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Ayoup MS, Rabee AR, Abdel-Hamid H, Harras MF, El Menofy NG, Ismail MMF. Exploration of Nitroaromatic Antibiotics via Sanger's Reagent: Synthesis, In Silico, and Antimicrobial Evaluation. ACS OMEGA 2022; 7:5254-5263. [PMID: 35187340 PMCID: PMC8851660 DOI: 10.1021/acsomega.1c06383] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
Facile synthesis of molecular hybrids containing a 2,4-dinitrophenyl moiety was achieved via nucleophilic aromatic substitution of the fluoride anion of Sanger's reagent (2,4-dinitrofluorobenzene) with various N, S, and O nucleophiles, considered as bioactive moieties. Antimicrobial evaluation of the new hybrids was carried out using amoxicillin and nystatin as antibacterial and antifungal reference standards, respectively. MIC test results identified the compounds 3, 4, and 7 as the most active hybrids against standard strains and multidrug-resistant strains (MDR) of Staphylococcus aureus, Escherichia coli, and Pseudomonas aurginosa. Most of the hybrids displayed two times the antibacterial activity of AMOX against MDR Pseudomonas aeruginosa, E. coli, and a standard strain of P. aeruginosa (ATCC 29853), while demonstrating a weak antifungal profile against Candida albicans. Selectivity profiles of the promising compounds 3, 4, 6, 7, 8, and 11 on WI-38 human cells were characterized, which indicated that compound 3 is the safest one (CC50 343.72 μM). The preferential anti-Gram-negative activity of our compounds led us to do docking studies on DNA gyrase B. Docking revealed that the potential antimicrobial compounds fit well into the active site of DNA gyrase B. Furthermore, in silico absorption, distribution, metabolism, and excretion (ADME) predictions revealed that most of the new compounds have high gastrointestinal absorption and a good oral bioavailability with no BBB permeability.
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Affiliation(s)
- Mohammed Salah Ayoup
- Department
of Chemistry, Faculty of Science, Alexandria
University, P.O. Box 426, Ibrahimia, 21525 Alexandria, Egypt
| | - Ahmed R. Rabee
- Department
of Chemistry, Faculty of Science, Alexandria
University, P.O. Box 426, Ibrahimia, 21525 Alexandria, Egypt
| | - Hamida Abdel-Hamid
- Department
of Chemistry, Faculty of Science, Alexandria
University, P.O. Box 426, Ibrahimia, 21525 Alexandria, Egypt
| | - Marwa F. Harras
- Department
of Pharmaceutical Medicinal Chemistry, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo 11651, Egypt
| | - Nagwan G. El Menofy
- Department
of Microbiology and Immunology, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo 11651, Egypt
| | - Magda M. F. Ismail
- Department
of Pharmaceutical Medicinal Chemistry, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo 11651, Egypt
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2
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Chen H, Xu Y, Chen H, Liu H, Yu Q, Han L. Isolation and Identification of Polyphenols From Fresh Sweet Sorghum Stems and Their Antibacterial Mechanism Against Foodborne Pathogens. Front Bioeng Biotechnol 2022; 9:770726. [PMID: 35223810 PMCID: PMC8878683 DOI: 10.3389/fbioe.2021.770726] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 12/03/2021] [Indexed: 11/17/2022] Open
Abstract
As a C4 energy crop widely planted all over the world, sweet sorghum is mainly used in sugar making and brewing. Fresh sweet sorghum stalks contain many natural ingredients that have antioxidant properties and can significantly inhibit the growth of foodborne pathogens. In this study, the polyphenols in sweet sorghum were extracted by acid ethanol and ion precipitation, and the types of polyphenols were determined by HPLC-MS. The polyphenol content in fresh sweet sorghum stalks was 5.77 mg/g after process optimization with 18 types of phenolic acids identified. The extract had a total antioxidant capacity of 9.4 μmol Trolox/mL. Polyphenol extract of sweet sorghum displayed antibacterial activity against Staphylococcus aureus, Escherichia coli, Listeria spp., and Salmonella spp. The extract increased the conductivity of cell suspensions by destroying the membrane structure, resulting in leakage of cell electrolytes. Changes in bacterial morphology and internal structure were indicated. The data describe an optimized process to extract polyphenols from sweet sorghum stalks and the methodology to identify the major components within the extract. The data provide a novel option for the comprehensive utilization of fresh sweet sorghum stalks.
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Affiliation(s)
- Hao Chen
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, China
| | - Yifei Xu
- Gansu Institute of Food Inspection, Lanzhou, China
| | - Haoyu Chen
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, China
| | - Hao Liu
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, China
| | - Qunli Yu
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, China
- *Correspondence: Qunli Yu,
| | - Ling Han
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, China
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3
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Shaker B, Ahmad S, Lee J, Jung C, Na D. In silico methods and tools for drug discovery. Comput Biol Med 2021; 137:104851. [PMID: 34520990 DOI: 10.1016/j.compbiomed.2021.104851] [Citation(s) in RCA: 138] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/05/2021] [Accepted: 09/05/2021] [Indexed: 12/28/2022]
Abstract
In the past, conventional drug discovery strategies have been successfully employed to develop new drugs, but the process from lead identification to clinical trials takes more than 12 years and costs approximately $1.8 billion USD on average. Recently, in silico approaches have been attracting considerable interest because of their potential to accelerate drug discovery in terms of time, labor, and costs. Many new drug compounds have been successfully developed using computational methods. In this review, we briefly introduce computational drug discovery strategies and outline up-to-date tools to perform the strategies as well as available knowledge bases for those who develop their own computational models. Finally, we introduce successful examples of anti-bacterial, anti-viral, and anti-cancer drug discoveries that were made using computational methods.
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Affiliation(s)
- Bilal Shaker
- Department of Biomedical Engineering, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, 25000, Pakistan
| | - Jingyu Lee
- Department of Biomedical Engineering, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Chanjin Jung
- Department of Biomedical Engineering, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Dokyun Na
- Department of Biomedical Engineering, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, 06974, Republic of Korea.
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4
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Tomašič T, Zubrienė A, Skok Ž, Martini R, Pajk S, Sosič I, Ilaš J, Matulis D, Bryant SD. Selective DNA Gyrase Inhibitors: Multi-Target in Silico Profiling with 3D-Pharmacophores. Pharmaceuticals (Basel) 2021; 14:ph14080789. [PMID: 34451886 PMCID: PMC8400042 DOI: 10.3390/ph14080789] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/02/2021] [Accepted: 08/09/2021] [Indexed: 11/17/2022] Open
Abstract
DNA gyrase is an important target for the development of novel antibiotics. Although ATP-competitive DNA gyrase (GyrB) inhibitors are a well-studied class of antibacterial agents, there is currently no representative used in therapy, largely due to unwanted off-target activities. Selectivity of GyrB inhibitors against closely related human ATP-binding enzymes should be evaluated early in development to avoid off-target binding to homologous binding domains. To address this challenge, we developed selective 3D-pharmacophore models for GyrB, human topoisomerase IIα (TopoII), and the Hsp90 N-terminal domain (NTD) to be used in in silico activity profiling paradigms to identify molecules selective for GyrB over TopoII and Hsp90, as starting points for hit expansion and lead optimization. The models were used to profile highly active GyrB, TopoII, and Hsp90 inhibitors. Selected compounds were tested in in vitro assays. GyrB inhibitors 1 and 2 were inactive against TopoII and Hsp90, while 3 and 4, potent Hsp90 inhibitors, displayed no inhibition of GyrB and TopoII, and TopoII inhibitors 5 and 6 were inactive at GyrB and Hsp90. The results provide a proof of concept for the use of target activity profiling methods to identify selective starting points for hit and lead identification.
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Affiliation(s)
- Tihomir Tomašič
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia; (Ž.S.); (S.P.); (I.S.); (J.I.)
- Correspondence: ; Tel.: +386-1-4769-556
| | - Asta Zubrienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania; (A.Z.); (D.M.)
| | - Žiga Skok
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia; (Ž.S.); (S.P.); (I.S.); (J.I.)
| | - Riccardo Martini
- Inte:Ligand Softwareentwicklungs- und Consulting GmbH, Mariahilferstrasse 74B, 1070 Vienna, Austria; (R.M.); (S.D.B.)
- Discngine S.A.S., 79 Avenue Ledru Rollin, 75012 Paris, France
| | - Stane Pajk
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia; (Ž.S.); (S.P.); (I.S.); (J.I.)
| | - Izidor Sosič
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia; (Ž.S.); (S.P.); (I.S.); (J.I.)
| | - Janez Ilaš
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia; (Ž.S.); (S.P.); (I.S.); (J.I.)
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania; (A.Z.); (D.M.)
| | - Sharon D. Bryant
- Inte:Ligand Softwareentwicklungs- und Consulting GmbH, Mariahilferstrasse 74B, 1070 Vienna, Austria; (R.M.); (S.D.B.)
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5
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Han J, Liu X, Zhang L, Quinn RJ, Feng Y. Anti-mycobacterial natural products and mechanisms of action. Nat Prod Rep 2021; 39:77-89. [PMID: 34226909 DOI: 10.1039/d1np00011j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Covering: up to June, 2020Tuberculosis (TB) continues to be a major disease with high mortality and morbidity globally. Drug resistance and long duration of treatment make antituberculosis drug discovery more challenging. In this review, we summarize recent advances on anti-TB natural products (NPs) and their potential molecular targets in cell wall synthesis, protein production, energy generation, nucleic acid synthesis and other emerging areas. We highlight compounds with activity against drug-resistant TB, and reveal several novel targets including Mtb biotin synthase, ATP synthase, 1,4-dihydroxy-2-naphthoate prenyltransferase and biofilms. These anti-TB NPs and their targets could facilitate target-based screening and accelerate TB drug discovery.
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Affiliation(s)
- Jianying Han
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia.
| | - Xueting Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Lixin Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Ronald J Quinn
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia.
| | - Yunjiang Feng
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia.
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6
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Beyzaei H, Mirzaei M, Hasan Fakhrabadi N, Ghasemi B. Synergistic effects of dual antimicrobial combinations of synthesized N-heterocycles or MgO nanoparticles with nisin against the growth of Aspergillus fumigatus: In vitro study. VETERINARY RESEARCH FORUM : AN INTERNATIONAL QUARTERLY JOURNAL 2021; 12:241-246. [PMID: 34345393 PMCID: PMC8328251 DOI: 10.30466/vrf.2019.103449.2460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 10/30/2019] [Indexed: 11/25/2022]
Abstract
Introduction of new inhibitory agents such as peptides, heterocyclic derivatives and nanoparticles (NPs) along with preventive proceedings are effective ways to deal with standard and drug-resistant strains of microorganisms. In this regard, inhibitory activities of some recently synthesized 4-thiazolylpyrazoles, imidazolidine- and tetrahydropyrimidine-2-thiones and magnesium oxide (MgO) NPs alone and in combination with nisin have been assessed against Aspergillus fumigatus. Antimicrobial susceptibility tests were done via broth microdilution, disk diffusion and streak plate methods according to the modified Clinical and Laboratory Standards Institute (CLSI) guidelines. Synergistic effects were also determined as fractional inhibitory concentration (FIC) and fractional fungicidal concentration (FFC) values. Inhibitory potentials of all heterocycles and NPs against A. fumigatus were proved based on inhibition zone diameter (IZD) values in the range of 7.72 - 16.85 mm, minimum inhibitory concentration (MIC) values in the range of 64.00 - 512 µg mL-1 and minimum fungicidal concentration (MFC) values in the range of 256 - 2048 µg mL-1. Tetrahydropyrimidine derivative 3f showed the best inhibitory properties. Inhibitory activity was not significant with nisin. While antifungal effects of major derivatives were improved by combination with it. The results indicated that the combined treatment of heterocycles used in the present study with nisin might be efficient for mold prevention and removal in foodstuffs or other products.
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Affiliation(s)
- Hamid Beyzaei
- Department of Chemistry, Faculty of Science, University of Zabol, Zabol, Iran
| | - Mojtaba Mirzaei
- Young Researchers and Elite Club, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | | | - Behzad Ghasemi
- Torbat-e Jam Faculty of Medical Sciences, Torbat-e Jam, Iran
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7
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Novel anti-tubercular and antibacterial based benzosuberone-thiazole moieties: Synthesis, molecular docking analysis, DNA gyrase supercoiling and ATPase activity. Bioorg Chem 2020; 104:104316. [PMID: 33022549 DOI: 10.1016/j.bioorg.2020.104316] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/18/2020] [Accepted: 09/20/2020] [Indexed: 12/20/2022]
Abstract
Herein, molecular hybridization strategy was utilized in the design of new benzosuberone-thiazole derivatives. The structures of the synthesized hybrids were determined on the basis of elemental and spectral analyses. These compounds were evaluated for their antibacterial activities against five bronchitis causing bacteria in addition to their anti-tubercular activities. Most compounds revealed promising activities. Amongst active compounds, benzosuberone-dithiazole derivatives 22a and 28 with MIC value = 1.95 µg/ml against H. influenza, M. pneumonia, and B. pertussis displayed four times the activity of ciprofloxacin (MIC = 7.81 µg/ml) against H. influenza, twice the activity of ciprofloxacin (MIC = 3.9 µg/ml) against M. pneumonia and were equipotent to ciprofloxacin against B. pertussis (MIC = 1.95 µg/ml). Additionally, benzosuberone-dithiazole derivatives 22a and 27 were the most promising anti-tubercular among the tested compounds with MIC values of 0.12 and 0.24 µg/ml, respectively against sensitive M. tuberculosis in addition to high activity against resistant strain of M. tuberculosis (MIC = 0.98 and 1.95 µg/ml, respectively) compared to isoniazid (MIC = 0.12 µg/ml against sensitive M. tuberculosis and no activity against resistant M. tuberculosis). Cytotoxicity study of the active dithiazole derivatives 22a, 27 and 28 against normal human lung cells (WI-38) indicated their high safety profile as showed from their high IC50 values (IC50 = 107, 74.8, and 117 µM, respectively). Furthermore, DNA gyrase supercoiling and ATPase activity assays showed that 22a, 27 and 28 have the potential to inhibit DNA gyrase at low micromolar levels (IC50 = 3.29-15.64 µM). Molecular docking analysis was also carried out to understand the binding profiles of the synthesized compounds into the ATPase binding sites of bacterial and mycobacterial DNA gyraseB.
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8
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Mamidala S, Mudigunda VS, Peddi SR, Bokara KK, Manga V, Vedula RR. Design and synthesis of new thiazoles by microwave-assisted method: Evaluation as an anti-breast cancer agents and molecular docking studies. SYNTHETIC COMMUN 2020. [DOI: 10.1080/00397911.2020.1781184] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Srikanth Mamidala
- Department of Chemistry, National Institute of Technology, Warangal, India
| | | | - Sudhir Reddy Peddi
- Molecular Modeling and Medicinal Chemistry Group, Department of Chemistry, University College of Science, Osmania University, Hyderabad, India
| | | | - Vijjulatha Manga
- Molecular Modeling and Medicinal Chemistry Group, Department of Chemistry, University College of Science, Osmania University, Hyderabad, India
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9
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Tambe PM, Bhowmick S, Chaudhary SK, Khan MR, Wabaidur SM, Muddassir M, Patil PC, Islam MA. Structure-Based Screening of DNA GyraseB Inhibitors for Therapeutic Applications in Tuberculosis: a Pharmacoinformatics Study. Appl Biochem Biotechnol 2020; 192:1107-1123. [PMID: 32686004 DOI: 10.1007/s12010-020-03374-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 06/22/2020] [Indexed: 11/27/2022]
Abstract
Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis (MTB) and considered as serious public health concern worldwide which kills approximately five thousand people every day. Therefore, TB drug development efforts are in gigantic need for identification of new potential chemical agents to eradicate TB from the society. The bacterial DNA gyrase B (GyrB) protein as an experimentally widely accepted effective drug target for the development of TB chemotherapeutics. In the present study, advanced pharmacoinformatics approaches were used to screen the Mcule database against the GyrB protein. Based on a number of chemometric parameters, five molecules were found to be crucial to inhibit the GyrB. A number of molecular binding interactions between the proposed inhibitors and important active site residues of GyrB were observed. The predicted drug-likeness properties of all molecules were indicated that compounds possess characteristics to be the drug-like candidates. The dynamic nature of each molecule was explored through the molecular dynamics (MD) simulation study. Various analyzing parameters from MD simulation trajectory have suggested rationality of the molecules to be potential GyrB inhibitor. Moreover, the binding free energy was calculated from the entire MD simulation trajectories highlighted greater binding free energy values for all newly identified compounds also substantiated the strong binding affection towards the GyrB in comparison to the novobiocin. Therefore, the proposed molecules might be considered as potential anti-TB chemical agents for future drug discovery purposes subjected to experimental validation. Graphical Abstract.
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Affiliation(s)
- Pranjali Mahadeo Tambe
- Department of Bioinformatics, Rajiv Gandhi Institute of IT and Biotechnology, Bharati Vidyapeeth Deemed University, Pune-Satara Road, Pune, India
| | - Shovonlal Bhowmick
- Department of Chemical Technology, University of Calcutta, 92 A.P.C. Road, Kolkata, India
| | - Sushil K Chaudhary
- Faculty of Pharmacy, DIT University, Mussoorie-Diversion Road, Makkawala, Dehradun, Uttarakhand, 248009, India
| | - Mohammad Rizwan Khan
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Saikh M Wabaidur
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Mohd Muddassir
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Preeti Chunarkar Patil
- Department of Bioinformatics, Rajiv Gandhi Institute of IT and Biotechnology, Bharati Vidyapeeth Deemed University, Pune-Satara Road, Pune, India
| | - Md Ataul Islam
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, M13 9PL, UK. .,School of Health Sciences, University of Kwazulu-Natal, Westville Campus, Durban, South Africa. .,Department of Chemical Pathology, Faculty of Health Sciences, University of Pretoria and National Health Laboratory Service Tshwane Academic Division, Pretoria, South Africa.
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10
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Xie W, Huang Y, Xiang Y, Xiong S, Manyande A, Du H. Insights into the Binding Mechanism of Polyphenols and Fish Myofibrillar Proteins Explored Using Multi-spectroscopic Methods. FOOD BIOPROCESS TECH 2020. [DOI: 10.1007/s11947-020-02439-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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11
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Ismail MM, Abdulwahab HG, Nossier ES, El Menofy NG, Abdelkhalek BA. Synthesis of novel 2-aminobenzothiazole derivatives as potential antimicrobial agents with dual DNA gyrase/topoisomerase IV inhibition. Bioorg Chem 2020; 94:103437. [DOI: 10.1016/j.bioorg.2019.103437] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 09/28/2019] [Accepted: 11/12/2019] [Indexed: 12/31/2022]
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12
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Qu S, Dai C, Shen Z, Tang Q, Wang H, Zhai B, Zhao L, Hao Z. Mechanism of Synergy Between Tetracycline and Quercetin Against Antibiotic Resistant Escherichia coli. Front Microbiol 2019; 10:2536. [PMID: 31824439 PMCID: PMC6882743 DOI: 10.3389/fmicb.2019.02536] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 10/21/2019] [Indexed: 11/13/2022] Open
Abstract
Treatment of multi-drug resistant (MDR) Escherichia coli intestinal infections are being hampered by the presence of the mcr-1 (colistin) and tet (tetracycline) resistance genes in these strains. We screened seven traditional Chinese medicines for their ability to synergize with tetracycline to provide an effective new drug for the treatment of animal intestinal diseases caused by MDR E. coli. Our primary screen identified quercetin as a compound that reduced the minimum inhibitory concentration (MIC) of tetracycline against the E. coli standard test strain American Type Culture Collection (ATCC) 25922 and clinical isolates fourfold from 4 and 256 μg/mL to 1 and 64 μg/mL, respectively. Low levels of quercetin in combination with tetracycline were bactericidal for clinical E. coli isolates and after 24 h, the differences between this combination and each drug singly were 108 CFU/mL. We used this combination therapy in a mouse infection model and found 100% survival after 48 h compared with <50% for each drug alone. This drug combination also synergized to disrupt the bacterial cell envelope resulting in increased permeability and cell lysis. These data demonstrate that combinatorial screening at low concentrations constitutes an efficient approach to identify clinically relevant quercetin/tetracycline combinations and is a valuable prototypical combination that has a high clinical potential against E. coli infections.
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Affiliation(s)
- Shaoqi Qu
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Cunchun Dai
- Agricultural Bio-Pharmaceutical Laboratory, Qingdao Agricultural University, Qingdao, China
| | - Zhangqi Shen
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Qihe Tang
- Agricultural Bio-Pharmaceutical Laboratory, Qingdao Agricultural University, Qingdao, China
| | - Haixia Wang
- Agricultural Bio-Pharmaceutical Laboratory, Qingdao Agricultural University, Qingdao, China
| | - Bing Zhai
- Agricultural Bio-Pharmaceutical Laboratory, Qingdao Agricultural University, Qingdao, China
| | - Li Zhao
- Agricultural Bio-Pharmaceutical Laboratory, Qingdao Agricultural University, Qingdao, China
| | - Zhihui Hao
- College of Veterinary Medicine, China Agricultural University, Beijing, China
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Ghasemi B, Abdollahi M, Beyzaei H, Hashemi S. Comparative antibacterial activity of synthetic N,S-Heterocyclic derivatives, MgO nanoparticles, and glycine on zoonotic Vibrio fluvialis. JOURNAL OF REPORTS IN PHARMACEUTICAL SCIENCES 2019. [DOI: 10.4103/jrptps.jrptps_49_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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14
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Badshah SL, Ullah A. New developments in non-quinolone-based antibiotics for the inhibiton of bacterial gyrase and topoisomerase IV. Eur J Med Chem 2018; 152:393-400. [DOI: 10.1016/j.ejmech.2018.04.059] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 04/23/2018] [Accepted: 04/29/2018] [Indexed: 01/06/2023]
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15
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Al-Nadaf AH, Salah SA, Taha MO. Discovery of new Gyrase β inhibitors via structure based modeling. Comput Biol Chem 2018; 74:263-272. [PMID: 29679863 DOI: 10.1016/j.compbiolchem.2018.03.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 03/10/2018] [Accepted: 03/13/2018] [Indexed: 11/16/2022]
Abstract
Gyrase B is an essential enzyme in the prokaryotes which became an attractive target for antibacterial agents. In our study, we implemented a wide range of docking configurations to dock 120 inhibitors into the in the ATP- binding pocket of Gyrase B enzyme (PDB code: 4GEE). LigandFit docking engines and six scoring functions were utilized in the study. Furthermore, the ligands were docked in their ionized and unionized forms into the hydrous and anhydrous binding pocket. We used docking-based Comparative Intermolecular Contacts Analysis (db-CICA) which is a novel methodology to validate and identify the optimal docking configurations. Three docking configurations were found to achieve self-consistent db-CICA models. The resulting db-CICA models were used to construct corresponding pharmacophoric models that were used to screen the National Cancer Institute (NCI) list of compounds. In-vitro study represents antibacterial activities for twelve hit molecules with the most active having IC50 of 20.9 μM.
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Affiliation(s)
- Afaf H Al-Nadaf
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Mu'tah University, Alkarak Jordan.
| | - Sajeda A Salah
- Department of Pharmaceutical Chemistry and Pharmacognacy, Faculty of Pharmacy, Applied Science Private University, Amman, Jordan
| | - Mutasem O Taha
- Drug Discovery Unit, Department of Pharmaceutical Sciences, Faculty of Pharmacy, University of Jordan, Amman, Jordan.
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16
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Nastasă C, Vodnar DC, Ionuţ I, Stana A, Benedec D, Tamaian R, Oniga O, Tiperciuc B. Antibacterial Evaluation and Virtual Screening of New Thiazolyl-Triazole Schiff Bases as Potential DNA-Gyrase Inhibitors. Int J Mol Sci 2018; 19:ijms19010222. [PMID: 29324679 PMCID: PMC5796171 DOI: 10.3390/ijms19010222] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 12/21/2017] [Accepted: 01/09/2018] [Indexed: 01/18/2023] Open
Abstract
The global spread of bacterial resistance to drugs used in therapy requires new potent and safe antimicrobial agents. DNA gyrases represent important targets in drug discovery. Schiff bases, thiazole, and triazole derivatives are considered key scaffolds in medicinal chemistry. Fifteen thiazolyl-triazole Schiff bases were evaluated for their antibacterial activity, measuring the growth inhibition zone diameter, the minimum inhibitory concentration (MIC), and the minimum bactericidal concentration (MBC), against Gram-positive (Staphylococcus aureus, Listeria monocytogenes) and Gram-negative (Escherichia coli, Salmonella typhimurium, Pseudomonas aeruginosa) bacteria. The inhibition of S. aureus and S. typhimurium was modest. Compounds B1, B2, and B9 showed a similar effect as ciprofloxacin, the antimicrobial reference, against L. monocytogenes. B10 displayed a better effect. Derivatives B1, B5–7, B9, and B11–15 expressed MIC values lower than the reference, against L. monocytogenes. B5, B6, and B11–15 strongly inhibited the growth of P. aeruginosa. All compounds were subjected to an in silico screening of the ADMET (absorption, distribution, metabolism, elimination, toxicity) properties. Molecular docking was performed on the gyrA and gyrB from L. monocytogenes. The virtual screening concluded that thiazolyl-triazole Schiff base B8 is the best drug-like candidate, satisfying requirements for both safety and efficacy, being more potent against the bacterial gyrA than ciprofloxacin.
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Affiliation(s)
- Cristina Nastasă
- Department of Pharmaceutical Chemistry, "Iuliu Haţieganu" University of Medicine and Pharmacy, 41 Victor Babeş Street, RO-400012 Cluj-Napoca, Romania.
| | - Dan C Vodnar
- Department of Food Science and Technology, University of Agricultural Sciences and Veterinary Medicine, 3-5 Mănăştur Street, RO-400372 Cluj-Napoca, Romania.
| | - Ioana Ionuţ
- Department of Pharmaceutical Chemistry, "Iuliu Haţieganu" University of Medicine and Pharmacy, 41 Victor Babeş Street, RO-400012 Cluj-Napoca, Romania.
| | - Anca Stana
- Department of Pharmaceutical Chemistry, "Iuliu Haţieganu" University of Medicine and Pharmacy, 41 Victor Babeş Street, RO-400012 Cluj-Napoca, Romania.
| | - Daniela Benedec
- Department of Pharmacognosy, "Iuliu Haţieganu" University of Medicine and Pharmacy, 12 Ion Creangă Street, RO-400010 Cluj-Napoca, Romania.
| | - Radu Tamaian
- National Institute for Research and Development for Cryogenic and Isotopic Technologies, 4th Uzinei Street, RO-240050 Râmnicu Vâlcea, Romania.
- SC Biotech Corp SRL, 4th Uzinei Street, RO-240050 Râmnicu Vâlcea, Romania.
| | - Ovidiu Oniga
- Department of Pharmaceutical Chemistry, "Iuliu Haţieganu" University of Medicine and Pharmacy, 41 Victor Babeş Street, RO-400012 Cluj-Napoca, Romania.
| | - Brînduşa Tiperciuc
- Department of Pharmaceutical Chemistry, "Iuliu Haţieganu" University of Medicine and Pharmacy, 41 Victor Babeş Street, RO-400012 Cluj-Napoca, Romania.
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17
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Wang S, Yao J, Zhou B, Yang J, Chaudry MT, Wang M, Xiao F, Li Y, Yin W. Bacteriostatic Effect of Quercetin as an Antibiotic Alternative In Vivo and Its Antibacterial Mechanism In Vitro. J Food Prot 2018; 81:68-78. [PMID: 29271686 DOI: 10.4315/0362-028x.jfp-17-214] [Citation(s) in RCA: 192] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Quercetin, a ubiquitous flavonoid, is known to have antibacterial effects. The purpose of this study was to investigate the effect of quercetin on cecal microbiota of Arbor Acre (AA) broiler chickens in vivo and the bacteriostatic effect and antibacterial mechanism of quercetin in vitro. In vivo, 480 AA broilers (1 day old) were randomly allotted to four treatments (negative control and 0.2, 0.4, or 0.6 g of quercetin per kg of diet) for 42 days. Cecal microbial population and distribution were measured at the end of the experiment. The cecal microflora in these broilers included Proteobacteria, Fimicutes, Bacteroidetes, and Deferribacteres. Compared with the negative control, quercetin significantly decreased the copies of Pseudomonas aeruginosa ( P < 0.05), Salmonella enterica serotype Typhimurium ( P < 0.01), Staphylococcus aureus ( P < 0.01), and Escherichia coli ( P < 0.01) but significantly increased the copies of Lactobacillus ( P < 0.01), Bifidobacterium ( P < 0.01), and total bacteria ( P < 0.01). In vitro, we investigated the bacteriostatic effect of quercetin on four kinds of bacteria ( E. coli, P. aeruginosa, S. enterica Typhimurium, and S. aureus) and the antibacterial mechanism of quercetin in E. coli and S. aureus. The bacteriostatic effect of quercetin was stronger on gram-positive bacteria than on gram-negative bacteria. Quercetin damaged the cell walls and membranes of E. coli (at 50 × MIC) and S. aureus (at 10 × MIC). Compared with the control, the activity of the extracellular alkaline phosphatase and β-galactosidase and concentrations of soluble protein in E. coli and S. aureus were significantly increased (all P < 0.01), and the activity of ATP in S. aureus was significantly increased ( P < 0.01); however, no significant change in ATP activity in E. coli was observed ( P > 0.05). These results suggest that quercetin has potential as an alternative antibiotic feed additive in animal production.
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Affiliation(s)
- Shengan Wang
- 1 Institute of Animal Nutrition, Northeast Agricultural University, Harbin, Heilongjiang Province 150030, People's Republic of China
| | - Jiaying Yao
- 1 Institute of Animal Nutrition, Northeast Agricultural University, Harbin, Heilongjiang Province 150030, People's Republic of China
| | - Bo Zhou
- 1 Institute of Animal Nutrition, Northeast Agricultural University, Harbin, Heilongjiang Province 150030, People's Republic of China
| | - Jiaxin Yang
- 1 Institute of Animal Nutrition, Northeast Agricultural University, Harbin, Heilongjiang Province 150030, People's Republic of China
| | - Maria T Chaudry
- 1 Institute of Animal Nutrition, Northeast Agricultural University, Harbin, Heilongjiang Province 150030, People's Republic of China
| | - Mi Wang
- 1 Institute of Animal Nutrition, Northeast Agricultural University, Harbin, Heilongjiang Province 150030, People's Republic of China
| | - Fenglin Xiao
- 1 Institute of Animal Nutrition, Northeast Agricultural University, Harbin, Heilongjiang Province 150030, People's Republic of China
| | - Yao Li
- 1 Institute of Animal Nutrition, Northeast Agricultural University, Harbin, Heilongjiang Province 150030, People's Republic of China
| | - Wenzhe Yin
- 2 Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang Province 150086, People's Republic of China
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18
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Tomašič T, Mirt M, Barančoková M, Ilaš J, Zidar N, Tammela P, Kikelj D. Design, synthesis and biological evaluation of 4,5-dibromo-N-(thiazol-2-yl)-1H-pyrrole-2-carboxamide derivatives as novel DNA gyrase inhibitors. Bioorg Med Chem 2017; 25:338-349. [DOI: 10.1016/j.bmc.2016.10.038] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 10/27/2016] [Accepted: 10/29/2016] [Indexed: 11/25/2022]
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19
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Biophysical Studies of Bacterial Topoisomerases Substantiate Their Binding Modes to an Inhibitor. Biophys J 2016; 109:1969-77. [PMID: 26536273 DOI: 10.1016/j.bpj.2015.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 09/25/2015] [Accepted: 10/01/2015] [Indexed: 12/18/2022] Open
Abstract
Bacterial DNA topoisomerases are essential for bacterial growth and are attractive, important targets for developing antibacterial drugs. Consequently, different potent inhibitors that target bacterial topoisomerases have been developed. However, the development of potent broad-spectrum inhibitors against both Gram-positive (G(+)) and Gram-negative (G(-)) bacteria has proven challenging. In this study, we carried out biophysical studies to better understand the molecular interactions between a potent bis-pyridylurea inhibitor and the active domains of the E-subunits of topoisomerase IV (ParE) from a G(+) strain (Streptococcus pneumoniae (sParE)) and a G(-) strain (Pseudomonas aeruginosa (pParE)). NMR results demonstrated that the inhibitor forms a tight complex with ParEs and the resulting complexes adopt structural conformations similar to those observed for free ParEs in solution. Further chemical-shift perturbation experiments and NOE analyses indicated that there are four regions in ParE that are important for inhibitor binding, namely, α2, the loop between β2 and α3, and the β2 and β6 strands. Surface plasmon resonance showed that this inhibitor binds to sParE with a higher KD than pParE. Point mutations in α2 of ParE, such as A52S (sParE), affected its binding affinity with the inhibitor. Taken together, these results provide a better understanding of the development of broad-spectrum antibacterial agents.
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20
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Xiabing M, Ablajan K, Obul M, Seydimemet M, Ruzi R, Wenbo L. Facial one-pot, three-component synthesis of thiazole compounds by the reactions of aldehyde/ketone, thiosemicarbazide and chlorinated carboxylic ester derivatives. Tetrahedron 2016. [DOI: 10.1016/j.tet.2016.03.053] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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21
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ghasemi B, Beyzaie H, Majidiani H. A Comparative Study on the Antibacterial Effects of Some Newly Synthesized Thiazole, Imidazolidine and Tetrahydropyrimidine Derivatives Against Bacillus cereus and Salmonella typhimurium. PHARMACEUTICAL SCIENCES 2016. [DOI: 10.15171/ps.2016.10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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22
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Mesleh MF, Cross JB, Zhang J, Kahmann J, Andersen OA, Barker J, Cheng RK, Felicetti B, Wood M, Hadfield AT, Scheich C, Moy TI, Yang Q, Shotwell J, Nguyen K, Lippa B, Dolle R, Ryan MD. Fragment-based discovery of DNA gyrase inhibitors targeting the ATPase subunit of GyrB. Bioorg Med Chem Lett 2016; 26:1314-8. [DOI: 10.1016/j.bmcl.2016.01.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 01/03/2016] [Accepted: 01/05/2016] [Indexed: 11/16/2022]
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23
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The antibiotic activity and mechanisms of sugarcane (Saccharum officinarum L.) bagasse extract against food-borne pathogens. Food Chem 2015; 185:112-8. [DOI: 10.1016/j.foodchem.2015.03.120] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 03/10/2015] [Accepted: 03/30/2015] [Indexed: 01/05/2023]
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24
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Li Y, Wong YX, Poh ZY, Wong YL, Lee MY, Ng HQ, Liu B, Hung AW, Cherian J, Hill J, Keller TH, Kang C. NMR structural characterization of the N-terminal active domain of the gyrase B subunit from Pseudomonas aeruginosa and its complex with an inhibitor. FEBS Lett 2015; 589:2683-9. [PMID: 26272827 DOI: 10.1016/j.febslet.2015.07.044] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 07/08/2015] [Accepted: 07/26/2015] [Indexed: 01/18/2023]
Abstract
The N-terminal ATP binding domain of the DNA gyrase B subunit is a validated drug target for antibacterial drug discovery. Structural information for this domain (pGyrB) from Pseudomonas aeruginosa is still missing. In this study, the interaction between pGyrB and a bis-pyridylurea inhibitor was characterized using several biophysical methods. We further carried out structural analysis of pGyrB using NMR spectroscopy. The secondary structures of free and inhibitor bound pGyrB were obtained based on backbone chemical shift assignment. Chemical shift perturbation and NOE experiments demonstrated that the inhibitor binds to the ATP binding pocket. The results of this study will be helpful for drug development targeting P. aeruginosa.
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Affiliation(s)
- Yan Li
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore
| | - Yun Xuan Wong
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore
| | - Zhi Ying Poh
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore
| | - Ying Lei Wong
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore
| | - Michelle Yueqi Lee
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore
| | - Hui Qi Ng
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore
| | - Boping Liu
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore
| | - Alvin W Hung
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore
| | - Joseph Cherian
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore
| | - Jeffrey Hill
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore
| | - Thomas H Keller
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore
| | - CongBao Kang
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore.
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25
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Pogorelčnik B, Janežič M, Sosič I, Gobec S, Solmajer T, Perdih A. 4,6-Substituted-1,3,5-triazin-2(1H)-ones as monocyclic catalytic inhibitors of human DNA topoisomerase IIα targeting the ATP binding site. Bioorg Med Chem 2015; 23:4218-4229. [PMID: 26183545 DOI: 10.1016/j.bmc.2015.06.049] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 06/15/2015] [Accepted: 06/18/2015] [Indexed: 10/23/2022]
Abstract
Human DNA topoisomerase IIα (htIIα) is a validated target for the development of novel anticancer agents. Starting from our discovered 4-amino-1,3,5-triazine inhibitors of htIIα, we investigated a library of 2,4,6-trisubstituted-1,3,5-triazines for novel inhibitors that bind to the htIIα ATP binding site using a combination of structure-based and ligand-based pharmacophore models and molecular docking. 4,6-substituted-1,3,5-triazin-2(1H)-ones 8, 9 and 14 were identified as novel inhibitors with activity comparable to the established drug etoposide (1). Compound 8 inhibits the htIIα decatenation in a superior fashion to etoposide. Cleavage assays demonstrated that selected compounds 8 and 14 do not act as poisons and antagonize the poison effect of etoposide. Microscale thermophoresis (MST) confirmed binding of compound 8 to the htIIα ATPase domain and compound 14 effectively inhibits the htIIα mediated ATP hydrolysis. The molecular dynamics simulation study provides further insight into the molecular recognition. The 4,6-disubstituted-1,3,5-triazin-2(1H)-ones represent the first validated monocyclic class of catalytic inhibitors that bind to the to the htIIα ATPase domain.
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Affiliation(s)
| | - Matej Janežič
- National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia
| | - Izidor Sosič
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Tom Solmajer
- National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia
| | - Andrej Perdih
- National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia.
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26
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Pogorelčnik B, Brvar M, Žegura B, Filipič M, Solmajer T, Perdih A. Discovery of Mono- and Disubstituted 1H-Pyrazolo[3,4]pyrimidines and 9H-Purines as Catalytic Inhibitors of Human DNA Topoisomerase IIα. ChemMedChem 2014; 10:345-59. [DOI: 10.1002/cmdc.201402459] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Indexed: 11/07/2022]
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27
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Pogorelčnik B, Brvar M, Zajc I, Filipič M, Solmajer T, Perdih A. Monocyclic 4-amino-6-(phenylamino)-1,3,5-triazines as inhibitors of human DNA topoisomerase IIα. Bioorg Med Chem Lett 2014; 24:5762-5768. [PMID: 25453816 DOI: 10.1016/j.bmcl.2014.10.042] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 10/09/2014] [Accepted: 10/14/2014] [Indexed: 10/24/2022]
Abstract
Human DNA topoisomerase IIα (htIIα) is a validated target for the development of anticancer agents. Starting from the available information about the binding of the purine-based htIIα inhibitors in the ATP binding site we designed a virtual screening campaign combining structure-based and ligand-based pharmacophores with a molecular docking calculation searching for compounds that would contain a monocycle mimetic of the purine moiety. We discovered novel 4-amino-6-(phenylamino)-1,3,5-triazines 6, 7 and 11 as monocyclic htIIα inhibitors targeting the ATP binding site. Compound 6 from the 1,3,5-triazine series also displayed cytotoxicity properties in hepatocellular carcinoma (HepG2) cell lines and selectivity against human umbilical vein endothelial (HUVEC) cell lines.
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Affiliation(s)
| | - Matjaž Brvar
- National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia
| | - Irena Zajc
- National Institute of Biology, Department of Genetic Toxicology and Cancer Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Metka Filipič
- National Institute of Biology, Department of Genetic Toxicology and Cancer Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Tom Solmajer
- National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia
| | - Andrej Perdih
- National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia.
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28
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Perdih A, Hrast M, Barreteau H, Gobec S, Wolber G, Solmajer T. Inhibitor design strategy based on an enzyme structural flexibility: a case of bacterial MurD ligase. J Chem Inf Model 2014; 54:1451-66. [PMID: 24724969 DOI: 10.1021/ci500104m] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Increasing bacterial resistance to available antibiotics stimulated the discovery of novel efficacious antibacterial agents. The biosynthesis of the bacterial peptidoglycan, where the MurD enzyme is involved in the intracellular phase of the UDP-MurNAc-pentapeptide formation, represents a collection of highly selective targets for novel antibacterial drug design. In our previous computational studies, the C-terminal domain motion of the MurD ligase was investigated using Targeted Molecular Dynamic (TMD) simulation and the Off-Path Simulation (OPS) technique. In this study, we present a drug design strategy using multiple protein structures for the identification of novel MurD ligase inhibitors. Our main focus was the ATP-binding site of the MurD enzyme. In the first stage, three MurD protein conformations were selected based on the obtained OPS/TMD data as the initial criterion. Subsequently, a two-stage virtual screening approach was utilized combining derived structure-based pharmacophores with molecular docking calculations. Selected compounds were then assayed in the established enzyme binding assays, and compound 3 from the aminothiazole class was discovered to act as a dual MurC/MurD inhibitor in the micomolar range. A steady-state kinetic study was performed on the MurD enzyme to provide further information about the mechanistic aspects of its inhibition. In the final stage, all used conformations of the MurD enzyme with compound 3 were simulated in classical molecular dynamics (MD) simulations providing atomistic insights of the experimental results. Overall, the study depicts several challenges that need to be addressed when trying to hit a flexible moving target such as the presently studied bacterial MurD enzyme and show the possibilities of how computational tools can be proficiently used at all stages of the drug discovery process.
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Affiliation(s)
- Andrej Perdih
- National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia
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29
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Prasad VGNV, krishna BV, Swamy PL, Rao TS, Rao GS. Antibacterial synergy between quercetin and polyphenolic acids against bacterial pathogens of fish. ASIAN PACIFIC JOURNAL OF TROPICAL DISEASE 2014. [DOI: 10.1016/s2222-1808(14)60464-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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30
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Abstract
Computer-aided drug discovery/design methods have played a major role in the development of therapeutically important small molecules for over three decades. These methods are broadly classified as either structure-based or ligand-based methods. Structure-based methods are in principle analogous to high-throughput screening in that both target and ligand structure information is imperative. Structure-based approaches include ligand docking, pharmacophore, and ligand design methods. The article discusses theory behind the most important methods and recent successful applications. Ligand-based methods use only ligand information for predicting activity depending on its similarity/dissimilarity to previously known active ligands. We review widely used ligand-based methods such as ligand-based pharmacophores, molecular descriptors, and quantitative structure-activity relationships. In addition, important tools such as target/ligand data bases, homology modeling, ligand fingerprint methods, etc., necessary for successful implementation of various computer-aided drug discovery/design methods in a drug discovery campaign are discussed. Finally, computational methods for toxicity prediction and optimization for favorable physiologic properties are discussed with successful examples from literature.
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Affiliation(s)
- Gregory Sliwoski
- Jr., Center for Structural Biology, 465 21st Ave South, BIOSCI/MRBIII, Room 5144A, Nashville, TN 37232-8725.
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31
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Mayer C, Janin YL. Non-quinolone inhibitors of bacterial type IIA topoisomerases: a feat of bioisosterism. Chem Rev 2013; 114:2313-42. [PMID: 24313284 DOI: 10.1021/cr4003984] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Claudine Mayer
- Unité de Microbiologie Structurale, Département de Biologie Structurale et Chimie, Institut Pasteur , 25 rue du Dr. Roux, 75724 Paris Cedex 15, France
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33
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Maharaj Y, Soliman MES. Identification of Novel Gyrase B Inhibitors as Potential Anti-TB drugs: Homology Modelling, Hybrid Virtual Screening and Molecular Dynamics Simulations. Chem Biol Drug Des 2013; 82:205-15. [DOI: 10.1111/cbdd.12152] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 04/15/2013] [Accepted: 04/18/2013] [Indexed: 12/16/2022]
Affiliation(s)
- Yushir Maharaj
- School of Health Sciences; University of KwaZulu-Natal; Durban; 4001; South Africa
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34
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Saeed A, Al-Masoudi NA, Latif M. Synthesis and Antiviral Activity of New Substituted Methyl [2-(arylmethylene-hydrazino)-4-oxo-thiazolidin-5-ylidene]acetates. Arch Pharm (Weinheim) 2013; 346:618-25. [DOI: 10.1002/ardp.201300057] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Revised: 04/03/2013] [Accepted: 04/12/2013] [Indexed: 01/24/2023]
Affiliation(s)
- Aamer Saeed
- Department of Chemistry; Quaid-I-Azam University; Islamabad; Pakistan
| | - Najim A. Al-Masoudi
- Department of Chemistry; College of Science, University of Basrah; Basrah; Iraq
| | - Muhammad Latif
- Cancer and Infectious Disease Research Center, Bio-Organic Science Division; Korea Research Institute of Chemical Technology, University of Science and Technology; Daejeon; Republic of Korea
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35
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Jayaraman P, Sakharkar KR, Lim C, Siddiqi MI, Dhillon SK, Sakharkar MK. Novel phytochemical-antibiotic conjugates as multitarget inhibitors of Pseudomononas aeruginosa GyrB/ParE and DHFR. DRUG DESIGN DEVELOPMENT AND THERAPY 2013; 7:449-75. [PMID: 23818757 PMCID: PMC3692347 DOI: 10.2147/dddt.s43964] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Background There is a dearth of treatment options for community-acquired and nosocomial Pseudomonas infections due to several rapidly emerging multidrug resistant phenotypes, which show resistance even to combination therapy. As an alternative, developing selective promiscuous hybrid compounds for simultaneous modulation of multiple targets is highly appreciated because it is difficult for the pathogen to develop resistance when an inhibitor has activity against multiple targets. Methods In line with our previous work on phytochemical–antibiotic combination assays and knowledge-based methods, using a fragment combination approach we here report a novel drug design strategy of conjugating synergistic phytochemical–antibiotic combinations into a single hybrid entity for multi-inhibition of P. aeruginosa DNA gyrase subunit B (GyrB)/topoisomerase IV subunit B (ParE) and dihydrofolate reductase (DHFR) enzymes. The designed conjugates were evaluated for their multitarget specificity using various computational methods including docking and dynamic simulations, drug-likeness using molecular properties calculations, and pharmacophoric features by stereoelectronic property predictions. Results Evaluation of the designed hybrid compounds based on their physicochemical properties has indicated that they are promising drug candidates with drug-like pharmacotherapeutic profiles. In addition, the stereoelectronic properties such as HOMO (highest occupied molecular orbital), LUMO (lowest unoccupied molecular orbital), and MEP (molecular electrostatic potential) maps calculated by quantum chemical methods gave a good correlation with the common pharmacophoric features required for multitarget inhibition. Furthermore, docking and dynamics simulations revealed that the designed compounds have favorable binding affinity and stability in both the ATP-binding sites of GyrB/ParE and the folate-binding site of DHFR, by forming strong hydrogen bonds and hydrophobic interactions with key active site residues. Conclusion This new design concept of hybrid “phyto-drug” scaffolds, and their simultaneous perturbation of well-established antibacterial targets from two unrelated pathways, appears to be very promising and could serve as a prospective lead in multitarget drug discovery.
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Affiliation(s)
- Premkumar Jayaraman
- Biomedical Engineering Research Centre, Nanyang Technological University, Singapore
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Saíz-Urra L, Pérez MÁC, Froeyen M. Thermodynamic computational approach to capture molecular recognition in the binding of different inhibitors to the DNA gyrase B subunit from Escherichia coli. J Mol Model 2013; 19:3187-200. [PMID: 23625033 DOI: 10.1007/s00894-013-1849-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 04/04/2013] [Indexed: 11/29/2022]
Abstract
DNA gyrase subunit B, that catalyzes the hydrolysis of ATP, is an attractive target for the development of antibacterial drugs. This work is intended to rationalize molecular recognition at DNA gyrase B enzyme - inhibitor binding interface through the evaluation of different scoring functions in finding the correct pose and scoring properly 50 Escherichia coli DNA Gyrase B inhibitors belonging to five different classes. Improving the binding free energy calculation accuracy is further attempted by using rescoring schemes after short molecular dynamic simulations of the obtained docked complexes. These data are then compared with the corresponding experimental enzyme activity data. The results are analyzed from a structural point of view emphasizing the strengths and limitations of the techniques applied in the study.
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Affiliation(s)
- Liane Saíz-Urra
- Laboratory for Medicinal Chemistry, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
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Brvar M, Perdih A, Renko M, Anderluh G, Turk D, Solmajer T. Structure-based discovery of substituted 4,5'-bithiazoles as novel DNA gyrase inhibitors. J Med Chem 2012; 55:6413-26. [PMID: 22731783 DOI: 10.1021/jm300395d] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Bacterial DNA gyrase is a well-established and validated target for the development of novel antibacterials. Starting from the available structural information about the binding of the natural product inhibitor, clorobiocin, we identified a novel series of 4'-methyl-N(2)-phenyl-[4,5'-bithiazole]-2,2'-diamine inhibitors of gyrase B with a low micromolar inhibitory activity by implementing a two-step structure-based design procedure. This novel class of DNA gyrase inhibitors was extensively investigated by various techniques (differential scanning fluorimetry, surface plasmon resonance, and microscale thermophoresis). The binding mode of the potent inhibitor 18 was revealed by X-ray crystallography, confirming our initial in silico binding model. Furthermore, the high resolution of the complex structure allowed for the placement of the Gly97-Ser108 flexible loop, thus revealing its role in binding of this class of compounds. The crystal structure of the complex protein G24 and inhibitor 18 provides valuable information for further optimization of this novel class of DNA gyrase B inhibitors.
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Affiliation(s)
- Matjaž Brvar
- National Institute of Chemistry, Laboratory for Biocomputing and Bioinformatics, 1001 Ljubljana, Slovenia
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Brvar M, Perdih A, Hodnik V, Renko M, Anderluh G, Jerala R, Solmajer T. In silico discovery and biophysical evaluation of novel 5-(2-hydroxybenzylidene) rhodanine inhibitors of DNA gyrase B. Bioorg Med Chem 2012; 20:2572-80. [DOI: 10.1016/j.bmc.2012.02.052] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Revised: 02/15/2012] [Accepted: 02/21/2012] [Indexed: 11/26/2022]
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Aboul-Fadl T, Abdel-Aziz HA, Abdel-Hamid MK, Elsaman T, Thanassi J, Pucci MJ. Schiff bases of indoline-2,3-dione: potential novel inhibitors of Mycobacterium tuberculosis (Mtb) DNA gyrase. Molecules 2011; 16:7864-79. [PMID: 22143547 PMCID: PMC6264139 DOI: 10.3390/molecules16097864] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Revised: 08/23/2011] [Accepted: 09/07/2011] [Indexed: 11/19/2022] Open
Abstract
In the present study a series of Schiff bases of indoline-2,3-dione were synthesized and investigated for their Mtb gyrase inhibitory activity. Promising inhibitory activity was demonstrated with some of these derivatives, which exhibited IC50 values ranging from 50–157 μM. The orientation and the ligand-receptor interactions of such molecules within the Mtb DNA gyrase A subunit active site were investigated applying a multi-step docking protocol using Molecular Operating Environment (MOE) and Autodock4 docking software. The results revealed the importance of the isatin moiety and the connecting side chain for strong interactions with the enzyme active site. Among the tested compounds the terminal aromatic ring benzofuran showed the best activity. Promising new leads for developing a novel class of Mtb gyrase inhibitors were obtained from Schiff bases of indoline-2,3-dione.
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Affiliation(s)
- Tarek Aboul-Fadl
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia.
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Angehrn P, Goetschi E, Gmuender H, Hebeisen P, Hennig M, Kuhn B, Luebbers T, Reindl P, Ricklin F, Schmitt-Hoffmann A. A New DNA Gyrase Inhibitor Subclass of the Cyclothialidine Family Based on a Bicyclic Dilactam−Lactone Scaffold. Synthesis and Antibacterial Properties. J Med Chem 2011; 54:2207-24. [DOI: 10.1021/jm1014023] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Peter Angehrn
- F. Hoffmann-La Roche Ltd., Discovery Chemistry, CH-4070 Basel, Switzerland
| | - Erwin Goetschi
- F. Hoffmann-La Roche Ltd., Discovery Chemistry, CH-4070 Basel, Switzerland
| | - Hans Gmuender
- F. Hoffmann-La Roche Ltd., Discovery Chemistry, CH-4070 Basel, Switzerland
| | - Paul Hebeisen
- F. Hoffmann-La Roche Ltd., Discovery Chemistry, CH-4070 Basel, Switzerland
| | - Michael Hennig
- F. Hoffmann-La Roche Ltd., Discovery Chemistry, CH-4070 Basel, Switzerland
| | - Bernd Kuhn
- F. Hoffmann-La Roche Ltd., Discovery Chemistry, CH-4070 Basel, Switzerland
| | - Thomas Luebbers
- F. Hoffmann-La Roche Ltd., Discovery Chemistry, CH-4070 Basel, Switzerland
| | - Peter Reindl
- F. Hoffmann-La Roche Ltd., Discovery Chemistry, CH-4070 Basel, Switzerland
| | - Fabienne Ricklin
- F. Hoffmann-La Roche Ltd., Discovery Chemistry, CH-4070 Basel, Switzerland
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