasumichi Fukuda
- Kyorin Pharmaceutical Co., Ltd, 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan.
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Hydroxy tricyclic 1,5-naphthyridinone oxabicyclooctane-linked novel bacterial topoisomerase inhibitors as broad-spectrum antibacterial agents-SAR of RHS moiety (Part-3). Bioorg Med Chem Lett 2015; 25:2473-8. [PMID: 25978963 DOI: 10.1016/j.bmcl.2015.04.063] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 04/18/2015] [Accepted: 04/21/2015] [Indexed: 12/22/2022]
Abstract
Novel bacterial topoisomerase inhibitors (NBTIs) are a new class of broad-spectrum antibacterial agents targeting bacterial Gyrase A and ParC and have potential utility in combating antibiotic resistance. (R)-Hydroxy-1,5-naphthyridinone left-hand side (LHS) oxabicyclooctane linked pyridoxazinone right-hand side (RHS) containing NBTIs showed a potent Gram-positive antibacterial profile. SAR around the RHS moiety, including substitutions around pyridooxazinone, pyridodioxane, and phenyl propenoids has been described. A fluoro substituted pyridoxazinone showed an MIC against Staphylococcus aureus of 0.5 μg/mL with reduced functional hERG activity (IC50 333 μM) and good in vivo efficacy [ED90 12 mg/kg, intravenous (iv) and 15 mg/kg, oral (p.o.)]. A pyridodioxane-containing NBTI showed a S. aureus MIC of 0.5 μg/mL, significantly improved hERG IC50 764 μM and strong efficacy of 11 mg/kg (iv) and 5 mg/kg (p.o.). A phenyl propenoid series of compounds showed potent antibacterial activity, but also showed potent hERG binding activity. Many of the compounds in the hydroxy-tricyclic series showed strong activity against Acinetobacter baumannii, but reduced activity against Escherichia coli and Pseudomonas aeruginosa. Bicyclic heterocycles appeared to be the best RHS moiety for the hydroxy-tricyclic oxabicyclooctane linked NBTIs.
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37
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Singh SB, Kaelin DE, Wu J, Miesel L, Tan CM, Meinke PT, Olsen DB, Lagrutta A, Wei C, Peng X, Wang X, Fukuda H, Kishii R, Takei M, Shibata T, Ohata K, Takano H, Kurasaki H, Takeuchi T, Nishimura A, Fukuda Y. Structure activity relationship of substituted 1,5-naphthyridine analogs of oxabicyclooctane-linked novel bacterial topoisomerase inhibitors as broad-spectrum antibacterial agents (Part-4). Bioorg Med Chem Lett 2015; 25:2409-15. [PMID: 25911300 DOI: 10.1016/j.bmcl.2015.04.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 03/30/2015] [Accepted: 04/01/2015] [Indexed: 11/25/2022]
Abstract
Bacterial resistance is rapidly growing, necessitating the need to discover new agents. Novel bacterial topoisomerase inhibitors (NBTIs) are new class of broad-spectrum antibacterial agents targeting bacterial DNA gyrase and topoisomerase IV. This class of inhibitors binds to an alternative binding site relative to fluoroquinolones and shows no cross-resistance to quinolones. NBTIs consist of three structural motifs. A structure activity relationship of the left hand motif 1,5-naphthyridine of oxabicyclooctane-linked NBTIs is described. Fifty five compounds were evaluated against a panel of key Gram-positive and Gram-negative strains of bacteria, as well as for hERG activity and five compounds were tested for in vivo efficacy in murine model of Staphylococcus aureus infection. These studies suggest that only a narrow range (activating and deactivating) of substitutions at C-2 and C-7 are tolerated for optimal antibacterial activity and spectrum. An alkoxy (methoxy) and CN at C-2, and a halogen and hydroxyl at C-7, appeared to be preferred in this series. Substitutions on the other three carbons generally have detrimental effect on the activity. No clear hERG activity SAR emerged from these substitutions.
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Affiliation(s)
- Sheo B Singh
- Merck Research Laboratories, Kenilworth, NJ 07033, United States.
| | - David E Kaelin
- Merck Research Laboratories, Kenilworth, NJ 07033, United States
| | - Jin Wu
- Merck Research Laboratories, Kenilworth, NJ 07033, United States
| | - Lynn Miesel
- Merck Research Laboratories, Kenilworth, NJ 07033, United States
| | | | - Peter T Meinke
- Merck Research Laboratories, Kenilworth, NJ 07033, United States
| | - David B Olsen
- Merck Research Laboratories, West Point, PA 19486, United States
| | - Armando Lagrutta
- Merck Research Laboratories, West Point, PA 19486, United States
| | | | - Xuanjia Peng
- WuXi AppTec, Shanghai, People's Republic of China
| | - Xiu Wang
- WuXi AppTec, Shanghai, People's Republic of China
| | - Hideyuki Fukuda
- Kyorin Pharmaceutical Co., Ltd, 2399-1, Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Ryuta Kishii
- Kyorin Pharmaceutical Co., Ltd, 2399-1, Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Masaya Takei
- Kyorin Pharmaceutical Co., Ltd, 2399-1, Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Takeshi Shibata
- Kyorin Pharmaceutical Co., Ltd, 2399-1, Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Kohei Ohata
- Kyorin Pharmaceutical Co., Ltd, 2399-1, Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Hisashi Takano
- Kyorin Pharmaceutical Co., Ltd, 2399-1, Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Haruaki Kurasaki
- Kyorin Pharmaceutical Co., Ltd, 2399-1, Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Tomoko Takeuchi
- Kyorin Pharmaceutical Co., Ltd, 2399-1, Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Akinori Nishimura
- Kyorin Pharmaceutical Co., Ltd, 2399-1, Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Yasumichi Fukuda
- Kyorin Pharmaceutical Co., Ltd, 2399-1, Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan.
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38
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Singh SB, Kaelin DE, Wu J, Miesel L, Tan CM, Black T, Nargund R, Meinke PT, Olsen DB, Lagrutta A, Lu J, Patel S, Rickert KW, Smith RF, Soisson S, Sherer E, Joyce LA, Wei C, Peng X, Wang X, Fukuda H, Kishii R, Takei M, Takano H, Shibasaki M, Yajima M, Nishimura A, Shibata T, Fukuda Y. Tricyclic 1,5-naphthyridinone oxabicyclooctane-linked novel bacterial topoisomerase inhibitors as broad-spectrum antibacterial agents-SAR of left-hand-side moiety (Part-2). Bioorg Med Chem Lett 2015; 25:1831-5. [PMID: 25851938 DOI: 10.1016/j.bmcl.2015.03.044] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 03/17/2015] [Accepted: 03/18/2015] [Indexed: 12/25/2022]
Abstract
Novel bacterial topoisomerase inhibitors (NBTIs) represent a new class of broad-spectrum antibacterial agents targeting bacterial Gyrase A and ParC and have potential utility in combating antibiotic resistance. A series of novel oxabicyclooctane-linked NBTIs with new tricyclic-1,5-naphthyridinone left hand side moieties have been described. Compounds with a (R)-hydroxy-1,5-naphthyridinone moiety (7) showed potent antibacterial activity (e.g., Staphylococcus aureus MIC 0.25 μg/mL), acceptable Gram-positive and Gram-negative spectrum with rapidly bactericidal activity. The compound 7 showed intravenous and oral efficacy (ED50) at 3.2 and 27 mg/kg doses, respectively, in a murine model of bacteremia. Most importantly they showed significant attenuation of functional hERG activity (IC50 >170 μM). In general, lower logD attenuated hERG activity but also reduced Gram-negative activity. The co-crystal structure of a hydroxy-tricyclic NBTI bound to a DNA-gyrase complex exhibited a binding mode that show enantiomeric preference for R isomer and explains the activity and SAR. The discovery, synthesis, SAR and X-ray crystal structure of the left-hand-side tricyclic 1,5-naphthyridinone based oxabicyclooctane linked NBTIs are described.
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Affiliation(s)
- Sheo B Singh
- Merck Research Laboratories, Kenilworth, NJ 07033, United States.
| | - David E Kaelin
- Merck Research Laboratories, Kenilworth, NJ 07033, United States
| | - Jin Wu
- Merck Research Laboratories, Kenilworth, NJ 07033, United States
| | - Lynn Miesel
- Merck Research Laboratories, Kenilworth, NJ 07033, United States
| | | | - Todd Black
- Merck Research Laboratories, Kenilworth, NJ 07033, United States
| | - Ravi Nargund
- Merck Research Laboratories, Kenilworth, NJ 07033, United States
| | - Peter T Meinke
- Merck Research Laboratories, Rahway 07065, United States
| | - David B Olsen
- Merck Research Laboratories, West Point, PA 19486, United States
| | - Armando Lagrutta
- Merck Research Laboratories, West Point, PA 19486, United States
| | - Jun Lu
- Merck Research Laboratories, West Point, PA 19486, United States
| | - Sangita Patel
- Merck Research Laboratories, West Point, PA 19486, United States
| | - Keith W Rickert
- Merck Research Laboratories, West Point, PA 19486, United States
| | - Robert F Smith
- Merck Research Laboratories, West Point, PA 19486, United States
| | - Stephen Soisson
- Merck Research Laboratories, West Point, PA 19486, United States
| | - Edward Sherer
- Merck Research Laboratories, Rahway 07065, United States
| | - Leo A Joyce
- Merck Research Laboratories, Rahway 07065, United States
| | | | - Xuanjia Peng
- WuXi AppTec, Shanghai, People's Republic of China
| | - Xiu Wang
- WuXi AppTec, Shanghai, People's Republic of China
| | - Hideyuki Fukuda
- Kyorin Pharmaceutical Co., Ltd, 2399-1, Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Ryuta Kishii
- Kyorin Pharmaceutical Co., Ltd, 2399-1, Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Masaya Takei
- Kyorin Pharmaceutical Co., Ltd, 2399-1, Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Hisashi Takano
- Kyorin Pharmaceutical Co., Ltd, 2399-1, Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Mitsuhito Shibasaki
- Kyorin Pharmaceutical Co., Ltd, 2399-1, Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Masanobu Yajima
- Kyorin Pharmaceutical Co., Ltd, 2399-1, Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Akinori Nishimura
- Kyorin Pharmaceutical Co., Ltd, 2399-1, Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Takeshi Shibata
- Kyorin Pharmaceutical Co., Ltd, 2399-1, Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Yasumichi Fukuda
- Kyorin Pharmaceutical Co., Ltd, 2399-1, Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan.
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39
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Singh SB, Kaelin DE, Wu J, Miesel L, Tan CM, Meinke PT, Olsen DB, Lagrutta A, Wei C, Liao Y, Peng X, Wang X, Fukuda H, Kishii R, Takei M, Shibata T, Takeuchi T, Ohata K, Nishimura A, Fukuda Y. C1–C2-linker substituted 1,5-naphthyridine analogues of oxabicyclooctane-linked NBTIs as broad-spectrum antibacterial agents (part 7). MEDCHEMCOMM 2015. [DOI: 10.1039/c5md00297d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Substitutions around linker positions C-1 and C-2 suggest that the C-2α hydroxy group is the best for activity.
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Affiliation(s)
| | | | - Jin Wu
- Merck Research Laboratories
- Kenilworth
- USA
| | | | | | | | | | | | | | | | | | - Xiu Wang
- WuXi AppTec
- Shanghai
- People's Republic of China
| | | | - Ryuta Kishii
- Kyorin Pharmaceutical Co., Ltd
- Tochigi
- 329-0114 Japan
| | - Masaya Takei
- Kyorin Pharmaceutical Co., Ltd
- Tochigi
- 329-0114 Japan
| | | | | | - Kohei Ohata
- Kyorin Pharmaceutical Co., Ltd
- Tochigi
- 329-0114 Japan
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Target-based resistance in Pseudomonas aeruginosa and Escherichia coli to NBTI 5463, a novel bacterial type II topoisomerase inhibitor. Antimicrob Agents Chemother 2014; 59:331-7. [PMID: 25348539 DOI: 10.1128/aac.04077-14] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
In a previous report (T. J. Dougherty, A. Nayar, J. V. Newman, S. Hopkins, G. G. Stone, M. Johnstone, A. B. Shapiro, M. Cronin, F. Reck, and D. E. Ehmann, Antimicrob Agents Chemother 58:2657-2664, 2014), a novel bacterial type II topoisomerase inhibitor, NBTI 5463, with activity against Gram-negative pathogens was described. First-step resistance mutations in Pseudomonas aeruginosa arose exclusively in the nfxB gene, a regulator of the MexCD-OprJ efflux pump system. The present report describes further resistance studies with NBTI 5463 in both Pseudomonas aeruginosa and Escherichia coli. Second-step mutations in P. aeruginosa arose at aspartate 82 of the gyrase A subunit and led to 4- to 8-fold increases in the MIC over those seen in the parental strain with a first-step nfxB efflux mutation. A third-step mutant showed additional GyrA changes, with no changes in topoisomerase IV. Despite repeated efforts, resistance mutations could not be selected in E. coli. Genetic introduction of the Asp82 mutations observed in P. aeruginosa did not significantly increase the NBTI MIC in E. coli. However, with the aspartate 82 mutation present, it was possible to select second-step mutations in topoisomerase IV that did lead to MIC increases of 16- and 128-fold. As with the gyrase aspartate 82 mutation, the mutations in topoisomerase IV did not by themselves raise the NBTI MIC in E. coli. Only the presence of mutations in both targets of E. coli led to an increase in NBTI MIC values. This represents a demonstration of the value of balanced dual-target activity in mitigating resistance development.
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41
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Optimization of physicochemical properties and safety profile of novel bacterial topoisomerase type II inhibitors (NBTIs) with activity against Pseudomonas aeruginosa. Bioorg Med Chem 2014; 22:5392-409. [DOI: 10.1016/j.bmc.2014.07.040] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 07/18/2014] [Accepted: 07/26/2014] [Indexed: 01/24/2023]
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42
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Ehmann DE, Lahiri SD. Novel compounds targeting bacterial DNA topoisomerase/DNA gyrase. Curr Opin Pharmacol 2014; 18:76-83. [PMID: 25271174 DOI: 10.1016/j.coph.2014.09.007] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 09/12/2014] [Indexed: 02/08/2023]
Abstract
Among the targets for the development of new antibacterial agents, bacterial topoisomerases remain a vibrant area of discovery. A structurally diverse set of inhibitors that bind to the adenosine 5'-triphosphate (ATP) site of type II topoisomerases have been disclosed recently. Seven compounds with this mechanism are highlighted, focusing on antibacterial potency and spectrum, as well as examples of in vivo efficacy against pathogens including Staphylococcus aureus and Mycobacterium tuberculosis. Five compounds from two structural classes are exemplified that are inhibitors that bind to the catalytic site of DNA gyrase and topoisomerase IV. The pharmacokinetic and pharmacodynamic properties of these molecules, derived from in vivo efficacy against Gram-positive and Gram-negative pathogens, define the potential for these agents with broad-spectrum and targeted-spectrum clinical utilities.
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Affiliation(s)
- David E Ehmann
- Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, USA.
| | - Sushmita D Lahiri
- Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, USA
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López Y, Tato M, Espinal P, Garcia-Alonso F, Gargallo-Viola D, Cantón R, Vila J. In vitro selection of mutants resistant to ozenoxacin compared with levofloxacin and ciprofloxacin in Gram-positive cocci. J Antimicrob Chemother 2014; 70:57-61. [PMID: 25261416 DOI: 10.1093/jac/dku375] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES To determine the frequency of selecting mutants resistant to ozenoxacin, a des-fluoro-(6)-quinolone active against pathogens involved in skin and skin structure infections, compared with levofloxacin and ciprofloxacin in quinolone-susceptible and -resistant Gram-positive cocci. METHODS Forty-nine quinolone-susceptible and -resistant Gram-positive cocci strains with different profiles of mutations in the quinolone resistance-determining region (QRDR) were examined to determine the frequency of selecting mutants resistant to ozenoxacin compared with levofloxacin and ciprofloxacin. MICs and mutations in the QRDR were determined by standard broth microdilution and PCR amplification and sequencing, respectively. RESULTS The mean resistance rates were 3.8 × 10(-9) (range <9 × 10(-11)-1 × 10(-8)) for ozenoxacin, 9.7 × 10(-9) (range <1.1 × 10(-11)-4.2 × 10(-8)) for levofloxacin and 1.2 × 10(-8) (range <1.6 × 10(-10)-2.6 × 10(-7)) for ciprofloxacin. Spontaneous mutants resistant to ozenoxacin showed lower MICs (≤ 16 mg/L) than mutants resistant to levofloxacin and ciprofloxacin (≤ 512 mg/L). Additional mutations were observed only in ParC at Ser-80 in Staphylococcus spp., Ser-79 in Streptococcus agalactiae and Asp-83 and Ser-89 in Streptococcus pyogenes. CONCLUSIONS The probability of ozenoxacin selecting spontaneous resistant mutants in quinolone-susceptible and -resistant strains with pre-existing mutations in the QRDR is low, supporting the potential utility of ozenoxacin as a therapeutic alternative in the treatment of skin infections caused by strains highly resistant to quinolones.
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Affiliation(s)
- Y López
- Centre for International Health Research (CRESIB), Barcelona, Spain Department of Clinical Microbiology, Hospital Clinic, School of Medicine, University of Barcelona, Barcelona, Spain Spanish Network for Research in Infectious Diseases (REIPI), Instituto de Salud Carlos III, Madrid, Spain
| | - M Tato
- Spanish Network for Research in Infectious Diseases (REIPI), Instituto de Salud Carlos III, Madrid, Spain Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - P Espinal
- Centre for International Health Research (CRESIB), Barcelona, Spain
| | | | | | - R Cantón
- Spanish Network for Research in Infectious Diseases (REIPI), Instituto de Salud Carlos III, Madrid, Spain Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - J Vila
- Centre for International Health Research (CRESIB), Barcelona, Spain Department of Clinical Microbiology, Hospital Clinic, School of Medicine, University of Barcelona, Barcelona, Spain Spanish Network for Research in Infectious Diseases (REIPI), Instituto de Salud Carlos III, Madrid, Spain
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Hameed P S, Raichurkar A, Madhavapeddi P, Menasinakai S, Sharma S, Kaur P, Nandishaiah R, Panduga V, Reddy J, Sambandamurthy VK, Sriram D. Benzimidazoles: novel mycobacterial gyrase inhibitors from scaffold morphing. ACS Med Chem Lett 2014; 5:820-5. [PMID: 25050172 DOI: 10.1021/ml5001728] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 06/02/2014] [Indexed: 01/25/2023] Open
Abstract
Type II topoisomerases are well conserved across the bacterial species, and inhibition of DNA gyrase by fluoroquinolones has provided an attractive option for treatment of tuberculosis (TB). However, the emergence of fluoroquinolone-resistant strains of Mycobacterium tuberculosis (Mtb) poses a threat for its sustainability. A scaffold hopping approach using the binding mode of novel bacterial topoisomerase inhibitors (NBTIs) led to the identification of a novel class of benzimidazoles as DNA gyrase inhibitors with potent anti-TB activity. Docking of benzimidazoles to a NBTI bound crystal structure suggested that this class of compound makes key contacts in the enzyme active site similar to the reported NBTIs. This observation was further confirmed through the measurement of DNA gyrase inhibition, and activity against Mtb strains harboring mutations that confer resistance to aminopiperidines based NBTIs and Mtb strains resistant to moxifloxacin. Structure-activity relationship modification at the C-7 position of the left-hand side ring provided further avenue to improve hERG selectivity for this chemical series that has been the major challenges for NBTIs.
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Affiliation(s)
- Shahul Hameed P
- AstraZeneca India Pvt. Ltd., Avishkar,
Bellary Road, Bangalore 560024, India
| | | | | | | | - Sreevalli Sharma
- AstraZeneca India Pvt. Ltd., Avishkar,
Bellary Road, Bangalore 560024, India
| | - Parvinder Kaur
- AstraZeneca India Pvt. Ltd., Avishkar,
Bellary Road, Bangalore 560024, India
| | - Radha Nandishaiah
- AstraZeneca India Pvt. Ltd., Avishkar,
Bellary Road, Bangalore 560024, India
| | - Vijender Panduga
- AstraZeneca India Pvt. Ltd., Avishkar,
Bellary Road, Bangalore 560024, India
| | - Jitendar Reddy
- AstraZeneca India Pvt. Ltd., Avishkar,
Bellary Road, Bangalore 560024, India
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45
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Singh SB. Confronting the challenges of discovery of novel antibacterial agents. Bioorg Med Chem Lett 2014; 24:3683-9. [PMID: 25017034 DOI: 10.1016/j.bmcl.2014.06.053] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 06/16/2014] [Accepted: 06/18/2014] [Indexed: 10/25/2022]
Abstract
Bacterial resistance is inevitable and is a growing concern. It can be addressed only by discovery and development of new agents. However the discovery and development of new antibacterial agents are at an all time low. This article broadly examines the historical as well as current status of antibacterial discovery and provides some perspective as how to address some of the challenges.
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Affiliation(s)
- Sheo B Singh
- SBS Pharma Consulting LLC, Edison, NJ 08820, United States.
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46
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Singh SB, Kaelin DE, Wu J, Miesel L, Tan CM, Meinke PT, Olsen D, Lagrutta A, Bradley P, Lu J, Patel S, Rickert KW, Smith RF, Soisson S, Wei C, Fukuda H, Kishii R, Takei M, Fukuda Y. Oxabicyclooctane-linked novel bacterial topoisomerase inhibitors as broad spectrum antibacterial agents. ACS Med Chem Lett 2014; 5:609-14. [PMID: 24900889 DOI: 10.1021/ml500069w] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 03/12/2014] [Indexed: 01/18/2023] Open
Abstract
Bacterial resistance is eroding the clinical utility of existing antibiotics necessitating the discovery of new agents. Bacterial type II topoisomerase is a clinically validated, highly effective, and proven drug target. This target is amenable to inhibition by diverse classes of inhibitors with alternative and distinct binding sites to quinolone antibiotics, thus enabling the development of agents that lack cross-resistance to quinolones. Described here are novel bacterial topoisomerase inhibitors (NBTIs), which are a new class of gyrase and topo IV inhibitors and consist of three distinct structural moieties. The substitution of the linker moiety led to discovery of potent broad-spectrum NBTIs with reduced off-target activity (hERG IC50 > 18 μM) and improved physical properties. AM8191 is bactericidal and selectively inhibits DNA synthesis and Staphylococcus aureus gyrase (IC50 = 1.02 μM) and topo IV (IC50 = 10.4 μM). AM8191 showed parenteral and oral efficacy (ED50) at less than 2.5 mg/kg doses in a S. aureus murine infection model. A cocrystal structure of AM8191 bound to S. aureus DNA-gyrase showed binding interactions similar to that reported for GSK299423, displaying a key contact of Asp83 with the basic amine at position-7 of the linker.
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Affiliation(s)
- Sheo B. Singh
- Merck Research Laboratories, Kenilworth, New Jersey 07033, United States
| | - David E. Kaelin
- Merck Research Laboratories, Kenilworth, New Jersey 07033, United States
| | - Jin Wu
- Merck Research Laboratories, Kenilworth, New Jersey 07033, United States
| | - Lynn Miesel
- Merck Research Laboratories, Kenilworth, New Jersey 07033, United States
| | - Christopher M. Tan
- Merck Research Laboratories, Kenilworth, New Jersey 07033, United States
| | - Peter T. Meinke
- Merck Research Laboratories, Kenilworth, New Jersey 07033, United States
| | - David Olsen
- Merck Research Laboratories, West Point, Pennsylvania 19486, United States
| | - Armando Lagrutta
- Merck Research Laboratories, West Point, Pennsylvania 19486, United States
| | - Prudence Bradley
- Merck Research Laboratories, Kenilworth, New Jersey 07033, United States
| | - Jun Lu
- Merck Research Laboratories, West Point, Pennsylvania 19486, United States
| | - Sangita Patel
- Merck Research Laboratories, West Point, Pennsylvania 19486, United States
| | - Keith W. Rickert
- Merck Research Laboratories, West Point, Pennsylvania 19486, United States
| | - Robert F. Smith
- Merck Research Laboratories, West Point, Pennsylvania 19486, United States
| | - Stephen Soisson
- Merck Research Laboratories, West Point, Pennsylvania 19486, United States
| | | | - Hideyuki Fukuda
- Kyorin Pharmaceutical Co., Ltd., 2399-1, Nogi,
Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Ryuta Kishii
- Kyorin Pharmaceutical Co., Ltd., 2399-1, Nogi,
Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Masaya Takei
- Kyorin Pharmaceutical Co., Ltd., 2399-1, Nogi,
Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Yasumichi Fukuda
- Kyorin Pharmaceutical Co., Ltd., 2399-1, Nogi,
Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
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Mayer C, Janin YL. Non-quinolone inhibitors of bacterial type IIA topoisomerases: a feat of bioisosterism. Chem Rev 2013; 114:2313-42. [PMID: 24313284 DOI: 10.1021/cr4003984] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Claudine Mayer
- Unité de Microbiologie Structurale, Département de Biologie Structurale et Chimie, Institut Pasteur , 25 rue du Dr. Roux, 75724 Paris Cedex 15, France
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48
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Surivet JP, Zumbrunn C, Rueedi G, Hubschwerlen C, Bur D, Bruyère T, Locher H, Ritz D, Keck W, Seiler P, Kohl C, Gauvin JC, Mirre A, Kaegi V, Dos Santos M, Gaertner M, Delers J, Enderlin-Paput M, Boehme M. Design, Synthesis, and Characterization of Novel Tetrahydropyran-Based Bacterial Topoisomerase Inhibitors with Potent Anti-Gram-Positive Activity. J Med Chem 2013; 56:7396-415. [DOI: 10.1021/jm400963y] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
| | - Cornelia Zumbrunn
- Actelion Pharmaceuticals Ltd, Gewerbestrasse
16, CH-4123 Allschwil, Switzerland
| | - Georg Rueedi
- Actelion Pharmaceuticals Ltd, Gewerbestrasse
16, CH-4123 Allschwil, Switzerland
| | | | - Daniel Bur
- Actelion Pharmaceuticals Ltd, Gewerbestrasse
16, CH-4123 Allschwil, Switzerland
| | - Thierry Bruyère
- Actelion Pharmaceuticals Ltd, Gewerbestrasse
16, CH-4123 Allschwil, Switzerland
| | - Hans Locher
- Actelion Pharmaceuticals Ltd, Gewerbestrasse
16, CH-4123 Allschwil, Switzerland
| | - Daniel Ritz
- Actelion Pharmaceuticals Ltd, Gewerbestrasse
16, CH-4123 Allschwil, Switzerland
| | - Wolfgang Keck
- Actelion Pharmaceuticals Ltd, Gewerbestrasse
16, CH-4123 Allschwil, Switzerland
| | - Peter Seiler
- Actelion Pharmaceuticals Ltd, Gewerbestrasse
16, CH-4123 Allschwil, Switzerland
| | - Christopher Kohl
- Actelion Pharmaceuticals Ltd, Gewerbestrasse
16, CH-4123 Allschwil, Switzerland
| | | | - Azely Mirre
- Actelion Pharmaceuticals Ltd, Gewerbestrasse
16, CH-4123 Allschwil, Switzerland
| | - Verena Kaegi
- Actelion Pharmaceuticals Ltd, Gewerbestrasse
16, CH-4123 Allschwil, Switzerland
| | - Marina Dos Santos
- Actelion Pharmaceuticals Ltd, Gewerbestrasse
16, CH-4123 Allschwil, Switzerland
| | - Mika Gaertner
- Actelion Pharmaceuticals Ltd, Gewerbestrasse
16, CH-4123 Allschwil, Switzerland
| | - Jonathan Delers
- Actelion Pharmaceuticals Ltd, Gewerbestrasse
16, CH-4123 Allschwil, Switzerland
| | | | - Maria Boehme
- Actelion Pharmaceuticals Ltd, Gewerbestrasse
16, CH-4123 Allschwil, Switzerland
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49
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Novel hydroxyl tricyclics (e.g., GSK966587) as potent inhibitors of bacterial type IIA topoisomerases. Bioorg Med Chem Lett 2013; 23:5437-41. [PMID: 23968823 DOI: 10.1016/j.bmcl.2013.07.013] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2013] [Revised: 07/07/2013] [Accepted: 07/09/2013] [Indexed: 11/23/2022]
Abstract
During the course of our research to find novel mode of action antibacterials, we discovered a series of hydroxyl tricyclic compounds that showed good potency against Gram-positive and Gram-negative pathogens. These compounds inhibit bacterial type IIA topoisomerases. Herein we will discuss structure-activity relationships in this series and report advanced studies on compound 1 (GSK966587) which demonstrates good PK and in vivo efficacy properties. X-ray crystallographic studies were used to provide insight into the structural basis for the difference in antibacterial potency between enantiomers.
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