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Jin X, Ding N, Guo HY, Hu Q. Macrocyclic-based strategy in drug design: From lab to the clinic. Eur J Med Chem 2024; 277:116733. [PMID: 39098132 DOI: 10.1016/j.ejmech.2024.116733] [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: 07/05/2024] [Revised: 07/24/2024] [Accepted: 07/25/2024] [Indexed: 08/06/2024]
Abstract
Macrocyclic compounds have emerged as potent tools in the field of drug design, offering unique advantages for enhancing molecular recognition, improving pharmacokinetic properties, and expanding the chemical space accessible to medicinal chemists. This review delves into the evolutionary trajectory of macrocyclic-based strategies, tracing their journey from laboratory innovations to clinical applications. Beginning with an exploration of the defining structural features of macrocycles and their impact on drug-like characteristics, this discussion progresses to highlight key design principles that have facilitated the development of diverse macrocyclic drug candidates. Through a series of illustrative representative case studies from approved macrocyclic drugs and candidates spanning various therapeutic areas, particular emphasis is placed on their efficacy in targeting challenging protein-protein interactions, enzymes, and receptors. Additionally, this review thoroughly examines how macrocycles effectively address critical issues such as metabolic stability, oral bioavailability and selectivity. Valuable insights into optimization strategies employed during both approved and clinical phases underscore successful translation of promising leads into efficacious therapies while providing valuable perspectives on harnessing the full potential of macrocycles in drug discovery and development endeavors.
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Affiliation(s)
- Xin Jin
- Department of Obstetrics and Gynaecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Ning Ding
- Department of Obstetrics and Gynaecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Hong-Yu Guo
- Department of Obstetrics and Gynaecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Qing Hu
- Department of Obstetrics and Gynaecology, Shengjing Hospital of China Medical University, Shenyang, China.
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2
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Dhamodiran M, Chinnaperumal K, J D, Venkatesan G, A Alshiekheid M, Suseem SR. Isolation, structural elucidation of bioactive compounds and their wound-healing ability, antibacterial and In silico molecular docking applications. ENVIRONMENTAL RESEARCH 2024; 252:119023. [PMID: 38685295 DOI: 10.1016/j.envres.2024.119023] [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: 03/13/2024] [Revised: 04/13/2024] [Accepted: 04/24/2024] [Indexed: 05/02/2024]
Abstract
Andrographis echioides has been extensively utilized in traditional Indian folk medicines for several skin disorders and other biological actions such as diuretic, antimicrobial, anthelmintic, anti-ulcer, and hepatoprotective properties. Different crude extracts were extracted from A. echioides leaves using various solvents such as methanol and water. The prepared crude extracts were utilized to formulate different herbal ointments. Further, the prepared ointments were examined against wounds and bacterial pathogens. The wound healing ability of the prepared formulations was observed for F1, F2, and F3, to be (89.84%, 95.11%, and 95.75%) respectively. Moreover, wound healing capabilities were compared with standard Betadine which exhibits 98.12%, those results indicating that the prepared herbal ointment also has a promising wound healing ability. The F2 formulations outperform the other two formulations (F1 and F2) in terms of their antibacterial ability to combat Staphylococcus aureus, Klebsiella pneumoniae Bacillus subtilis, and Escherichia coli. Moreover, there are two compounds were successfully isolated and identified from methanolic extract, which are 2-(3,4-dihydroxyphenyl)-3,4-dihydro-2H-chromene-3,5,7-triol and 3-(3,4-Dihydroxyphenyl)-2-propenoic acid. Meanwhile, the molecular docking investigation exposed high binding energy Staphylococcus aureus TyrRS (-8.9 kcal/mol), Isoleucyl-tRNA synthetase (-7.5 kcal/mol), Penicillin-binding protein 2a (-8.0 kcal/mol), S. aureus DNA Gyrase (-7.2 kcal/mol), GSK-3beta (Glycogen synthase kinase-3 beta) (-8.3 kcal/mol) and TGF - Beta Receptor Type 1 Kinase Domain (-8.7 kcal/mol) indicating high degree of interaction between Compound-1 2-(3,4-dihydroxyphenyl)-3,4-dihydro-2H-chromene-3,5,7-triol (DHPDHC) and 7 clinically important skin infective pathogen Staphylococcus aureus proteins at the active sites. Additionally, the standard drug Povidone iodine, Sulphothiazole, and Nitrofurazone (<-8 kcal/mol), displayed low binding affinity on targeted proteins. A molecular dynamics simulation research with high free energy showed stable interaction between the ligand and protein. Which endorses the capabilities of A. echioides derived compounds as a potential wound healer and antibacterial therapeutic candidate for drug development in the future.
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Affiliation(s)
- Mathivanan Dhamodiran
- Department of Chemistry, School of Advanced Sciences, VIT University, Vellore, 632014, Tamil Nadu, India
| | - Kamaraj Chinnaperumal
- Interdisciplinary Institute of Indian System of Medicine (IIISM), Directorate of Research, SRM Institute of Science and Technology (SRMIST), Chengalpattu District, Kattankulathur, 603203, Tamil Nadu, India.
| | - Dhanish J
- Department of Chemistry, School of Advanced Sciences, VIT University, Vellore, 632014, Tamil Nadu, India
| | - Geetha Venkatesan
- Department of Biomaterials, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, 600 077, India
| | - Maha A Alshiekheid
- Department of Botany and Microbiology, College of Science, King Saud University, PO Box -2455, Riyadh - 11451, Saudi Arabia
| | - S R Suseem
- Department of Chemistry, School of Advanced Sciences, VIT University, Vellore, 632014, Tamil Nadu, India.
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Fayed EA, Al-Arab EME, Saleh AS, Bayoumi AH, Ammar YA. Design, synthesis, in silico studies, in vivo and in vitro assessment of pyridones and thiazolidinones as anti-inflammatory, antipyretic and ulcerogenic hits. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132839] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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4
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EVREN AE, DAWBAA S, NUHA D, YAVUZ ŞA, GÜL ÜD, YURTTAŞ L. Design and synthesis of new 4-methylthiazole derivatives: In vitro and in silico studies of antimicrobial activity. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130692] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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5
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Singh VP, Dowarah J, Marak BN, Sran BS, Tewari AK. Study of the structure-bioactivity of fleximers: synthesis, crystal structure, Hirshfeld surface analysis, and anti-inflammatory assays. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130513] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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6
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Shi Y, Jiang K, Zheng R, Fu J, Yan L, Gu Q, Zhang Y, Lin F. Design, Microwave‐Assisted Synthesis and in Vitro Antibacterial and Antifungal Activity of 2,5‐Disubstituted Benzimidazole. Chem Biodivers 2019; 16:e1800510. [DOI: 10.1002/cbdv.201800510] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 11/16/2018] [Indexed: 12/19/2022]
Affiliation(s)
- Yanpeng Shi
- College of ChemistryJilin University Changchun 130012 P. R. China
| | - Kai Jiang
- School of life SciencesJilin University Changchun 130012 P. R. China
| | - Ran Zheng
- College of ChemistryJilin University Changchun 130012 P. R. China
| | - Jiaxu Fu
- College of ChemistryJilin University Changchun 130012 P. R. China
| | - Liuqing Yan
- College of ChemistryJilin University Changchun 130012 P. R. China
| | - Qiang Gu
- College of ChemistryJilin University Changchun 130012 P. R. China
| | - Yumin Zhang
- College of ChemistryJilin University Changchun 130012 P. R. China
| | - Feng Lin
- School of life SciencesJilin University Changchun 130012 P. R. China
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Hosseini H, Bayat M. Cyanoacetohydrazides in Synthesis of Heterocyclic Compounds. Top Curr Chem (Cham) 2018; 376:40. [DOI: 10.1007/s41061-018-0218-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/03/2018] [Indexed: 11/24/2022]
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8
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Ahmed M, Kelley SO. Enhancing the Potency of Nalidixic Acid toward a Bacterial DNA Gyrase with Conjugated Peptides. ACS Chem Biol 2017; 12:2563-2569. [PMID: 28825963 DOI: 10.1021/acschembio.7b00540] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Quinolones and fluoroquinolones are widely used antibacterial agents. Nalidixic acid (NA) is a first-generation quinolone-based antibiotic that has a narrow spectrum and poor pharmacokinetics. Here, we describe a family of peptide-nalidixic acid conjugates featuring different levels of hydrophobicity and molecular charge prepared by solid-phase peptide synthesis that exhibit intriguing improvements in potency. In comparison to NA, which has a low level of potency in S. aureus, the NA peptide conjugates with optimized hydrophobicities and molecular charges exhibited significantly improved antibacterial activity. The most potent NA conjugate-featuring a peptide containing cyclohexylalanine and arginine-exhibited efficient bacterial uptake and, notably, specific inhibition of S. aureus DNA gyrase. A systematic study of peptide-NA conjugates revealed that a fine balance of cationic charge and hydrophobicity in an appendage anchored to the core of the drug is required to overcome the intrinsic resistance of S. aureus DNA gyrase toward this quinolone-based drug.
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Affiliation(s)
- Marya Ahmed
- Department of Pharmaceutical
Sciences, Leslie Dan Faculty of Pharmacy, and Department of Biochemistry,
Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Shana O. Kelley
- Department of Pharmaceutical
Sciences, Leslie Dan Faculty of Pharmacy, and Department of Biochemistry,
Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
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Alneyadi SS, Abdulqader AA, Salem AA, Abdou IM. Synthesis and antimicrobial activity of 4-trifluoromethylpyridine nucleosides. HETEROCYCL COMMUN 2017. [DOI: 10.1515/hc-2017-0019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract4-Trifluoromethylpyridine derivatives 4–8 represent good candidates for the discovery of new antibacterial agents. Fluorinated pyridine nucleosides 4–7 and non-nucleoside analogues 8a,b were synthesized and evaluated for their antibacterial activities against Staphylococcus aureus, Bacillus infantis, Escherichia coli and Stenotrophomonas maltophilia. The minimum inhibitory concentrations (MICs) of the new nucleosides 4–7 range from 1.3 to 4.9 μg/mL and MICs of fluoroaryl derivatives 8a,b are in the range of 1.8–5.5 μg/mL. Activity of amoxicillin, the reference drug, is 1.0–2.0 μg/mL under similar conditions.
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Affiliation(s)
| | | | - Alaa A. Salem
- Department of Chemistry, College of Science, UAEUAl-Ain 15551, UAE
| | - Ibrahim M. Abdou
- Department of Chemistry, College of Science, UAEUAl-Ain 15551, UAE,
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Ma Z, Lynch AS. Development of a Dual-Acting Antibacterial Agent (TNP-2092) for the Treatment of Persistent Bacterial Infections. J Med Chem 2016; 59:6645-57. [PMID: 27336583 DOI: 10.1021/acs.jmedchem.6b00485] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The clinical management of prosthetic joint infections and other persistent bacterial infections represents a major unmet medical need. The rifamycins are one of the most potent antibiotic classes against persistent bacterial infections, but bacteria can develop resistance to rifamycins rapidly and the clinical utility of the rifamycin class is typically limited to antibiotic combinations to minimize the development of resistance. To develop a better therapy against persistent bacterial infections, a series of rifamycin based bifunctional molecules were designed, synthesized, and evaluated with the goal to identify a dual-acting drug that maintains the potent activity of rifamycins against persistent pathogens and at the same time minimize the development of rifamycin resistance. TNP-2092 was identified as a drug candidate and is currently in an early stage of clinical development for the treatment of prosthetic joint infections.
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Affiliation(s)
- Zhenkun Ma
- TenNor Therapeutics Ltd. , 218 Xinghu Street, Suzhou Industrial Park, Suzhou 215123, China
| | - Anthony Simon Lynch
- Janssen Research & Development LLC. , 1400 McKean Road, Spring House, Pennsylvania 18940, United States
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11
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Song D, Ma S. Recent Development of Benzimidazole-Containing Antibacterial Agents. ChemMedChem 2016; 11:646-59. [PMID: 26970352 DOI: 10.1002/cmdc.201600041] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Revised: 02/20/2016] [Indexed: 11/11/2022]
Abstract
Clinically significant antibiotic resistance is one of the greatest challenges of the twenty-first century. However, new antibacterial agents are currently being developed at a much slower pace than our growing need for such drugs. Given their diverse biological activities and clinical applications, many bioactive heterocyclic compounds containing a benzimidazole nucleus have been the focus of interest for many researchers. The benzimidazole nucleus is a structural isostere of naturally occurring nucleotides. This advantage allows benzimidazoles to readily interact with the various biopolymers found in living systems. In view of this situation, much attention has been given to the exploration of benzimidazole-based antibacterial agents, leading to the discovery of many new chemical entities with intriguing profiles. In this minireview we summarize novel benzimidazole derivatives active against various bacterial strains. In particular, we outline the relationship between the structures of variously modified benzimidazoles and their antibacterial activity.
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Affiliation(s)
- Di Song
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Jinan, 250012, P.R. China
| | - Shutao Ma
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Jinan, 250012, P.R. China.
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12
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Desai N, Shihory N, Kotadiya G, Desai P. Synthesis, antibacterial and antitubercular activities of benzimidazole bearing substituted 2-pyridone motifs. Eur J Med Chem 2014; 82:480-9. [DOI: 10.1016/j.ejmech.2014.06.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 04/05/2014] [Accepted: 06/03/2014] [Indexed: 10/25/2022]
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13
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Desai N, Shihory N, Kotadiya G. Facile synthesis of benzimidazole bearing 2-pyridone derivatives as potential antimicrobial agents. CHINESE CHEM LETT 2014. [DOI: 10.1016/j.cclet.2013.11.026] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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14
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Khokhani K, Khatri T, Patel P. One Pot Synthesis of Bioactive Novel Cyanopyridones. JOURNAL OF THE KOREAN CHEMICAL SOCIETY-DAEHAN HWAHAK HOE JEE 2013. [DOI: 10.5012/jkcs.2013.57.4.476] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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15
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Desai NC, Rajpara KM, Joshi VV. Synthesis of pyrazole encompassing 2-pyridone derivatives as antibacterial agents. Bioorg Med Chem Lett 2013; 23:2714-7. [DOI: 10.1016/j.bmcl.2013.02.077] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Revised: 02/06/2013] [Accepted: 02/15/2013] [Indexed: 11/28/2022]
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16
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Alt S, Mitchenall LA, Maxwell A, Heide L. Inhibition of DNA gyrase and DNA topoisomerase IV of Staphylococcus aureus and Escherichia coli by aminocoumarin antibiotics. J Antimicrob Chemother 2011; 66:2061-9. [DOI: 10.1093/jac/dkr247] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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17
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18
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Heravi MM, Tahershamsi L, Oskooie HA, Baghernejad B. 1,4-Diaza-bicyclo[2,2,2]octane as a Novel and Efficient Catalyst for the Synthesis of 3,4,6-Trisubstituted 2-Pyridone Derivatives. CHINESE J CHEM 2010. [DOI: 10.1002/cjoc.201090130] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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19
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Aiello D, Barnes MH, Biswas EE, Biswas SB, Gu S, Williams JD, Bowlin TL, Moir DT. Discovery, characterization and comparison of inhibitors of Bacillus anthracis and Staphylococcus aureus replicative DNA helicases. Bioorg Med Chem 2009; 17:4466-76. [PMID: 19477652 DOI: 10.1016/j.bmc.2009.05.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2008] [Revised: 05/01/2009] [Accepted: 05/07/2009] [Indexed: 12/19/2022]
Abstract
Antibacterial compounds with new mechanisms of action are needed for effective therapy against drug-resistant pathogens in the clinic and in biodefense. Screens for inhibitors of the essential replicative helicases of Bacillus anthracis and Staphylococcus aureus yielded 18 confirmed hits (IC(50)25 microM). Several (5 of 18) of the inhibitors were also shown to inhibit DNA replication in permeabilized polA-deficient B. anthracis cells. One of the most potent inhibitors also displayed antibacterial activity (MIC approximately 5 microg/ml against a range of Gram-positive species including bacilli and staphylococci) together with good selectivity for bacterial versus mammalian cells (CC(50)/MIC>16) suitable for further optimization. This compound shares the bicyclic ring of the clinically proven aminocoumarin scaffold, but is not a gyrase inhibitor. It exhibits a mixed mode of helicase inhibition including a component of competitive inhibition with the DNA substrate (K(i)=8 microM) and is rapidly bactericidal at 4 x MIC.
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20
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Robertson GT, Bonventre EJ, Doyle TB, Du Q, Duncan L, Morris TW, Roche ED, Yan D, Lynch AS. In vitro evaluation of CBR-2092, a novel rifamycin-quinolone hybrid antibiotic: studies of the mode of action in Staphylococcus aureus. Antimicrob Agents Chemother 2008; 52:2313-23. [PMID: 18443108 PMCID: PMC2443886 DOI: 10.1128/aac.01649-07] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2007] [Revised: 03/03/2008] [Accepted: 04/22/2008] [Indexed: 01/12/2023] Open
Abstract
Rifamycins have proven efficacy in the treatment of persistent bacterial infections. However, the frequency with which bacteria develop resistance to rifamycin agents restricts their clinical use to antibiotic combination regimens. In a program directed toward the synthesis of rifamycins with a lower propensity to elicit resistance development, a series of compounds were prepared that covalently combine rifamycin and quinolone pharmacophores to form stable hybrid antibacterial agents. We describe mode-of-action studies with Staphylococcus aureus of CBR-2092, a novel hybrid that combines the rifamycin SV and 4H-4-oxo-quinolizine pharmacophores. In biochemical studies, CBR-2092 exhibited rifampin-like potency as an inhibitor of RNA polymerase, was an equipotent (balanced) inhibitor of DNA gyrase and DNA topoisomerase IV, and retained activity against a prevalent quinolone-resistant variant. Macromolecular biosynthesis studies confirmed that CBR-2092 has rifampin-like effects on RNA synthesis in rifampin-susceptible strains and quinolone-like effects on DNA synthesis in rifampin-resistant strains. Studies of mutant strains that exhibited reduced susceptibility to CBR-2092 further substantiated RNA polymerase as the primary cellular target of CBR-2092, with DNA gyrase and DNA topoisomerase IV being secondary and tertiary targets, respectively, in strains exhibiting preexisting rifampin resistance. In contrast to quinolone comparator agents, no strains with altered susceptibility to CBR-2092 were found to exhibit changes consistent with altered efflux properties. The combined data indicate that CBR-2092 may have potential utility in monotherapy for the treatment of persistent S. aureus infections.
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Butler MM, Lamarr WA, Foster KA, Barnes MH, Skow DJ, Lyden PT, Kustigian LM, Zhi C, Brown NC, Wright GE, Bowlin TL. Antibacterial activity and mechanism of action of a novel anilinouracil-fluoroquinolone hybrid compound. Antimicrob Agents Chemother 2006; 51:119-27. [PMID: 17074800 PMCID: PMC1797695 DOI: 10.1128/aac.01311-05] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The anilinouracils (AUs) such as 6-(3-ethyl-4-methylanilino)uracil (EMAU) are a novel class of gram-positive, selective, bactericidal antibacterials which inhibit pol IIIC, the gram-positive-specific replicative DNA polymerase. We have linked various fluoroquinolones (FQs) to the N-3 position of EMAU to generate a variety of AU-FQ "hybrids" offering the potential for targeting two distinct steps in DNA replication. In this study, the properties of a hybrid, "251D," were compared with those of representative AUs and FQs in a variety of in vitro assays, including pol IIIC and topoisomerase/gyrase enzyme assays, antibacterial, bactericidal, and mammalian cytotoxicity assays. Compound 251D potently inhibited pol IIIC and topoisomerase/gyrase, displayed gram-positive antibacterial potency at least 15 times that of the corresponding AU compound, and as expected, acted selectively on bacterial DNA synthesis. Compound 251D was active against a broad panel of antibiotic-resistant gram-positive pathogens as well as several gram-negative organisms and was also active against both AU- and FQ-resistant gram-positive organisms, demonstrating its capacity for attacking both of its potential targets in the bacterium. 251D also was bactericidal for gram-positive organisms and lacked toxicity in vitro. Although we obtained strains of Staphylococcus aureus resistant to the individual parent compounds, spontaneous resistance to 251D was not observed. We obtained 251D resistance in multiple-passage experiments, but resistance developed at a pace comparable to those for the parent compounds. This class of AU-FQ hybrids provides a promising new pharmacophore with an unusual dual mechanism of action and potent activity against antibiotic-sensitive and -resistant gram-positive pathogens.
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Aubry A, Fisher LM, Jarlier V, Cambau E. First functional characterization of a singly expressed bacterial type II topoisomerase: the enzyme from Mycobacterium tuberculosis. Biochem Biophys Res Commun 2006; 348:158-65. [PMID: 16876125 DOI: 10.1016/j.bbrc.2006.07.017] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2006] [Accepted: 07/07/2006] [Indexed: 10/24/2022]
Abstract
Genome deciphering revealed that Mycobacterium tuberculosis encodes a single type II topoisomerase contrary to common bacteria harboring two type II topoisomerases (DNA gyrase and topoisomerase IV). Functions of the M. tuberculosis type II topoisomerase were explored after cloning and expressing the subunits encoding genes in Escherichia coli. M. tuberculosis type II topoisomerase supercoiled relaxed pBR322 with a specific activity close to that of DNA gyrases of common bacteria whereas it exhibited DNA relaxation and formation of cleavable complexes with activities significantly higher than other DNA gyrases. Intermolecular passage activity evaluated by the decatenation of kinetoplast DNA was 25-fold lower than that of the topoisomerase IV from Streptococcus pneumoniae, but was markedly higher than that of the E. coli gyrase. Overall, the type II topoisomerase of M. tuberculosis exhibits classical polyvalent activities of DNA gyrase for supercoiling but enhanced relaxation, cleavage, and decatenation activities.
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Affiliation(s)
- Alexandra Aubry
- Laboratoire de Bactériologie, Faculté de Médecine Pitié-Salpêtrière, EA1541, Université Paris 6, France
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Strahilevitz J, Onodera Y, Hooper DC. An improved expression plasmid for affinity purification of Staphylococcus aureus gyrase A subunit. Protein Expr Purif 2005; 47:10-5. [PMID: 16289915 DOI: 10.1016/j.pep.2005.08.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2005] [Accepted: 08/18/2005] [Indexed: 11/26/2022]
Abstract
Of the bacterial topoisomerases, the gyrase A subunit (GyrA) of Staphylococcus aureus is particularly difficult to purify because of its tendency to form inclusion bodies. Previous attempts at purification yielded low concentrations of protein with reduced specific activity. To overcome this problem, we modified the commercially available plasmid expression vector, pBAD/Thio-TOPO, via the addition of DNA sequences encoding a hexahistidine tag upstream and a cleavage site for tobacco etch virus protease downstream of the gene encoding thioredoxin. The resulting expression system consisting of the modified plasmid, pSAGA7, and the recommended host strain, Escherichia coli TOP 10, facilitated high level expression of soluble GyrA and its affinity purification to over 95% homogeneity. Purified GyrA had high biological activity as evidenced by a specific activity of 4.3x10(5)U/mg. The pSAGA7/TOP10 expression system also facilitated the expression and purification of a subunit of S. aureus topoisomerase IV, ParE, and a recently discovered protein unrelated to topoisomerases, QnrB, two "hard to purify" proteins. We conclude that pSAGA7 might be useful for high-level soluble expression and purification of diverse microbial proteins.
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Affiliation(s)
- Jacob Strahilevitz
- Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
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24
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Song G, Yan Q, He Y. Studies on Interaction of Norfloxacin, Cu2+, and DNA by Spectral Methods. J Fluoresc 2005; 15:673-8. [PMID: 16341784 DOI: 10.1007/s10895-005-2974-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2005] [Accepted: 07/26/2005] [Indexed: 10/25/2022]
Abstract
The interactions of norfloxacin (NFA), DNA, and Cu2+ are studied by fluorescence and UV-spectra method. According to the experimental results, it can be concluded that NFA can form a steady binary complex with Cu2+. There is a linear relationship between the Fluorescence intensity of the norfloxacin-Cu2+-DNA system and the concentration of DNA. And when the concentration of the NFA is 1.95x10(-5) mol L-1, they possess a good linearity in the concentration of DNA ranged from 4.7x10(-6) to 2.8x10(-5) mol L-1. It is a good method due to the high sensitivity and selectivity.
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Affiliation(s)
- Gongwu Song
- Faculty of Chemistry and Material Science, Hubei University, Wuhan, 430062, People's Republic of China.
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Mitscher LA. Bacterial topoisomerase inhibitors: quinolone and pyridone antibacterial agents. Chem Rev 2005; 105:559-92. [PMID: 15700957 DOI: 10.1021/cr030101q] [Citation(s) in RCA: 591] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lester A Mitscher
- Department of Medicinal Chemistry and Molecular Biosciences and The Chemical Methodologies and Library Development Center of Excellence, The University of Kansas, Lawrence, Kansas 66045-7582, USA.
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26
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Song G, He Y, Cai Z, Lou Z. The Fluorescence Studies of Interaction between 4‐(n‐2′‐Glucosyl) Acetamidyl Triphenyl Phosphonium Chloride and DNA. ANAL LETT 2005. [DOI: 10.1081/al-200047785] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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27
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Li W, Chen Y, Lam Y. A facile solid-phase synthesis of 3,4,6-trisubstituted-2-pyridones using sodium benzenesulfinate as a traceless linker. Tetrahedron Lett 2004. [DOI: 10.1016/j.tetlet.2004.07.051] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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28
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Bronstein JC, Olson SL, LeVier K, Tomilo M, Weber PC. Purification and characterization of recombinant Staphylococcus haemolyticus DNA gyrase and topoisomerase IV expressed in Escherichia coli. Antimicrob Agents Chemother 2004; 48:2708-11. [PMID: 15215131 PMCID: PMC434177 DOI: 10.1128/aac.48.7.2708-2711.2004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The subunits of DNA gyrase and topoisomerase IV from Staphylococcus haemolyticus were expressed in Escherichia coli, purified to homogeneity, and used to reconstitute active enzymes that were sensitive to known topoisomerase inhibitors. This represents the first description of a method for isolating type II topoisomerases of a coagulase-negative staphylococcal species.
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Affiliation(s)
- Joel C Bronstein
- Pfizer Global Research and Development, 2800 Plymouth Road, Ann Arbor, MI 48105, USA.
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Aubry A, Pan XS, Fisher LM, Jarlier V, Cambau E. Mycobacterium tuberculosis DNA gyrase: interaction with quinolones and correlation with antimycobacterial drug activity. Antimicrob Agents Chemother 2004; 48:1281-8. [PMID: 15047530 PMCID: PMC375300 DOI: 10.1128/aac.48.4.1281-1288.2004] [Citation(s) in RCA: 181] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Genome studies suggest that DNA gyrase is the sole type II topoisomerase and likely the unique target of quinolones in Mycobacterium tuberculosis. Despite the emerging importance of quinolones in the treatment of mycobacterial disease, the slow growth and high pathogenicity of M. tuberculosis have precluded direct purification of its gyrase and detailed analysis of quinolone action. To address these issues, we separately overexpressed the M. tuberculosis DNA gyrase GyrA and GyrB subunits as His-tagged proteins in Escherichia coli from pET plasmids carrying gyrA and gyrB genes. The soluble 97-kDa GyrA and 72-kDa GyrB subunits were purified by nickel chelate chromatography and shown to reconstitute an ATP-dependent DNA supercoiling activity. The drug concentration that inhibited DNA supercoiling by 50% (IC(50)) was measured for 22 different quinolones, and values ranged from 2 to 3 microg/ml (sparfloxacin, sitafloxacin, clinafloxacin, and gatifloxacin) to >1,000 microg/ml (pipemidic acid and nalidixic acid). By comparison, MICs measured against M. tuberculosis ranged from 0.12 microg/ml (for gatifloxacin) to 128 microg/ml (both pipemidic acid and nalidixic acid) and correlated well with the gyrase IC(50)s (R(2) = 0.9). Quinolones promoted gyrase-mediated cleavage of plasmid pBR322 DNA due to stabilization of the cleavage complex, which is thought to be the lethal lesion. Surprisingly, the measured concentrations of drug inducing 50% plasmid linearization correlated less well with the MICs (R(2) = 0.7). These findings suggest that the DNA supercoiling inhibition assay may be a useful screening test in identifying quinolones with promising activity against M. tuberculosis. The quinolone structure-activity relationship demonstrated here shows that C-8, the C-7 ring, the C-6 fluorine, and the N-1 cyclopropyl substituents are desirable structural features in targeting M. tuberculosis gyrase.
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Affiliation(s)
- Alexandra Aubry
- Laboratoire de Bactériologie, Faculté de Médecine Pitié-Salpêtrière, Université Pierre et Marie Curie, Paris, France
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Nilius AM, Shen LL, Hensey-Rudloff D, Almer LS, Beyer JM, Balli DJ, Cai Y, Flamm RK. In vitro antibacterial potency and spectrum of ABT-492, a new fluoroquinolone. Antimicrob Agents Chemother 2004; 47:3260-9. [PMID: 14506039 PMCID: PMC201153 DOI: 10.1128/aac.47.10.3260-3269.2003] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
ABT-492 demonstrated potent antibacterial activity against most quinolone-susceptible pathogens. The rank order of potency was ABT-492 > trovafloxacin > levofloxacin > ciprofloxacin against quinolone-susceptible staphylococci, streptococci, and enterococci. ABT-492 had activity comparable to those of trovafloxacin, levofloxacin, and ciprofloxacin against seven species of quinolone-susceptible members of the family Enterobacteriaceae, although it was less active than the comparators against Citrobacter freundii and Serratia marcescens. The activity of ABT-492 was greater than those of the comparators against fastidious gram-negative species, including Haemophilus influenzae, Moraxella catarrhalis, Neisseria gonorrhoeae, and Legionella spp. and against Pseudomonas aeruginosa and Helicobacter pylori. ABT-492 was as active as trovafloxacin against Chlamydia trachomatis, indicating good intracellular penetration and antibacterial activity. In particular, ABT-492 was more active than trovafloxacin and levofloxacin against multidrug-resistant Streptococcus pneumoniae, including strains resistant to penicillin and macrolides, and H. influenzae, including beta-lactam-resistant strains. It retained greater in vitro activity than the comparators against S. pneumoniae and H. influenzae strains resistant to other quinolones due to amino acid alterations in the quinolone resistance-determining regions of the target topoisomerases. ABT-492 was a potent inhibitor of bacterial topoisomerases, and unlike the comparators, DNA gyrase and topoisomerase IV from either Staphylococcus aureus or Escherichia coli were almost equally sensitive to ABT-492. The profile of ABT-492 suggested that it may be a useful agent for the treatment of community-acquired respiratory tract infections, as well as infections of the urinary tract, bloodstream, and skin and skin structure and nosocomial lung infections.
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Affiliation(s)
- Angela M Nilius
- Infectious Diseases Research, Abbott Laboratories, Abbott Park, Illinois 60064-3537, USA.
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31
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Dandliker PJ, Pratt SD, Nilius AM, Black-Schaefer C, Ruan X, Towne DL, Clark RF, Englund EE, Wagner R, Weitzberg M, Chovan LE, Hickman RK, Daly MM, Kakavas S, Zhong P, Cao Z, David CA, Xuei X, Lerner CG, Soni NB, Bui M, Shen LL, Cai Y, Merta PJ, Saiki AYC, Beutel BA. Novel antibacterial class. Antimicrob Agents Chemother 2004; 47:3831-9. [PMID: 14638491 PMCID: PMC296205 DOI: 10.1128/aac.47.12.3831-3839.2003] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report the discovery and characterization of a novel ribosome inhibitor (NRI) class that exhibits selective and broad-spectrum antibacterial activity. Compounds in this class inhibit growth of many gram-positive and gram-negative bacteria, including the common respiratory pathogens Streptococcus pneumoniae, Haemophilus influenzae, Staphylococcus aureus, and Moraxella catarrhalis, and are nontoxic to human cell lines. The first NRI was discovered in a high-throughput screen designed to identify inhibitors of cell-free translation in extracts from S. pneumoniae. The chemical structure of the NRI class is related to antibacterial quinolones, but, interestingly, the differences in structure are sufficient to completely alter the biochemical and intracellular mechanisms of action. Expression array studies and analysis of NRI-resistant mutants confirm this difference in intracellular mechanism and provide evidence that the NRIs inhibit bacterial protein synthesis by inhibiting ribosomes. Furthermore, compounds in the NRI series appear to inhibit bacterial ribosomes by a new mechanism, because NRI-resistant strains are not cross-resistant to other ribosome inhibitors, such as macrolides, chloramphenicol, tetracycline, aminoglycosides, or oxazolidinones. The NRIs are a promising new antibacterial class with activity against all major drug-resistant respiratory pathogens.
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Affiliation(s)
- Peter J Dandliker
- Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, Illinois 60064, USA.
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Barnes MH, LaMarr WA, Foster KA. DNA gyrase and DNA topoisomerase of Bacillus subtilis: expression and characterization of recombinant enzymes encoded by the gyrA, gyrB and parC, parE genes. Protein Expr Purif 2003; 29:259-64. [PMID: 12767818 DOI: 10.1016/s1046-5928(03)00068-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Bacillus subtilis Bs gyrA and gyrB genes specifying the DNA gyrase subunits, and parC and parE genes specifying the DNA topoisomerase IV subunits, have been separately cloned and expressed in Escherichia coli as hexahistidine (his6)-tagged recombinant proteins. Purification of the gyrA and gyrB subunits together resulted in predominantly two bands at molecular weights of 94 and 73kDa; purification of the parC and parE subunits together resulted in predominantly two bands at molecular weights of 93 and 75kDa, as predicted by their respective sequences. The ability of the subunits to complement their partner was tested in an ATP-dependent decatenation/supercoiling assay system. The results demonstrated that the DNA gyrase and the topoisomerase IV subunits produce the expected supercoiled DNA and relaxed DNA products, respectively. Additionally, inhibition of these two enzymes by fluoroquinolones has been shown to be comparable to those of the DNA gyrases and topoisomerases of other bacterial strains. In sum, the biological and enzymatic properties of these products are consistent with their authenticity as DNA gyrase and DNA topoisomerase IV enzymes from B. subtilis.
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Hiasa H, Shea ME, Richardson CM, Gwynn MN. Staphylococcus aureus gyrase-quinolone-DNA ternary complexes fail to arrest replication fork progression in vitro. Effects of salt on the DNA binding mode and the catalytic activity of S. aureus gyrase. J Biol Chem 2003; 278:8861-8. [PMID: 12511566 DOI: 10.1074/jbc.m209207200] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Type II topoisomerases bind to DNA at the catalytic domain across the DNA gate. DNA gyrases also bind to DNA at the non-homologous C-terminal domain of the GyrA subunit, which causes the wrapping of DNA about itself. This unique mode of DNA binding allows gyrases to introduce the negative supercoils into DNA molecules. We have investigated the biochemical characteristics of Staphylococcus aureus (S. aureus) gyrase. S. aureus gyrase is known to require high concentrations of potassium glutamate (K-Glu) for its supercoiling activity. However, high concentrations of K-Glu are not required for its relaxation and decatenation activities. This is due to the requirement of high concentrations of K-Glu for S. aureus gyrase-mediated wrapping of DNA. These results suggest that S. aureus gyrase can bind to DNA at the catalytic domain independent of K-Glu concentration, but high concentrations of K-Glu are required for the binding of the C-terminal domain of GyrA to DNA and the wrapping of DNA. Thus, salt modulates the DNA binding mode and the catalytic activity of S. aureus gyrase. Quinolone drugs can stimulate the formation of covalent S. aureus gyrase-DNA complexes, but high concentrations of K-Glu inhibit the formation of S. aureus gyrase-quinolone-DNA ternary complexes. In the absence of K-Glu, ternary complexes formed with S. aureus gyrase cannot arrest replication fork progression in vitro, demonstrating that the formation of a wrapped ternary complex is required for replication fork arrest by a S. aureus gyrase-quinolone-DNA ternary complex.
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Affiliation(s)
- Hiroshi Hiasa
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis 55455, USA.
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34
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Wu Song G, Xia Cai Z. Studies on the Interaction of Enoxacin, Fe(III), and DNA by Spectral Methods. ANAL LETT 2003. [DOI: 10.1081/al-120026421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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35
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Zhanel GG, Ennis K, Vercaigne L, Walkty A, Gin AS, Embil J, Smith H, Hoban DJ. A critical review of the fluoroquinolones: focus on respiratory infections. Drugs 2002; 62:13-59. [PMID: 11790155 DOI: 10.2165/00003495-200262010-00002] [Citation(s) in RCA: 269] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The new fluoroquinolones (clinafloxacin, gatifloxacin, gemifloxacin, grepafloxacin, levofloxacin, moxifloxacin, sitafloxacin, sparfloxacin and trovafloxacin) offer excellent activity against Gram-negative bacilli and improved Gram-positive activity (e.g. against Streptococcus pneumoniae and Staphylococcus aureus) over ciprofloxacin. Ciprofloxacin still maintains the best in vitro activity against Pseudomonas aeruginosa. Clinafloxacin, gatifloxacin, moxifloxacin, sitafloxacin, sparfloxacin and trovafloxacin display improved activity against anaerobes (e.g. Bacteroides fragilis) versus ciprofloxacin. All of the new fluoroquinolones display excellent bioavailability and have longer serum half-lives than ciprofloxacin allowing for once daily dose administration. Clinical trials comparing the new fluoroquinolones to each other or to standard therapy have demonstrated good efficacy in a variety of community-acquired respiratory infections (e.g. pneumonia, acute exacerbations of chronic bronchitis and acute sinusitis). Limited data suggest that the new fluoroquinolones as a class may lead to better outcomes in community-acquired pneumonia and acute exacerbations of chronic bronchitis versus comparators. Several of these agents have either been withdrawn from the market, had their use severely restricted because of adverse effects (clinafloxacin because of phototoxicity and hypoglycaemia; grepafloxacin because of prolongation of the QTc and resultant torsades de pointes; sparfloxacin because of phototoxicity; and trovafloxacin because of hepatotoxicity), or were discontinued during developmental phases. The remaining fluoroquinolones such as gatifloxacin, gemifloxacin, levofloxacin and moxifloxacin have adverse effect profiles similar to ciprofloxacin. Extensive post-marketing safety surveillance data (as are available with ciprofloxacin and levofloxacin) are required for all new fluoroquinolones before safety can be definitively established. Drug interactions are limited; however, all fluoroquinolones interact with metal ion containing drugs (eg. antacids). The new fluoroquinolones (gatifloxacin, gemifloxacin, levofloxacin and moxifloxacin) offer several advantages over ciprofloxacin and are emerging as important therapeutic agents in the treatment of community-acquired respiratory infections. Their broad spectrum of activity which includes respiratory pathogens such as penicillin and macrolide resistant S. pneumoniae, favourable pharmacokinetic parameters, good bacteriological and clinical efficacy will lead to growing use of these agents in the treatment of community-acquired pneumonia, acute exacerbations of chronic bronchitis and acute sinusitis. These agents may result in cost savings especially in situations where, because of their potent broad-spectrum activity and excellent bioavailability, they may be used orally in place of intravenous antibacterials. Prudent use of the new fluoroquinolones will be required to minimise the development of resistance to these agents.
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Affiliation(s)
- George G Zhanel
- Department of Medical Microbiology, Faculty of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada.
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Wu P, Lawrence LE, Denbleyker KL, Barrett JF. Mechanism of action of the des-F(6) quinolone BMS-284756 measured by supercoiling inhibition and cleavable complex assays. Antimicrob Agents Chemother 2001; 45:3660-2. [PMID: 11709365 PMCID: PMC90894 DOI: 10.1128/aac.45.12.3660-3662.2001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
BMS-284756 (T-3811ME), a novel des-F(6) quinolone, was tested in the supercoiling inhibition and cleavable complex assays against Escherichia coli DNA gyrase, a target of quinolones. The results suggest that BMS-284756 has the same mechanism of action against DNA gyrase as other quinolones and a similar level of potency.
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Affiliation(s)
- P Wu
- Bristol-Myers Squibb Company Pharmaceutical Research Institute, Wallingford, Connecticut, USA
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