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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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2
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Zhou G, Li Y. Investigation of bacterial DNA gyrase Inhibitor classification models and structural requirements utilizing multiple machine learning methods. Mol Divers 2024:10.1007/s11030-024-10806-y. [PMID: 38372837 DOI: 10.1007/s11030-024-10806-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 01/04/2024] [Indexed: 02/20/2024]
Abstract
Infections from multidrug-resistant (MDR) bacteria have emerged as a paramount global health concern, and the therapeutic effectiveness of current treatments is swiftly diminishing. An urgent need exists to explore innovative strategies for countering drug-resistant bacteria. Bacterial DNA gyrase, functioning as an ATP-dependent enzyme, plays a pivotal role in the intricate processes of transcription, replication, and chromosome segregation within bacterial DNA. This renders it a prime target for the development of innovative antibacterial agents. However, the experimental identification of bacterial DNA gyrase inhibitors faces multifaceted challenges due to current methodological constraints. Recognizing its significance, this study developed 56 computational models designed for predicting bacterial DNA gyrase inhibitors. These models employed seven distinct molecular fingerprints and eight machine learning algorithms. Among these models, Model_2D, created using KlekotaRoth fingerprints and the SVM algorithm, stands out as the most robust performer (ACC = 0.86, MCC = 0.63, G-mean = 0.82). Moreover, given the limited exploration of structural fragments required for DNA Gyrase B inhibitors, crucial structural fingerprints influencing DNA Gyrase B inhibitors were identified through Bayesian classification. Subsequently, we conducted molecular docking to reveal the binding modes between these crucial structural fingerprints and the active site of DNA gyrase B. In conclusion, the present study aimed to develop the optimal classification model for bacterial DNA gyrase inhibitors, offering invaluable support to medicinal chemists creating innovative DNA gyrase inhibitors.
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Affiliation(s)
- Guozheng Zhou
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian, 116024, Liaoning, China
| | - Yan Li
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian, 116024, Liaoning, China.
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3
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Gardner ED, Johnson BP, Dimas DA, McClurg HE, Severance ZC, Burgett AW, Singh S. Unlocking New Prenylation Modes: Azaindoles as a New Substrate Class for Indole Prenyltransferases. ChemCatChem 2023; 15:e202300650. [PMID: 37954549 PMCID: PMC10634513 DOI: 10.1002/cctc.202300650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Indexed: 11/14/2023]
Abstract
Aza-substitution, the replacement of aromatic CH groups with nitrogen atoms, is an established medicinal chemistry strategy for increasing solubility, but current methods of accessing functionalized azaindoles are limited. In this work, indole-alkylating aromatic prenyltransferases (PTs) were explored as a strategy to directly functionalize azaindole-substituted analogs of natural products. For this, a series of aza-l-tryptophans (Aza-Trp) featuring N-substitution of every aromatic CH position of the indole ring and their corresponding cyclic Aza-l-Trp-l-proline dipeptides (Aza-CyWP), were synthesized as substrate mimetics for the indole-alkylating PTs FgaPT2, CdpNPT, and FtmPT1. We then demonstrated most of these substrate analogs were accepted by a PT, and the regioselectivity of each prenylation was heavily influenced by the position of the N-substitution. Remarkably, FgaPT2 was found to produce cationic N-prenylpyridinium products, representing not only a new substrate class for indole PTs but also a previously unobserved prenylation mode. The discovery that nitrogenous indole bioisosteres can be accepted by PTs thus provides access to previously unavailable chemical space in the search for bioactive indolediketopiperazine analogs.
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Affiliation(s)
- Eric D. Gardner
- Department of Chemistry and Biochemistry, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, Oklahoma 73019, United States
| | - Bryce P. Johnson
- Department of Chemistry and Biochemistry, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, Oklahoma 73019, United States
| | - Dustin A. Dimas
- Department of Chemistry and Biochemistry, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, Oklahoma 73019, United States
| | - Heather E. McClurg
- Department of Chemistry and Biochemistry, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, Oklahoma 73019, United States
| | - Zachary C. Severance
- Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73117, United States
| | - Anthony W. Burgett
- Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73117, United States
| | - Shanteri Singh
- Department of Chemistry and Biochemistry, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, Oklahoma 73019, United States
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4
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Hilmy KMH, Kishk FNM, Shahen EBA, Sobh EA, Hawata MA. New pyrrole derivatives as DNA gyrase and 14α-demethylase inhibitors: Design, synthesis, antimicrobial evaluation, and molecular docking. Drug Dev Res 2023; 84:1204-1230. [PMID: 37165799 DOI: 10.1002/ddr.22080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/01/2023] [Accepted: 03/12/2023] [Indexed: 05/12/2023]
Abstract
An efficient one-pot reaction utilizing readily available chemical reagents was used to prepare novel 2-amino-1,5-diaryl-1H-pyrrole-3-carbonitrile derivatives and the structures of these compounds were validated by spectroscopic data and elemental analyses. All the synthetic compounds were evaluated for their antimicrobial activities (MZI assay). The tested compounds proved high activities on Staphylococcus aureus (Gram-positive bacteria) and Candida albicans (Pathogenic fungi). However, they did not show any activity on Escherichia coli (Gram-negative bacteria). The most effective compounds in MZI assay 7c, 9a, 9b, 11a, and 11b were selected to determine their MIC on S. aureus and C. albicans. Furthermore, DNA gyrase and 14-α demethylase inhibitory assays were performed to study the inhibitory activities of 7c, 9a, 9b, 11a, and 11b. The results illustrated that compound 9b was the most DNA gyrase inhibitor (IC50 of 0.0236 ± 0.45 µM, which was 1.3- fold higher than gentamicin reference IC50 values of 0.0323 ± 0.81 µM). In addition, compound 9b demonstrated the highest 14-α demethylase inhibitory effect with IC50 of 0.0013 ± 0.02 µM, compared to ketoconazole (IC50 of 0.0008 ± 0.03 µM) and fluconazole (IC50 of 0.00073 ± 0.01 µM), as antifungal reference drugs. Lastly, docking studies were performed to rationalize the dual inhibitory activities of the highly active compounds on both DNA gyrase and 14-α demethylase enzymes.
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Affiliation(s)
- Khaled M H Hilmy
- Department of Chemistry, Faculty of Science, El-Menoufia University, Shebin El-Kom, Egypt
| | - Fawzya N M Kishk
- Department of Chemistry, Faculty of Science, El-Menoufia University, Shebin El-Kom, Egypt
| | - Esmat B A Shahen
- Depatment of Biochemistry, Faculty of Medicine, Al-Azhar University for Girls, Cairo, Egypt
| | - Eman A Sobh
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Menoufia University, Menoufia, Shebin El-Kom, Egypt
| | - Mohamed A Hawata
- Department of Chemistry, Faculty of Science, El-Menoufia University, Shebin El-Kom, Egypt
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5
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Ommi O, Naiyaz Ahmad M, Gajula SNR, Wanjari P, Sau S, Agnivesh PK, Sahoo SK, Kalia NP, Sonti R, Nanduri S, Dasgupta A, Chopra S, Yaddanapudi VM. Synthesis and pharmacological evaluation of 1,3-diaryl substituted pyrazole based (thio)urea derivatives as potent antimicrobial agents against multi-drug resistant Staphylococcus aureus and Mycobacterium tuberculosis. RSC Med Chem 2023; 14:1296-1308. [PMID: 37484564 PMCID: PMC10357928 DOI: 10.1039/d3md00079f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/08/2023] [Indexed: 07/25/2023] Open
Abstract
The urgent development of newer alternatives has been deemed a panacea for tackling emerging antimicrobial resistance effectively. Herein, we report the design, synthesis, and biological evaluation of 1,3-diaryl substituted pyrazole-based urea and thiourea derivatives as antimicrobial agents. Preliminary screening results revealed that compound 7a (3,4-dichlorophenyl derivative) exhibited potent activity against S. aureus (MIC = 0.25 μg mL-1) and compound 7j (2,4-difluorophenyl derivative) against Mycobacterium tuberculosis (MIC = 1 μg mL-1). Compounds 7a and 7j were non-toxic to Vero cells with a favorable selectivity index of 40 and 200, respectively, and demonstrated good microsomal stability. Compound 7a exhibited equipotent activity (MIC = 0.25 μg mL-1) against various multidrug-resistant strains of S. aureus, which include various strains of MRSA and VRSA, and elicited bacteriostatic properties. In an enzymatic assay, 7a effectively inhibited DNA gyrase supercoiling activity at a concentration of 8 times MIC. Further, molecular modeling studies suggested that compound 7a binds at the active site of DNA gyrase with good affinity.
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Affiliation(s)
- Ojaswitha Ommi
- Department of Chemical Sciences, National Institute of Pharmaceutical Education and Research (NIPER) Balanagar Hyderabad 500037 Telangana India
| | - Mohammad Naiyaz Ahmad
- Division of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute Sector 10, Jankipuram Extension, Sitapur Road Lucknow 226031 UP India
- AcSIR: Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
| | - Siva Nageswara Rao Gajula
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER) Balanagar Hyderabad 500037 Telangana India
| | - Parita Wanjari
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER) Balanagar Hyderabad 500037 Telangana India
| | - Shashikanta Sau
- Department of Biological Sciences, National Institute of Pharmaceutical Education and Research (NIPER) Balanagar Hyderabad 500037 Telangana India
| | - Puja Kumari Agnivesh
- Department of Biological Sciences, National Institute of Pharmaceutical Education and Research (NIPER) Balanagar Hyderabad 500037 Telangana India
| | - Santosh Kumar Sahoo
- Department of Pharmaceutical Chemistry, GITAM School of Pharmacy, GITAM University Visakhapatnam 530045 India
| | - Nitin Pal Kalia
- Department of Biological Sciences, National Institute of Pharmaceutical Education and Research (NIPER) Balanagar Hyderabad 500037 Telangana India
| | - Rajesh Sonti
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER) Balanagar Hyderabad 500037 Telangana India
| | - Srinivas Nanduri
- Department of Chemical Sciences, National Institute of Pharmaceutical Education and Research (NIPER) Balanagar Hyderabad 500037 Telangana India
| | - Arunava Dasgupta
- Division of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute Sector 10, Jankipuram Extension, Sitapur Road Lucknow 226031 UP India
- AcSIR: Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
| | - Sidharth Chopra
- Division of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute Sector 10, Jankipuram Extension, Sitapur Road Lucknow 226031 UP India
- AcSIR: Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
| | - Venkata Madhavi Yaddanapudi
- Department of Chemical Sciences, National Institute of Pharmaceutical Education and Research (NIPER) Balanagar Hyderabad 500037 Telangana India
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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: 1] [Impact Index Per Article: 0.5] [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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Wang L, Linares-Otoya V, Liu Y, Mettal U, Marner M, Armas-Mantilla L, Willbold S, Kurtán T, Linares-Otoya L, Schäberle TF. Discovery and Biosynthesis of Antimicrobial Phenethylamine Alkaloids from the Marine Flavobacterium Tenacibaculum discolor sv11. JOURNAL OF NATURAL PRODUCTS 2022; 85:1039-1051. [PMID: 35416664 DOI: 10.1021/acs.jnatprod.1c01173] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The bacterial genus Tenacibaculum has been associated with various ecological roles in marine environments. Members of this genus can act, for example, as pathogens, predators, or episymbionts. However, natural products produced by these bacteria are still unknown. In the present work, we investigated a Tenacibaculum strain for the production of antimicrobial metabolites. Six new phenethylamine (PEA)-containing alkaloids, discolins A and B (1 and 2), dispyridine (3), dispyrrolopyridine A and B (4 and 5), and dispyrrole (6), were isolated from media produced by the predatory bacterium Tenacibaculum discolor sv11. Chemical structures were elucidated by analysis of spectroscopic data. Alkaloids 4 and 5 exhibited strong activity against Gram-positive Bacillus subtilis DSM10, Mycobacterium smegmatis ATCC607, Listeria monocytogenes DSM20600, and Staphylococcus aureus ATCC25923, with minimum inhibitory concentration (MIC) values ranging from 0.5 to 4 μg/mL, and moderate activity against Candida albicans FH2173 and Aspergillus flavus ATCC9170. Compound 6 displayed moderate antibacterial activities against Gram-positive bacteria. Dispyrrolopyridine A (4) was active against efflux pump deficient Escherichia coli ATCC25922 ΔtolC, with an MIC value of 8 μg/mL, as well as against Caenorhabditis elegans N2 with an MIC value of 32 μg/mL. Other compounds were inactive against these microorganisms. The biosynthetic route toward discolins A and B (1 and 2) was investigated using in vivo and in vitro experiments. It comprises an enzymatic decarboxylation of phenylalanine to PEA catalyzed by DisA, followed by a nonenzymatic condensation to form the central imidazolium ring. This spontaneous formation of the imidazolium core was verified by means of a synthetic one-pot reaction using the respective building blocks. Six additional strains belonging to three Tenacibaculum species were able to produce discolins, and several DisA analogues were identified in various marine flavobacterial genera, suggesting the widespread presence of PEA-derived compounds in marine ecosystems.
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Affiliation(s)
- Lei Wang
- Institute for Insect Biotechnology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Branch for Bioresources, 35392 Giessen, Germany
| | - Virginia Linares-Otoya
- Department of Pharmacology, Faculty of Pharmacy and Biochemistry, National University of Trujillo, 13011 Trujillo, Peru
- Research Centre for Sustainable Development Uku Pacha, 13011 Trujillo, Peru
| | - Yang Liu
- Institute for Insect Biotechnology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Branch for Bioresources, 35392 Giessen, Germany
| | - Ute Mettal
- Institute for Insect Biotechnology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Branch for Bioresources, 35392 Giessen, Germany
| | - Michael Marner
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Branch for Bioresources, 35392 Giessen, Germany
| | - Lizbeth Armas-Mantilla
- Department of Pharmacology, Faculty of Pharmacy and Biochemistry, National University of Trujillo, 13011 Trujillo, Peru
- Research Centre for Sustainable Development Uku Pacha, 13011 Trujillo, Peru
| | - Sabine Willbold
- Central Institute for Engineering, Electronics and Analytics, Analytics, Forschungszentrum Juelich GmbH, 52425 Juelich, Germany
| | - Tibor Kurtán
- Department of Organic Chemistry, University of Debrecen, H-4002 Debrecen, Hungary
| | - Luis Linares-Otoya
- Institute for Insect Biotechnology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Branch for Bioresources, 35392 Giessen, Germany
- Department of Pharmacology, Faculty of Pharmacy and Biochemistry, National University of Trujillo, 13011 Trujillo, Peru
| | - Till F Schäberle
- Institute for Insect Biotechnology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Branch for Bioresources, 35392 Giessen, Germany
- German Center for Infection Research, Partner Site Giessen-Marburg-Langen, 35392 Giessen, Germany
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8
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GyrB inhibitors as potential antibacterial agents: a review. MONATSHEFTE FUR CHEMIE 2021. [DOI: 10.1007/s00706-021-02800-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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9
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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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10
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Discovery of novel multi-substituted benzo-indole pyrazole schiff base derivatives with antibacterial activity targeting DNA gyrase. Bioorg Chem 2020; 99:103807. [DOI: 10.1016/j.bioorg.2020.103807] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/25/2020] [Accepted: 03/28/2020] [Indexed: 01/14/2023]
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11
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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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12
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Masci D, Hind C, Islam MK, Toscani A, Clifford M, Coluccia A, Conforti I, Touitou M, Memdouh S, Wei X, La Regina G, Silvestri R, Sutton JM, Castagnolo D. Switching on the activity of 1,5-diaryl-pyrrole derivatives against drug-resistant ESKAPE bacteria: Structure-activity relationships and mode of action studies. Eur J Med Chem 2019; 178:500-514. [DOI: 10.1016/j.ejmech.2019.05.087] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 05/29/2019] [Accepted: 05/29/2019] [Indexed: 12/13/2022]
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13
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Rizk OH, Bekhit MG, Hazzaa AAB, El‐Khawass EM, Abdelwahab IA. Synthesis, antibacterial evaluation, and DNA gyrase inhibition profile of some new quinoline hybrids. Arch Pharm (Weinheim) 2019; 352:e1900086. [DOI: 10.1002/ardp.201900086] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 06/19/2019] [Accepted: 07/02/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Ola H. Rizk
- Department of Pharmaceutical ChemistryFaculty of PharmacyUniversity of AlexandriaAlexandria Egypt
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy & Drug ManufacturingPharos University in AlexandriaAlexandria Egypt
| | - Mohamed G. Bekhit
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy & Drug ManufacturingPharos University in AlexandriaAlexandria Egypt
| | - Aly A. B. Hazzaa
- Department of Pharmaceutical ChemistryFaculty of PharmacyUniversity of AlexandriaAlexandria Egypt
| | - El‐Sayeda M. El‐Khawass
- Department of Pharmaceutical ChemistryFaculty of PharmacyUniversity of AlexandriaAlexandria Egypt
| | - Ibrahim A. Abdelwahab
- Department of Microbiology and Immunology, Faculty of Pharmacy & Drug ManufacturingPharos University in AlexandriaAlexandria Egypt
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14
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Le Fouler V, Duret G, Bisseret P, Blanchard N. Copper-mediated synthesis of N-vinyl ynamides from N-vinyl carbamates. Tetrahedron Lett 2018. [DOI: 10.1016/j.tetlet.2018.07.053] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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15
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Szulczyk D, Dobrowolski MA, Roszkowski P, Bielenica A, Stefańska J, Koliński M, Kmiecik S, Jóźwiak M, Wrzosek M, Olejarz W, Struga M. Design and synthesis of novel 1H-tetrazol-5-amine based potent antimicrobial agents: DNA topoisomerase IV and gyrase affinity evaluation supported by molecular docking studies. Eur J Med Chem 2018; 156:631-640. [PMID: 30031974 DOI: 10.1016/j.ejmech.2018.07.041] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Revised: 07/11/2018] [Accepted: 07/15/2018] [Indexed: 12/27/2022]
Abstract
A total of 14 of 1,5-disubstituted tetrazole derivatives were prepared by reacting appropriate thiourea and sodium azide in the presence of mercury (II) chloride and triethylamine. All compounds were evaluated in vitro for their antimicrobial activity. Derivatives 10 and 11 showed the highest inhibition against Gram-positive and Gram-negative strains (standard and hospital strains). The observed minimal inhibitory concentrations values were in the range of 1-208 μM (0.25-64 μg/ml). Inhibitory activity of 1,5-tetrazole derivatives 10 and 11 against gyrase and topoisomerase IV isolated from S. aureus was studied. Evaluation was supported by molecular docking studies for all synthesized derivatives and reference ciprofloxacin. Moreover, selected tetrazoles (2, 3, 5, 6, 8, 9, 10 and 11) were evaluated for their cytotoxicity. All tested compounds are non-cytotoxic against HaCaT and A549 cells (CC50 ≤ 60 μM).
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Affiliation(s)
- Daniel Szulczyk
- Chair and Department of Biochemistry, Medical University, 02-097 Warszawa, Poland.
| | | | - Piotr Roszkowski
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Anna Bielenica
- Chair and Department of Biochemistry, Medical University, 02-097 Warszawa, Poland
| | - Joanna Stefańska
- Laboratory of Centre for Preclinical Research, Medical University of Warsaw, Banacha 1B, 02-097 Warsaw, Poland; Department of Pharmaceutical Microbiology, Medical University, 02-007 Warszawa, Poland
| | - Michał Koliński
- Bioinformatics Laboratory, Mossakowski Medical Research Centre, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Sebastian Kmiecik
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, 02-089 Warsaw, Poland
| | - Michał Jóźwiak
- Department of Biochemistry and Pharmacogenomics, Faculty of Pharmacy, Medical University of Warsaw, 02-097 Warszawa, Poland; Laboratory of Centre for Preclinical Research, Medical University of Warsaw, Banacha 1B, 02-097 Warsaw, Poland; Department of Biochemistry, Second Faculty of Medicine, Medical University of Warsaw, 02-097 Warszawa, Poland
| | - Małgorzata Wrzosek
- Department of Biochemistry and Pharmacogenomics, Faculty of Pharmacy, Medical University of Warsaw, 02-097 Warszawa, Poland; Laboratory of Centre for Preclinical Research, Medical University of Warsaw, Banacha 1B, 02-097 Warsaw, Poland
| | - Wioletta Olejarz
- Department of Biochemistry and Pharmacogenomics, Faculty of Pharmacy, Medical University of Warsaw, 02-097 Warszawa, Poland; Laboratory of Centre for Preclinical Research, Medical University of Warsaw, Banacha 1B, 02-097 Warsaw, Poland
| | - Marta Struga
- Chair and Department of Biochemistry, Medical University, 02-097 Warszawa, Poland; Laboratory of Centre for Preclinical Research, Medical University of Warsaw, Banacha 1B, 02-097 Warsaw, Poland
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16
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McGarry DH, Cooper IR, Walker R, Warrilow CE, Pichowicz M, Ratcliffe AJ, Salisbury AM, Savage VJ, Moyo E, Maclean J, Smith A, Charrier C, Stokes NR, Lindsay DM, Kerr WJ. Design, synthesis and antibacterial properties of pyrimido[4,5-b]indol-8-amine inhibitors of DNA gyrase. Bioorg Med Chem Lett 2018; 28:2998-3003. [PMID: 30122228 DOI: 10.1016/j.bmcl.2018.05.049] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 05/24/2018] [Accepted: 05/26/2018] [Indexed: 01/12/2023]
Abstract
According to the World Health Organization (WHO), approximately 1.7 million deaths per year are caused by tuberculosis infections. Furthermore, it has been predicted that, by 2050, antibacterial resistance will be the cause of approximately 10 million deaths annually if the issue is not tackled. As a result, novel approaches to treating broad-spectrum bacterial infections are of vital importance. During the course of our wider efforts to discover unique methods of targeting multidrug-resistant (MDR) pathogens, we identified a novel series of amide-linked pyrimido[4,5-b]indol-8-amine inhibitors of bacterial type II topoisomerases. Compounds from the series were highly potent against gram-positive bacteria and mycobacteria, with excellent potency being retained against a panel of relevant Mycobacterium tuberculosis drug-resistant clinical isolates.
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Affiliation(s)
- David H McGarry
- Redx Pharma, Alderley Park, Cheshire SK10 4TG, United Kingdom.
| | - Ian R Cooper
- Redx Pharma, Alderley Park, Cheshire SK10 4TG, United Kingdom
| | - Rolf Walker
- Redx Pharma, Alderley Park, Cheshire SK10 4TG, United Kingdom
| | | | - Mark Pichowicz
- Redx Pharma, Alderley Park, Cheshire SK10 4TG, United Kingdom
| | | | | | | | - Emmanuel Moyo
- Redx Pharma, Alderley Park, Cheshire SK10 4TG, United Kingdom
| | - John Maclean
- Redx Pharma, Alderley Park, Cheshire SK10 4TG, United Kingdom
| | - Andrew Smith
- Redx Pharma, Alderley Park, Cheshire SK10 4TG, United Kingdom
| | - Cédric Charrier
- Redx Pharma, Alderley Park, Cheshire SK10 4TG, United Kingdom
| | - Neil R Stokes
- Redx Pharma, Alderley Park, Cheshire SK10 4TG, United Kingdom
| | - David M Lindsay
- Department of Pure and Applied Chemistry, University of Strathclyde, WestCHEM, Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - William J Kerr
- Department of Pure and Applied Chemistry, University of Strathclyde, WestCHEM, Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
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17
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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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18
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New N-phenylpyrrolamide DNA gyrase B inhibitors: Optimization of efficacy and antibacterial activity. Eur J Med Chem 2018; 154:117-132. [PMID: 29778894 DOI: 10.1016/j.ejmech.2018.05.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 03/27/2018] [Accepted: 05/07/2018] [Indexed: 01/04/2023]
Abstract
The ATP binding site located on the subunit B of DNA gyrase is an attractive target for the development of new antibacterial agents. In recent decades, several small-molecule inhibitor classes have been discovered but none has so far reached the market. We present here the discovery of a promising new series of N-phenylpyrrolamides with low nanomolar IC50 values against DNA gyrase, and submicromolar IC50 values against topoisomerase IV from Escherichia coli and Staphylococcus aureus. The most potent compound in the series has an IC50 value of 13 nM against E. coli gyrase. Minimum inhibitory concentrations (MICs) against Gram-positive bacteria are in the low micromolar range. The oxadiazolone derivative 11a, with an IC50 value of 85 nM against E. coli DNA gyrase displays the most potent antibacterial activity, with MIC values of 1.56 μM against Enterococcus faecalis, and 3.13 μM against wild type S. aureus, methicillin-resistant S. aureus (MRSA) and vancomycin-resistant Enterococcus (VRE). The activity against wild type E. coli in the presence of efflux pump inhibitor phenylalanine-arginine β-naphthylamide (PAβN) is 4.6 μM.
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19
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Synthesis, antimicrobial activity, and molecular docking study of fluorine-substituted indole-based imidazolines. Med Chem Res 2018. [DOI: 10.1007/s00044-018-2177-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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20
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Synthesis, structural and antimicrobial studies of type II topoisomerase-targeted copper(II) complexes of 1,3-disubstituted thiourea ligands. J Inorg Biochem 2018; 182:61-70. [PMID: 29499458 DOI: 10.1016/j.jinorgbio.2018.01.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 12/20/2017] [Accepted: 01/07/2018] [Indexed: 12/12/2022]
Abstract
A series of Cu(II) complexes of 3-(trifluoromethyl)phenylthiourea derivatives was synthesized. Their structural properties were investigated by spectroscopic techniques (infrared and electron paramagnetic resonance), as well as molecular modeling. All studied coordination compounds are mononuclear complexes containing two chelating ligands bonded to the metal cation via S and deprotonated N atoms. The new chelates were evaluated for their antimicrobial potency. The complex of 1-(3,4-dichlorophenyl)-3-[3-(trifluoromethyl)phenyl]thiourea (3) presented the highest activity against Gram-positive pathogens, even stronger than the activity of its non-complexed counterpart and the reference drug. The compound also prevented the biofilm formation of methicillin-resistant and standard strains of staphylococcal cocci. The title derivatives were found to be effective inhibitors of DNA gyrase and topoisomerase IV isolated from Staphylococcus aureus. The binding modes of the ligand L3 with DNA gyrase and topoisomerase IV were presented.
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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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Qiu Z, Li JS, Li CJ. Formal aromaticity transfer for palladium-catalyzed coupling between phenols and pyrrolidines/indolines. Chem Sci 2017; 8:6954-6958. [PMID: 29147521 PMCID: PMC5642148 DOI: 10.1039/c7sc02578e] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 08/09/2017] [Indexed: 12/15/2022] Open
Abstract
We herein describe a palladium-catalyzed formal aromaticity transfer coupling reaction between phenols and pyrrolidines or indolines to generate the corresponding N-cyclohexyl pyrroles or indoles. In this transformation, the aromaticity of phenols is formally passed on to the pyrrolidine or indoline units. Substituted phenols thus can serve as latent cyclohexyl equivalents for the fast construction of various N-cyclohexyl pyrroles and indoles.
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Affiliation(s)
- Zihang Qiu
- Department of Chemistry , FQRNT Centre for Green Chemistry and Catalysis , McGill University , 801 Sherbrooke St. W. , Montreal , Quebec H3A 0B8 , Canada .
| | - Jiang-Sheng Li
- Department of Chemistry , FQRNT Centre for Green Chemistry and Catalysis , McGill University , 801 Sherbrooke St. W. , Montreal , Quebec H3A 0B8 , Canada .
- School of Chemistry and Biological Engineering , Changsha University of Science & Technology , Changsha 410114 , China
| | - Chao-Jun Li
- Department of Chemistry , FQRNT Centre for Green Chemistry and Catalysis , McGill University , 801 Sherbrooke St. W. , Montreal , Quebec H3A 0B8 , Canada .
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23
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Linker-switch approach towards new ATP binding site inhibitors of DNA gyrase B. Eur J Med Chem 2016; 125:500-514. [PMID: 27689732 DOI: 10.1016/j.ejmech.2016.09.040] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 08/18/2016] [Accepted: 09/13/2016] [Indexed: 12/30/2022]
Abstract
Due to increasing emergence of bacterial resistance, compounds with new mechanisms of action are of paramount importance. One of modestly researched therapeutic targets in the field of antibacterial discovery is DNA gyrase B. In the present work we synthesized a focused library of potential DNA gyrase B inhibitors composed of two key pharmacophoric moieties linked by three types of sp3-rich linkers to obtain three structural classes of compounds. Using molecular docking, molecular dynamics and analysis of conserved waters in the binding site, we identified a favourable binding mode for piperidin-4-yl and 4-cyclohexyl pyrrole-2-carboxamides while predicting unfavourable interactions with the active site for piperazine pyrrole-2-carboxamides. Biological evaluation of prepared compounds on isolated enzyme DNA gyrase B confirmed our predictions and afforded multiple moderately potent inhibitors of DNA gyrase B. Namely trans-4-(4,5-dibromo-1H-pyrrole-2-carboxamide)cyclohexyl)glycine and 4-(4-(3,4-dichloro-5-methyl-1H-pyrrole-2-carboxamido)piperidin-1-yl)-4-oxobutanoic acid with an IC50 value of 16 and 0.5 μM respectively.
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