1
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Zidar N, Onali A, Peršolja P, Benedetto Tiz D, Dernovšek J, Skok Ž, Durcik M, Cotman AE, Hrast Rambaher M, Cruz CD, Tammela P, Senerovic L, Jovanovic M, Szili PÉ, Czikkely MS, Pál C, Zega A, Peterlin Mašič L, Ilaš J, Tomašič T, Kikelj D. Improved N-phenylpyrrolamide inhibitors of DNA gyrase as antibacterial agents for high-priority bacterial strains. Eur J Med Chem 2024; 278:116823. [PMID: 39236496 DOI: 10.1016/j.ejmech.2024.116823] [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: 04/11/2024] [Revised: 08/29/2024] [Accepted: 08/30/2024] [Indexed: 09/07/2024]
Abstract
In this work, we describe an improved series of N-phenylpyrrolamide inhibitors that exhibit potent activity against DNA gyrase and are highly effective against high-priority gram-positive bacteria. The most potent compounds show low nanomolar IC50 values against Escherichia coli DNA gyrase, and in addition, compound 7c also inhibits E. coli topoisomerase IV in the nanomolar concentration range, making it a promising candidate for the development of potent dual inhibitors for these enzymes. All tested compounds show high selectivity towards the human isoform DNA topoisomerase IIα. Compounds 6a, 6d, 6e and 6f show MIC values between 0.031 and 0.0625 μg/mL against vancomycin-intermediate S. aureus (VISA) and Enterococcus faecalis strains. Compound 6g shows an inhibitory effect against the methicillin-resistant S. aureus strain (MRSA) with a MIC of 0.0625 μg/mL and against the E. faecalis strain with a MIC of 0.125 μg/mL. In a time-kill assay, compound 6d showed a dose-dependent bactericidal effect on the MRSA strain and achieved bactericidal activity at 8 × MIC after 8 h. The duration of the post-antibiotic effect (PAE) on the MRSA strain for compound 6d was 2 h, which corresponds to the PAE duration for ciprofloxacin. The compounds were not cytotoxic at effective concentrations, as determined in an MTS assay on the MCF-7 breast cancer cell line.
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Affiliation(s)
- Nace Zidar
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia.
| | - Alessia Onali
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Peter Peršolja
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Davide Benedetto Tiz
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Jaka Dernovšek
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Žiga Skok
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Martina Durcik
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Andrej Emanuel Cotman
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Martina Hrast Rambaher
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Cristina D Cruz
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, Viikinkaari 5E, Helsinki, 00014, Finland
| | - Päivi Tammela
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, Viikinkaari 5E, Helsinki, 00014, Finland
| | - Lidija Senerovic
- Laboratory for Microbial Molecular Genetics and Ecology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11 042, Belgrade, Serbia
| | - Milija Jovanovic
- Laboratory for Microbial Molecular Genetics and Ecology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11 042, Belgrade, Serbia
| | - Petra Éva Szili
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, H-6726, Hungary
| | - Márton Simon Czikkely
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, H-6726, Hungary; Doctoral School of Multidisciplinary Medical Sciences, University of Szeged, Szeged, HU-6722, Hungary; Department of Forensic Medicine, Albert-Szent-Györgyi Medical School, University of Szeged, Szeged, HU-6722, Hungary
| | - Csaba Pál
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, H-6726, Hungary
| | - Anamarija Zega
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Lucija Peterlin Mašič
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Janez Ilaš
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Tihomir Tomašič
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Danijel Kikelj
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
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2
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Cotman AE, Fulgheri F, Piga M, Peršolja P, Tiz DB, Skok Ž, Durcik M, Sterle M, Dernovšek J, Cruz CD, Tammela P, Szili PÉ, Daruka L, Pál C, Zega A, Mašič LP, Ilaš J, Tomašič T, Kikelj D, Zidar N. New N-phenylpyrrolamide inhibitors of DNA gyrase with improved antibacterial activity. RSC Adv 2024; 14:28423-28454. [PMID: 39247510 PMCID: PMC11378028 DOI: 10.1039/d4ra04802d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Accepted: 08/30/2024] [Indexed: 09/10/2024] Open
Abstract
This study presents the discovery of a new series of N-phenylpyrrolamide inhibitors of bacterial DNA gyrase with improved antibacterial activity. The most potent inhibitors had low nanomolar IC50 values against Escherichia coli DNA gyrase (IC50; 2-20 nM) and E. coli topoisomerase IV (22i, IC50 = 143 nM). Importantly, none of the compounds showed activity against human DNA topoisomerase IIα, indicating selectivity for bacterial targets. Among the tested compounds, 22e emerged as the most effective against Gram-positive bacteria with minimum inhibitory concentration (MIC) values of 0.25 μg mL-1 against Staphylococcus aureus ATCC 29213 and MRSA, and 0.125 μg mL-1 against Enterococcus faecalis ATCC 29212. For Gram-negative bacteria, compounds 23b and 23c showed the greatest efficacy with MIC values ranging from 4 to 32 μg mL-1 against E. coli ATCC 25922, Pseudomonas aeruginosa ATCC 27853, Acinetobacter baumannii ATCC 17978 and A. baumannii ATCC 19606. Notably, compound 23b showed promising activity against the clinically relevant Gram-negative pathogen Klebsiella pneumoniae ATCC 10031, with an MIC of 0.0625 μg mL-1. Furthermore, compounds 23a and 23c exhibited significantly lower susceptibility to resistance development compared to novobiocin in S. aureus ATCC 29213 and K. pneumoniae ATCC 10031. Overall, the most promising compounds of this series showed excellent on-target potency, marking a significant improvement over previous N-phenylpyrrolamide inhibitors.
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Affiliation(s)
- Andrej Emanuel Cotman
- University of Ljubljana, Faculty of Pharmacy Aškerčeva cesta 7 1000 Ljubljana Slovenia
| | - Federica Fulgheri
- University of Ljubljana, Faculty of Pharmacy Aškerčeva cesta 7 1000 Ljubljana Slovenia
| | - Martina Piga
- University of Ljubljana, Faculty of Pharmacy Aškerčeva cesta 7 1000 Ljubljana Slovenia
| | - Peter Peršolja
- University of Ljubljana, Faculty of Pharmacy Aškerčeva cesta 7 1000 Ljubljana Slovenia
| | - Davide Benedetto Tiz
- University of Ljubljana, Faculty of Pharmacy Aškerčeva cesta 7 1000 Ljubljana Slovenia
| | - Žiga Skok
- University of Ljubljana, Faculty of Pharmacy Aškerčeva cesta 7 1000 Ljubljana Slovenia
| | - Martina Durcik
- University of Ljubljana, Faculty of Pharmacy Aškerčeva cesta 7 1000 Ljubljana Slovenia
| | - Maša Sterle
- University of Ljubljana, Faculty of Pharmacy Aškerčeva cesta 7 1000 Ljubljana Slovenia
| | - Jaka Dernovšek
- University of Ljubljana, Faculty of Pharmacy Aškerčeva cesta 7 1000 Ljubljana Slovenia
| | - Cristina D Cruz
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki P.O. Box 56, Viikinkaari 5E Helsinki 00014 Finland
| | - Päivi Tammela
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki P.O. Box 56, Viikinkaari 5E Helsinki 00014 Finland
| | - Petra Éva Szili
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences Szeged H-6726 Hungary
| | - Lejla Daruka
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences Szeged H-6726 Hungary
| | - Csaba Pál
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences Szeged H-6726 Hungary
| | - Anamarija Zega
- University of Ljubljana, Faculty of Pharmacy Aškerčeva cesta 7 1000 Ljubljana Slovenia
| | - Lucija Peterlin Mašič
- University of Ljubljana, Faculty of Pharmacy Aškerčeva cesta 7 1000 Ljubljana Slovenia
| | - Janez Ilaš
- University of Ljubljana, Faculty of Pharmacy Aškerčeva cesta 7 1000 Ljubljana Slovenia
| | - Tihomir Tomašič
- University of Ljubljana, Faculty of Pharmacy Aškerčeva cesta 7 1000 Ljubljana Slovenia
| | - Danijel Kikelj
- University of Ljubljana, Faculty of Pharmacy Aškerčeva cesta 7 1000 Ljubljana Slovenia
| | - Nace Zidar
- University of Ljubljana, Faculty of Pharmacy Aškerčeva cesta 7 1000 Ljubljana Slovenia
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3
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Gutierrez L, Peršolja P, Tosso R, Zidar N, Kikelj D, Enriz RD. New ATP-competitive inhibitors of E. coli GyrB obtained from the mapping of the hydrophobic floor at the binding site: synthesis and biological evaluation. RSC Med Chem 2024:d4md00498a. [PMID: 39290385 PMCID: PMC11403825 DOI: 10.1039/d4md00498a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Accepted: 08/21/2024] [Indexed: 09/19/2024] Open
Abstract
We mapped the hydrophobic floor, an interesting subsite at the active site of DNA gyrase B (GyrB) from E. coli. We synthesized three new compounds with pendant groups targeting the hydrophobic floor and evaluated their inhibitory activities on DNA gyrase. A new benzothiazole derivative with a benzyl substituent at position 3 of the benzothiazole ring exhibited strong inhibitory activity against E. coli DNA gyrase (IC50 = 19 ± 3 nM). An exhaustive conformational study using potential energy surfaces (PESs) allowed us to map the new subsite evaluating all critical points on the surface and conformational interconversion pathways. We analyzed the molecular interactions using QTAIM calculations. Our data provide insights into the mechanism of action of these new ligands at the molecular level. Theoretical and experimental data suggest that new ligand optimization strategies should focus on strengthening interactions at the hydrophobic floor while preserving the binding mode of the main scaffold.
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Affiliation(s)
- Lucas Gutierrez
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL) Ejercito de los Andes 950 5700 San Luis Argentina
| | - Peter Peršolja
- Faculty of Pharmacy, University of Ljubljana Aškerčeva cesta 7 1000 Ljubljana Slovenia
| | - Rodrigo Tosso
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL) Ejercito de los Andes 950 5700 San Luis Argentina
| | - Nace Zidar
- Faculty of Pharmacy, University of Ljubljana Aškerčeva cesta 7 1000 Ljubljana Slovenia
| | - Danijel Kikelj
- Faculty of Pharmacy, University of Ljubljana Aškerčeva cesta 7 1000 Ljubljana Slovenia
| | - Ricardo D Enriz
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL) Ejercito de los Andes 950 5700 San Luis Argentina
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4
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Xue W, Zuo X, Zhao X, Wang X, Zhang X, Xia J, Cheng M, Yang H. Bioisosteric replacement strategy leads to novel DNA gyrase B inhibitors with improved potencies and properties. Bioorg Chem 2024; 147:107314. [PMID: 38581967 DOI: 10.1016/j.bioorg.2024.107314] [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: 02/05/2024] [Revised: 03/12/2024] [Accepted: 03/25/2024] [Indexed: 04/08/2024]
Abstract
The identification of novel 4-hydroxy-2-quinolone-3-carboxamide antibacterials with improved properties is of great value for the control of antibiotic resistance. In this study, a series of N-heteroaryl-substituted 4-hydroxy-2-quinolone-3-carboxamides were developed using the bioisosteric replacement strategy. As a result of our research, we discovered the two most potent GyrB inhibitors (WBX7 and WBX18), with IC50 values of 0.816 µM and 0.137 µM, respectively. Additional antibacterial activity screening indicated that WBX18 possesses the best antibacterial activity against MRSA, VISA, and VRE strains, with MIC values rangingbetween0.5and 2 µg/mL, which was 2 to over 32 times more potent than that of vancomycin. In vitro safety and metabolic stability, as well as in vivo pharmacokinetics assessments revealed that WBX18 is non-toxic to HUVEC and HepG2, metabolically stable in plasma and liver microsomes (mouse), and displays favorable in vivo pharmacokinetic properties. Finally, docking studies combined with molecular dynamic simulation showed that WBX18 could stably fit in the active site cavity of GyrB.
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Affiliation(s)
- Wenjie Xue
- Department of Pharmacy, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan 030032, China; Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Xueping Zuo
- School of Materials and Environment, Shanxi Jinzhong Institute of Technology, Jinzhong 030600, China
| | - Xueqi Zhao
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Xiaomin Wang
- Department of Pharmacy, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan 030032, China; Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xiangyu Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Jie Xia
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Maosheng Cheng
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China.
| | - Huali Yang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China.
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5
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Dobričić V, Savić J, Tomašič T, Durcik M, Zidar N, Mašič LP, Ilaš J, Kikelj D, Čudina O. High-performance liquid chromatography evaluation of lipophilicity and QSRR modeling of a series of dual DNA gyrase and topoisomerase IV inhibitors. ACTA CHROMATOGR 2022. [DOI: 10.1556/1326.2022.01096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Abstract
AbstractBacterial DNA gyrase and topoisomerase IV control the topological state of DNA during replication and represent important antibacterial drug targets. To be successful as drug candidates, newly synthesized compounds must possess optimal lipophilicity, which enables efficient delivery to the site of action. In this study, retention behavior of twenty-three previously synthesized dual DNA gyrase and topoisomerase IV inhibitors was tested in RP-HPLC system, consisting of C8 column and acetonitrile/phosphate buffer (pH 5.5 and pH 7.4) mobile phase. logD was calculated at both pH values and the best correlation with logD was obtained for retention parameter φ0, indicating that this RP-HPLC system could be used as an alternative to the shake-flask determination of lipophilicity. Subsequent QSRR analysis revealed that intrinsic lipophilicity (logP) and molecular weight (bcutm13) have a positive, while solubility (bcutp3) has a negative influence on this retention parameter.
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Affiliation(s)
- Vladimir Dobričić
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11000 Belgrade, Serbia
| | - Jelena Savić
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11000 Belgrade, Serbia
| | - Tihomir Tomašič
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Martina Durcik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Nace Zidar
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Lucija Peterlin Mašič
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Janez Ilaš
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Danijel Kikelj
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Olivera Čudina
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11000 Belgrade, Serbia
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6
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Xue W, Wang Y, Lian X, Li X, Pang J, Kirchmair J, Wu K, Han Z, You X, Zhang H, Xia J, Wu S. Discovery of N-quinazolinone-4-hydroxy-2-quinolone-3-carboxamides as DNA gyrase B-targeted antibacterial agents. J Enzyme Inhib Med Chem 2022; 37:1620-1631. [PMID: 36278813 PMCID: PMC9186351 DOI: 10.1080/14756366.2022.2084088] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Emerging drug resistance is generating an urgent need for novel and effective antibiotics. A promising target that has not yet been addressed by approved antibiotics is the bacterial DNA gyrase subunit B (GyrB), and GyrB inhibitors could be effective against drug-resistant bacteria, such as methicillin-resistant S. aureus (MRSA). Here, we used the 4-hydroxy-2-quinolone fragment to search the Specs database of purchasable compounds for potential inhibitors of GyrB and identified AG-690/11765367, or f1, as a novel and potent inhibitor of the target protein (IC50: 1.21 µM). Structural modification was used to further identify two more potent GyrB inhibitors: f4 (IC50: 0.31 µM) and f14 (IC50: 0.28 µM). Additional experiments indicated that compound f1 is more potent than the others in terms of antibacterial activity against MRSA (MICs: 4–8 µg/mL), non-toxic to HUVEC and HepG2 (CC50: approximately 50 µM), and metabolically stable (t1/2: > 372.8 min for plasma; 24.5 min for liver microsomes). In summary, this study showed that the discovered N-quinazolinone-4-hydroxy-2-quinolone-3-carboxamides are novel GyrB-targeted antibacterial agents; compound f1 is promising for further development.
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Affiliation(s)
- Wenjie Xue
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Department of Pharmacy, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
| | - Yaling Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- School of Pharmacy, Jiangsu Ocean University, Lianyungang, China
| | - Xu Lian
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xueyao Li
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jing Pang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Johannes Kirchmair
- Division of Pharmaceutical Chemistry, Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Kebin Wu
- Department of Biology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment and SUSTech-HKU Joint Laboratories for Matrix Biology, Southern University of Science and Technology, Shenzhen, China
| | - Zunsheng Han
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xuefu You
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hongmin Zhang
- Department of Biology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment and SUSTech-HKU Joint Laboratories for Matrix Biology, Southern University of Science and Technology, Shenzhen, China
| | - Jie Xia
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Song Wu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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7
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Five-Membered Cyclic Carbonates: Versatility for Applications in Organic Synthesis, Pharmaceutical, and Materials Sciences. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11115024] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
This review presents the recent advances involving several applications of five-membered cyclic carbonates and derivatives. With more than 150 references, it covers the period from 2012 to 2020, with special emphasis on the use of five-membered cyclic carbonates as building blocks for organic synthesis and material elaboration. We demonstrate the application of cyclic carbonates in several important chemical transformations, such as decarboxylation, hydrogenation, and transesterification reactions, among others. The presence of cyclic carbonates in molecules with high biological potential is also displayed, together with the importance of these compounds in the preparation of materials such as urethanes, polyurethanes, and flame retardants.
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8
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Cotman A, Guérin T, Kovačević I, Benedetto Tiz D, Durcik M, Fulgheri F, Možina Š, Secci D, Sterle M, Ilaš J, Zega A, Zidar N, Mašič LP, Tomašič T, Leroux F, Hanquet G, Kikelj D. Practical Synthesis and Application of Halogen-Doped Pyrrole Building Blocks. ACS OMEGA 2021; 6:9723-9730. [PMID: 33869952 PMCID: PMC8047689 DOI: 10.1021/acsomega.1c00331] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/18/2021] [Indexed: 06/12/2023]
Abstract
A practical access to four new halogen-substituted pyrrole building blocks was realized in two to five synthetic steps from commercially available starting materials. The target compounds were prepared on a 50 mg to 1 g scale, and their conversion to nanomolar inhibitors of bacterial DNA gyrase B was demonstrated for three of the prepared building blocks to showcase the usefulness of such chemical motifs in medicinal chemistry.
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Affiliation(s)
- Andrej
Emanuel Cotman
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Thomas Guérin
- Université
de Strasbourg, CNRS, UMR 7042-LIMA, ECPM, 25 Rue Becquerel, Strasbourg 67087, France
| | - Ivana Kovačević
- Faculty
of Sciences, Department of Chemistry, Biochemistry and Environmental
Protection, University of Novi Sad, Trg Dositeja Obradovića 3, 21000 Novi Sad, Serbia
| | - Davide Benedetto Tiz
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Martina Durcik
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Federica Fulgheri
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Štefan Možina
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Daniela Secci
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Maša Sterle
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Janez Ilaš
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Anamarija Zega
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Nace Zidar
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Lucija Peterlin Mašič
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Tihomir Tomašič
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Frédéric
R. Leroux
- Université
de Strasbourg, CNRS, UMR 7042-LIMA, ECPM, 25 Rue Becquerel, Strasbourg 67087, France
| | - Gilles Hanquet
- Université
de Strasbourg, CNRS, UMR 7042-LIMA, ECPM, 25 Rue Becquerel, Strasbourg 67087, France
| | - Danijel Kikelj
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
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9
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Skok Ž, Barančoková M, Benek O, Cruz CD, Tammela P, Tomašič T, Zidar N, Mašič LP, Zega A, Stevenson CEM, Mundy JEA, Lawson DM, Maxwell A, Kikelj D, Ilaš J. Exploring the Chemical Space of Benzothiazole-Based DNA Gyrase B Inhibitors. ACS Med Chem Lett 2020; 11:2433-2440. [PMID: 33329764 PMCID: PMC7734788 DOI: 10.1021/acsmedchemlett.0c00416] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 10/13/2020] [Indexed: 12/22/2022] Open
Abstract
![]()
We
designed and synthesized a series of inhibitors of the bacterial
enzymes DNA gyrase and DNA topoisomerase IV, based on our recently
published benzothiazole-based inhibitor bearing an oxalyl moiety.
To improve the antibacterial activity and retain potent enzymatic
activity, we systematically explored the chemical space. Several strategies
of modification were followed: varying substituents on the pyrrole
carboxamide moiety, alteration of the central scaffold, including
variation of substitution position and, most importantly, modification
of the oxalyl moiety. Compounds with acidic, basic, and neutral properties
were synthesized. To understand the mechanism of action and binding
mode, we have obtained a crystal structure of compound 16a, bearing a primary amino group, in complex with the N-terminal domain
of E. coli gyrase B (24 kDa) (PDB: 6YD9). Compound 15a, with a low molecular weight of 383
Da, potent inhibitory activity on E. coli gyrase
(IC50 = 9.5 nM), potent antibacterial activity on E. faecalis (MIC = 3.13 μM), and efflux impaired E. coli strain (MIC = 0.78 μM), is an important contribution
for the development of novel gyrase and topoisomerase IV inhibitors
in Gram-negative bacteria.
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Affiliation(s)
- Žiga Skok
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Michaela Barančoková
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Ondřej Benek
- University of Hradec Králové, Faculty of Science, Department of Chemistry, Rokitanského 62, 500 03 Hradec Králové, Czech Republic
| | - Cristina Durante Cruz
- Centre for Drug Research, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), Helsinki FI-00014, Finland
| | - Päivi Tammela
- Centre for Drug Research, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), Helsinki FI-00014, Finland
| | - Tihomir Tomašič
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Nace Zidar
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Lucija Peterlin Mašič
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Anamarija Zega
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Clare E. M. Stevenson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | - Julia E. A. Mundy
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | - David M. Lawson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | - Anthony Maxwell
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | - Danijel Kikelj
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Janez Ilaš
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
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10
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Jaswal S, Nehra B, Kumar S, Monga V. Recent advancements in the medicinal chemistry of bacterial type II topoisomerase inhibitors. Bioorg Chem 2020; 104:104266. [PMID: 33142421 DOI: 10.1016/j.bioorg.2020.104266] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/14/2020] [Accepted: 08/31/2020] [Indexed: 02/06/2023]
Abstract
Replication proteins are sought as a potential targets for antimicrobial agents. Despite their promising target characteristics, only topoisomerase II inhibitors targeting DNA gyrase and/or topoisomerase IV have reached clinical use. Topoisomerases are the enzymes that are essential for cellular functions and various biological activities. A wide range of natural and synthetic compounds have been identified as potential topoisomerase inhibitors but the resistance is most commonly found in these drugs. The emergence of FQ resistance has increased the need for the development of novel topoisomerase inhibitors with efficacy and high potency against FQ-resistant strains. Besides structural modifications of existing FQ scaffolds, novel non-quinolone topoisomerase II inhibitors, known as novel bacterial topoisomerase inhibitors, have been developed which showed remarkable inhibitory activity against DNA gyrase/topoisomerase IV or both with an improved spectrum of antibacterial potency including drug-resistant strains. This review aims to summarize various recent advancements in the medicinal chemistry of topoisomerase inhibitors with the following objectives: (1) To represent inclusive data on types of topoisomerases and various marketed topoisomerase inhibitors as drugs; (2) To discuss the recent advances in the medicinal chemistry of various topoisomerase inhibitors (DNA gyrase and topo IV) belonging to different structural classes as potential antibacterial agents; (3) To summarizes the structure activity relationship (SAR) including in silico and mechanistic studies to afford ideas and to provide focused direction for the development of new chemical entities which are effective against drug-resistant bacterial pathogens and biofilms.
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Affiliation(s)
- Shalini Jaswal
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, GT Road, Ghal Kalan, Moga 142001, Punjab, India
| | - Bhupender Nehra
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, GT Road, Ghal Kalan, Moga 142001, Punjab, India
| | - Shubham Kumar
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, GT Road, Ghal Kalan, Moga 142001, Punjab, India
| | - Vikramdeep Monga
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, GT Road, Ghal Kalan, Moga 142001, Punjab, India.
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11
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Recent advances in DNA gyrase-targeted antimicrobial agents. Eur J Med Chem 2020; 199:112326. [DOI: 10.1016/j.ejmech.2020.112326] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 04/07/2020] [Accepted: 04/08/2020] [Indexed: 12/16/2022]
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12
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Second-generation 4,5,6,7-tetrahydrobenzo[ d]thiazoles as novel DNA gyrase inhibitors. Future Med Chem 2020; 12:277-297. [PMID: 32043377 DOI: 10.4155/fmc-2019-0127] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Aim: DNA gyrase and topoisomerase IV are essential bacterial enzymes, and in the fight against bacterial resistance, they are important targets for the development of novel antibacterial drugs. Results: Building from our first generation of 4,5,6,7-tetrahydrobenzo[d]thiazole-based DNA gyrase inhibitors, we designed and prepared an optimized series of analogs that show improved inhibition of DNA gyrase and topoisomerase IV from Staphylococcus aureus and Escherichia coli, with IC50 values in the nanomolar range. Importantly, these inhibitors also show improved antibacterial activity against Gram-positive strains. Conclusion: The most promising inhibitor, 29, is active against Enterococcus faecalis, Enterococcus faecium and S. aureus wild-type and resistant strains, with minimum inhibitory concentrations between 4 and 8 μg/ml, which represents good starting point for development of novel antibacterials.
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13
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Xue W, Li X, Ma G, Zhang H, Chen Y, Kirchmair J, Xia J, Wu S. N-thiadiazole-4-hydroxy-2-quinolone-3-carboxamides bearing heteroaromatic rings as novel antibacterial agents: Design, synthesis, biological evaluation and target identification. Eur J Med Chem 2019; 188:112022. [PMID: 31901744 DOI: 10.1016/j.ejmech.2019.112022] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 12/22/2019] [Accepted: 12/29/2019] [Indexed: 12/12/2022]
Abstract
Due to the occurrence of antibiotic resistance, bacterial infectious diseases have become a serious threat to public health. To overcome antibiotic resistance, novel antibiotics are urgently needed. N-thiadiazole-4-hydroxy-2-quinolone-3-carboxamides are a potential new class of antibacterial agents, as one of its derivatives was identified as an antibacterial agent against S. aureus. However, no potency-directed structural optimization has been performed. In this study, we designed and synthesized 37 derivatives, and evaluated their antibacterial activity against S. aureus ATCC29213, which led to the identification of ten potent antibacterial agents with minimum inhibitory concentration (MIC) values below 1 μg/mL. Next, we performed bacterial growth inhibition assays against a panel of drug-resistant clinical isolates, including methicillin-resistant S. aureus, and cytotoxicity assays with HepG2 and HUVEC cells. One of the tested compounds named 1-ethyl-4-hydroxy-2-oxo-N-(5-(thiazol-2-yl)-1,3,4-thiadiazol-2-yl)-1,2-dihydroquinoline-3-carboxamide (g37) showed 2 to 128-times improvement compared with vancomycin in term of antibacterial potency against the tested strains (MICs: 0.25-1 μg/mL vs. 1-64 μg/mL) and an optimal selective toxicity (HepG2/MRSA, 110.6 to 221.2; HUVEC/MRSA, 77.6-155.2). Further, comprehensive evaluation indicated that g37 did not induce resistance development of MRSA over 20 passages, and it has been confirmed as a bactericidal, metabolically stable, orally active antibacterial agent. More importantly, we have identified the S. aureus DNA gyrase B as its potential target and proposed a potential binding mode by molecular docking. Taken together, the present work reports the most potent derivative of this chemical series (g37) and uncovers its potential target, which lays a solid foundation for further lead optimization facilitated by the structure-based drug design technique.
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Affiliation(s)
- Wenjie Xue
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Xueyao Li
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Guixing Ma
- Department of Biology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment and SUSTech-HKU Joint Laboratories for Matrix Biology, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Hongmin Zhang
- Department of Biology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment and SUSTech-HKU Joint Laboratories for Matrix Biology, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Ya Chen
- Center for Bioinformatics (ZBH), Department of Computer Science, Faculty of Mathematics, Informatics and Natural Sciences, Universität Hamburg, Hamburg, Germany
| | - Johannes Kirchmair
- Center for Bioinformatics (ZBH), Department of Computer Science, Faculty of Mathematics, Informatics and Natural Sciences, Universität Hamburg, Hamburg, Germany; Department of Chemistry, Faculty of Mathematics and Natural Sciences, University of Bergen, Bergen, Norway; Computational Biology Unit (CBU), University of Bergen, Bergen, Norway
| | - Jie Xia
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
| | - Song Wu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
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14
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Prasannan D, Sareena C, Arunkumar C, Vasu ST. Synthesis, structure, photophysical, electrochemical properties and antibacterial activity of brominated BODIPYs as an inhibitor of DNA gyrase B of S. aureus. J PORPHYR PHTHALOCYA 2019. [DOI: 10.1142/s1088424619500433] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
BODIPYs with 3-thienyl and 4-acetamido phenyl groups substituted at the meso-position are subjected to regioselective bromination using three equivalents of [Formula: see text]-bromosuccinimide (NBS) to yield their 2-mono and 2,6-di bromoderivatives. Their photophysical, electrochemical and antimicrobial properties are investigated. This paper presents a mechanistic investigation of the antibacterial effect of brominated BODIPYs, particularly against Staphylococcus aureus. Fluorescence microscopic images reveal that the compounds are internalized effectively within the bacterial cells, making it an ideal antibacterial drug. Morphological analysis of the bacterial cells after the treatment with the test compounds showed that the compounds did not affect the cell membrane or cell wall and the antibacterial effect of these compounds is achieved via a different mechanism. The most effective compound was selected to explore the target of action. Molecular docking studies were performed on 22 selected proteins in S. aureus and the in silico results were validated by in vitro experiments. It was observed that the supercoiling activity of DNA gyrase was completely inhibited by the 2,6-dibromo-1,3,5,7-tetramethyl-8-(4-acetamido)-4-bora-3a,4a-diaza-[Formula: see text]-indacene, 3c by forming H-bonds with the ASP 81 residue of the enzyme.
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Affiliation(s)
- Dijo Prasannan
- Bioinorganic Materials Research Laboratory, Department of Chemistry, National Institute of Technology Calicut, NIT Campus, P.O., Calicut, India-673 601, India
| | - Chennakkandathil Sareena
- School of Biotechnology, National Institute of Technology Calicut, NIT Campus, P.O., Calicut, India-673 601, India
| | - Chellaiah Arunkumar
- Bioinorganic Materials Research Laboratory, Department of Chemistry, National Institute of Technology Calicut, NIT Campus, P.O., Calicut, India-673 601, India
| | - Suchithra Tharamel Vasu
- School of Biotechnology, National Institute of Technology Calicut, NIT Campus, P.O., Calicut, India-673 601, India
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15
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Zidar N, Macut H, Tomašič T, Peterlin Mašič L, Ilaš J, Zega A, Tammela P, Kikelj D. New N-phenyl-4,5-dibromopyrrolamides as DNA gyrase B inhibitors. MEDCHEMCOMM 2019; 10:1007-1017. [PMID: 31303999 DOI: 10.1039/c9md00224c] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 05/18/2019] [Indexed: 11/21/2022]
Abstract
Due to the rapid development of antimicrobial resistance, the discovery of new antibacterials is essential in the fight against potentially lethal infections. The DNA gyrase B (GyrB) subunit of bacterial DNA gyrase is an excellent target for the design of antibacterials, as it has been clinically validated by novobiocin. However, there are currently no drugs in clinical use that target GyrB. We prepared a new series of N-phenyl-4,5-dibromopyrrolamides and evaluated them against DNA gyrase and against the structurally and functionally similar enzyme, topoisomerase IV. The most active compound, 28, had an IC50 of 20 nM against Escherichia coli DNA gyrase. The IC50 values of 28 against Staphylococcus aureus DNA gyrase, and E. coli and S. aureus topoisomerase IV were in the low micromolar range. However, the compounds evaluated did not show significant antibacterial activities against selected Gram-positive and Gram-negative bacteria. Our results indicate that for potent inhibition of DNA gyrase, a combination of polar groups on the carboxylic end of the molecule and substituents that reach into the 'lipophilic floor' of the enzyme is required.
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Affiliation(s)
- Nace Zidar
- University of Ljubljana , Faculty of Pharmacy , Aškerčeva cesta 7 , 1000 Ljubljana , Slovenia . ; ; Tel: +386 1 4769578
| | - Helena Macut
- University of Ljubljana , Faculty of Pharmacy , Aškerčeva cesta 7 , 1000 Ljubljana , Slovenia . ; ; Tel: +386 1 4769578
| | - Tihomir Tomašič
- University of Ljubljana , Faculty of Pharmacy , Aškerčeva cesta 7 , 1000 Ljubljana , Slovenia . ; ; Tel: +386 1 4769578
| | - Lucija Peterlin Mašič
- University of Ljubljana , Faculty of Pharmacy , Aškerčeva cesta 7 , 1000 Ljubljana , Slovenia . ; ; Tel: +386 1 4769578
| | - Janez Ilaš
- University of Ljubljana , Faculty of Pharmacy , Aškerčeva cesta 7 , 1000 Ljubljana , Slovenia . ; ; Tel: +386 1 4769578
| | - Anamarija Zega
- University of Ljubljana , Faculty of Pharmacy , Aškerčeva cesta 7 , 1000 Ljubljana , Slovenia . ; ; Tel: +386 1 4769578
| | - Päivi Tammela
- Drug Research Program , Division of Pharmaceutical Biosciences , Faculty of Pharmacy , University of Helsinki , P.O. Box 56 (Viikinkaari 5 E) , Helsinki FI-00014 , Finland
| | - Danijel Kikelj
- University of Ljubljana , Faculty of Pharmacy , Aškerčeva cesta 7 , 1000 Ljubljana , Slovenia . ; ; Tel: +386 1 4769578
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16
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Tiz DB, Skok Ž, Durcik M, Tomašič T, Mašič LP, Ilaš J, Zega A, Draskovits G, Révész T, Nyerges Á, Pál C, Cruz CD, Tammela P, Žigon D, Kikelj D, Zidar N. An optimised series of substituted N-phenylpyrrolamides as DNA gyrase B inhibitors. Eur J Med Chem 2019; 167:269-290. [PMID: 30776691 DOI: 10.1016/j.ejmech.2019.02.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 01/18/2019] [Accepted: 02/01/2019] [Indexed: 10/27/2022]
Abstract
ATP competitive inhibitors of DNA gyrase and topoisomerase IV have great therapeutic potential, but none of the described synthetic compounds has so far reached the market. To optimise the activities and physicochemical properties of our previously reported N-phenylpyrrolamide inhibitors, we have synthesized an improved, chemically variegated selection of compounds and evaluated them against DNA gyrase and topoisomerase IV enzymes, and against selected Gram-positive and Gram-negative bacteria. The most potent compound displayed IC50 values of 6.9 nM against Escherichia coli DNA gyrase and 960 nM against Staphylococcus aureus topoisomerase IV. Several compounds displayed minimum inhibitory concentrations (MICs) against Gram-positive strains in the 1-50 μM range, one of which inhibited the growth of Enterococcus faecalis, Enterococcus faecium, S. aureus and Streptococcus pyogenes with MIC values of 1.56 μM, 1.56 μM, 0.78 μM and 0.72 μM, respectively. This compound has been investigated further on methicillin-resistant S. aureus (MRSA) and on ciprofloxacin non-susceptible and extremely drug resistant strain of S. aureus (MRSA VISA). It exhibited the MIC value of 2.5 μM on both strains, and MIC value of 32 μM against MRSA in the presence of inactivated human blood serum. Further studies are needed to confirm its mode of action.
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Affiliation(s)
- Davide Benedetto Tiz
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Žiga Skok
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Martina Durcik
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Tihomir Tomašič
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Lucija Peterlin Mašič
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Janez Ilaš
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Anamarija Zega
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Gábor Draskovits
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, H-6726, Hungary
| | - Tamás Révész
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, H-6726, Hungary
| | - Ákos Nyerges
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, H-6726, Hungary
| | - Csaba Pál
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), Helsinki, FI-00014, Finland
| | - Cristina D Cruz
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), Helsinki, FI-00014, Finland
| | - Päivi Tammela
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), Helsinki, FI-00014, Finland
| | - Dušan Žigon
- Jožef Stefan Institute, Department of Environmental Science, Jamova cesta 39, 1000, Ljubljana, Slovenia
| | - Danijel Kikelj
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Nace Zidar
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia.
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17
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Mermer A, Faiz O, Demirbas A, Demirbas N, Alagumuthu M, Arumugam S. Piperazine-azole-fluoroquinolone hybrids: Conventional and microwave irradiated synthesis, biological activity screening and molecular docking studies. Bioorg Chem 2019; 85:308-318. [PMID: 30654222 DOI: 10.1016/j.bioorg.2019.01.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 01/01/2019] [Accepted: 01/06/2019] [Indexed: 01/18/2023]
Abstract
A series of new 1,2,4-triazole and 1,3,4-oxadiazole derivatives was obtained via several steps sequential reactions of phenyl piperazine. Then, these compounds were converted to the corresponding fluoroquinolone hybrids via one pot three component Mannich reaction. All the reactions were examined under conventional and microwave mediated conditions, and optimum conditions were determined. The effect of different solvents and microwave power on microwave prompted reactions was investigated as well. All the newly synthesized compounds were characterized by FTIR, 1H NMR, 13C NMR and EI MS spectral techniques. The antimicrobial activity, DNA gyrase and Topoisomerase IV inhibition potentials were performed. The results obtained showed that fluoroquinolone hybrids possess good antimicrobial activity. Moreover, Fluoroquinolone-azole-piperazine hybrids synthesized in the present study displayed excellent DNA gyrase inhibition. To unveil the interaction mode of compounds to receptor, a molecular docking study was performed. With an average least binding energy of -9.5 kcal/mol, all compounds were found to have remarkable inhibitory potentials against DNA gyrase (E. coli).
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Affiliation(s)
- Arif Mermer
- Karadeniz Technical University, Department of Chemistry 61080 Trabzon, Turkey
| | - Ozlem Faiz
- Recep Tayyip Erdogan University, Department of Chemistry, 53100 Rize, Turkey
| | - Ahmet Demirbas
- Karadeniz Technical University, Department of Chemistry 61080 Trabzon, Turkey
| | - Neslihan Demirbas
- Karadeniz Technical University, Department of Chemistry 61080 Trabzon, Turkey.
| | - Manikandan Alagumuthu
- Dept. of Biotechnology, School of Bio-Sciences and Technology, VIT, Vellore 632014, India
| | - Sivakumar Arumugam
- Dept. of Biotechnology, School of Bio-Sciences and Technology, VIT, Vellore 632014, India
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18
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Mane YD, Patil SS, Biradar DO, Khade BC. 5-Bromo-1-(4-chlorobenzyl)-1H-indole-2-carboxamides as new potent antibacterial agents. HETEROCYCL COMMUN 2018. [DOI: 10.1515/hc-2018-0107] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
Ten 5-bromoindole-2-carboxamides were synthesized, characterized and evaluated for antibacterial activity against pathogenic Gram-negative bacteria Klebsiella pneumoniae, Escherichia coli, Pseudomonas aeruginosa and Salmonella Typhi using gentamicin and ciprofloxacin as internal standards. Compounds 7a–c, 7g and 7h exhibit high antibacterial activity with a minimum inhibitory concentration (MIC) of 0.35–1.25 μg/mL. Compounds 7a–c exhibit antibacterial activities that are higher than those of the standards against E. coli and P. aeruginosa.
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19
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Abstract
New antibacterials that modulate less explored targets are needed to fight the emerging bacterial resistance. DNA gyrase and topoisomerase IV are attractive targets in this search. These are both type II topoisomerases that can cleave both DNA strands, and can thus alter DNA topology during replication or similar processes. Currently, there are no ATP-competitive inhibitors of these two enzymes on the market, as the only aminocoumarin representative, novobiocin, was withdrawn due to safety concerns. The search for novel ATP-competitive inhibitors is a focus of ongoing industrial and academical research. This review summarizes the recent efforts in the design, synthesis and evaluation of GyrB/ParE inhibitors. The various approaches to achieve improved antibacterial activities are described, with particular reference to Gram-negative bacteria.
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20
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Durcik M, Tammela P, Barančoková M, Tomašič T, Ilaš J, Kikelj D, Zidar N. Synthesis and Evaluation of N-Phenylpyrrolamides as DNA Gyrase B Inhibitors. ChemMedChem 2018; 13:186-198. [PMID: 29206345 DOI: 10.1002/cmdc.201700549] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 12/01/2017] [Indexed: 01/05/2023]
Abstract
ATP-competitive inhibitors of DNA gyrase and topoisomerase IV are among the most interesting classes of antibacterial drugs that are unrepresented in the antibacterial pipeline. We developed 32 new N-phenylpyrrolamides and evaluated them against DNA gyrase and topoisomerase IV from E. coli and Staphylococcus aureus. Antibacterial activities were studied against Gram-positive and Gram-negative bacterial strains. The most potent compound displayed an IC50 of 47 nm against E. coli DNA gyrase, and a minimum inhibitory concentration (MIC) of 12.5 μm against the Gram-positive Enterococcus faecalis. Some compounds displayed good antibacterial activities against an efflux-pump-deficient E. coli strain (MIC=6.25 μm) and against wild-type E. coli in the presence of efflux pump inhibitor PAβN (MIC=3.13 μm). Here we describe new findings regarding the structure-activity relationships of N-phenylpyrrolamide DNA gyrase B inhibitors and investigate the factors that are important for the antibacterial activity of this class of compounds.
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Affiliation(s)
- Martina Durcik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Päivi Tammela
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, Viikinkaari 5E, Helsinki, 00014, Finland
| | - Michaela Barančoková
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Tihomir Tomašič
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Janez Ilaš
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Danijel Kikelj
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Nace Zidar
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
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21
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Tomašič T, Barančoková M, Zidar N, Ilaš J, Tammela P, Kikelj D. Design, synthesis, and biological evaluation of 1-ethyl-3-(thiazol-2-yl)urea derivatives as Escherichia coli
DNA gyrase inhibitors. Arch Pharm (Weinheim) 2017; 351. [DOI: 10.1002/ardp.201700333] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 11/22/2017] [Accepted: 11/24/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Tihomir Tomašič
- Faculty of Pharmacy; University of Ljubljana; Ljubljana Slovenia
| | | | - Nace Zidar
- Faculty of Pharmacy; University of Ljubljana; Ljubljana Slovenia
| | - Janez Ilaš
- Faculty of Pharmacy; University of Ljubljana; Ljubljana Slovenia
| | - Päivi Tammela
- Division of Pharmaceutical Biosciences; Faculty of Pharmacy; University of Helsinki; Helsinki Finland
| | - Danijel Kikelj
- Faculty of Pharmacy; University of Ljubljana; Ljubljana Slovenia
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22
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Cotman AE, Trampuž M, Brvar M, Kikelj D, Ilaš J, Peterlin-Mašič L, Montalvão S, Tammela P, Frlan R. Design, Synthesis, and Evaluation of Novel Tyrosine-Based DNA Gyrase B Inhibitors. Arch Pharm (Weinheim) 2017. [PMID: 28621824 DOI: 10.1002/ardp.201700087] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The discovery and synthesis of new tyrosine-based inhibitors of DNA gyrase B (GyrB), which target its ATPase subunit, is reported. Twenty-four compounds were synthesized and evaluated for activity against DNA gyrase and DNA topoisomerase IV. The antibacterial properties of selected GyrB inhibitors were demonstrated by their activity against Staphylococcus aureus and Enterococcus faecalis in the low micromolar range. The most promising compounds, 8a and 13e, inhibited Escherichia coli and S. aureus GyrB with IC50 values of 40 and 30 µM. The same compound also inhibited the growth of S. aureus and E. faecalis with minimal inhibitory concentrations (MIC90 ) of 14 and 28 µg/mL, respectively.
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Affiliation(s)
- Andrej E Cotman
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia.,National Institute of Chemistry, Ljubljana, Slovenia
| | - Marko Trampuž
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia.,National Institute of Chemistry, Ljubljana, Slovenia
| | - Matjaž Brvar
- National Institute of Chemistry, Ljubljana, Slovenia
| | - Danijel Kikelj
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Janez Ilaš
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | | | - Sofia Montalvão
- Faculty of Pharmacy, Division of Pharmaceutical Biosciences, University of Helsinki, Helsinki, Finland
| | - Päivi Tammela
- Faculty of Pharmacy, Division of Pharmaceutical Biosciences, University of Helsinki, Helsinki, Finland
| | - Rok Frlan
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
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23
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Discovery of substituted oxadiazoles as a novel scaffold for DNA gyrase inhibitors. Eur J Med Chem 2017; 130:171-184. [DOI: 10.1016/j.ejmech.2017.02.046] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 02/13/2017] [Accepted: 02/17/2017] [Indexed: 01/06/2023]
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24
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Mane YD, Surwase SM, Biradar DO, Sarnikar YP, Jawle BH, Shinde VS, Khade BC. Design and Synthesis of Diverse Pyrrole-2-carboxamide Derivatives as a Potent Antibacterial Agents. J Heterocycl Chem 2017. [DOI: 10.1002/jhet.2859] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yogesh D. Mane
- Shri Chhatrapati Shivaji College; Omerga Dist-Osmanabad, M.S. India
| | | | | | | | - Balaji H. Jawle
- Arts, Science and Commerce College; Makni Dist-Osmanabad, M.S. India
| | - Vishnu S. Shinde
- Shri Chhatrapati Shivaji College; Omerga Dist-Osmanabad, M.S. India
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25
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Gjorgjieva M, Tomašič T, Barančokova M, Katsamakas S, Ilaš J, Tammela P, Peterlin Mašič L, Kikelj D. Discovery of Benzothiazole Scaffold-Based DNA Gyrase B Inhibitors. J Med Chem 2016; 59:8941-8954. [DOI: 10.1021/acs.jmedchem.6b00864] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Marina Gjorgjieva
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Tihomir Tomašič
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Michaela Barančokova
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Sotirios Katsamakas
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
- Department
of Pharmaceutical Chemistry, School of Pharmacy, Faculty of Health
Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Janez Ilaš
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Päivi Tammela
- Division
of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014 Helsinki, Finland
| | | | - Danijel Kikelj
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
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