1
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Powell J, Mann CA, Toth PD, Nolan S, Steinert A, Ove C, Seffernick JT, Wozniak DJ, Kebriaei R, Lindert S, Osheroff N, Yalowich JC, Mitton-Fry MJ. Development of Novel Bacterial Topoisomerase Inhibitors Assisted by Computational Screening. ACS Med Chem Lett 2024; 15:1287-1297. [PMID: 39140037 PMCID: PMC11318591 DOI: 10.1021/acsmedchemlett.4c00162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 06/16/2024] [Accepted: 06/20/2024] [Indexed: 08/15/2024] Open
Abstract
Multidrug-resistant bacterial infections pose an ever-evolving threat to public health. Since the outset of the antibacterial age, bacteria have developed a multitude of diverse resistance mechanisms that suppress the effectiveness of current therapies. New drug entities, such as Novel Bacterial Topoisomerase Inhibitors (NBTIs), can circumvent this major issue. A computational docking model was employed to predict the binding to DNA gyrase of atypical NBTIs with novel pharmacophores. Synthesis of NBTIs based on computational docking and subsequent antibacterial evaluation against both Gram-positive and Gram-negative bacteria yielded congeners with outstanding anti-staphylococcal activity and varying activity against select Gram-negative pathogens.
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Affiliation(s)
- Joshua
W. Powell
- Division
of Medicinal Chemistry and Pharmacognosy, Department of Chemistry and Biochemistry, Microbial Infection
and Immunity, Division of Outcomes and Translational Sciences, Department of Microbiology, and Division of Pharmaceutics
and Pharmacology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Chelsea A. Mann
- Division
of Medicinal Chemistry and Pharmacognosy, Department of Chemistry and Biochemistry, Microbial Infection
and Immunity, Division of Outcomes and Translational Sciences, Department of Microbiology, and Division of Pharmaceutics
and Pharmacology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Paul D. Toth
- Division
of Medicinal Chemistry and Pharmacognosy, Department of Chemistry and Biochemistry, Microbial Infection
and Immunity, Division of Outcomes and Translational Sciences, Department of Microbiology, and Division of Pharmaceutics
and Pharmacology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Sheri Nolan
- Division
of Medicinal Chemistry and Pharmacognosy, Department of Chemistry and Biochemistry, Microbial Infection
and Immunity, Division of Outcomes and Translational Sciences, Department of Microbiology, and Division of Pharmaceutics
and Pharmacology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Anja Steinert
- Division
of Medicinal Chemistry and Pharmacognosy, Department of Chemistry and Biochemistry, Microbial Infection
and Immunity, Division of Outcomes and Translational Sciences, Department of Microbiology, and Division of Pharmaceutics
and Pharmacology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Clarissa Ove
- Division
of Medicinal Chemistry and Pharmacognosy, Department of Chemistry and Biochemistry, Microbial Infection
and Immunity, Division of Outcomes and Translational Sciences, Department of Microbiology, and Division of Pharmaceutics
and Pharmacology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Justin T. Seffernick
- Division
of Medicinal Chemistry and Pharmacognosy, Department of Chemistry and Biochemistry, Microbial Infection
and Immunity, Division of Outcomes and Translational Sciences, Department of Microbiology, and Division of Pharmaceutics
and Pharmacology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Daniel J. Wozniak
- Division
of Medicinal Chemistry and Pharmacognosy, Department of Chemistry and Biochemistry, Microbial Infection
and Immunity, Division of Outcomes and Translational Sciences, Department of Microbiology, and Division of Pharmaceutics
and Pharmacology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Razieh Kebriaei
- Division
of Medicinal Chemistry and Pharmacognosy, Department of Chemistry and Biochemistry, Microbial Infection
and Immunity, Division of Outcomes and Translational Sciences, Department of Microbiology, and Division of Pharmaceutics
and Pharmacology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Steffen Lindert
- Division
of Medicinal Chemistry and Pharmacognosy, Department of Chemistry and Biochemistry, Microbial Infection
and Immunity, Division of Outcomes and Translational Sciences, Department of Microbiology, and Division of Pharmaceutics
and Pharmacology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Neil Osheroff
- Department of Biochemistry and Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
| | - Jack C. Yalowich
- Division
of Medicinal Chemistry and Pharmacognosy, Department of Chemistry and Biochemistry, Microbial Infection
and Immunity, Division of Outcomes and Translational Sciences, Department of Microbiology, and Division of Pharmaceutics
and Pharmacology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Mark J. Mitton-Fry
- Division
of Medicinal Chemistry and Pharmacognosy, Department of Chemistry and Biochemistry, Microbial Infection
and Immunity, Division of Outcomes and Translational Sciences, Department of Microbiology, and Division of Pharmaceutics
and Pharmacology, The Ohio State University, Columbus, Ohio 43210, United States
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2
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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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3
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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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4
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Zorman M, Hrast Rambaher M, Kokot M, Minovski N, Anderluh M. The overview of development of novel bacterial topoisomerase inhibitors effective against multidrug-resistant bacteria in an academic environment: From early hits to in vivo active antibacterials. Eur J Pharm Sci 2024; 192:106632. [PMID: 37949194 DOI: 10.1016/j.ejps.2023.106632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 09/29/2023] [Accepted: 11/06/2023] [Indexed: 11/12/2023]
Abstract
Antimicrobial resistance caused by the excessive and inappropriate use of antibacterial drugs is a global health concern. Currently, we are walking a fine line between the fact that most bacterial infections can still be cured with the antibiotics known so far, and the emergence of infections with bacteria resistant to several drugs at the same time, against which we no longer have an effective drug. Therefore, new antibacterial drugs are urgently needed to curb the hard-to-treat infections. Our group has developed new antibacterials from the class of novel bacterial topoisomerase inhibitors (NBTIs) that exhibit broad-spectrum antibacterial activity. This article reviews our efforts in developing highly potent NBTIs over the past decade. Following the discovery of an initial hit with potent enzyme inhibitory and broad-spectrum antibacterial activity, an extensive hit-to-lead campaign was conducted with the goal of optimizing physicochemical properties, reducing hERG inhibition, and maintaining antibacterial activity against both Gram-positive and Gram-negative bacteria, with a focus on methicillin-resistant Staphylococcus aureus (MRSA). This optimization strategy resulted in an amide-containing, focused NBTI library with compounds exhibiting potent antibacterial activity against Gram-positive bacteria, reduced hERG inhibition, no cardiotoxicity in in vivo zebrafish model, and favorable in vivo efficacy in a neutropenic murine thigh infection model for MRSA infections.
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Affiliation(s)
- Maša Zorman
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, Ljubljana 1000, Slovenia; Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, Hajdrihova 19, Ljubljana 1001, Slovenia
| | - Martina Hrast Rambaher
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, Ljubljana 1000, Slovenia
| | - Maja Kokot
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, Ljubljana 1000, Slovenia; Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, Hajdrihova 19, Ljubljana 1001, Slovenia
| | - Nikola Minovski
- Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, Hajdrihova 19, Ljubljana 1001, Slovenia.
| | - Marko Anderluh
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, Ljubljana 1000, Slovenia.
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5
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Mann CA, Carvajal Moreno JJ, Lu Y, Dellos-Nolan S, Wozniak DJ, Yalowich JC, Mitton-Fry MJ. Novel bacterial topoisomerase inhibitors: unique targeting activities of amide enzyme-binding motifs for tricyclic analogs. Antimicrob Agents Chemother 2023; 67:e0048223. [PMID: 37724886 PMCID: PMC10583662 DOI: 10.1128/aac.00482-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 07/14/2023] [Indexed: 09/21/2023] Open
Abstract
Antimicrobial resistance has made a sizeable impact on public health and continues to threaten the effectiveness of antibacterial therapies. Novel bacterial topoisomerase inhibitors (NBTIs) are a promising class of antibacterial agents with a unique binding mode and distinct pharmacology that enables them to evade existing resistance mechanisms. The clinical development of NBTIs has been plagued by several issues, including cardiovascular safety. Herein, we report a sub-series of tricyclic NBTIs bearing an amide linkage that displays promising antibacterial activity, potent dual-target inhibition of DNA gyrase and topoisomerase IV (TopoIV), as well as improved cardiovascular safety and metabolic profiles. These amide NBTIs induced both single- and double-strand breaks in pBR322 DNA mediated by Staphylococcus aureus DNA gyrase, in contrast to prototypical NBTIs that cause only single-strand breaks. Unexpectedly, amides 1a and 1b targeted human topoisomerase IIα (TOP2α) causing both single- and double-strand breaks in pBR322 DNA, and induced DNA strand breaks in intact human leukemia K562 cells. In addition, anticancer drug-resistant K/VP.5 cells containing decreased levels of TOP2α were cross-resistant to amides 1a and 1b. Together, these results demonstrate broad spectrum antibacterial properties of selected tricyclic NBTIs, desirable safety profiles, an unusual ability to induce DNA double-stranded breaks, and activity against human TOP2α. Future work will be directed toward optimization and development of tricyclic NBTIs with potent and selective activity against bacteria. Finally, the current results may provide an additional avenue for development of selective anticancer agents.
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Affiliation(s)
- Chelsea A. Mann
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio, USA
| | - Jessika J. Carvajal Moreno
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio, USA
| | - Yanran Lu
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio, USA
| | - Sheri Dellos-Nolan
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Daniel J. Wozniak
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Jack C. Yalowich
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio, USA
| | - Mark J. Mitton-Fry
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio, USA
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6
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Phelps HA, Kuhn M, Lu Y, Vibhute S, Watts JL, Mitton-Fry MJ. Antibacterial activity of novel bacterial topoisomerase inhibitors against key veterinary pathogens. Vet Microbiol 2023; 284:109840. [PMID: 37531840 DOI: 10.1016/j.vetmic.2023.109840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 07/07/2023] [Accepted: 07/28/2023] [Indexed: 08/04/2023]
Abstract
Multidrug-resistant bacteria infect companion animals and livestock in addition to their devastating impact on human health. Novel Bacterial Topoisomerase Inhibitors (NBTIs) with excellent activity against Gram-positive bacteria have previously been identified as promising new antibacterial agents. Herein, we evaluate the antibacterial activity of these NBTIs against a variety of important veterinary pathogens and demonstrate outstanding in vitro activity, especially against staphylococci.
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Affiliation(s)
- Hilary A Phelps
- Global Therapeutics, Anti-Infectives Research, Zoetis, 333 Portage Street, Kalamazoo, MI 49007, United States
| | - Michael Kuhn
- Global Therapeutics, Anti-Infectives Research, Zoetis, 333 Portage Street, Kalamazoo, MI 49007, United States
| | - Yanran Lu
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, 500 West 12th Avenue, Columbus, OH 43210, United States
| | - Sandip Vibhute
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, 500 West 12th Avenue, Columbus, OH 43210, United States
| | - Jeffrey L Watts
- Global Therapeutics, Anti-Infectives Research, Zoetis, 333 Portage Street, Kalamazoo, MI 49007, United States
| | - Mark J Mitton-Fry
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, 500 West 12th Avenue, Columbus, OH 43210, United States.
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7
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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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8
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Khade VV, Bhowmick A, Thube AS, Bhat RG. Direct Access to Strained Fused Dihalo-Aziridino Quinoxalinones via C3-Alkylation Followed by Tandem Cyclization. J Org Chem 2023. [PMID: 37262098 DOI: 10.1021/acs.joc.3c00033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Quinoxalinones are a privileged class of compounds, and their structural framework is found in many bioactive compounds, natural compounds, and pharmaceuticals. Quinoxalinone is a promising scaffold for different types of functionalization, and the slight modification of the quinoxalinone skeleton is known to offer a wide range of compounds for drug discovery. Owing to the importance of the quinoxalinone scaffold, we have developed a base-mediated protocol for the C3-alkylation of quinoxalinone followed by tandem cyclization to access novel types of strenuous and fused dihalo-aziridino-quinoxalinone heterocycles via the construction of C-C and C-N bonds. The protocol proved to be simple and practical to access desired fused quinoxalinone heterocycles in excellent yields (up to 98% yield). As an application, the highly functionalized fused dihalo-aziridino-quinoxalinone molecule has been further utilized for mono-dehalogenation under visible light irradiation and selective amide reduction. Moreover, the protocol has also been demonstrated on a gram scale.
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Affiliation(s)
- Vikas V Khade
- Department of Chemistry, Indian Institute of Science Education and Research (IISER)-Pune, Pune, Maharashtra 411008, India
| | - Anindita Bhowmick
- Department of Chemistry, Indian Institute of Science Education and Research (IISER)-Pune, Pune, Maharashtra 411008, India
| | - Archana S Thube
- Department of Chemistry, Indian Institute of Science Education and Research (IISER)-Pune, Pune, Maharashtra 411008, India
| | - Ramakrishna G Bhat
- Department of Chemistry, Indian Institute of Science Education and Research (IISER)-Pune, Pune, Maharashtra 411008, India
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9
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Kokot M, Novak D, Zdovc I, Anderluh M, Hrast M, Minovski N. Exploring Alternative Pathways to Target Bacterial Type II Topoisomerases Using NBTI Antibacterials: Beyond Halogen-Bonding Interactions. Antibiotics (Basel) 2023; 12:antibiotics12050930. [PMID: 37237833 DOI: 10.3390/antibiotics12050930] [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: 03/27/2023] [Revised: 05/15/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
Novel bacterial topoisomerase inhibitors (NBTIs) are a new class of antibacterial agents that target bacterial type II topoisomerases (DNA gyrase and topoisomerase IV). Our recently disclosed crystal structure of an NBTI ligand in complex with DNA gyrase and DNA revealed that the halogen atom in the para position of the phenyl right hand side (RHS) moiety is able to establish strong symmetrical bifurcated halogen bonds with the enzyme; these are responsible for the excellent enzyme inhibitory potency and antibacterial activity of these NBTIs. To further assess the possibility of any alternative interactions (e.g., hydrogen-bonding and/or hydrophobic interactions), we introduced various non-halogen groups at the p-position of the phenyl RHS moiety. Considering the hydrophobic nature of amino acid residues delineating the NBTI's binding pocket in bacterial topoisomerases, we demonstrated that designed NBTIs cannot establish any hydrogen-bonding interactions with the enzyme; hydrophobic interactions are feasible in all respects, while halogen-bonding interactions are apparently the most preferred.
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Affiliation(s)
- Maja Kokot
- Laboratory for Cheminformatics, Theory Department, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Doroteja Novak
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Irena Zdovc
- Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1000 Ljubljana, Slovenia
| | - Marko Anderluh
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Martina Hrast
- 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, 1000 Ljubljana, Slovenia
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10
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Kokot M, Weiss M, Zdovc I, Senerovic L, Radakovic N, Anderluh M, Minovski N, Hrast M. Amide containing NBTI antibacterials with reduced hERG inhibition, retained antimicrobial activity against gram-positive bacteria and in vivo efficacy. Eur J Med Chem 2023; 250:115160. [PMID: 36753879 DOI: 10.1016/j.ejmech.2023.115160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/23/2023] [Accepted: 01/24/2023] [Indexed: 02/05/2023]
Abstract
Novel bacterial topoisomerase inhibitors (NBTIs) are new promising antimicrobials for the treatment of multidrug-resistant bacterial infections. In recent years, many new NBTIs have been discovered, however most of them struggle with the same issue - the balance between antibacterial activity and hERG-related toxicity. We started a new campaign by optimizing the previous series of NBTIs, followed by the design and synthesis of a new, amide-containing focused NBTI library to reduce hERG inhibition and maintain antibacterial activity against Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus (MRSA). This optimization strategy yielded the lead compound 12 that exhibits potent antibacterial activity against Gram-positive bacteria, reduced hERG inhibition, no cardiotoxicity in zebrafish model, and a favorable in vivo efficacy in a neutropenic murine thigh infection model of MRSA infection.
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Affiliation(s)
- Maja Kokot
- Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, 1000, Ljubljana, Slovenia
| | - Matjaž Weiss
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, 1000, Ljubljana, Slovenia
| | - Irena Zdovc
- Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1000, Ljubljana, Slovenia
| | - Lidija Senerovic
- Laboratory for Microbial Molecular Genetics and Ecology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11 042, Belgrade, Serbia
| | - Natasa Radakovic
- Laboratory for Microbial Molecular Genetics and Ecology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11 042, Belgrade, Serbia
| | - Marko Anderluh
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, 1000, Ljubljana, Slovenia
| | - Nikola Minovski
- Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia.
| | - Martina Hrast
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, 1000, Ljubljana, Slovenia.
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11
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Kokot M, Weiss M, Zdovc I, Anderluh M, Hrast M, Minovski N. Diminishing hERG inhibitory activity of aminopiperidine-naphthyridine linked NBTI antibacterials by structural and physicochemical optimizations. Bioorg Chem 2022; 128:106087. [PMID: 35970069 DOI: 10.1016/j.bioorg.2022.106087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 08/05/2022] [Accepted: 08/05/2022] [Indexed: 11/02/2022]
Abstract
Novel bacterial topoisomerase inhibitors (NBTIs) are an important new class of antibacterials targeting bacterial type II topoisomerases (DNA gyrase and topoisomerase IV). Notwithstanding their potent antibacterial activity, they suffer from a detrimental class-related hERG blockage. In this study, we designed and synthesized an optimized library of NBTIs comprising different linker moieties that exhibit reduced hERG inhibition and retain inhibitory potencies on DNA gyrase and topoisomerase IV of Staphylococcus aureus and Escherichia coli, respectively, as well as potent antibacterial activities. Substitution of the linker's tertiary amine with polar groups outcome in diminished hERG inhibition. Compound 17 expresses nanomolar enzyme inhibitory potency and antibacterial activity against both Gram-positive and Gram-negative bacteria as well as reduced hERG inhibition relative to our previously published NBTI analogs. Here, we point to some important NBTI's structural features that influence their hERG inhibitory activity.
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Affiliation(s)
- Maja Kokot
- Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia; The Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Matjaž Weiss
- The Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Irena Zdovc
- Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1000 Ljubljana, Slovenia
| | - Marko Anderluh
- The Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Martina Hrast
- The Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia.
| | - Nikola Minovski
- Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia.
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12
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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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13
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Tang ML, Li H, Ning JF, Shen X, Sun X. Discovery of First-in-Class TAK1-MKK3 Protein-Protein Interaction (PPI) Inhibitor (R)-STU104 for the Treatment of Ulcerative Colitis through Modulating TNF-α Production. J Med Chem 2022; 65:6690-6709. [PMID: 35442672 DOI: 10.1021/acs.jmedchem.1c02198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tumor necrosis factor α (TNF-α) has been demonstrated to be a therapeutic target for autoimmune diseases. However, this biological therapy exhibits some inevitable disadvantages, such as risk of infection. Thus, small-molecule alternatives by targeting TNF-α production signaling pathway are still in demand. Herein, we describe the design, synthesis, and structure-activity relationships of 3-aryindanone compounds regarding their modulation of TNF-α production. Among them, (R)-STU104 exhibited the most potent inhibitory activity on TNF-α production, which suppressed the TAK1/MKK3/p38/MnK1/MK2/elF4E signal pathways through binding with MKK3 and disrupting the TAK1 phosphorylating MKK3. As a result, (R)-STU104 demonstrated remarkable dose-effect relationships on both acute and chronic mouse UC models. In addition to its good pharmacokinetic (PK) and safety profile, (R)-STU104 showed better anti-UC efficacy in vivo at 10 mg/kg/d than mesalazine at the dose of 50 mg/kg/d. These results suggested that TAK1-MKK3 interaction inhibitors could be potentially utilized for the treatment of UC.
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Affiliation(s)
- Mei-Lin Tang
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - Haidong Li
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - Jin-Feng Ning
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - Xiaoyan Shen
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - Xun Sun
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China.,The Institutes of Integrative Medicine of Fudan University, 12 Wulumuqi Zhong Road, Shanghai 200040, China
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14
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Beuchel A, Robaa D, Negatu DA, Madani A, Alvarez N, Zimmerman MD, Richter A, Mann L, Hoenke S, Csuk R, Dick T, Imming P. Structure-Activity Relationship of Anti- Mycobacterium abscessus Piperidine-4-carboxamides, a New Class of NBTI DNA Gyrase Inhibitors. ACS Med Chem Lett 2022; 13:417-427. [PMID: 35300094 PMCID: PMC8919391 DOI: 10.1021/acsmedchemlett.1c00549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 02/24/2022] [Indexed: 11/28/2022] Open
Abstract
Mycobacterium abscessus causes difficult-to-cure pulmonary infections. The bacterium is resistant to most anti-infective agents, including first line antituberculosis (anti-TB) drugs. MMV688844 (844) is a piperidine-4-carboxamide (P4C) with bactericidal properties against M. abscessus. We recently identified DNA gyrase as the molecular target of 844. Here, we present in silico docking and genetic evidence suggesting that P4Cs display a similar binding mode to DNA gyrase as gepotidacin. Gepotidacin is a member of the Novel Bacterial Topoisomerase Inhibitors (NBTIs), a new class of nonfluoroquinolone DNA gyrase poisons. Thus, our work suggests that P4Cs present a novel structural subclass of NBTI. We describe structure-activity relationship studies of 844 leading to analogues showing increased antibacterial activity. Selected derivatives were tested for their inhibitory activity against recombinant M. abscessus DNA gyrase. Further optimization of the lead structures led to improved stability in mouse plasma and increased oral bioavailability.
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Affiliation(s)
- Andreas Beuchel
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany, Kurt-Mothes-Str. 3, 06120 Halle (Saale), Germany
| | - Dina Robaa
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany, Kurt-Mothes-Str. 3, 06120 Halle (Saale), Germany
| | - Dereje A Negatu
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey 07110, United States.,Center for Innovative Drug Development and Therapeutic Trials for Africa (CDT-Africa), Addis Ababa University, Addis Ababa 1000, Ethiopia
| | - Abdeldjalil Madani
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey 07110, United States
| | - Nadine Alvarez
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey 07110, United States
| | - Matthew D Zimmerman
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey 07110, United States
| | - Adrian Richter
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany, Kurt-Mothes-Str. 3, 06120 Halle (Saale), Germany
| | - Lea Mann
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany, Kurt-Mothes-Str. 3, 06120 Halle (Saale), Germany
| | - Sophie Hoenke
- Institut für Chemie, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 2, 06120 Halle (Saale), Germany
| | - René Csuk
- Institut für Chemie, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 2, 06120 Halle (Saale), Germany
| | - Thomas Dick
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey 07110, United States.,Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, New Jersey 07110, United States.,Department of Microbiology and Immunology, Georgetown University, Washington, D.C. 20057, United States
| | - Peter Imming
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany, Kurt-Mothes-Str. 3, 06120 Halle (Saale), Germany
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15
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Jiang X, Wu K, Bai R, Zhang P, Zhang Y. Functionalized quinoxalinones as privileged structures with broad-ranging pharmacological activities. Eur J Med Chem 2022; 229:114085. [PMID: 34998058 DOI: 10.1016/j.ejmech.2021.114085] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/16/2021] [Accepted: 12/24/2021] [Indexed: 02/08/2023]
Abstract
Quinoxalinones are a class of heterocyclic compounds which attract extensive attention owing to their potential in the field of organic synthesis and medicinal chemistry. During the past few decades, many new synthetic strategies toward the functionalization of quinoxalinone based scaffolds have been witnessed. Regrettably, there are only a few reports on the pharmacological activities of quinoxalinone scaffolds from a medicinal chemistry perspective. Therefore, herein we intend to outline the applications of multifunctional quinoxalinones as privileged structures possessing various biological activities, including anticancer, neuroprotective, antibacterial, antiviral, antiparasitic, anti-inflammatory, antiallergic, anti-cardiovascular, anti-diabetes, antioxidation, etc. We hope that this review will facilitate the development of quinoxalinone derivatives in medicinal chemistry.
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Affiliation(s)
- Xiaoying Jiang
- Hunan Provincial Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, PR China; College of Material, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Hangzhou Normal University, Hangzhou, 311121, PR China
| | - Kaiyu Wu
- College of Material, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Hangzhou Normal University, Hangzhou, 311121, PR China
| | - Renren Bai
- School of Pharmacy, Hangzhou Normal University, Hangzhou, 311121, PR China; Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, 311121, PR China.
| | - Pengfei Zhang
- College of Material, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Hangzhou Normal University, Hangzhou, 311121, PR China.
| | - Yi Zhang
- Hunan Provincial Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, PR China.
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16
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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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17
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Kokot M, Weiss M, Zdovc I, Hrast M, Anderluh M, Minovski N. Structurally Optimized Potent Dual-Targeting NBTI Antibacterials with an Enhanced Bifurcated Halogen-Bonding Propensity. ACS Med Chem Lett 2021; 12:1478-1485. [PMID: 34527181 PMCID: PMC8436411 DOI: 10.1021/acsmedchemlett.1c00345] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 08/12/2021] [Indexed: 11/30/2022] Open
Abstract
![]()
We designed and synthesized
an optimized library of novel bacterial
topoisomerase inhibitors with p-halogenated phenyl
right-hand side fragments and significantly enhanced and balanced
dual-targeted DNA gyrase and topoisomerase IV activities of Staphylococcus aureus and Escherichia coli. By increasing the electron-withdrawing properties of the p-halogenated phenyl right-hand side fragment and maintaining
a similar lipophilicity and size, an increased potency was achieved,
indicating that the antibacterial activities of this series of novel
bacterial topoisomerase inhibitors against all target enzymes are
determined by halogen-bonding rather than van der Waals interactions.
They show nanomolar enzyme inhibitory and whole-cell antibacterial
activities against S. aureus and methicillin-resistant S. aureus (MRSA) strains. However, due to the relatively
high substrate specificity for the bacterial efflux pumps, they tend
to be less potent against E. coli and other Gram-negative
pathogens.
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Affiliation(s)
- Maja Kokot
- Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
- The Chair of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, SI-1000 Ljubljana, Slovenia
| | - Matjaž Weiss
- The Chair of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, SI-1000 Ljubljana, Slovenia
| | - Irena Zdovc
- Veterinary Faculty, Institute of Microbiology and Parasitology, University of Ljubljana, Gerbičeva 60, SI-1000 Ljubljana, Slovenia
| | - Martina Hrast
- The Chair of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, SI-1000 Ljubljana, Slovenia
| | - Marko Anderluh
- The Chair of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, SI-1000 Ljubljana, Slovenia
| | - Nikola Minovski
- Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
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18
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A Fine-Tuned Lipophilicity/Hydrophilicity Ratio Governs Antibacterial Potency and Selectivity of Bifurcated Halogen Bond-Forming NBTIs. Antibiotics (Basel) 2021; 10:antibiotics10070862. [PMID: 34356782 PMCID: PMC8300687 DOI: 10.3390/antibiotics10070862] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/12/2021] [Accepted: 07/12/2021] [Indexed: 12/15/2022] Open
Abstract
Herein, we report the design of a focused library of novel bacterial topoisomerase inhibitors (NBTIs) based on innovative mainly monocyclic right-hand side fragments active against DNA gyrase and Topo IV. They exhibit a very potent and wide range of antibacterial activity, even against some of the most concerning hard-to-treat pathogens for which new antibacterials are urgently needed, as reported by the WHO and CDC. NBTIs enzyme activity and whole cell potency seems to depend on the fine-tuned lipophilicity/hydrophilicity ratio that governs the permeability of those compounds through the bacterial membranes. Lipophilicity of NBTIs is apparently optimal for passing through the membrane of Gram-positive bacteria, but the higher, although not excessive lipophilicity and suitable hydrophilicity seems to determine the passage through Gram-negative bacterial membranes. However, due to the considerable hERG inhibition, which is still at least two orders of magnitude away from MICs, continued optimization is required to realize their full potential.
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19
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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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20
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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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21
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Synthetic Strategies, Reactivity and Applications of 1,5-Naphthyridines. Molecules 2020; 25:molecules25143252. [PMID: 32708796 PMCID: PMC7397193 DOI: 10.3390/molecules25143252] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/11/2020] [Accepted: 07/15/2020] [Indexed: 11/17/2022] Open
Abstract
This review covers the synthesis and reactivity of 1,5-naphthyridine derivatives published in the last 18 years. These heterocycles present a significant importance in the field of medicinal chemistry because many of them exhibit a great variety of biological activities. First, the published strategies related to the synthesis of 1,5-naphthyridines are presented followed by the reactivity of these compounds with electrophilic or nucleophilic reagents, in oxidations, reductions, cross-coupling reactions, modification of side chains or formation of metal complexes. Finally, some properties and applications of these heterocycles studied during this period are examined.
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22
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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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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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Gibson EG, Oviatt AA, Cacho M, Neuman KC, Chan PF, Osheroff N. Bimodal Actions of a Naphthyridone/Aminopiperidine-Based Antibacterial That Targets Gyrase and Topoisomerase IV. Biochemistry 2019; 58:4447-4455. [PMID: 31617352 PMCID: PMC7450530 DOI: 10.1021/acs.biochem.9b00805] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Gyrase and topoisomerase IV are the targets of fluoroquinolone antibacterials. However, the rise in antimicrobial resistance has undermined the clinical use of this important drug class. Therefore, it is critical to identify new agents that maintain activity against fluoroquinolone-resistant strains. One approach is to develop non-fluoroquinolone drugs that also target gyrase and topoisomerase IV but interact differently with the enzymes. This has led to the development of the "novel bacterial topoisomerase inhibitor" (NBTI) class of antibacterials. Despite the clinical potential of NBTIs, there is a relative paucity of data describing their mechanism of action against bacterial type II topoisomerases. Consequently, we characterized the activity of GSK126, a naphthyridone/aminopiperidine-based NBTI, against a variety of Gram-positive and Gram-negative bacterial type II topoisomerases, including gyrase from Mycobacterium tuberculosis and gyrase and topoisomerase IV from Bacillus anthracis and Escherichia coli. GSK126 enhanced single-stranded DNA cleavage and suppressed double-stranded cleavage mediated by these enzymes. It was also a potent inhibitor of gyrase-catalyzed DNA supercoiling and topoisomerase IV-catalyzed decatenation. Thus, GSK126 displays a similar bimodal mechanism of action across a variety of species. In contrast, GSK126 displayed a variable ability to overcome fluoroquinolone resistance mutations across these same species. Our results suggest that NBTIs elicit their antibacterial effects by two different mechanisms: inhibition of gyrase/topoisomerase IV catalytic activity or enhancement of enzyme-mediated DNA cleavage. Furthermore, the relative importance of these two mechanisms appears to differ from species to species. Therefore, we propose that the mechanistic basis for the antibacterial properties of NBTIs is bimodal in nature.
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Affiliation(s)
- Elizabeth G. Gibson
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN 37232, United States
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, United States
| | - Alexandria A. Oviatt
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, United States
| | - Monica Cacho
- Department of Diseases of the Developing World, GlaxoSmithKline, Parque Tecnológico de Madrid, Calle de Severo Ochoa, 2, 28760 Tres Cantos, Madrid, Spain
| | - Keir C. Neuman
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20982, United States
| | - Pan F. Chan
- Infectious Diseases Discovery, Medicines Opportunities Research Unit, GlaxoSmithKline, Collegeville, PA 19426, United States
| | - Neil Osheroff
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, United States
- Department of Medicine (Hematology/Oncology), Vanderbilt University School of Medicine, Nashville, TN 37232, United States
- VA Tennessee Valley Healthcare System, Nashville, TN 37212, United States
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