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Liu R, Sun J, Li LF, Cheng Y, Li M, Fu L, Li S, Peng G, Wang Y, Liu S, Qu X, Ran J, Li X, Pang E, Qiu HJ, Wang Y, Qi J, Wang H, Gao GF. Structural basis for difunctional mechanism of m-AMSA against African swine fever virus pP1192R. Nucleic Acids Res 2024:gkae703. [PMID: 39166497 DOI: 10.1093/nar/gkae703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 07/24/2024] [Accepted: 08/07/2024] [Indexed: 08/23/2024] Open
Abstract
The African swine fever virus (ASFV) type II topoisomerase (Topo II), pP1192R, is the only known Topo II expressed by mammalian viruses and is essential for ASFV replication in the host cytoplasm. Herein, we report the structures of pP1192R in various enzymatic stages using both X-ray crystallography and single-particle cryo-electron microscopy. Our data structurally define the pP1192R-modulated DNA topology changes. By presenting the A2+-like metal ion at the pre-cleavage site, the pP1192R-DNA-m-AMSA complex structure provides support for the classical two-metal mechanism in Topo II-mediated DNA cleavage and a better explanation for nucleophile formation. The unique inhibitor selectivity of pP1192R and the difunctional mechanism of pP1192R inhibition by m-AMSA highlight the specificity of viral Topo II in the poison binding site. Altogether, this study provides the information applicable to the development of a pP1192R-targeting anti-ASFV strategy.
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Affiliation(s)
- Ruili Liu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan Province 450046, China
- Beijing Life Science Academy, Beijing 102200, China
| | - Junqing Sun
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, Shanxi Province 030801, China
| | - Lian-Feng Li
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High-Containment Facilities for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin Province 150069, China
| | - Yingxian Cheng
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan Province 450046, China
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Meilin Li
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High-Containment Facilities for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin Province 150069, China
| | - Lifeng Fu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Su Li
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High-Containment Facilities for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin Province 150069, China
| | - Guorui Peng
- China/WOAH Reference Laboratory for Classical Swine Fever, China Institute of Veterinary Drug Control, Beijing 100081, China
| | - Yanjin Wang
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High-Containment Facilities for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin Province 150069, China
| | - Sheng Liu
- SUSTech Cryo-EM Centre, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xiao Qu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jiaqi Ran
- Department of Biological Sciences, School of life Science, Liaoning University, Shenyang, Liaoning Province 110030, China
| | - Xiaomei Li
- Shanxi Academy of Advanced Research and Innovation, Taiyuan, Shanxi Province 030032, China
| | - Erqi Pang
- Shanxi Academy of Advanced Research and Innovation, Taiyuan, Shanxi Province 030032, China
| | - Hua-Ji Qiu
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High-Containment Facilities for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin Province 150069, China
| | - Yanli Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Han Wang
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing 100091, China
| | - George Fu Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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Collins J, Basarab GS, Chibale K, Osheroff N. Interactions between Zoliflodacin and Neisseria gonorrhoeae Gyrase and Topoisomerase IV: Enzymological Basis for Cellular Targeting. ACS Infect Dis 2024; 10:3071-3082. [PMID: 39082980 PMCID: PMC11320581 DOI: 10.1021/acsinfecdis.4c00438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 07/09/2024] [Accepted: 07/16/2024] [Indexed: 08/10/2024]
Abstract
Gyrase and topoisomerase IV are the cellular targets for fluoroquinolones, a critically important class of antibacterial agents used to treat a broad spectrum of human infections. Unfortunately, the clinical efficacy of the fluoroquinolones has been curtailed by the emergence of target-mediated resistance. This is especially true for Neisseria gonorrhoeae, the causative pathogen of the sexually transmitted infection gonorrhea. Spiropyrimidinetriones (SPTs), a new class of antibacterials, were developed to combat the growing antibacterial resistance crisis. Zoliflodacin is the most clinically advanced SPT and displays efficacy against uncomplicated urogenital gonorrhea in human trials. Like fluoroquinolones, the primary target of zoliflodacin in N. gonorrhoeae is gyrase, and topoisomerase IV is a secondary target. Because unbalanced gyrase/topoisomerase IV targeting has facilitated the evolution of fluoroquinolone-resistant bacteria, it is important to understand the underlying basis for the differential targeting of zoliflodacin in N. gonorrhoeae. Therefore, we assessed the effects of this SPT on the catalytic and DNA cleavage activities of N. gonorrhoeae gyrase and topoisomerase IV. In all reactions examined, zoliflodacin displayed higher potency against gyrase than topoisomerase IV. Moreover, zoliflodacin generated more DNA cleavage and formed more stable enzyme-cleaved DNA-SPT complexes with gyrase. The SPT also maintained higher activity against fluoroquinolone-resistant gyrase than topoisomerase IV. Finally, when compared to zoliflodacin, the novel SPT H3D-005722 induced more balanced double-stranded DNA cleavage with gyrase and topoisomerase IV from N. gonorrhoeae, Escherichia coli, and Bacillus anthracis. This finding suggests that further development of the SPT class could yield compounds with a more balanced targeting against clinically important bacterial infections.
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Affiliation(s)
- Jessica
A. Collins
- Department
of Biochemistry, Vanderbilt University School
of Medicine, Nashville, Tennessee 37232, United States
| | - Gregory S. Basarab
- Holistic
Drug Discovery and Development (H3D) Centre, University of Cape Town, Rondebosch 7701, South Africa
| | - Kelly Chibale
- Holistic
Drug Discovery and Development (H3D) Centre, and South African Medical
Research Council Drug Discovery and Development Research Unit, Department
of Chemistry and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch 7701, South Africa
| | - Neil Osheroff
- Department
of Biochemistry, Vanderbilt University School
of Medicine, Nashville, Tennessee 37232, United States
- Department
of Medicine (Hematology/Oncology), Vanderbilt
University School of Medicine, Nashville, Tennessee 37232, United States
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3
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Aguilar-Ayala DA, Sanz-García F, Rabodoarivelo MS, Susanto BO, Bailo R, Eveque-Mourroux MR, Willand N, Simonsson USH, Ramón-García S, Lucía A. Evaluation of critical parameters in the hollow-fibre system for tuberculosis: A case study of moxifloxacin. Br J Clin Pharmacol 2024; 90:1711-1727. [PMID: 38632083 DOI: 10.1111/bcp.16068] [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: 12/04/2023] [Revised: 03/06/2024] [Accepted: 03/14/2024] [Indexed: 04/19/2024] Open
Abstract
AimsThe hollow‐fibre system for tuberculosis (HFS‐TB) is a preclinical model qualified by the European Medicines Agency to underpin the anti‐TB drug development process. It can mimic in vivo pharmacokinetic (PK)–pharmacodynamic (PD) attributes of selected antimicrobials, which could feed into in silico models to inform the design of clinical trials. However, historical data and published protocols are insufficient and omit key information to allow experiments to be reproducible. Therefore, in this work, we aim to optimize and standardize various HFS‐TB operational procedures.MethodsFirst, we characterized bacterial growth dynamics with different types of hollow‐fibre cartridges, Mycobacterium tuberculosis strains and media. Second, we mimicked a moxifloxacin PK profile within hollow‐fibre cartridges, in order to check drug–fibres compatibility. Lastly, we mimicked the moxifloxacin total plasma PK profile in human after once daily oral dose of 400 mg to assess PK–PD after different sampling methods, strains, cartridge size and bacterial adaptation periods before drug infusion into the system.ResultsWe found that final bacterial load inside the HFS‐TB was contingent on the studied variables. Besides, we demonstrated that drug–fibres compatibility tests are critical preliminary HFS‐TB assays, which need to be properly reported. Lastly, we uncovered that the sampling method and bacterial adaptation period before drug infusion significantly impact actual experimental conclusions.ConclusionOur data contribute to the necessary standardization of HFS‐TB experiments, draw attention to multiple aspects of this preclinical model that should be considered when reporting novel results and warn about critical parameters in the HFS‐TB currently overlooked.
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Affiliation(s)
- Diana A Aguilar-Ayala
- Department of Microbiology, Pediatrics, Radiology and Public Health, University of Zaragoza, Zaragoza, Spain
| | - Fernando Sanz-García
- Department of Microbiology, Pediatrics, Radiology and Public Health, University of Zaragoza, Zaragoza, Spain
| | | | - Budi O Susanto
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Rebeca Bailo
- Department of Microbiology, Pediatrics, Radiology and Public Health, University of Zaragoza, Zaragoza, Spain
| | - Maxime R Eveque-Mourroux
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, Lille, France
| | - Nicolas Willand
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, Lille, France
| | | | - Santiago Ramón-García
- Department of Microbiology, Pediatrics, Radiology and Public Health, University of Zaragoza, Zaragoza, Spain
- Spanish Network for Research on Respiratory Diseases (CIBERES), Carlos III Health Institute, Madrid, Spain
- Research and Development Agency of Aragón (ARAID) Foundation, Zaragoza, Spain
| | - Ainhoa Lucía
- Department of Microbiology, Pediatrics, Radiology and Public Health, University of Zaragoza, Zaragoza, Spain
- Spanish Network for Research on Respiratory Diseases (CIBERES), Carlos III Health Institute, Madrid, Spain
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4
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Collins J, Oviatt AA, Chan PF, Osheroff N. Target-Mediated Fluoroquinolone Resistance in Neisseria gonorrhoeae: Actions of Ciprofloxacin against Gyrase and Topoisomerase IV. ACS Infect Dis 2024; 10:1351-1360. [PMID: 38606464 PMCID: PMC11015056 DOI: 10.1021/acsinfecdis.4c00041] [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: 01/12/2024] [Revised: 02/08/2024] [Accepted: 02/13/2024] [Indexed: 04/13/2024]
Abstract
Fluoroquinolones make up a critically important class of antibacterials administered worldwide to treat human infections. However, their clinical utility has been curtailed by target-mediated resistance, which is caused by mutations in the fluoroquinolone targets, gyrase and topoisomerase IV. An important pathogen that has been affected by this resistance is Neisseria gonorrhoeae, the causative agent of gonorrhea. Over 82 million new cases of this sexually transmitted infection were reported globally in 2020. Despite the impact of fluoroquinolone resistance on gonorrhea treatment, little is known about the interactions of this drug class with its targets in this bacterium. Therefore, we investigated the effects of the fluoroquinolone ciprofloxacin on the catalytic and DNA cleavage activities of wild-type gyrase and topoisomerase IV and the corresponding enzymes that harbor mutations associated with cellular and clinical resistance to fluoroquinolones. Results indicate that ciprofloxacin interacts with both gyrase (its primary target) and topoisomerase IV (its secondary target) through a water-metal ion bridge that has been described in other species. Moreover, mutations in amino acid residues that anchor this bridge diminish the susceptibility of the enzymes for the drug, leading to fluoroquinolone resistance. Results further suggest that ciprofloxacin primarily induces its cytotoxic effects by enhancing gyrase-mediated DNA cleavage as opposed to inhibiting the DNA supercoiling activity of the enzyme. In conclusion, this work links the effects of ciprofloxacin on wild-type and resistant gyrase to results reported for cellular and clinical studies and provides a mechanistic explanation for the targeting and resistance of fluoroquinolones in N. gonorrhoeae.
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Affiliation(s)
- Jessica
A. Collins
- Department
of Biochemistry, Vanderbilt University School
of Medicine, Nashville, Tennessee 37232, United States
| | - Alexandria A. Oviatt
- Department
of Biochemistry, Vanderbilt University School
of Medicine, Nashville, Tennessee 37232, 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
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5
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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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6
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Collins J, Osheroff N. Gyrase and Topoisomerase IV: Recycling Old Targets for New Antibacterials to Combat Fluoroquinolone Resistance. ACS Infect Dis 2024; 10:1097-1115. [PMID: 38564341 PMCID: PMC11019561 DOI: 10.1021/acsinfecdis.4c00128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 03/14/2024] [Accepted: 03/18/2024] [Indexed: 04/04/2024]
Abstract
Beyond their requisite functions in many critical DNA processes, the bacterial type II topoisomerases, gyrase and topoisomerase IV, are the targets of fluoroquinolone antibacterials. These drugs act by stabilizing gyrase/topoisomerase IV-generated DNA strand breaks and by robbing the cell of the catalytic activities of these essential enzymes. Since their clinical approval in the mid-1980s, fluoroquinolones have been used to treat a broad spectrum of infectious diseases and are listed among the five "highest priority" critically important antimicrobial classes by the World Health Organization. Unfortunately, the widespread use of fluoroquinolones has been accompanied by a rise in target-mediated resistance caused by specific mutations in gyrase and topoisomerase IV, which has curtailed the medical efficacy of this drug class. As a result, efforts are underway to identify novel antibacterials that target the bacterial type II topoisomerases. Several new classes of gyrase/topoisomerase IV-targeted antibacterials have emerged, including novel bacterial topoisomerase inhibitors, Mycobacterium tuberculosis gyrase inhibitors, triazaacenaphthylenes, spiropyrimidinetriones, and thiophenes. Phase III clinical trials that utilized two members of these classes, gepotidacin (triazaacenaphthylene) and zoliflodacin (spiropyrimidinetrione), have been completed with positive outcomes, underscoring the potential of these compounds to become the first new classes of antibacterials introduced into the clinic in decades. Because gyrase and topoisomerase IV are validated targets for established and emerging antibacterials, this review will describe the catalytic mechanism and cellular activities of the bacterial type II topoisomerases, their interactions with fluoroquinolones, the mechanism of target-mediated fluoroquinolone resistance, and the actions of novel antibacterials against wild-type and fluoroquinolone-resistant gyrase and topoisomerase IV.
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Affiliation(s)
- Jessica
A. Collins
- Department
of Biochemistry, Vanderbilt University School
of Medicine, Nashville, Tennessee 37232, United States
| | - Neil Osheroff
- Department
of Biochemistry, Vanderbilt University School
of Medicine, Nashville, Tennessee 37232, United States
- Department
of Medicine (Hematology/Oncology), Vanderbilt
University School of Medicine, Nashville, Tennessee 37232, United States
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Gargvanshi S, Heravi G, Ayon NJ, Gutheil WG. Screening the NCI diversity set V for anti-MRSA activity: cefoxitin synergy and LC-MS/MS confirmation of folate/thymidine biosynthesis inhibition. Microbiol Spectr 2023; 11:e0054123. [PMID: 37888993 PMCID: PMC10715016 DOI: 10.1128/spectrum.00541-23] [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: 02/06/2023] [Accepted: 09/19/2023] [Indexed: 10/28/2023] Open
Abstract
IMPORTANCE New antibacterial agents are urgently needed to counter increasingly resistant bacteria. One approach to this problem is library screening for new antibacterial agents. Library screening efforts can be improved by increasing the information content of the screening effort. In this study, we screened the National Cancer Institute diversity set V against methicillin-resistant Staphylococcus aureus (MRSA) with several enhancements. One of these is to screen the library before and after microsomal metabolism as means to identify potential active metabolites. A second enhancement is to screen the library in the absence and presence of sub-minimum inhibitory concentration levels of another antibiotic, such as cefoxitin in this study. This identified four agents with synergistic activity with cefoxitin out of 16 agents with good MRSA activity alone. Finally, active agents from this effort were counter-screened in the presence of thymidine, which quickly identified three folate/thymidine biosynthesis inhibitors, and also screened for bactericidal vs bacteriostatic activity.
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Affiliation(s)
- Shivani Gargvanshi
- Division of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, Kansas City, Missouri, USA
| | - Gioia Heravi
- Division of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, Kansas City, Missouri, USA
| | - Navid J. Ayon
- Division of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, Kansas City, Missouri, USA
| | - William G. Gutheil
- Division of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, Kansas City, Missouri, USA
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Medellín-Luna MF, Hernández-López H, Castañeda-Delgado JE, Martinez-Gutierrez F, Lara-Ramírez E, Espinoza-Rodríguez JJ, García-Cruz S, Portales-Pérez DP, Cervantes-Villagrana AR. Fluoroquinolone Analogs, SAR Analysis, and the Antimicrobial Evaluation of 7-Benzimidazol-1-yl-fluoroquinolone in In Vitro, In Silico, and In Vivo Models. Molecules 2023; 28:6018. [PMID: 37630269 PMCID: PMC10458221 DOI: 10.3390/molecules28166018] [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: 07/14/2023] [Revised: 07/30/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
Structure-activity relationship (SAR) studies allow the evaluation of the relationship between structural chemical changes and biological activity. Fluoroquinolones have chemical characteristics that allow their structure to be modified and new analogs with different therapeutic properties to be generated. The objective of this research is to identify and select the C-7 heterocycle fluoroquinolone analog (FQH 1-5) with antibacterial activity similar to the reference fluoroquinolone through in vitro, in silico, and in vivo evaluations. First, SAR analysis was conducted on the FQH 1-5, using an in vitro antimicrobial sensibility model in order to select the best compound. Then, an in silico model mechanism of action analysis was carried out by molecular docking. The non-bacterial cell cytotoxicity was evaluated, and finally, the antimicrobial potential was determined by an in vivo model of topical infection in mice. The results showed antimicrobial differences between the FQH 1-5 and Gram-positive and Gram-negative bacteria, identifying the 7-benzimidazol-1-yl-fluoroquinolone (FQH-2) as the most active against S. aureus. Suggesting the same mechanism of action as the other fluoroquinolones; no cytotoxic effects on non-bacterial cells were found. FQH-2 was demonstrated to decrease the amount of bacteria in infected wound tissue.
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Affiliation(s)
- Mitzzy Fátima Medellín-Luna
- Ciencias Farmacobiológicas, Facultad de Ciencias Químicas, Universidad Autónoma de San Luís Potosí, San Luis Potosí 78210, Mexico; (M.F.M.-L.)
- Unidad Académica de Ciencias Químicas, Universidad Autónoma de Zacatecas, Zacatecas 98160, Mexico
- Unidad de Investigación Biomédica de Zacatecas, Instituto Mexicano del Seguro Social, Zacatecas 98000, Mexico
| | - Hiram Hernández-López
- Unidad Académica de Ciencias Químicas, Universidad Autónoma de Zacatecas, Zacatecas 98160, Mexico
| | - Julio Enrique Castañeda-Delgado
- Unidad de Investigación Biomédica de Zacatecas, Instituto Mexicano del Seguro Social, Zacatecas 98000, Mexico
- Investigadores por México, CONAHCYT, Consejo Nacional de Humanidades, Ciencias y Tecnologias, Ciudad de México 03940, Mexico
| | - Fidel Martinez-Gutierrez
- Ciencias Farmacobiológicas, Facultad de Ciencias Químicas, Universidad Autónoma de San Luís Potosí, San Luis Potosí 78210, Mexico; (M.F.M.-L.)
- Centro de Investigación en Ciencias de la Salud y Biomedicina, UASLP, Sierra Leona No. 550, Lomas, San Luis Potosí 28210, Mexico
| | - Edgar Lara-Ramírez
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reyonsa 88710, Mexico
| | | | - Salvador García-Cruz
- Departamento de Cirugía Experimental e Investigación Quirúrgica y Bioterio, “Claude Bernard”, Área de Ciencias de la Salud, Universidad Autónoma de Zacatecas, Zacatecas 98160, Mexico
| | - Diana Patricia Portales-Pérez
- Ciencias Farmacobiológicas, Facultad de Ciencias Químicas, Universidad Autónoma de San Luís Potosí, San Luis Potosí 78210, Mexico; (M.F.M.-L.)
- Centro de Investigación en Ciencias de la Salud y Biomedicina, UASLP, Sierra Leona No. 550, Lomas, San Luis Potosí 28210, Mexico
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9
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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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10
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Fedorowicz J, Cruz CD, Morawska M, Ciura K, Gilbert-Girard S, Mazur L, Mäkkylä H, Ilina P, Savijoki K, Fallarero A, Tammela P, Sączewski J. Antibacterial and antibiofilm activity of permanently ionized quaternary ammonium fluoroquinolones. Eur J Med Chem 2023; 254:115373. [PMID: 37084595 DOI: 10.1016/j.ejmech.2023.115373] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/29/2023] [Accepted: 04/11/2023] [Indexed: 04/23/2023]
Abstract
A series of quaternary ammonium fluoroquinolones was obtained by exhaustive methylation of the amine groups present at the 7-position of fluoroquinolones, including ciprofloxacin, enoxacin, gatifloxacin, lomefloxacin, and norfloxacin. The synthesized molecules were tested for their antibacterial and antibiofilm activities against Gram-positive and Gram-negative human pathogens, i.e. Staphylococcus aureus and Pseudomonas aeruginosa. The study showed that the synthesized compounds are potent antibacterial agents (MIC values at the lowest 6.25 μM) with low cytotoxicity in vitro as assessed on the BALB 3T3 mouse embryo cell line. Further experiments proved that the tested derivatives are able to bind to the DNA gyrase and topoisomerase IV active sites in a fluoroquinolone-characteristic manner. The most active quaternary ammonium fluoroquinolones, in contrast to ciprofloxacin, reduce the total biomass of P. aeruginosa ATCC 15442 biofilm in post-exposure experiments. The latter effect may be due to the dual mechanism of action of the quaternary fluoroquinolones, which also involves disruption of bacterial cell membranes. IAM-HPLC chromatographic experiments with immobilized artificial membranes (phospholipids) showed that the most active compounds were those with moderate lipophilicity and containing a cyclopropyl group at the N1 nitrogen atom in the fluoroquinolone core.
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Affiliation(s)
- Joanna Fedorowicz
- Department of Chemical Technology of Drugs, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416, Gdańsk, Poland; Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5E), FI-00014, Helsinki, Finland.
| | - Cristina D Cruz
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5E), FI-00014, Helsinki, Finland
| | - Małgorzata Morawska
- Department of Chemical Technology of Drugs, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416, Gdańsk, Poland; Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5E), FI-00014, Helsinki, Finland; Department of Organic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416, Gdańsk, Poland
| | - Krzesimir Ciura
- Department of Physical Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416, Gdańsk, Poland; QSAR Lab Ltd., Trzy Lipy 3 St., 80-172, Gdańsk, Poland
| | - Shella Gilbert-Girard
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5E), FI-00014, Helsinki, Finland
| | - Liliana Mazur
- Institute of Chemical Sciences, Faculty of Chemistry, Maria Curie-Sklodowska University, Plac Marii Curie-Skłodowskiej 5, 20-031, Lublin, Poland
| | - Heidi Mäkkylä
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5E), FI-00014, Helsinki, Finland
| | - Polina Ilina
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5E), FI-00014, Helsinki, Finland
| | - Kirsi Savijoki
- Infection Biology, Faculty of Medicine and Health Technology, Tampere University, Kalevantie 4, FI-33100, Tampere, Finland; Department of Food and Nutrition, Faculty of Agriculture and Forestry, University of Helsinki, Agnes Sjöbergin katu 2, P.O. Box, FI-00014, Helsinki, Finland
| | - Adyary Fallarero
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5E), FI-00014, Helsinki, Finland
| | - Päivi Tammela
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5E), FI-00014, Helsinki, Finland
| | - Jarosław Sączewski
- Department of Organic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416, Gdańsk, Poland
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11
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Byl JAW, Mueller R, Bax B, Basarab GS, Chibale K, Osheroff N. A Series of Spiropyrimidinetriones that Enhances DNA Cleavage Mediated by Mycobacterium tuberculosis Gyrase. ACS Infect Dis 2023; 9:706-715. [PMID: 36802491 PMCID: PMC10006343 DOI: 10.1021/acsinfecdis.3c00012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
The rise in drug-resistant tuberculosis has necessitated the search for alternative antibacterial treatments. Spiropyrimidinetriones (SPTs) represent an important new class of compounds that work through gyrase, the cytotoxic target of fluoroquinolone antibacterials. The present study analyzed the effects of a novel series of SPTs on the DNA cleavage activity of Mycobacterium tuberculosis gyrase. H3D-005722 and related SPTs displayed high activity against gyrase and increased levels of enzyme-mediated double-stranded DNA breaks. The activities of these compounds were similar to those of the fluoroquinolones, moxifloxacin, and ciprofloxacin and greater than that of zoliflodacin, the most clinically advanced SPT. All the SPTs overcame the most common mutations in gyrase associated with fluoroquinolone resistance and, in most cases, were more active against the mutant enzymes than wild-type gyrase. Finally, the compounds displayed low activity against human topoisomerase IIα. These findings support the potential of novel SPT analogues as antitubercular drugs.
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Affiliation(s)
- Jo Ann W Byl
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
| | - Rudolf Mueller
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Ben Bax
- Medicines Discovery Institute, Cardiff University, Cardiff CF10 3AT, United Kingdom
| | - Gregory S Basarab
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Kelly Chibale
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa.,South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch 7701, South Africa
| | - Neil Osheroff
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States.,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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12
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da Silva RA, Wong JJ, Antypas H, Choo PY, Goh K, Jolly S, Liang C, Tay Kwan Sing L, Veleba M, Hu G, Chen J, Kline KA. Mitoxantrone targets both host and bacteria to overcome vancomycin resistance in Enterococcus faecalis. SCIENCE ADVANCES 2023; 9:eadd9280. [PMID: 36812322 PMCID: PMC9946351 DOI: 10.1126/sciadv.add9280] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
Antibiotic resistance critically limits treatment options for infection caused by opportunistic pathogens such as enterococci. Here, we investigate the antibiotic and immunological activity of the anticancer agent mitoxantrone (MTX) in vitro and in vivo against vancomycin-resistant Enterococcus faecalis (VRE). We show that, in vitro, MTX is a potent antibiotic against Gram-positive bacteria through induction of reactive oxygen species and DNA damage. MTX also synergizes with vancomycin against VRE, rendering the resistant strains more permeable to MTX. In a murine wound infection model, single-dose MTX treatment effectively reduces VRE numbers, with further reduction when combined with vancomycin. Multiple MTX treatments accelerate wound closure. MTX also promotes macrophage recruitment and proinflammatory cytokine induction at the wound site and augments intracellular bacterial killing in macrophages by up-regulating the expression of lysosomal enzymes. These results show that MTX represents a promising bacterium- and host-targeted therapeutic for overcoming vancomycin resistance.
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Affiliation(s)
- Ronni A. G. da Silva
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Drug Resistance Interdisciplinary Research Group, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Jun Jie Wong
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Interdisciplinary Graduate Programme, Nanyang Technological University, Singapore, Singapore
| | - Haris Antypas
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Pei Yi Choo
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Karlyn Goh
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Shreya Jolly
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Cui Liang
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Drug Resistance Interdisciplinary Research Group, Singapore, Singapore
| | - Leona Tay Kwan Sing
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Drug Resistance Interdisciplinary Research Group, Singapore, Singapore
| | - Mark Veleba
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Guangan Hu
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jianzhu Chen
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Drug Resistance Interdisciplinary Research Group, Singapore, Singapore
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kimberly A. Kline
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Drug Resistance Interdisciplinary Research Group, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
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13
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Alwali AY, Parkinson EI. Small molecule inducers of actinobacteria natural product biosynthesis. J Ind Microbiol Biotechnol 2023; 50:kuad019. [PMID: 37587009 PMCID: PMC10549211 DOI: 10.1093/jimb/kuad019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 08/14/2023] [Indexed: 08/18/2023]
Abstract
Actinobacteria are a large and diverse group of bacteria that are known to produce a wide range of secondary metabolites, many of which have important biological activities, including antibiotics, anti-cancer agents, and immunosuppressants. The biosynthesis of these compounds is often highly regulated with many natural products (NPs) being produced at very low levels in laboratory settings. Environmental factors, such as small molecule elicitors, can induce the production of secondary metabolites. Specifically, they can increase titers of known NPs as well as enabling discovery of novel NPs typically produced at undetectable levels. These elicitors can be NPs, including antibiotics or hormones, or synthetic compounds. In recent years, there has been a growing interest in the use of small molecule elicitors to induce the production of secondary metabolites from actinobacteria, especially for the discovery of NPs from "silent" biosynthetic gene clusters. This review aims to highlight classes of molecules that induce secondary metabolite production in actinobacteria and to describe the potential mechanisms of induction. ONE-SENTENCE SUMMARY This review describes chemical elicitors of actinobacteria natural products described to date and the proposed mechanisms of induction.
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Affiliation(s)
- Amir Y Alwali
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Elizabeth I Parkinson
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
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14
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Grossman S, Fishwick CWG, McPhillie MJ. Developments in Non-Intercalating Bacterial Topoisomerase Inhibitors: Allosteric and ATPase Inhibitors of DNA Gyrase and Topoisomerase IV. Pharmaceuticals (Basel) 2023; 16:261. [PMID: 37259406 PMCID: PMC9964621 DOI: 10.3390/ph16020261] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 10/15/2023] Open
Abstract
Increases in antibiotic usage and antimicrobial resistance occurrence have caused a dramatic reduction in the effectiveness of many frontline antimicrobial treatments. Topoisomerase inhibitors including fluoroquinolones are broad-spectrum antibiotics used to treat a range of infections, which stabilise a topoisomerase-DNA cleavage complex via intercalation of the bound DNA. However, these are subject to bacterial resistance, predominantly in the form of single-nucleotide polymorphisms in the active site. Significant research has been undertaken searching for novel bioactive molecules capable of inhibiting bacterial topoisomerases at sites distal to the fluoroquinolone binding site. Notably, researchers have undertaken searches for anti-infective agents that can inhibit topoisomerases through alternate mechanisms. This review summarises work looking at the inhibition of topoisomerases predominantly through non-intercalating agents, including those acting at a novel allosteric site, ATPase domain inhibitors, and those offering unique binding modes and mechanisms of action.
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Affiliation(s)
- Scott Grossman
- School of Chemistry, University of Leeds, Leeds LS2 9JT, UK
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15
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Jiang X, Wang D, Wu W, Li F. Ecotoxicological effect of enrofloxacin on Spirulina platensis and the corresponding detoxification mechanism. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2023; 25:85-93. [PMID: 36511301 DOI: 10.1039/d2em00284a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Enrofloxacin is a widely used antibiotic targeting DNA gyrase and has become the commonly detected micropollutant in aquatic environments. Thus, the potential toxicity of enrofloxacin to Spirulina platensis which is a kind of prokaryote similar to Gram-negative bacteria has been hypothesized. However, little is known about the toxicity and degradation mechanism of enrofloxacin during the growth process of Spirulina platensis. Herein, the biomass accumulation of Spirulina platensis was stimulated to 115% of the control group by 0.1 mg L-1 enrofloxacin (10th day), which could be removed probably through the metabolism. Further increasing the enrofloxacin level to 5.0 mg L-1 almost inhibited the growth and remediation ability of Spirulina platensis for 35 days. Environmental stress also caused the variations of photosynthetic pigments (chlorophyll a and carotenoids) and primary biocomponents (proteins, lipids, and carbohydrates), reflecting the adaptation of Spirulina platensis for handling the negative effects of enrofloxacin. The detoxification mechanism was studied by identifying the degradation products of enrofloxacin, suggesting the occurrence of dealkylation and oxidation reactions primarily at the piperazine group. The decreased antimicrobial activity was confirmed by the reduced binding affinity of degradation products with enzymes. The obtained results could help us understand the role of enrofloxacin in the growth of Spirulina platensis, thus providing great support for employing Spirulina platensis in risk assessment and hazard reduction.
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Affiliation(s)
- Xiaohua Jiang
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Dabin Wang
- The State Agriculture Ministry Laboratory of Quality & Safety Risk Assessment for Tobacco, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Weiran Wu
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Fengmin Li
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
- Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, China
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16
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Jiang X, Wang D, Wu W, Li F. The different toxicological effects and removal efficiencies of norfloxacin and sulfadiazine in culturing Arthrospira (Spirulina) platensis. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 250:114468. [PMID: 36592587 DOI: 10.1016/j.ecoenv.2022.114468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/20/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
Norfloxacin (NFX) and sulfadiazine (SDZ) are two widely used antibiotics belonging to fluoroquinolone and sulfonamide groups, respectively, and have become the commonly detected micropollutants in aquatic environments. However, only few works have been conducted to investigate the highly probable inhibition of these antibiotic pollutants to Arthrospira platensis, which is an important species of cyanobacteria that is one of primary producers in aquatic ecosystems and should be remarkably sensitive to environmental pollutants due to its prokaryotic characteristics. Hence, the toxicological effects and removal efficiencies of NFX and SDZ in culturing A. platensis were studied by analyzing the biomass growth, photosynthetic pigments, primary biocomponents, and antibiotics concentration. The corresponding variations of these characteristics showed the higher sensitivity of A. platensis to NFX than to SDZ, indicating the specifically targeted effect of NFX on A. platensis, which could be confirmed in silico by the higher binding affinity of NFX with the critical enzyme. The obtained results illustrated the roles of NFX and SDZ on the growth of A. platensis, thus providing the great support in employing A. platensis to reduce hazards from contaminated water and recover biomass resources.
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Affiliation(s)
- Xiaohua Jiang
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Dabin Wang
- The State Agriculture Ministry Laboratory of Quality & Safety Risk Assessment for Tobacco, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
| | - Weiran Wu
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Fengmin Li
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China; Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, China.
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17
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A 2.8 Å Structure of Zoliflodacin in a DNA Cleavage Complex with Staphylococcus aureus DNA Gyrase. Int J Mol Sci 2023; 24:ijms24021634. [PMID: 36675148 PMCID: PMC9865888 DOI: 10.3390/ijms24021634] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/04/2023] [Accepted: 01/07/2023] [Indexed: 01/17/2023] Open
Abstract
Since 2000, some thirteen quinolones and fluoroquinolones have been developed and have come to market. The quinolones, one of the most successful classes of antibacterial drugs, stabilize DNA cleavage complexes with DNA gyrase and topoisomerase IV (topo IV), the two bacterial type IIA topoisomerases. The dual targeting of gyrase and topo IV helps decrease the likelihood of resistance developing. Here, we report on a 2.8 Å X-ray crystal structure, which shows that zoliflodacin, a spiropyrimidinetrione antibiotic, binds in the same DNA cleavage site(s) as quinolones, sterically blocking DNA religation. The structure shows that zoliflodacin interacts with highly conserved residues on GyrB (and does not use the quinolone water-metal ion bridge to GyrA), suggesting it may be more difficult for bacteria to develop target mediated resistance. We show that zoliflodacin has an MIC of 4 µg/mL against Acinetobacter baumannii (A. baumannii), an improvement of four-fold over its progenitor QPT-1. The current phase III clinical trial of zoliflodacin for gonorrhea is due to be read out in 2023. Zoliflodacin, together with the unrelated novel bacterial topoisomerase inhibitor gepotidacin, is likely to become the first entirely novel chemical entities approved against Gram-negative bacteria in the 21st century. Zoliflodacin may also become the progenitor of a new safer class of antibacterial drugs against other problematic Gram-negative bacteria.
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18
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Evren AE, Karaduman AB, Sağlik BN, Özkay Y, Yurttaş L. Investigation of Novel Quinoline-Thiazole Derivatives as Antimicrobial Agents: In Vitro and In Silico Approaches. ACS OMEGA 2023; 8:1410-1429. [PMID: 36643421 PMCID: PMC9835529 DOI: 10.1021/acsomega.2c06871] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Infectious diseases are a major concern around the world. Today, it is an urgent need for new chemotherapeutics for infectious diseases. Because of that, our group designed, synthesized, and analyzed 14 new quinoline derivatives endowed with the pharmacophore moiety of fluoroquinolones primarily for their antimicrobial effects. Their cytotoxicity effects were tested against six bacterial and four fungal strains and NIH/3T3 cell line. Additionally, their action mechanisms were evaluated against DNA gyrase and lanosterol 14α-demethylase (LMD). Furthermore, to eliminate the potential side effects, the active compounds were evaluated against the aromatase enzyme. The experimental enzymatic results were evaluated for active compounds' binding modes using molecular docking and molecular dynamics simulation studies. The results were utilized to clarify the structure-activity relationship (SAR). Finally, compound 4m was the most potent compound for its antifungal activity with low cytotoxicity against healthy cells and fewer possible side effects, while compounds 4j and 4l can be used alone for special patients who are suffering from fungal infections in addition to the primer disease.
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Affiliation(s)
- Asaf Evrim Evren
- Department
of Pharmacy Services, Vocational School of Health Services, Bilecik Şeyh Edebali University, Bilecik 11000, Turkey
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, Eskişehir 26470, Turkey
| | - Abdullah Burak Karaduman
- Department
of Pharmaceutical Toxicology, Faculty of Pharmacy, Anadolu University, Eskişehir 26470, Turkey
| | - Begüm Nurpelin Sağlik
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, Eskişehir 26470, Turkey
- Central
Research Laboratory, Faculty of Pharmacy, Anadolu University, Eskişehir 26470, Turkey
| | - Yusuf Özkay
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, Eskişehir 26470, Turkey
- Central
Research Laboratory, Faculty of Pharmacy, Anadolu University, Eskişehir 26470, Turkey
| | - Leyla Yurttaş
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, Eskişehir 26470, Turkey
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19
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Tang T, Liu M, Du Y, Chen Y. Deciphering the internal mechanisms of ciprofloxacin affected anaerobic digestion, its degradation and detoxification mechanism. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 842:156718. [PMID: 35760173 DOI: 10.1016/j.scitotenv.2022.156718] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 06/02/2022] [Accepted: 06/11/2022] [Indexed: 06/15/2023]
Abstract
Ciprofloxacin (CIP) is widely used in livestock farms, but the internal mechanism of the effect of residual CIP in actual livestock wastewater on anaerobic digestion (AD) performance remains unknown. This study examined the dose-specific effects of CIP (0.5-2 mg/L) on livestock wastewater AD by analyzing acidogenesis and methanogenesis. 0.5 mg/L CIP promoted methane production by facilitating acidogenesis and acetogenesis. Compared with the control, the cumulative methane production increased from 331.38 to 407.44 mL/g VS at a dose of 0.5 mg/L, an increase of 22.95 %. However, as the dose of CIP increased, the cumulative methane production gradually decreased to 217.64 mL/g VS (2 mg/L). Microbial community analysis revealed that CIP had the greatest impact on methane production by influencing the activity of acidogenic bacteria. Meanwhile, acidogenesis was critical for CIP degradation. In acidogenesis, hydroxylation, amination, defluorination, decarboxylation, and piperazine ring breaking not only degraded CIP but also reduced its toxicity. Therefore, a large number of intermediates could be continuously degraded by microorganisms. However, as the dosage of CIP increased, the ability of microorganisms to degrade intermediates decreased.
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Affiliation(s)
- Taotao Tang
- College of Architecture and Environment, Sichuan University, Chengdu 610065, PR China
| | - Min Liu
- College of Architecture and Environment, Sichuan University, Chengdu 610065, PR China
| | - Ye Du
- College of Architecture and Environment, Sichuan University, Chengdu 610065, PR China
| | - Ying Chen
- College of Architecture and Environment, Sichuan University, Chengdu 610065, PR China.
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20
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A potent antibiotic-loaded bone-cement implant against staphylococcal bone infections. Nat Biomed Eng 2022; 6:1180-1195. [PMID: 36229662 PMCID: PMC10101771 DOI: 10.1038/s41551-022-00950-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 09/08/2022] [Indexed: 12/14/2022]
Abstract
New antibiotics should ideally exhibit activity against drug-resistant bacteria, delay the development of bacterial resistance to them and be suitable for local delivery at desired sites of infection. Here, we report the rational design, via molecular-docking simulations, of a library of 17 candidate antibiotics against bone infection by wild-type and mutated bacterial targets. We screened this library for activity against multidrug-resistant clinical isolates and identified an antibiotic that exhibits potent activity against resistant strains and the formation of biofilms, decreases the chances of bacterial resistance and is compatible with local delivery via a bone-cement matrix. The antibiotic-loaded bone cement exhibited greater efficacy than currently used antibiotic-loaded bone cements against staphylococcal bone infections in rats. Potent and locally delivered antibiotic-eluting polymers may help address antimicrobial resistance.
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21
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Mohammed Musthafa T, Snigdha K, Asiri AM, Sobahi TR, Asad M. Green synthesis of Chromonyl Chalcone and Pyrazoline as Potential Antimicrobial Agents - DFT, Molecular Docking and Antimicrobial Studies. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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22
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Palladium(II) Complexes of Substituted Salicylaldehydes: Synthesis, Characterization and Investigation of Their Biological Profile. Pharmaceuticals (Basel) 2022; 15:ph15070886. [PMID: 35890184 PMCID: PMC9323974 DOI: 10.3390/ph15070886] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/06/2022] [Accepted: 07/14/2022] [Indexed: 02/04/2023] Open
Abstract
Five palladium(II) complexes of substituted salicylaldehydes (X-saloH, X = 4-Et2N (for 1), 3,5-diBr (for 2), 3,5-diCl (for 3), 5-F (for 4) or 4-OMe (for 5)) bearing the general formula [Pd(X-salo)2] were synthesized and structurally characterized. The crystal structure of complex [Pd(4-Et2N-salo)2] was determined by single-crystal X-ray crystallography. The complexes can scavenge 1,1-diphenyl-picrylhydrazyl and 2,2′-azinobis(3-ethylbenzothiazoline-6-sulfonic acid) radicals and reduce H2O2. They are active against two Gram-positive (Staphylococcus aureus and Bacillus subtilis) and two Gram-negative (Escherichia coli and Xanthomonas campestris) bacterial strains. The complexes interact strongly with calf-thymus DNA via intercalation, as deduced by diverse techniques and via the determination of their binding constants. Complexes interact reversibly with bovine and human serum albumin. Complementary insights into their possible mechanisms of bioactivity at the molecular level were provided by molecular docking calculations, exploring in silico their ability to bind to calf-thymus DNA, Escherichia coli and Staphylococcus aureus DNA-gyrase, 5-lipoxygenase, and membrane transport lipid protein 5-lipoxygenase-activating protein, contributing to the understanding of the role complexes 1–5 can play both as antioxidant and antibacterial agents. Furthermore, in silico predictive tools have been employed to study the chemical reactivity, molecular properties and drug-likeness of the complexes, and also the drug-induced changes of gene expression profile (as protein- and mRNA-based prediction results), the sites of metabolism, the substrate/metabolite specificity, the cytotoxicity for cancer and non-cancer cell lines, the acute rat toxicity, the rodent organ-specific carcinogenicity, the anti-target interaction profiles, the environmental ecotoxicity, and finally the activity spectra profile of the compounds.
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Govender P, Müller R, Singh K, Reddy V, Eyermann CJ, Fienberg S, Ghorpade SR, Koekemoer L, Myrick A, Schnappinger D, Engelhart C, Meshanni J, Byl JAW, Osheroff N, Singh V, Chibale K, Basarab GS. Spiropyrimidinetrione DNA Gyrase Inhibitors with Potent and Selective Antituberculosis Activity. J Med Chem 2022; 65:6903-6925. [PMID: 35500229 DOI: 10.1021/acs.jmedchem.2c00266] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
New antibiotics with either a novel mode of action or novel mode of inhibition are urgently needed to overcome the threat of drug-resistant tuberculosis (TB). The present study profiles new spiropyrimidinetriones (SPTs), DNA gyrase inhibitors having activity against drug-resistant Mycobacterium tuberculosis (Mtb), the causative agent of TB. While the clinical candidate zoliflodacin has progressed to phase 3 trials for the treatment of gonorrhea, compounds herein demonstrated higher inhibitory potency against Mtb DNA gyrase (e.g., compound 42 with IC50 = 2.0) and lower Mtb minimum inhibitor concentrations (0.49 μM for 42). Notably, 42 and analogues showed selective Mtb activity relative to representative Gram-positive and Gram-negative bacteria. DNA gyrase inhibition was shown to involve stabilization of double-cleaved DNA, while on-target activity was supported by hypersensitivity against a gyrA hypomorph. Finally, a docking model for SPTs with Mtb DNA gyrase was developed, and a structural hypothesis was built for structure-activity relationship expansion.
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Affiliation(s)
- Preshendren Govender
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Rudolf Müller
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Kawaljit Singh
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Virsinha Reddy
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Charles J Eyermann
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Stephen Fienberg
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Sandeep R Ghorpade
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Lizbé Koekemoer
- Drug Discovery and Development Centre (H3D) South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Alissa Myrick
- Drug Discovery and Development Centre (H3D) South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065, United States
| | - Curtis Engelhart
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065, United States
| | - Jaclynn Meshanni
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065, United States
| | - Jo Ann W Byl
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
| | - Neil Osheroff
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States.,Department of Medicine (Hematology/Oncology), Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States.,VA Tennessee Valley Healthcare System, Nashville, Tennessee 37212, United States
| | - Vinayak Singh
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch, Cape Town 7701, South Africa.,Drug Discovery and Development Centre (H3D) South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Kelly Chibale
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch, Cape Town 7701, South Africa.,Drug Discovery and Development Centre (H3D) South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Gregory S Basarab
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch, Cape Town 7701, South Africa.,Drug Discovery and Development Centre (H3D), Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Observatory, Cape Town, 7935, South Africa
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Spiropyrimidinetriones: a Class of DNA Gyrase Inhibitors with Activity against Mycobacterium tuberculosis and without Cross-Resistance to Fluoroquinolones. Antimicrob Agents Chemother 2022; 66:e0219221. [PMID: 35266826 PMCID: PMC9017349 DOI: 10.1128/aac.02192-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Described here is a series of spiropyrimidinetrione (SPT) compounds with activity against Mycobacterium tuberculosis through inhibition of DNA gyrase. The SPT class operates via a novel mode of inhibition, which involves Mg2+-independent stabilization of the DNA cleavage complex with DNA gyrase and is thereby not cross-resistant with other DNA gyrase-inhibiting antibacterials, including fluoroquinolones. Compound 22 from the series was profiled broadly and showed in vitro cidality as well as intracellular activity against M. tuberculosis in macrophages. Evidence for the DNA gyrase mode of action was supported by inhibition of the target in a DNA supercoiling assay and elicitation of an SOS response seen in a recA reporter strain of M. tuberculosis. Pharmacokinetic properties of 22 supported evaluation of efficacy in an acute model of M. tuberculosis infection, where modest reduction in CFU numbers was seen. This work offers promise for deriving a novel drug class of tuberculosis agent without preexisting clinical resistance.
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Moussaoui O, Bhadane R, Sghyar R, Ilaš J, El Hadrami EM, Chakroune S, Salo‐Ahen OMH. Design, Synthesis, in vitro and in silico Characterization of 2-Quinolone-L-alaninate-1,2,3-triazoles as Antimicrobial Agents. ChemMedChem 2022; 17:e202100714. [PMID: 34978160 PMCID: PMC9305408 DOI: 10.1002/cmdc.202100714] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 12/16/2021] [Indexed: 11/07/2022]
Abstract
Due to the ever-increasing antimicrobial resistance there is an urgent need to continuously design and develop novel antimicrobial agents. Inspired by the broad antibacterial activities of various heterocyclic compounds such as 2-quinolone derivatives, we designed and synthesized new methyl-(2-oxo-1,2-dihydroquinolin-4-yl)-L-alaninate-1,2,3-triazole derivatives via 1,3-dipolar cycloaddition reaction of 1-propargyl-2-quinolone-L-alaninate with appropriate azide groups. The synthesized compounds were obtained in good yield ranging from 75 to 80 %. The chemical structures of these novel hybrid molecules were determined by spectroscopic methods and the antimicrobial activity of the compounds was investigated against both bacterial and fungal strains. The tested compounds showed significant antimicrobial activity and weak to moderate antifungal activity. Despite the evident similarity of the quinolone moiety of our compounds with fluoroquinolones, our compounds do not function by inhibiting DNA gyrase. Computational characterization of the compounds shows that they have attractive physicochemical and pharmacokinetic properties and could serve as templates for developing potential antimicrobial agents for clinical use.
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Affiliation(s)
- Oussama Moussaoui
- Laboratory of Applied Organic ChemistrySidi Mohamed Ben Abdellah University30000FezMorocco
| | - Rajendra Bhadane
- Structural Bioinformatics Laboratory, BiochemistryÅbo Akademi University20520TurkuFinland
- Pharmaceutical Sciences Laboratory, PharmacyÅbo Akademi University20520TurkuFinland
| | - Riham Sghyar
- Laboratory of Applied Organic ChemistrySidi Mohamed Ben Abdellah University30000FezMorocco
| | - Janez Ilaš
- Faculty of PharmacyUniversity of Ljubljana1000LjubljanaSlovenia
| | - El Mestafa El Hadrami
- Laboratory of Applied Organic ChemistrySidi Mohamed Ben Abdellah University30000FezMorocco
| | - Said Chakroune
- Laboratory of Applied Organic ChemistrySidi Mohamed Ben Abdellah University30000FezMorocco
| | - Outi M. H. Salo‐Ahen
- Structural Bioinformatics Laboratory, BiochemistryÅbo Akademi University20520TurkuFinland
- Pharmaceutical Sciences Laboratory, PharmacyÅbo Akademi University20520TurkuFinland
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Rząd K, Paluszkiewicz E, Neubauer D, Olszewski M, Kozłowska-Tylingo K, Kamysz W, Gabriel I. The Effect of Conjugation with Octaarginine, a Cell-Penetrating Peptide on Antifungal Activity of Imidazoacridinone Derivative. Int J Mol Sci 2021; 22:ijms222413190. [PMID: 34947987 PMCID: PMC8705783 DOI: 10.3390/ijms222413190] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/26/2021] [Accepted: 12/02/2021] [Indexed: 12/31/2022] Open
Abstract
Acridine cell-penetrating peptide conjugates are an extremely important family of compounds in antitumor chemotherapy. These conjugates are not so widely analysed in antimicrobial therapy, although bioactive peptides could be used as nanocarriers to smuggle antimicrobial compounds. An octaarginine conjugate of an imidazoacridinone derivative (Compound 1-R8) synthetized by us exhibited high antifungal activity against reference and fluconazole-resistant clinical strains (MICs ≤ 4 μg mL−1). Our results clearly demonstrate the qualitative difference in accumulation of the mother compound and Compound 1-R8 conjugate into fungal cells. Only the latter was transported and accumulated effectively. Microscopic and flow cytometry analysis provide some evidence that the killing activity of Compound 1-R8 may be associated with a change in the permeability of the fungal cell membrane. The conjugate exhibited low cytotoxicity against human embryonic kidney (HEK-293) and human liver (HEPG2) cancer cell lines. Nevertheless, the selectivity index value of the conjugate for human pathogenic strains remained favourable and no hemolytic activity was observed. The inhibitory effect of the analysed compound on yeast topoisomerase II activity suggested its molecular target. In summary, conjugation with R8 effectively increased imidazoacridinone derivative ability to enter the fungal cell and achieve a concentration inside the cell that resulted in a high antifungal effect.
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Affiliation(s)
- Kamila Rząd
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry and BioTechMed Center, Gdańsk University of Technology, 11/12 Narutowicza Str., 80-233 Gdańsk, Poland; (K.R.); (E.P.); (M.O.); (K.K.-T.)
| | - Ewa Paluszkiewicz
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry and BioTechMed Center, Gdańsk University of Technology, 11/12 Narutowicza Str., 80-233 Gdańsk, Poland; (K.R.); (E.P.); (M.O.); (K.K.-T.)
| | - Damian Neubauer
- Department of Inorganic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Gen. J. Hallera 107th Avenue, 80-416 Gdańsk, Poland; (D.N.); (W.K.)
| | - Mateusz Olszewski
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry and BioTechMed Center, Gdańsk University of Technology, 11/12 Narutowicza Str., 80-233 Gdańsk, Poland; (K.R.); (E.P.); (M.O.); (K.K.-T.)
| | - Katarzyna Kozłowska-Tylingo
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry and BioTechMed Center, Gdańsk University of Technology, 11/12 Narutowicza Str., 80-233 Gdańsk, Poland; (K.R.); (E.P.); (M.O.); (K.K.-T.)
| | - Wojciech Kamysz
- Department of Inorganic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Gen. J. Hallera 107th Avenue, 80-416 Gdańsk, Poland; (D.N.); (W.K.)
| | - Iwona Gabriel
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry and BioTechMed Center, Gdańsk University of Technology, 11/12 Narutowicza Str., 80-233 Gdańsk, Poland; (K.R.); (E.P.); (M.O.); (K.K.-T.)
- Correspondence: ; Tel.: +48-58-348-6078; Fax: +48-58-347-1144
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Sanguiin H-6 Fractionated from Cloudberry ( Rubus chamaemorus) Seeds Can Prevent the Methicillin-Resistant Staphylococcus aureus Biofilm Development during Wound Infection. Antibiotics (Basel) 2021; 10:antibiotics10121481. [PMID: 34943693 PMCID: PMC8698471 DOI: 10.3390/antibiotics10121481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 11/25/2021] [Accepted: 11/29/2021] [Indexed: 11/16/2022] Open
Abstract
Staphylococcus aureus is the most common cause of surgical site infections and its treatment is challenging due to the emergence of multi-drug resistant strains such as methicillin-resistant S. aureus (MRSA). Natural berry-derived compounds have shown antimicrobial potential, e.g., ellagitannins such as sanguiin H-6 and lambertianin C, the main phenolic compounds in Rubus seeds, have shown antimicrobial activity. The aim of this study was to evaluate the effect of sanguiin H-6 and lambertianin C fractionated from cloudberry seeds, on the MRSA growth, and as treatment of a MRSA biofilm development in different growth media in vitro and in vivo by using a murine wound infection model where sanguiin H-6 and lambertianin C were used to prevent the MRSA infection. Sanguiin H-6 and lambertianin C inhibited the in vitro biofilm development and growth of MRSA. Furthermore, sanguiin H-6 showed significant anti-MRSA effect in the in vivo wound model. Our study shows the possible use of sanguiin H-6 as a preventive measure in surgical sites to avoid postoperative infections, whilst lambertianin C showed no anti-MRSA activity.
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Analysis of fluoroquinolone-resistance using MIC determination and homology modelling of ParC of contemporary Mycoplasma genitalium strains. J Infect Chemother 2021; 28:377-383. [PMID: 34836778 DOI: 10.1016/j.jiac.2021.11.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 09/22/2021] [Accepted: 11/12/2021] [Indexed: 11/23/2022]
Abstract
INTRODUCTION The mechanisms of fluoroquinolone-resistance of Mycoplasma genitalium were analysed by a new method. METHODS M. genitalium strains from urinary sediments of patients with urethritis were isolated and examined antimicrobial susceptibilities and the mutations in ParC, GyrA and 23S rRNA. Docking models between gyrase and topoisomerase IV with sitafloxacin showed that two binding modes in which the amine moiety at the C-7 position rotated could be constructed. RESULTS Among 18 strains, 13 strains had mutations with amino-acid changes at Serine 83 in ParC. The MICs of moxifloxacin or sitafloxacin for three strains with only S83I in ParC were 2, 1 and 8 mg/L (moxifloxacin) or 0.13, 0.13 and 1 mg/L (sitafloxacin), respectively. In contrast, the MICs of moxifloxacin or sitafloxacin for 3 strain with S83N in ParC were 0.25, 0.13 and 0.25 mg/L (moxifloxacin) or 0.06, 0.03, and 0,03 mg/L (sitafloxacin), respectively, not significantly different from wild-type isolates. The docking model of sitafloxacin and topoisomerase IV showed that the oxygen atom at the gamma position of Serine 83 of ParC interacted with the sitafloxacin carboxylate moiety. When the S83I substitution occurs, the isoleucine side chain is lipophilic and the residue hydropathy changes from hydrophilicity to hydrophobicity and important H-bond interactions between serine and the carboxylate moiety are lost. When the serine 83 to asparagine substitution (S83N) occurred, the asparagine side chain is hydrophilic and the residue hydropathy does not change. CONCLUSION The docking model suggests that Ser83 replacements causes attenuation or loss of activity of fluoroquinolones such as sitafloxacin.
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Ibrahim TS, Almalki AJ, Moustafa AH, Allam RM, Abuo-Rahma GEDA, El Subbagh HI, Mohamed MFA. Novel 1,2,4-oxadiazole-chalcone/oxime hybrids as potential antibacterial DNA gyrase inhibitors: Design, synthesis, ADMET prediction and molecular docking study. Bioorg Chem 2021; 111:104885. [PMID: 33838559 DOI: 10.1016/j.bioorg.2021.104885] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/26/2021] [Accepted: 03/28/2021] [Indexed: 01/19/2023]
Abstract
New antibacterial drugs are urgently needed to tackle the rapid rise in multi-drug resistant bacteria. DNA gyrase is a validated target for the development of new antibacterial drugs. Thus, in the present investigation, a novel series of 1,2,4-oxadiazole-chalcone/oxime (6a-f) and (7a-f) were synthesized and characterized by IR, NMR (1H and 13C) and elemental analyses. The title compounds were evaluated for their in-vitro antimicrobial activity by the modified agar diffusion method as well as their E. coli DNA gyrase inhibitory activity. The minimum inhibitory concentration (MIC) and the structure activity relationships (SARs) were evaluated. Among all, compounds 6a, 6c-e, 7b and 7e were the most potent and proved to possess broad spectrum activity against the tested Gram-positive and Gram-negative organisms. Additionally, compounds 6a (against S. aureus), 6c (against B. subtilis and E. hirae), 6e (against E. hirae), 6f, 7a and 7c (against E. coli) and 7d (against B. subtilis), with MIC value of 3.12 μM were two-fold more potent than the standard ciprofloxacin (MIC = 6.25 μM). Mechanistically, compounds 6c, 7c, 7e and 7b had good inhibitory activity against E. coli gyrase with IC50 values of 17.05, 13.4, 16.9, and 19.6 µM, respectively, in comparison with novobiocin (IC50 = 12.3 µM) and ciprofloxacin (IC50 = 10.5 µM). The molecular docking results at DNA gyrase active site revealed that the most potent compounds 6c and 7c have binding mode and docking scores comparable to that of ciprofloxacin and novobiocin suggesting their antibacterial activity via inhibition of DNA gyrase. Finally, the predicted parameters of Lipinski's rule of five and ADMET analysis showed that 6c and 7c had good drug-likeness and acceptable physicochemical properties. Therefore, the hybridization of the chalcone and oxadiazole moieties could be promising lead as antibacterial candidate which merit further future structural optimizations.
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Affiliation(s)
- Tarek S Ibrahim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt.
| | - Ahmad J Almalki
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Amr H Moustafa
- Department of Chemistry, Faculty of Science, Sohag University, Sohag 82524, Egypt
| | - Rasha M Allam
- Pharmacology Department, National Research Centre, Cairo 12622 (ID: 60014618), Egypt
| | - Gamal El-Din A Abuo-Rahma
- Department of Medicinal Chemistry, Faculty of Pharmacy, Minia University, Minia 61519, Egypt; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Deraya University, New Minia, Minia, Egypt
| | - Hussein I El Subbagh
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, 35516 Mansoura, Egypt
| | - Mamdouh F A Mohamed
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Sohag University, 82524 Sohag, Egypt.
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Towards Conformation-Sensitive Inhibition of Gyrase: Implications of Mechanistic Insight for the Identification and Improvement of Inhibitors. Molecules 2021; 26:molecules26051234. [PMID: 33669078 PMCID: PMC7956263 DOI: 10.3390/molecules26051234] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 02/19/2021] [Accepted: 02/20/2021] [Indexed: 12/17/2022] Open
Abstract
Gyrase is a bacterial type IIA topoisomerase that catalyzes negative supercoiling of DNA. The enzyme is essential in bacteria and is a validated drug target in the treatment of bacterial infections. Inhibition of gyrase activity is achieved by competitive inhibitors that interfere with ATP- or DNA-binding, or by gyrase poisons that stabilize cleavage complexes of gyrase covalently bound to the DNA, leading to double-strand breaks and cell death. Many of the current inhibitors suffer from severe side effects, while others rapidly lose their antibiotic activity due to resistance mutations, generating an unmet medical need for novel, improved gyrase inhibitors. DNA supercoiling by gyrase is associated with a series of nucleotide- and DNA-induced conformational changes, yet the full potential of interfering with these conformational changes as a strategy to identify novel, improved gyrase inhibitors has not been explored so far. This review highlights recent insights into the mechanism of DNA supercoiling by gyrase and illustrates the implications for the identification and development of conformation-sensitive and allosteric inhibitors.
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Martins-Duarte ÉS, Sheiner L, Reiff SB, de Souza W, Striepen B. Replication and partitioning of the apicoplast genome of Toxoplasma gondii is linked to the cell cycle and requires DNA polymerase and gyrase. Int J Parasitol 2021; 51:493-504. [PMID: 33581138 PMCID: PMC8113025 DOI: 10.1016/j.ijpara.2020.11.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 10/30/2020] [Accepted: 11/08/2020] [Indexed: 10/26/2022]
Abstract
Apicomplexans are the causative agents of numerous important infectious diseases including malaria and toxoplasmosis. Most of them harbour a chloroplast-like organelle called the apicoplast that is essential for the parasites' metabolism and survival. While most apicoplast proteins are nuclear encoded, the organelle also maintains its own genome, a 35 kb circle. In this study we used Toxoplasma gondii to identify and characterise essential proteins involved in apicoplast genome replication and to understand how apicoplast genome segregation unfolds over time. We demonstrated that the DNA replication enzymes Prex, DNA gyrase and DNA single stranded binding protein localise to the apicoplast. We show in knockdown experiments that apicoplast DNA Gyrase A and B, and Prex are required for apicoplast genome replication and growth of the parasite. Analysis of apicoplast genome replication by structured illumination microscopy in T. gondii tachyzoites showed that apicoplast nucleoid division and segregation initiate at the beginning of S phase and conclude during mitosis. Thus, the replication and division of the apicoplast nucleoid is highly coordinated with nuclear genome replication and mitosis. Our observations highlight essential components of apicoplast genome maintenance and shed light on the timing of this process in the context of the overall parasite cell cycle.
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Affiliation(s)
- Érica S Martins-Duarte
- Laboratório de Quimioterapia de Protozoários Egler Chiari, Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil; Núcleo de Biologia Estrutural e Bioimagens (CENABIO) - Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Biomagens (INBEB), Rio de Janeiro, RJ, Brazil.
| | - Lilach Sheiner
- Wellcome Centre for Integrative Parasitology, University of Glasgow, 120 University Place Glasgow, United Kingdom
| | - Sarah B Reiff
- Department of Cellular Biology, University of Georgia, Athens, GA, USA
| | - Wanderley de Souza
- Núcleo de Biologia Estrutural e Bioimagens (CENABIO) - Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Biomagens (INBEB), Rio de Janeiro, RJ, Brazil; Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Boris Striepen
- Department of Cellular Biology, University of Georgia, Athens, GA, USA; Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA. USA
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Mallikarjuna Reddy G, Raul Garcia J, Venkata Subbaiah M, Wen J. An efficient green approach for the synthesis of benzothiazole‐linked pyranopyrazoles as promising pharmacological agents and docking studies. J Heterocycl Chem 2021. [DOI: 10.1002/jhet.4194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Guda Mallikarjuna Reddy
- Chemical Engineering Institute Ural Federal University, 620002 Yekaterinburg Russian Federation
| | - Jarem Raul Garcia
- Department of Chemistry University of Ponta Grossa Ponta Grossa Parana state Brazil
| | - Munagapati Venkata Subbaiah
- Research Centre for Soil & Water Resources and Natural Disaster Prevention (SWAN) National Yunlin University of Science & Technology Douliou Taiwan
| | - Jet‐Chau Wen
- Research Centre for Soil & Water Resources and Natural Disaster Prevention (SWAN) National Yunlin University of Science & Technology Douliou Taiwan
- Department of Safety, Health and Environmental Engineering National Yunlin University of Science & Technology Douliou Taiwan
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Jia Z, Lv R, Guo L, Zhang J, Li R, Liu J, Fan C. Rapid degradation of ciprofloxacin over BiOCl: Insight into the molecular structure transformation and antibacterial activity elimination. Sep Purif Technol 2021. [DOI: 10.1016/j.seppur.2020.117872] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Rząd K, Paluszkiewicz E, Gabriel I. A new 1-nitro-9-aminoacridine derivative targeting yeast topoisomerase II able to overcome fluconazole-resistance. Bioorg Med Chem Lett 2021; 35:127815. [PMID: 33486051 DOI: 10.1016/j.bmcl.2021.127815] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 01/05/2021] [Accepted: 01/17/2021] [Indexed: 02/02/2023]
Abstract
Fungal resistance remains a significant threat and a leading cause of death worldwide. Thus, overcoming microbial infections have again become a serious clinical problem. Although acridine derivatives are widely analyzed as anticancer agents, only a few reports have demonstrated their antifungal activity. In an effort to develop biologically active antifungals, twelve novel C-857 (9-(2'-hydroxyethylamino)-1-nitroacridine) and C-1748 (9-(2'-hydroxyethylamino)-4-methyl-1-nitroacridine) derivatives were synthesized. The evaluation of biological properties suggests that starting compounds: C-1748, C-857 and IE3 (2-[(4-methyl-1-nitroacridin-9-yl)amino]ethyl lysinate), IE4 (2-[(1-nitroacridin-9-yl)amino]ethyl lysinate) antifungal mode of action differ from that determined for IE5 (N'-{3-[(4-methyl-1-nitroacridin-9-yl)amino]propyl}lysinamide), IE6 (N'-{3-[(1-nitroacridin-9-yl)amino]propyl}lysinamide) and IE10 (3,3'-Bis-(1-nitroacridin-9-ylamino)-aminoethylaminoethylaminoethylamine). Although MIC values determined for the latter were higher, in contrast to C-857 and C-1748, newly synthesized IE5, IE6 and IE10 reduced C. albicans hyphal growth in different inducing media. Those compounds also exhibited antibiofilm activity, whereas IE10 was the most effective. Moreover, only IE6 exhibited antifungal activity against fluconazole resistant C. albicans strains with MICs values in the range of 16-64 μg mL-1. Our results also indicate that, in contrast to other analyzed derivatives, novel synthetized compounds IE6 and IE10 with antifungal activity target yeast topoisomerase II activity.
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Affiliation(s)
- Kamila Rząd
- Department of Pharmaceutical Technology and Biochemistry, Gdańsk University of Technology, 11/12 Narutowicza Str., 80-233 Gdańsk, Poland
| | - Ewa Paluszkiewicz
- Department of Pharmaceutical Technology and Biochemistry, Gdańsk University of Technology, 11/12 Narutowicza Str., 80-233 Gdańsk, Poland
| | - Iwona Gabriel
- Department of Pharmaceutical Technology and Biochemistry, Gdańsk University of Technology, 11/12 Narutowicza Str., 80-233 Gdańsk, Poland.
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35
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Kolarič A, Germe T, Hrast M, Stevenson CEM, Lawson DM, Burton NP, Vörös J, Maxwell A, Minovski N, Anderluh M. Potent DNA gyrase inhibitors bind asymmetrically to their target using symmetrical bifurcated halogen bonds. Nat Commun 2021; 12:150. [PMID: 33420011 PMCID: PMC7794245 DOI: 10.1038/s41467-020-20405-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 11/25/2020] [Indexed: 12/13/2022] Open
Abstract
Novel bacterial type II topoisomerase inhibitors (NBTIs) stabilize single-strand DNA cleavage breaks by DNA gyrase but their exact mechanism of action has remained hypothetical until now. We have designed a small library of NBTIs with an improved DNA gyrase-binding moiety resulting in low nanomolar inhibition and very potent antibacterial activity. They stabilize single-stranded cleavage complexes and, importantly, we have obtained the crystal structure where an NBTI binds gyrase–DNA in a single conformation lacking apparent static disorder. This directly proves the previously postulated NBTI mechanism of action and shows that they stabilize single-strand cleavage through asymmetric intercalation with a shift of the scissile phosphate. This crystal stucture shows that the chlorine forms a halogen bond with the backbone carbonyls of the two symmetry-related Ala68 residues. To the best of our knowledge, such a so-called symmetrical bifurcated halogen bond has not been identified in a biological system until now. The mechanism of DNA gyrase inhibitor stabilization of single-strand DNA cleavage breaks by DNA gyrase has been hypothetical. Here, the authors show experimental evidence of the mechanism using a library of inhibitors with improved binding and employ crystal analysis to show bifurcated halogen bonding.
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Affiliation(s)
- Anja Kolarič
- Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000, Ljubljana, Slovenia
| | - Thomas Germe
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Martina Hrast
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000, Ljubljana, Slovenia
| | - Clare E M Stevenson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - David M Lawson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Nicolas P Burton
- Inspiralis Ltd., Innovation Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7GJ, UK
| | - Judit Vörös
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Anthony Maxwell
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Nikola Minovski
- Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia.
| | - Marko Anderluh
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000, Ljubljana, Slovenia.
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36
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Usman M, Husain FM, Khan RA, Alharbi W, Alsalme A, Al-Lohedan HA, Tabassum S. Organometallic ruthenium (η 6- p-cymene) complexes interfering with quorum sensing and biofilm formation: an anti-infective approach to combat multidrug-resistance in bacteria. NEW J CHEM 2021; 45:2184-2199. [DOI: 10.1039/d0nj05068g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Organometallic ruthenium complexes of flavonoids as antiquorum sensing agents against pathogens likeChromobacterium violaceumATCC 12472,Pseudomonas aeruginosaPAO1 and methicillin-resistantS. aureus(MRSA).
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Affiliation(s)
- Mohammad Usman
- Department of Chemistry
- Aligarh Muslim University
- Aligarh-202002
- India
| | - Fohad Mabood Husain
- Department of Food Science and Nutrition
- College of Food and Agriculture Sciences
- King Saud University
- Riyadh 11451
- Kingdom of Saudi Arabia
| | - Rais Ahmad Khan
- Department of Chemistry
- College of Sciences
- King Saud University
- Riyadh 11451
- Kingdom of Saudi Arabia
| | - Walaa Alharbi
- Department of Chemistry, Faculty of Science
- King Khalid University
- Abha 62529
- Kingdom of Saudi Arabia
| | - Ali Alsalme
- Department of Chemistry
- College of Sciences
- King Saud University
- Riyadh 11451
- Kingdom of Saudi Arabia
| | - Hamad A. Al-Lohedan
- Surfactant Research Chair
- Department of Chemistry
- College of Sciences
- King Saud University
- Riyadh 11451
| | - Sartaj Tabassum
- Department of Chemistry
- Aligarh Muslim University
- Aligarh-202002
- India
- Surfactant Research Chair
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37
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Meghrazi Ahadi E, Azizian H, Fathi Vavsari V, Aliahmadi A, Shahsavari Z, Bijanzadeh HR, Balalaie S. Synthesis and Decarboxylation of Functionalized 2-Pyridone-3-carboxylic Acids and Evaluation of their Antimicrobial Activity and Molecular Docking. IRANIAN JOURNAL OF PHARMACEUTICAL RESEARCH : IJPR 2021; 20:456-475. [PMID: 34904001 PMCID: PMC8653659 DOI: 10.22037/ijpr.2021.114749.15018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The functionalized 2-pyridone-3-carboxylic acids were synthesized starting from 3-formylchromone. Meanwhile, a decarboxylation reaction of 2-pyridone-3-carboxylic acid was performed by potassium carbonate in toluene. All compounds were evaluated against two Gram-negative bacteria (Escherichia coli (E. coli), Acinetobacter baumannii (A. baumannii)) and two Gram-positive (Staphylococcus aureus (S. aureus)) and fungus (Candida albicans (C. albicans)) using serial broth dilution method. The antimicrobial screening revealed that S. aureus is the highest sensitive microorganism towards the synthesized compounds. Among all analogs, derivatives, 4p and 5c showed excellent activities in comparison with the other compounds against S. aureus. Molecular docking showed that the most active anti S. aureus are compounds 4p and 5c exhibiting primary interaction as with fluoroquinolones by cross-linking over DNA gyrase active site via metal ion bridge and H-bonding interaction with Ser84 and Glu88 from GyrA subunit along with Arg458 and Asp437 located at GyrB subunit. In addition, based on the molecular dynamic simulation as like the standard fluoroquinolones, the mentioned compounds were stabilized for significant amount of simulation time over DNA gyrase which potentiate the importance of the mentioned residues in the DNA gate region of DNA gyrase.
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Affiliation(s)
- Elmira Meghrazi Ahadi
- Peptide Chemistry Research Institute, K. N. Toosi University of Technology, Tehran, Iran.
| | - Homa Azizian
- Department of Medicinal Chemistry, School of Pharmacy, International Campus, Iran University of Medical Sciences, Tehran, Iran.
| | - Vaezeh Fathi Vavsari
- Peptide Chemistry Research Institute, K. N. Toosi University of Technology, Tehran, Iran.
| | - Atousa Aliahmadi
- Medicinal Plant and Drug Research Institute, Shahid Beheshti University, Tehran, Iran.
| | - Zeinab Shahsavari
- Medicinal Plant and Drug Research Institute, Shahid Beheshti University, Tehran, Iran.
| | - Hamid R. Bijanzadeh
- Department of Environmental Sciences, Faculty of Natural Resources and Marine Sciences, Tarbiat Modares University, Tehran, Iran.
| | - Saeed Balalaie
- Peptide Chemistry Research Institute, K. N. Toosi University of Technology, Tehran, Iran. ,Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran.,Corresponding author: E-mail:
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38
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Durcik M, Skok Ž, Ilaš J, Zidar N, Zega A, Szili PÉ, Draskovits G, Révész T, Kikelj D, Nyerges A, Pál C, Mašič LP, Tomašič T. Hybrid Inhibitors of DNA Gyrase A and B: Design, Synthesis and Evaluation. Pharmaceutics 2020; 13:pharmaceutics13010006. [PMID: 33374964 PMCID: PMC7822030 DOI: 10.3390/pharmaceutics13010006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/15/2020] [Accepted: 12/19/2020] [Indexed: 11/16/2022] Open
Abstract
The discovery of multi-targeting ligands of bacterial enzymes is an important strategy to combat rapidly spreading antimicrobial resistance. Bacterial DNA gyrase and topoisomerase IV are validated targets for the development of antibiotics. They can be inhibited at their catalytic sites or at their ATP binding sites. Here we present the design of new hybrids between the catalytic inhibitor ciprofloxacin and ATP-competitive inhibitors that show low nanomolar inhibition of DNA gyrase and antibacterial activity against Gram-negative pathogens. The most potent hybrid 3a has MICs of 0.5 µg/mL against Klebsiella pneumoniae, 4 µg/mL against Enterobacter cloacae, and 2 µg/mL against Escherichia coli. In addition, inhibition of mutant E. coli strains shows that these hybrid inhibitors interact with both subunits of DNA gyrase (GyrA, GyrB), and that binding to both of these sites contributes to their antibacterial activity.
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Affiliation(s)
- Martina Durcik
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia; (M.D.); (Ž.S.); (J.I.); (N.Z.); (A.Z.); (D.K.)
| | - Žiga Skok
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia; (M.D.); (Ž.S.); (J.I.); (N.Z.); (A.Z.); (D.K.)
| | - Janez Ilaš
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia; (M.D.); (Ž.S.); (J.I.); (N.Z.); (A.Z.); (D.K.)
| | - Nace Zidar
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia; (M.D.); (Ž.S.); (J.I.); (N.Z.); (A.Z.); (D.K.)
| | - Anamarija Zega
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia; (M.D.); (Ž.S.); (J.I.); (N.Z.); (A.Z.); (D.K.)
| | - Petra Éva Szili
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, H-6726 Szeged, Hungary; (P.É.S.); (G.D.); (T.R.); (A.N.); (C.P.)
| | - Gábor Draskovits
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, H-6726 Szeged, Hungary; (P.É.S.); (G.D.); (T.R.); (A.N.); (C.P.)
| | - Tamás Révész
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, H-6726 Szeged, Hungary; (P.É.S.); (G.D.); (T.R.); (A.N.); (C.P.)
| | - Danijel Kikelj
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia; (M.D.); (Ž.S.); (J.I.); (N.Z.); (A.Z.); (D.K.)
| | - Akos Nyerges
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, H-6726 Szeged, Hungary; (P.É.S.); (G.D.); (T.R.); (A.N.); (C.P.)
- Department of Genetics, Harvard Medical School, Boston, MA 02215, USA
| | - Csaba Pál
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, H-6726 Szeged, Hungary; (P.É.S.); (G.D.); (T.R.); (A.N.); (C.P.)
| | - Lucija Peterlin Mašič
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia; (M.D.); (Ž.S.); (J.I.); (N.Z.); (A.Z.); (D.K.)
- Correspondence: (L.P.M.); (T.T.); Tel.: +386-1-4769-635 (L.P.M.); +386-1-4769-556 (T.T.)
| | - Tihomir Tomašič
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia; (M.D.); (Ž.S.); (J.I.); (N.Z.); (A.Z.); (D.K.)
- Correspondence: (L.P.M.); (T.T.); Tel.: +386-1-4769-635 (L.P.M.); +386-1-4769-556 (T.T.)
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39
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Kirk R, Ratcliffe A, Noonan G, Uosis-Martin M, Lyth D, Bardell-Cox O, Massam J, Schofield P, Hindley S, Jones DR, Maclean J, Smith A, Savage V, Mohmed S, Charrier C, Salisbury AM, Moyo E, Metzger R, Chalam-Judge N, Cheung J, Stokes NR, Best S, Craighead M, Armer R, Huxley A. Rational design, synthesis and testing of novel tricyclic topoisomerase inhibitors for the treatment of bacterial infections part 1. RSC Med Chem 2020; 11:1366-1378. [PMID: 34095844 DOI: 10.1039/d0md00174k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 08/07/2020] [Indexed: 12/17/2022] Open
Abstract
The alarming reduction in drug effectiveness against bacterial infections has created an urgent need for the development of new antibacterial agents that circumvent bacterial resistance mechanisms. We report here a series of DNA gyrase and topoisomerase IV inhibitors that demonstrate potent activity against a range of Gram-positive and selected Gram-negative organisms, including clinically-relevant and drug-resistant strains. In part 1, we present a detailed structure activity relationship (SAR) analysis that led to the discovery of our previously disclosed compound, REDX05931, which has a minimum inhibitory concentration (MIC) of 0.06 μg mL-1 against fluoroquinolone-resistant Staphylococcus aureus. Although in vitro hERG and CYP inhibition precluded further development, it validates a rational design approach to address this urgent unmet medical need and provides a scaffold for further optimisation, which is presented in part 2.
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Affiliation(s)
- R Kirk
- Redx Anti-Infectives Ltd, Alderley Park, Mereside Macclesfield SK10 4TG UK
| | - A Ratcliffe
- Redx Anti-Infectives Ltd, Alderley Park, Mereside Macclesfield SK10 4TG UK
| | - G Noonan
- Redx Anti-Infectives Ltd, Alderley Park, Mereside Macclesfield SK10 4TG UK
| | - M Uosis-Martin
- Redx Anti-Infectives Ltd, Alderley Park, Mereside Macclesfield SK10 4TG UK
| | - D Lyth
- Redx Anti-Infectives Ltd, Alderley Park, Mereside Macclesfield SK10 4TG UK
| | - O Bardell-Cox
- Redx Anti-Infectives Ltd, Alderley Park, Mereside Macclesfield SK10 4TG UK
| | - J Massam
- Redx Anti-Infectives Ltd, Alderley Park, Mereside Macclesfield SK10 4TG UK
| | - P Schofield
- Redx Anti-Infectives Ltd, Alderley Park, Mereside Macclesfield SK10 4TG UK
| | - S Hindley
- Redx Anti-Infectives Ltd, Alderley Park, Mereside Macclesfield SK10 4TG UK
| | - D R Jones
- Redx Anti-Infectives Ltd, Alderley Park, Mereside Macclesfield SK10 4TG UK
| | - J Maclean
- Redx Anti-Infectives Ltd, Alderley Park, Mereside Macclesfield SK10 4TG UK
| | - A Smith
- Redx Anti-Infectives Ltd, Alderley Park, Mereside Macclesfield SK10 4TG UK
| | - V Savage
- Redx Anti-Infectives Ltd, Alderley Park, Mereside Macclesfield SK10 4TG UK
| | - S Mohmed
- Redx Anti-Infectives Ltd, Alderley Park, Mereside Macclesfield SK10 4TG UK
| | - C Charrier
- Redx Anti-Infectives Ltd, Alderley Park, Mereside Macclesfield SK10 4TG UK
| | - A-M Salisbury
- Redx Anti-Infectives Ltd, Alderley Park, Mereside Macclesfield SK10 4TG UK
| | - E Moyo
- Redx Anti-Infectives Ltd, Alderley Park, Mereside Macclesfield SK10 4TG UK
| | - R Metzger
- Redx Anti-Infectives Ltd, Alderley Park, Mereside Macclesfield SK10 4TG UK
| | - N Chalam-Judge
- Redx Anti-Infectives Ltd, Alderley Park, Mereside Macclesfield SK10 4TG UK
| | - J Cheung
- Redx Anti-Infectives Ltd, Alderley Park, Mereside Macclesfield SK10 4TG UK
| | - N R Stokes
- Redx Anti-Infectives Ltd, Alderley Park, Mereside Macclesfield SK10 4TG UK
| | - S Best
- Redx Anti-Infectives Ltd, Alderley Park, Mereside Macclesfield SK10 4TG UK
| | - M Craighead
- Redx Anti-Infectives Ltd, Alderley Park, Mereside Macclesfield SK10 4TG UK
| | - R Armer
- Redx Anti-Infectives Ltd, Alderley Park, Mereside Macclesfield SK10 4TG UK
| | - A Huxley
- Redx Anti-Infectives Ltd, Alderley Park, Mereside Macclesfield SK10 4TG UK
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40
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Ramachandran B, Srinivasadesikan V, Chou TM, Jeyakanthan J, Lee SL. Atomistic simulation on flavonoids derivatives as potential inhibitors of bacterial gyrase of Staphylococcus aureus. J Biomol Struct Dyn 2020; 40:4314-4327. [PMID: 33308046 DOI: 10.1080/07391102.2020.1856184] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The bacterial DNA gyrase is an attractive target to identify the novel antibacterial agents. The flavonoid derivatives possess various biological activities such as antimicrobial, anti-inflammatory and anticancer activities. The aim of present study is to identify the potential molecule from flavonoid derivatives against Staphylococcus aureus using atomistic simulation namely Molecular Docking, Quantum Chemical and Molecular Dynamics. The molecules Cpd58, Cpd65 and Cpd70 are identified as potential molecules through molecular docking approaches by exploring through the N - H…O hydrogen bonding interactions with Asn31 and Glu35 of Gyrase B. To confirm the intramolecular charge transfer in the flavonoid derivatives, Frontier Molecular Orbital (FMO) calculation was performed at M06/6-31g(d) level in gas phase. The lowest HOMO-LUMO gap was calculated for Cpd58, Cpd65 and Cpd70 among the selected compounds used in this study. Molecular dynamics simulation were carried out for Cpd58 and Cpd70 for a time period of 50 ns and found to be stable throughout the analysis. Therefore, the identified compounds are found to be a potent inhibitor for GyrB of S. aureus that can be validated by experimental studies. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Balajee Ramachandran
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Venkatesan Srinivasadesikan
- Division of Chemistry, Department of Sciences & Humanities, Vignan's Foundation for Science, Technology and Research, Vadlamudi, Andhra Pradesh, India
| | - Tsz-Min Chou
- Department of Chemistry and Biochemistry, National Chung Cheng University, Chia-Yi, Taiwan
| | - Jeyaraman Jeyakanthan
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Shyi-Long Lee
- Department of Chemistry and Biochemistry, National Chung Cheng University, Chia-Yi, Taiwan
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41
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Srinivas S, Neeraja P, Banothu V, Kumar Dubey P, Mukkanti K, Pal S. Synthesis, Biological Evaluation and
In silico
Studies of Compounds Based on Tryptophan‐Naproxen‐Triazole Hybrids. ChemistrySelect 2020. [DOI: 10.1002/slct.202003786] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Suryapeta Srinivas
- Alembic Pharmaceuticals Ltd, 450 MN Park, Genome Valley, Turkapally Village, Shameerpet, Medchal Malkajgiri 500101 India
| | - Papigani Neeraja
- Department of Chemistry DVR College of Engineering & Technology, Kashipur (village), Sangareddy District Telangana 502285 India
| | | | | | - Khagga Mukkanti
- Center for Chemical Sciences and Technology, IST, JNTUH Hyderabad 500085 India
| | - Sarbani Pal
- Department of Chemistry MNR Degree & PG College, Kukatpally Hyderabad 500085 India
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42
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Basarab GS, Doig P, Eyermann CJ, Galullo V, Kern G, Kimzey A, Kutschke A, Morningstar M, Schuck V, Vishwanathan K, Zhou F, Gowravaram M, Hauck S. Antibacterial Spiropyrimidinetriones with N-Linked Azole Substituents on a Benzisoxazole Scaffold Targeting DNA Gyrase. J Med Chem 2020; 63:11882-11901. [DOI: 10.1021/acs.jmedchem.0c01100] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Gregory S. Basarab
- Department of Chemistry, Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Peter Doig
- Department of Biosciences, Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Charles J. Eyermann
- Department of Chemistry, Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Vincent Galullo
- Department of Chemistry, Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Gunther Kern
- Department of Biosciences, Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Amy Kimzey
- Discovery Safety, Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Amy Kutschke
- Department of Chemistry, Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Marshall Morningstar
- Department of Chemistry, Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Virna Schuck
- Drug Safety and Metabolism, Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Karthick Vishwanathan
- Drug Safety and Metabolism, Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Fei Zhou
- Department of Chemistry, Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Madhusudhan Gowravaram
- Department of Chemistry, Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Sheila Hauck
- Department of Chemistry, Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
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43
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Sharma P, Kumar M, Dahiya S, Sood S, Das BK, Kaur P, Kapil A. Structure based drug discovery and in vitro activity testing for DNA gyrase inhibitors of Salmonella enterica serovar Typhi. Bioorg Chem 2020; 104:104244. [PMID: 32966903 DOI: 10.1016/j.bioorg.2020.104244] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 07/23/2020] [Accepted: 08/25/2020] [Indexed: 11/24/2022]
Abstract
The emerged resistance in Typhoidal Salmonella has limited the treatment options for typhoid fever. In this scenario, there is a need to find alternate treatment modalities against this pathogen. Amongst the therapeutic agents currently being used to treat enteric fever, quinolones have enjoyed considerable success since past three decades. These drugs act upon DNA gyrase and the acquired resistance is due to mutations at Ser83 and Asp87 of gyrase A subunit. In the present study DNA gyrase enzyme was targeted to seek out potential new inhibitors which are not affected by these mutations. Molecular modelling and docking studies were performed in Schrödinger's molecular modelling software. Homology model of DNA gyrase-DNA complex was built using templates 1AB4 and 3LTN. Molecular dynamic simulations were performed in SPC solvent for 100 ns. Total 17,900,742 drug like molecules were downloaded from ZINC library of chemical compounds. The Glide XP score of the compounds ranged from -5.285 to -13.692. All the ligands bound at the four base pair staggered nick in the DNA binding groove of DNA gyrase enzyme with their aromatic rings intercalating between the bases of two successive nucleotides stabilized by π - π stacking interactions. The binding pocket of DNA gyrase B comprising conserved residues Lys 447, Gly 448, Lys 449, Ile 450, Leu 451, Gln 465 and Val 467 interacts with the ligand molecules through van der Waals interactions. The MIC (minimum inhibitory concentration), MBC (minimum bactericidal concentration) and IC50 of the tested compounds ranged from 500 to 125 mg/L, 750 to 500 mg/L and 100 to 12.5 mg/L, respectively. The selected hits bind to quinolone binding pocket, but their mode of binding and conformation is different to fluoroquinolones, and hence, their binding is not affected by mutations at Ser83 or Asp87 positions. These lead compounds can be further explored as a scaffold to design inhibitors against DNA gyrase to bypass quinolone resistance.
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Affiliation(s)
- Priyanka Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Manoj Kumar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Sushila Dahiya
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Seema Sood
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Bimal Kumar Das
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Punit Kaur
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.
| | - Arti Kapil
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India.
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44
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Long S, Resende DISP, Palmeira A, Kijjoa A, Silva AMS, Tiritan ME, Pereira-Terra P, Freitas-Silva J, Barreiro S, Silva R, Remião F, Pinto E, Martins da Costa P, Sousa E, Pinto MMM. New marine-derived indolymethyl pyrazinoquinazoline alkaloids with promising antimicrobial profiles. RSC Adv 2020; 10:31187-31204. [PMID: 35520644 PMCID: PMC9056383 DOI: 10.1039/d0ra05319h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 08/11/2020] [Indexed: 01/03/2023] Open
Abstract
Due to the emergence of multidrug-resistant pathogenic microorganisms, the search for novel antimicrobials is urgent. Inspired by marine alkaloids, a series of indolomethyl pyrazino [1,2-b]quinazoline-3,6-diones was prepared using a one-pot microwave-assisted multicomponent polycondensation of amino acids. The compounds were evaluated for their antimicrobial activity against a panel of nine bacterial strains and five fungal strains. Compounds 26 and 27 were the most effective against Staphylococcus aureus ATCC 29213 reference strain with MIC values of 4 μg mL−1, and a methicillin-resistant Staphylococcus aureus (MRSA) isolate with MIC values of 8 μg mL−1. It was possible to infer that enantiomer (−)-26 was responsible for the antibacterial activity (MIC 4 μg mL−1) while (+)-26 had no activity. Furthermore, compound (−)-26 was able to impair S. aureus biofilm production and no significant cytotoxicity towards differentiated and non-differentiated SH-SY5Y cells was observed. Compounds 26, 28, and 29 showed a weak antifungal activity against Trichophyton rubrum clinical isolate with MIC 128 μg mL−1 and presented a synergistic effect with fluconazole. Indolomethyl pyrazino [1,2-b]quinazoline-3,6-diones were prepared using a one-pot multicomponent polycondensation of amino acids and were evaluated for their antimicrobial activity against a panel of nine bacterial strains and five fungal strains.![]()
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Affiliation(s)
- Solida Long
- LQOF - Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto Rua de Jorge Viterbo Ferreira, 228 4050-313 Porto Portugal
| | - Diana I S P Resende
- LQOF - Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto Rua de Jorge Viterbo Ferreira, 228 4050-313 Porto Portugal .,CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Terminal de Cruzeiros do Porto de Leixões Av. General Norton de Matos S/N 4450-208 Matosinhos Portugal
| | - Andreia Palmeira
- LQOF - Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto Rua de Jorge Viterbo Ferreira, 228 4050-313 Porto Portugal .,CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Terminal de Cruzeiros do Porto de Leixões Av. General Norton de Matos S/N 4450-208 Matosinhos Portugal
| | - Anake Kijjoa
- CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Terminal de Cruzeiros do Porto de Leixões Av. General Norton de Matos S/N 4450-208 Matosinhos Portugal.,ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto Rua de Jorge Viterbo Ferreira, 228 4050-313 Porto Portugal
| | - Artur M S Silva
- QOPNA - Química Orgânica, Produtos Naturais e Agroalimentares, Departamento de Química, Universidade de Aveiro 3810-193 Aveiro Portugal
| | - Maria Elizabeth Tiritan
- LQOF - Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto Rua de Jorge Viterbo Ferreira, 228 4050-313 Porto Portugal .,CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Terminal de Cruzeiros do Porto de Leixões Av. General Norton de Matos S/N 4450-208 Matosinhos Portugal.,CESPU, Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde (IINFACTS) Rua Central de Gandra, 1317 4585-116 Gandra PRD Portugal
| | - Patrícia Pereira-Terra
- CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Terminal de Cruzeiros do Porto de Leixões Av. General Norton de Matos S/N 4450-208 Matosinhos Portugal.,ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto Rua de Jorge Viterbo Ferreira, 228 4050-313 Porto Portugal
| | - Joana Freitas-Silva
- CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Terminal de Cruzeiros do Porto de Leixões Av. General Norton de Matos S/N 4450-208 Matosinhos Portugal.,ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto Rua de Jorge Viterbo Ferreira, 228 4050-313 Porto Portugal
| | - Sandra Barreiro
- UCIBIO-REQUIMTE, Laboratório de Toxicologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto Rua de Jorge Viterbo Ferreira, 228 4050-313 Porto Portugal
| | - Renata Silva
- UCIBIO-REQUIMTE, Laboratório de Toxicologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto Rua de Jorge Viterbo Ferreira, 228 4050-313 Porto Portugal
| | - Fernando Remião
- UCIBIO-REQUIMTE, Laboratório de Toxicologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto Rua de Jorge Viterbo Ferreira, 228 4050-313 Porto Portugal
| | - Eugénia Pinto
- CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Terminal de Cruzeiros do Porto de Leixões Av. General Norton de Matos S/N 4450-208 Matosinhos Portugal.,Laboratório de Microbiologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto Rua de Jorge Viterbo Ferreira, 228 4050-313 Porto Portugal
| | - Paulo Martins da Costa
- CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Terminal de Cruzeiros do Porto de Leixões Av. General Norton de Matos S/N 4450-208 Matosinhos Portugal.,ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto Rua de Jorge Viterbo Ferreira, 228 4050-313 Porto Portugal
| | - Emília Sousa
- LQOF - Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto Rua de Jorge Viterbo Ferreira, 228 4050-313 Porto Portugal .,CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Terminal de Cruzeiros do Porto de Leixões Av. General Norton de Matos S/N 4450-208 Matosinhos Portugal
| | - Madalena M M Pinto
- LQOF - Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto Rua de Jorge Viterbo Ferreira, 228 4050-313 Porto Portugal .,CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Terminal de Cruzeiros do Porto de Leixões Av. General Norton de Matos S/N 4450-208 Matosinhos Portugal
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45
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Zhang B, Zhang J, Kang Z, Liang L, Liu Y, Wang Q. On interactions of P-glycoprotein with various anti-tumor drugs by binding free energy calculations. J Biomol Struct Dyn 2020; 39:5335-5347. [PMID: 32608321 DOI: 10.1080/07391102.2020.1786456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
P-glycoprotein (P-gp, MDR1), one of ATP-binding cassette transporters, may confer tumor cells cross-resistance to chemotherapeutics. A large amount of P-gp inhibitors were designed to inhibit the multidrug resistance (MDR) feature of P-gp. However, no sufficient researches were reported to explore the correlation between binding capacity and drug property by experiment. Without particular drug property found to inhibit the MDR feature of P-gp, the orientation of drug design is indefinite. In this work, 10 representative cancer drugs with various properties are used to bind with P-gp by molecular dynamics simulation. Binding free energy between P-gp and 10 drugs ranges -139 to -253 kJ/mol. It reveals that the promiscuity nature of P-gp is in light of the similar binding free energy in separate P-gp-ligand binding systems. The binding effect of P-gp and drugs correlates well with the size of drugs and has no apparent correlation with the polarity of each drug. The key reason is that van der Waal's interaction occupies most of the total binding free energy, and it is led by the number of atoms in the drugs. Two transmembrane segments (TM6 and TM12) and three types of amino acids (PHE, MET, and GLN) are vital in binding drugs with van der Waal's energy, which evident the influence between binding stability and size of drugs. This work provides the cause and theoretical basis for the promiscuity nature of P-gp.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Bo Zhang
- Department of Chemistry and Soft Matter Research Center, Zhejiang University, Hangzhou, People's Republic of China
| | - Junqiao Zhang
- Department of Chemistry and Soft Matter Research Center, Zhejiang University, Hangzhou, People's Republic of China
| | - Zhengzhong Kang
- Department of Chemistry and Soft Matter Research Center, Zhejiang University, Hangzhou, People's Republic of China
| | - Lijun Liang
- Department of Chemistry and Soft Matter Research Center, Zhejiang University, Hangzhou, People's Republic of China.,College of Life Information Science and Instrument Engineering, Hangzhou Dianzi University, Hangzhou, People's Republic of China
| | - Yingchun Liu
- Department of Chemistry and Soft Matter Research Center, Zhejiang University, Hangzhou, People's Republic of China
| | - Qi Wang
- Department of Chemistry and Soft Matter Research Center, Zhejiang University, Hangzhou, People's Republic of China
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46
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Ghosh S, Pal S, Praveena K, Mareddy J. 2-Chloro-7-methyl-3-((4-((p-tolyloxy)methyl)-1H-1,2,3-triazol-1-yl)methyl) quinoline: Crystal structure, hydrogen bonding and anti-bacterial activity. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128137] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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47
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Wang D, Ning Q, Dong J, Brooks BW, You J. Predicting mixture toxicity and antibiotic resistance of fluoroquinolones and their photodegradation products in Escherichia coli. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 262:114275. [PMID: 32142973 DOI: 10.1016/j.envpol.2020.114275] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 02/24/2020] [Accepted: 02/24/2020] [Indexed: 06/10/2023]
Abstract
Antibiotics in the environment usually co-exist with their transformation products with retained toxicity, raising concerns about environmental risks of their combined exposure. Herein, we reported a novel predictive approach for evaluating the individual and combined toxicity for photodegradation products of fluoroquinolone antibiotics (FQs). Quantitative structure-activity relationship (QSAR) models with promising predictive performance were constructed and validated using experimental data obtained with 13 FQs and 78 mixtures towards E. coli. A structural descriptor reflecting the interaction among FQ molecules and the target protein was employed in the QSAR models, which was obtained through molecular docking and thus provided a rational mechanistic explanation for these models. The predicted results indicated that the degradation products displayed varying degrees of changes compared to the parent FQs, while the combined toxicity of FQs and their degradation products was mostly additive. Furthermore, following UV irradiation the degradation products displayed elevated capacity of inducing resistance mutations in E. coli, though their overall toxicity was reduced. This result highlights the implications of antibiotic degradation products on resistance development in bacteria and stresses the importance of considering such impacts during environmental risk assessments of antibiotics.
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Affiliation(s)
- Dali Wang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 511443, China
| | - Qing Ning
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 511443, China
| | - Jiayu Dong
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 511443, China
| | - Bryan W Brooks
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 511443, China; Department of Environmental Science, Institute of Biomedical Studies, Baylor University, Waco, TX, USA
| | - Jing You
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 511443, China.
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48
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Suryapeta S, Papigani N, Banothu V, Dubey PK, Mukkanti K, Pal S. Synthesis, biological evaluation, and docking study of a series of 1,4‐disubstituted 1,2,3‐triazole derivatives with an indole‐triazole‐peptide conjugate. J Heterocycl Chem 2020. [DOI: 10.1002/jhet.4020] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Srinivas Suryapeta
- Research and Development DepartmentAlembic Pharmaceuticals Ltd, Genome Valley, Shameerpet Hyderabad India
| | - Neeraja Papigani
- Department of ChemistryDVR College of Engineering & Technology Kashipur Village, Sangareddy District, Hyderabad India
| | | | | | - Khagga Mukkanti
- Center for Chemical Sciences and TechnologyIST JNTUH Hyderabad India
| | - Sarbani Pal
- Department of ChemistryMNR Degree & PG College Kukatpally, Hyderabad India
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49
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Bradford PA, Miller AA, O’Donnell J, Mueller JP. Zoliflodacin: An Oral Spiropyrimidinetrione Antibiotic for the Treatment of Neisseria gonorrheae, Including Multi-Drug-Resistant Isolates. ACS Infect Dis 2020; 6:1332-1345. [PMID: 32329999 DOI: 10.1021/acsinfecdis.0c00021] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The Centers for Disease Control and the World Health Organization have issued a list of priority pathogens for which there are dwindling therapeutic options, including antibiotic-resistant Neisseria gonorrheae, for which novel oral agents are urgently needed. Zoliflodacin, the first in a new class of antibacterial agents called the spiropyrimidinetriones, is being developed for the treatment of gonorrhea. It has a unique mode of inhibition against bacterial type II topoisomerases with binding sites in bacterial gyrase that are distinct from those of the fluoroquinolones. Zoliflodacin is bactericidal, with a low frequency of resistance and potent antibacterial activity against N. gonorrheae, including multi-drug-resistant strains (MICs ranging from ≤0.002 to 0.25 μg/mL). Although being developed for the treatment of gonorrhea, zoliflodacin also has activity against Gram-positive, fastidious Gram-negative, and atypical pathogens. A hollow-fiber infection model using S. aureus showed that that pharmacokinetic/pharmacodynamic index of fAUC/MIC best correlated with efficacy in in vivo neutropenic thigh models in mice. This data and unbound exposure magnitudes derived from the thigh models were subsequently utilized in a surrogate pathogen approach to establish dose ranges for clinical development with N. gonorrheae. In preclinical studies, a wide safety margin supported progression to phase 1 studies in healthy volunteers, which showed linear pharmacokinetics, good oral bioavailability, and no significant safety findings. In a phase 2 study, zoliflodacin was effective in treating gonococcal urogenital and rectal infections. In partnership with the Global Antibiotic Research Development Program (GARDP), zoliflodacin is currently being studied in a global phase 3 clinical trial. Zoliflodacin represents a promising new oral therapy for drug-resistant infections caused by N. gonorrheae.
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Affiliation(s)
- Patricia A. Bradford
- Antimicrobial Development Specialists, LLC, Nyack, New York 10960, United States
| | - Alita A. Miller
- Entasis Therapeutics, Waltham, Massachusetts 02451, United States
| | - John O’Donnell
- Entasis Therapeutics, Waltham, Massachusetts 02451, United States
| | - John P. Mueller
- Entasis Therapeutics, Waltham, Massachusetts 02451, United States
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50
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Srinivas S, Neeraja P, Naveen K, Banothu V, Dubey PK, Mukkanti K, Pal S. Synthesis, Chemotherapeutic Screening and Docking Studies of NSAID Inserted Peptide‐Triazole Hybrid Molecules. ChemistrySelect 2020. [DOI: 10.1002/slct.202000492] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Suryapeta Srinivas
- Alembic pharmaceuticals ltd 450 MN Park, Genome Valley, Turkapally Village, Shameerpet Medchal, Malkajgiri 500101 India
| | - Papigani Neeraja
- Department of ChemistryDVR College of Engineering & Technology Kashipur (village), Sangareddy District, Telangana 502285 India
| | - Kuntala Naveen
- Centre for Chemical Sciences and Technology IST, JNTUH Hyderabad 500085
| | | | | | - Khagga Mukkanti
- Centre for Chemical Sciences and Technology IST, JNTUH Hyderabad 500085
| | - Sarbani Pal
- Department of ChemistryMNR Degree & PG College, Kukatpally Hyderabad 500085 India
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