1
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Durcik M, Cotman AE, Toplak Ž, Možina Š, Skok Ž, Szili PE, Czikkely M, Maharramov E, Vu TH, Piras MV, Zidar N, Ilaš J, Zega A, Trontelj J, Pardo LA, Hughes D, Huseby D, Berruga-Fernández T, Cao S, Simoff I, Svensson R, Korol SV, Jin Z, Vicente F, Ramos MC, Mundy JEA, Maxwell A, Stevenson CEM, Lawson DM, Glinghammar B, Sjöström E, Bohlin M, Oreskär J, Alvér S, Janssen GV, Sterk GJ, Kikelj D, Pal C, Tomašič T, Peterlin Mašič L. New Dual Inhibitors of Bacterial Topoisomerases with Broad-Spectrum Antibacterial Activity and In Vivo Efficacy against Vancomycin-Intermediate Staphylococcus aureus. J Med Chem 2023; 66:3968-3994. [PMID: 36877255 PMCID: PMC10041525 DOI: 10.1021/acs.jmedchem.2c01905] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
A new series of dual low nanomolar benzothiazole inhibitors of bacterial DNA gyrase and topoisomerase IV were developed. The resulting compounds show excellent broad-spectrum antibacterial activities against Gram-positive Enterococcus faecalis, Enterococcus faecium and multidrug resistant (MDR) Staphylococcus aureus strains [best compound minimal inhibitory concentrations (MICs): range, <0.03125-0.25 μg/mL] and against the Gram-negatives Acinetobacter baumannii and Klebsiella pneumoniae (best compound MICs: range, 1-4 μg/mL). Lead compound 7a was identified with favorable solubility and plasma protein binding, good metabolic stability, selectivity for bacterial topoisomerases, and no toxicity issues. The crystal structure of 7a in complex with Pseudomonas aeruginosa GyrB24 revealed its binding mode at the ATP-binding site. Expanded profiling of 7a and 7h showed potent antibacterial activity against over 100 MDR and non-MDR strains of A. baumannii and several other Gram-positive and Gram-negative strains. Ultimately, in vivo efficacy of 7a in a mouse model of vancomycin-intermediate S. aureus thigh infection was also demonstrated.
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Affiliation(s)
- Martina Durcik
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, Ljubljana 1000, Slovenia
| | - Andrej Emanuel Cotman
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, Ljubljana 1000, Slovenia
| | - Žan Toplak
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, Ljubljana 1000, Slovenia
| | - Štefan Možina
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, Ljubljana 1000, Slovenia
| | - Žiga Skok
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, Ljubljana 1000, Slovenia
| | - Petra Eva Szili
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged H-6726, Hungary
| | - Márton Czikkely
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged H-6726, Hungary
| | - Elvin Maharramov
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged H-6726, Hungary
| | - Thu Hien Vu
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged H-6726, Hungary
| | - Maria Vittoria Piras
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, Ljubljana 1000, Slovenia
| | - Nace Zidar
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, Ljubljana 1000, Slovenia
| | - Janez Ilaš
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, Ljubljana 1000, Slovenia
| | - Anamarija Zega
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, Ljubljana 1000, Slovenia
| | - Jurij Trontelj
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, Ljubljana 1000, Slovenia
| | - Luis A Pardo
- Max Planck Institute for Multidisciplinary Sciences, Oncophysiology, Hermann-Rein-Str. 3, Göttingen 37075, Germany
| | - Diarmaid Hughes
- Department of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, Uppsala 75123, Sweden
| | - Douglas Huseby
- Department of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, Uppsala 75123, Sweden
| | - Tália Berruga-Fernández
- Department of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, Uppsala 75123, Sweden
| | - Sha Cao
- Department of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, Uppsala 75123, Sweden
| | - Ivailo Simoff
- Drug Optimization and Pharmaceutical Profiling Platform (UDOPP) Department of Pharmacy, Uppsala University, Husargatan 3, Uppsala 75123, Sweden
| | - Richard Svensson
- Drug Optimization and Pharmaceutical Profiling Platform (UDOPP) Department of Pharmacy, Uppsala University, Husargatan 3, Uppsala 75123, Sweden
| | - Sergiy V Korol
- Department of Medical Cell Biology, Uppsala University, Husargatan 3, Uppsala 75123, Sweden
| | - Zhe Jin
- Department of Medical Cell Biology, Uppsala University, Husargatan 3, Uppsala 75123, Sweden
| | - Francisca Vicente
- Fundación Medina, Avenida del Conocimiento 34, Parque Tecnológico Ciencias de la Salud, Granada 18016, Spain
| | - Maria C Ramos
- Fundación Medina, Avenida del Conocimiento 34, Parque Tecnológico Ciencias de la Salud, Granada 18016, Spain
| | - Julia E A Mundy
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | - Anthony Maxwell
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | - Clare E M Stevenson
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | - David M Lawson
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | - Björn Glinghammar
- Department of Chemical and Pharmaceutical Toxicology, RISE Research Institutes of Sweden, Södertälje 15136, Sweden
| | - Eva Sjöström
- Department of Chemical Processes and Pharmaceutical Development, RISE Research Institutes of Sweden, Södertälje 15136, Sweden
| | - Martin Bohlin
- Department of Chemical Processes and Pharmaceutical Development, RISE Research Institutes of Sweden, Södertälje 15136, Sweden
| | - Joanna Oreskär
- Department of Chemical Processes and Pharmaceutical Development, RISE Research Institutes of Sweden, Södertälje 15136, Sweden
| | - Sofie Alvér
- Department of Chemical Processes and Pharmaceutical Development, RISE Research Institutes of Sweden, Södertälje 15136, Sweden
| | - Guido V Janssen
- Medicinal Chemistry Division, Vrije Universiteit Amsterdam, De Boelelaan 1108, Amsterdam 1081 HZ, The Netherlands
| | - Geert Jan Sterk
- Medicinal Chemistry Division, Vrije Universiteit Amsterdam, De Boelelaan 1108, Amsterdam 1081 HZ, The Netherlands
| | - Danijel Kikelj
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, Ljubljana 1000, Slovenia
| | - Csaba Pal
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged H-6726, Hungary
| | - Tihomir Tomašič
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, Ljubljana 1000, Slovenia
| | - Lucija Peterlin Mašič
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, Ljubljana 1000, Slovenia
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2
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Skok Ž, Durcik M, Zajec Ž, Gramec Skledar D, Bozovičar K, Pišlar A, Tomašič T, Zega A, Peterlin Mašič L, Kikelj D, Zidar N, Ilaš J. ATP-competitive inhibitors of human DNA topoisomerase IIα with improved antiproliferative activity based on N-phenylpyrrolamide scaffold. Eur J Med Chem 2023; 249:115116. [PMID: 36689894 DOI: 10.1016/j.ejmech.2023.115116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 01/05/2023] [Accepted: 01/10/2023] [Indexed: 01/20/2023]
Abstract
ATP-competitive inhibitors of human DNA topoisomerase II show potential for becoming the successors of topoisomerase II poisons, the clinically successful anticancer drugs. Based on our recent screening hits, we designed, synthesized and biologically evaluated new, improved series of N-phenylpyrrolamide DNA topoisomerase II inhibitors. Six structural classes were prepared to systematically explore the chemical space of N-phenylpyrrolamide based inhibitors. The most potent inhibitor, 47d, had an IC50 value of 0.67 μM against DNA topoisomerase IIα. Compound 53b showed exceptional activity on cancer cell lines with IC50 values of 130 nM against HepG2 and 140 nM against MCF-7 cancer cell lines. The reported compounds have no structurally similarity to published structures, they are metabolically stable, have reasonable solubility and thus can serve as promising leads in the development of anticancer ATP-competitive inhibitors of human DNA topoisomerase IIα.
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Affiliation(s)
- 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
| | - Živa Zajec
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Darja Gramec Skledar
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Krištof Bozovičar
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Anja Pišlar
- 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
| | - 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
| | - 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
| | - Janez Ilaš
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia.
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3
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Cotman A, Durcik M, Benedetto Tiz D, Fulgheri F, Secci D, Sterle M, Možina Š, Skok Ž, Zidar N, Zega A, Ilaš J, Peterlin Mašič L, Tomašič T, Hughes D, Huseby DL, Cao S, Garoff L, Berruga Fernández T, Giachou P, Crone L, Simoff I, Svensson R, Birnir B, Korol SV, Jin Z, Vicente F, Ramos MC, de la Cruz M, Glinghammar B, Lenhammar L, Henderson SR, Mundy JEA, Maxwell A, Stevenson CEM, Lawson DM, Janssen GV, Sterk GJ, Kikelj D. Discovery and Hit-to-Lead Optimization of Benzothiazole Scaffold-Based DNA Gyrase Inhibitors with Potent Activity against Acinetobacter baumannii and Pseudomonas aeruginosa. J Med Chem 2023; 66:1380-1425. [PMID: 36634346 PMCID: PMC9884090 DOI: 10.1021/acs.jmedchem.2c01597] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
We have developed compounds with a promising activity against Acinetobacter baumannii and Pseudomonas aeruginosa, which are both on the WHO priority list of antibiotic-resistant bacteria. Starting from DNA gyrase inhibitor 1, we identified compound 27, featuring a 10-fold improved aqueous solubility, a 10-fold improved inhibition of topoisomerase IV from A. baumannii and P. aeruginosa, a 10-fold decreased inhibition of human topoisomerase IIα, and no cross-resistance to novobiocin. Cocrystal structures of 1 in complex with Escherichia coli GyrB24 and (S)-27 in complex with A. baumannii GyrB23 and P. aeruginosa GyrB24 revealed their binding to the ATP-binding pocket of the GyrB subunit. In further optimization steps, solubility, plasma free fraction, and other ADME properties of 27 were improved by fine-tuning of lipophilicity. In particular, analogs of 27 with retained anti-Gram-negative activity and improved plasma free fraction were identified. The series was found to be nongenotoxic, nonmutagenic, devoid of mitochondrial toxicity, and possessed no ion channel liabilities.
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Affiliation(s)
- Andrej
Emanuel Cotman
- 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
| | - Davide Benedetto Tiz
- 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
| | - 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
| | - Štefan Možina
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Žiga Skok
- 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
| | - Anamarija Zega
- 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
| | - 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
| | - Diarmaid Hughes
- Department
of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, 75123 Uppsala, Sweden
| | - Douglas L. Huseby
- Department
of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, 75123 Uppsala, Sweden
| | - Sha Cao
- Department
of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, 75123 Uppsala, Sweden
| | - Linnéa Garoff
- Department
of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, 75123 Uppsala, Sweden
| | - Talía Berruga Fernández
- Department
of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, 75123 Uppsala, Sweden
| | - Paraskevi Giachou
- Department
of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, 75123 Uppsala, Sweden
| | - Lisa Crone
- Department
of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, 75123 Uppsala, Sweden
| | - Ivailo Simoff
- Drug
Optimization and Pharmaceutical Profiling Platform (UDOPP), Department
of Pharmacy, Uppsala University, Husargatan 3, 75123 Uppsala, Sweden
| | - Richard Svensson
- Drug
Optimization and Pharmaceutical Profiling Platform (UDOPP), Department
of Pharmacy, Uppsala University, Husargatan 3, 75123 Uppsala, Sweden
| | - Bryndis Birnir
- Department
of Medical Cell Biology, Uppsala University, Husargatan 3, 75123 Uppsala, Sweden
| | - Sergiy V. Korol
- Department
of Medical Cell Biology, Uppsala University, Husargatan 3, 75123 Uppsala, Sweden
| | - Zhe Jin
- Department
of Medical Cell Biology, Uppsala University, Husargatan 3, 75123 Uppsala, Sweden
| | - Francisca Vicente
- Fundación
MEDINA, Avenida del Conocimiento
34, Parque Tecnológico Ciencias de la Salud, 18016 Granada, Spain
| | - Maria C. Ramos
- Fundación
MEDINA, Avenida del Conocimiento
34, Parque Tecnológico Ciencias de la Salud, 18016 Granada, Spain
| | - Mercedes de la Cruz
- Fundación
MEDINA, Avenida del Conocimiento
34, Parque Tecnológico Ciencias de la Salud, 18016 Granada, Spain
| | - Björn Glinghammar
- Department
Chemical Process and Pharmaceutical Development, Unit Chemical and
Pharmaceutical Safety, RISE Research Institutes
of Sweden, 15136 Södertälje, Sweden
| | - Lena Lenhammar
- Department
of Medical Sciences, Uppsala University
Hospital, 75185 Uppsala, Sweden
| | - Sara R. Henderson
- Department
of Biochemistry and Metabolism, John Innes
Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | - Julia E. A. Mundy
- Department
of Biochemistry and Metabolism, John Innes
Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | - Anthony Maxwell
- Department
of Biochemistry and Metabolism, John Innes
Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | - Clare E. M. Stevenson
- Department
of Biochemistry and Metabolism, John Innes
Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | - David M. Lawson
- Department
of Biochemistry and Metabolism, John Innes
Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | - Guido V. Janssen
- Medicinal
Chemistry Division, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Geert Jan Sterk
- Medicinal
Chemistry Division, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Danijel Kikelj
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia,. Phone: (+386)1476-9500. Fax: (+386)1425-8031
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4
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Tomašič T, Zubrienė A, Skok Ž, Martini R, Pajk S, Sosič I, Ilaš J, Matulis D, Bryant SD. Selective DNA Gyrase Inhibitors: Multi-Target in Silico Profiling with 3D-Pharmacophores. Pharmaceuticals (Basel) 2021; 14:ph14080789. [PMID: 34451886 PMCID: PMC8400042 DOI: 10.3390/ph14080789] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/02/2021] [Accepted: 08/09/2021] [Indexed: 11/17/2022] Open
Abstract
DNA gyrase is an important target for the development of novel antibiotics. Although ATP-competitive DNA gyrase (GyrB) inhibitors are a well-studied class of antibacterial agents, there is currently no representative used in therapy, largely due to unwanted off-target activities. Selectivity of GyrB inhibitors against closely related human ATP-binding enzymes should be evaluated early in development to avoid off-target binding to homologous binding domains. To address this challenge, we developed selective 3D-pharmacophore models for GyrB, human topoisomerase IIα (TopoII), and the Hsp90 N-terminal domain (NTD) to be used in in silico activity profiling paradigms to identify molecules selective for GyrB over TopoII and Hsp90, as starting points for hit expansion and lead optimization. The models were used to profile highly active GyrB, TopoII, and Hsp90 inhibitors. Selected compounds were tested in in vitro assays. GyrB inhibitors 1 and 2 were inactive against TopoII and Hsp90, while 3 and 4, potent Hsp90 inhibitors, displayed no inhibition of GyrB and TopoII, and TopoII inhibitors 5 and 6 were inactive at GyrB and Hsp90. The results provide a proof of concept for the use of target activity profiling methods to identify selective starting points for hit and lead identification.
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Affiliation(s)
- Tihomir Tomašič
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia; (Ž.S.); (S.P.); (I.S.); (J.I.)
- Correspondence: ; Tel.: +386-1-4769-556
| | - Asta Zubrienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania; (A.Z.); (D.M.)
| | - Žiga Skok
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia; (Ž.S.); (S.P.); (I.S.); (J.I.)
| | - Riccardo Martini
- Inte:Ligand Softwareentwicklungs- und Consulting GmbH, Mariahilferstrasse 74B, 1070 Vienna, Austria; (R.M.); (S.D.B.)
- Discngine S.A.S., 79 Avenue Ledru Rollin, 75012 Paris, France
| | - Stane Pajk
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia; (Ž.S.); (S.P.); (I.S.); (J.I.)
| | - Izidor Sosič
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia; (Ž.S.); (S.P.); (I.S.); (J.I.)
| | - Janez Ilaš
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia; (Ž.S.); (S.P.); (I.S.); (J.I.)
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania; (A.Z.); (D.M.)
| | - Sharon D. Bryant
- Inte:Ligand Softwareentwicklungs- und Consulting GmbH, Mariahilferstrasse 74B, 1070 Vienna, Austria; (R.M.); (S.D.B.)
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5
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Durcik M, Skok Ž, Ilaš J, Zidar N, Zega A, Szili PÉ, Draskovits G, Révész T, Kikelj D, Nyerges A, Pál C, Mašič LP, Tomašič T. Hybrid Inhibitors of DNA Gyrase A and B: Design, Synthesis and Evaluation. Pharmaceutics 2020; 13:pharmaceutics13010006. [PMID: 33374964 PMCID: PMC7822030 DOI: 10.3390/pharmaceutics13010006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/15/2020] [Accepted: 12/19/2020] [Indexed: 11/16/2022] Open
Abstract
The discovery of multi-targeting ligands of bacterial enzymes is an important strategy to combat rapidly spreading antimicrobial resistance. Bacterial DNA gyrase and topoisomerase IV are validated targets for the development of antibiotics. They can be inhibited at their catalytic sites or at their ATP binding sites. Here we present the design of new hybrids between the catalytic inhibitor ciprofloxacin and ATP-competitive inhibitors that show low nanomolar inhibition of DNA gyrase and antibacterial activity against Gram-negative pathogens. The most potent hybrid 3a has MICs of 0.5 µg/mL against Klebsiella pneumoniae, 4 µg/mL against Enterobacter cloacae, and 2 µg/mL against Escherichia coli. In addition, inhibition of mutant E. coli strains shows that these hybrid inhibitors interact with both subunits of DNA gyrase (GyrA, GyrB), and that binding to both of these sites contributes to their antibacterial activity.
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Affiliation(s)
- Martina Durcik
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia; (M.D.); (Ž.S.); (J.I.); (N.Z.); (A.Z.); (D.K.)
| | - Žiga Skok
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia; (M.D.); (Ž.S.); (J.I.); (N.Z.); (A.Z.); (D.K.)
| | - Janez Ilaš
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia; (M.D.); (Ž.S.); (J.I.); (N.Z.); (A.Z.); (D.K.)
| | - Nace Zidar
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia; (M.D.); (Ž.S.); (J.I.); (N.Z.); (A.Z.); (D.K.)
| | - Anamarija Zega
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia; (M.D.); (Ž.S.); (J.I.); (N.Z.); (A.Z.); (D.K.)
| | - Petra Éva Szili
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, H-6726 Szeged, Hungary; (P.É.S.); (G.D.); (T.R.); (A.N.); (C.P.)
| | - Gábor Draskovits
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, H-6726 Szeged, Hungary; (P.É.S.); (G.D.); (T.R.); (A.N.); (C.P.)
| | - Tamás Révész
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, H-6726 Szeged, Hungary; (P.É.S.); (G.D.); (T.R.); (A.N.); (C.P.)
| | - Danijel Kikelj
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia; (M.D.); (Ž.S.); (J.I.); (N.Z.); (A.Z.); (D.K.)
| | - Akos Nyerges
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, H-6726 Szeged, Hungary; (P.É.S.); (G.D.); (T.R.); (A.N.); (C.P.)
- Department of Genetics, Harvard Medical School, Boston, MA 02215, USA
| | - Csaba Pál
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, H-6726 Szeged, Hungary; (P.É.S.); (G.D.); (T.R.); (A.N.); (C.P.)
| | - Lucija Peterlin Mašič
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia; (M.D.); (Ž.S.); (J.I.); (N.Z.); (A.Z.); (D.K.)
- Correspondence: (L.P.M.); (T.T.); Tel.: +386-1-4769-635 (L.P.M.); +386-1-4769-556 (T.T.)
| | - Tihomir Tomašič
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia; (M.D.); (Ž.S.); (J.I.); (N.Z.); (A.Z.); (D.K.)
- Correspondence: (L.P.M.); (T.T.); Tel.: +386-1-4769-635 (L.P.M.); +386-1-4769-556 (T.T.)
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6
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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7
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Nyerges A, Tomašič T, Durcik M, Revesz T, Szili P, Draskovits G, Bogar F, Skok Ž, Zidar N, Ilaš J, Zega A, Kikelj D, Daruka L, Kintses B, Vasarhelyi B, Foldesi I, Kata D, Welin M, Kimbung R, Focht D, Mašič LP, Pal C. Rational design of balanced dual-targeting antibiotics with limited resistance. PLoS Biol 2020; 18:e3000819. [PMID: 33017402 PMCID: PMC7561186 DOI: 10.1371/journal.pbio.3000819] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 10/15/2020] [Accepted: 08/26/2020] [Indexed: 12/02/2022] Open
Abstract
Antibiotics that inhibit multiple bacterial targets offer a promising therapeutic strategy against resistance evolution, but developing such antibiotics is challenging. Here we demonstrate that a rational design of balanced multitargeting antibiotics is feasible by using a medicinal chemistry workflow. The resultant lead compounds, ULD1 and ULD2, belonging to a novel chemical class, almost equipotently inhibit bacterial DNA gyrase and topoisomerase IV complexes and interact with multiple evolutionary conserved amino acids in the ATP-binding pockets of their target proteins. ULD1 and ULD2 are excellently potent against a broad range of gram-positive bacteria. Notably, the efficacy of these compounds was tested against a broad panel of multidrug-resistant Staphylococcus aureus clinical strains. Antibiotics with clinical relevance against staphylococcal infections fail to inhibit a significant fraction of these isolates, whereas both ULD1 and ULD2 inhibit all of them (minimum inhibitory concentration [MIC] ≤1 μg/mL). Resistance mutations against these compounds are rare, have limited impact on compound susceptibility, and substantially reduce bacterial growth. Based on their efficacy and lack of toxicity demonstrated in murine infection models, these compounds could translate into new therapies against multidrug-resistant bacterial infections.
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Affiliation(s)
- Akos Nyerges
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, Hungary
| | - Tihomir Tomašič
- University of Ljubljana, Faculty of Pharmacy, Ljubljana, Slovenia
| | - Martina Durcik
- University of Ljubljana, Faculty of Pharmacy, Ljubljana, Slovenia
| | - Tamas Revesz
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, Hungary
- Doctoral School of Theoretical Medicine, University of Szeged, Szeged, Hungary
| | - Petra Szili
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, Hungary
- Doctoral School of Multidisciplinary Medical Sciences, University of Szeged, Szeged, Hungary
| | - Gabor Draskovits
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, Hungary
| | - Ferenc Bogar
- MTA-SZTE Biomimetic Systems Research Group, Department of Medical Chemistry, University of Szeged, Hungary
| | - Žiga Skok
- University of Ljubljana, Faculty of Pharmacy, Ljubljana, Slovenia
| | - Nace Zidar
- University of Ljubljana, Faculty of Pharmacy, Ljubljana, Slovenia
| | - Janez Ilaš
- University of Ljubljana, Faculty of Pharmacy, Ljubljana, Slovenia
| | - Anamarija Zega
- University of Ljubljana, Faculty of Pharmacy, Ljubljana, Slovenia
| | - Danijel Kikelj
- University of Ljubljana, Faculty of Pharmacy, Ljubljana, Slovenia
| | - Lejla Daruka
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, Hungary
- Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Balint Kintses
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, Hungary
- HCEMM-BRC Translational Microbiology Lab, Szeged, Hungary
| | - Balint Vasarhelyi
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, Hungary
| | - Imre Foldesi
- Department of Laboratory Medicine, University of Szeged, Szeged, Hungary
| | - Diána Kata
- Department of Laboratory Medicine, University of Szeged, Szeged, Hungary
| | - Martin Welin
- SARomics Biostructures, Medicon Village, Lund, Sweden
| | | | - Dorota Focht
- SARomics Biostructures, Medicon Village, Lund, Sweden
| | | | - Csaba Pal
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, Hungary
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8
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Rupar J, Dobričić V, Grahovac J, Radulović S, Skok Ž, Ilaš J, Aleksić M, Brborić J, Čudina O. Synthesis and evaluation of anticancer activity of new 9-acridinyl amino acid derivatives. RSC Med Chem 2020; 11:378-386. [PMID: 33479643 DOI: 10.1039/c9md00597h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 01/19/2020] [Indexed: 01/25/2023] Open
Abstract
A series of eleven 9-acridinyl amino acid derivatives were synthesized using a two-step procedure. Cytotoxicity was tested on the K562 and A549 cancer cell lines and normal diploid cell line MRC5 using the MTT assay. Compounds 6, 7, 8 and 9 were the most active, with IC50 values comparable to or lower than that of chemotherapeutic agent amsacrine. 8 and 9 were especially effective in the A549 cell line (IC50 ≈ 6 μM), which is of special interest since amsacrine is not sufficiently active in lung cancer patients. Cell cycle analysis revealed that 7 and 9 caused G2/M block, amsacrine caused arrest in the S phase, while 6 and 8 induced apoptotic cell death independently of the cell cycle regulation. In comparison to amsacrine, 6, 7, 8, and 9 showed similar inhibitory potential towards topoisomerase II, whereas only 7 showed DNA intercalation properties. In contrast to amsacrine, 6, 7, 8 and 9 showed a lack of toxicity towards unstimulated normal human leucocytes.
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Affiliation(s)
- Jelena Rupar
- Department of Pharmaceutical Chemistry , University of Belgrade - Faculty of Pharmacy , Vojvode Stepe 450 , 11000 Belgrade , Serbia . .,Department of Physical Chemistry and Instrumental Methods , University of Belgrade - Faculty of Pharmacy , Vojvode Stepe 450 , 11000 Belgrade , Serbia
| | - Vladimir Dobričić
- Department of Pharmaceutical Chemistry , University of Belgrade - Faculty of Pharmacy , Vojvode Stepe 450 , 11000 Belgrade , Serbia .
| | - Jelena Grahovac
- Department of Experimental Oncology , Institute for Oncology and Radiology of Serbia , Pasterova 14 , Belgrade , Serbia
| | - Siniša Radulović
- Department of Experimental Oncology , Institute for Oncology and Radiology of Serbia , Pasterova 14 , Belgrade , Serbia
| | - Žiga Skok
- Chair of Pharmaceutical Chemistry , University of Ljubljana, Faculty of Pharmacy , Aškerčeva 7 , SI-1000 Ljubljana , Slovenia
| | - Janez Ilaš
- Chair of Pharmaceutical Chemistry , University of Ljubljana, Faculty of Pharmacy , Aškerčeva 7 , SI-1000 Ljubljana , Slovenia
| | - Mara Aleksić
- Department of Physical Chemistry and Instrumental Methods , University of Belgrade - Faculty of Pharmacy , Vojvode Stepe 450 , 11000 Belgrade , Serbia
| | - Jasmina Brborić
- Department of Pharmaceutical Chemistry , University of Belgrade - Faculty of Pharmacy , Vojvode Stepe 450 , 11000 Belgrade , Serbia .
| | - Olivera Čudina
- Department of Pharmaceutical Chemistry , University of Belgrade - Faculty of Pharmacy , Vojvode Stepe 450 , 11000 Belgrade , Serbia .
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9
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Fois B, Skok Ž, Tomašič T, Ilaš J, Zidar N, Zega A, Peterlin Mašič L, Szili P, Draskovits G, Nyerges Á, Pál C, Kikelj D. Cover Feature: Dual
Escherichia coli
DNA Gyrase A and B Inhibitors with Antibacterial Activity (ChemMedChem 3/2020). ChemMedChem 2020. [DOI: 10.1002/cmdc.202000031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Benedetta Fois
- Faculty of Pharmacy University of Ljubljana Aškerčeva cesta 7 1000 Ljubljana Slovenia
- Faculty of Biology and Pharmacy University of Cagliari Via Ospedale 72 09124 Cagliari Italy
| | - Žiga Skok
- 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
| | - Janez Ilaš
- 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
| | - Anamarija Zega
- 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
| | - Petra Szili
- Synthetic and Systems Biology Unit Hungarian Academy of Sciences Szeged 6726 Hungary
- Doctoral School of Multidisciplinary Medical Sciences University of Szeged Szeged 6720 Hungary
| | - Gábor Draskovits
- Synthetic and Systems Biology Unit Hungarian Academy of Sciences Szeged 6726 Hungary
| | - Ákos Nyerges
- Synthetic and Systems Biology Unit Hungarian Academy of Sciences Szeged 6726 Hungary
| | - Csaba Pál
- Synthetic and Systems Biology Unit Hungarian Academy of Sciences Szeged 6726 Hungary
| | - Danijel Kikelj
- Faculty of Pharmacy University of Ljubljana Aškerčeva cesta 7 1000 Ljubljana Slovenia
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10
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Lamut A, Cruz CD, Skok Ž, Barančoková M, Zidar N, Zega A, Mašič LP, Ilaš J, Tammela P, Kikelj D, Tomašič T. Design, synthesis and biological evaluation of novel DNA gyrase inhibitors and their siderophore mimic conjugates. Bioorg Chem 2019; 95:103550. [PMID: 31911309 DOI: 10.1016/j.bioorg.2019.103550] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 12/19/2019] [Accepted: 12/21/2019] [Indexed: 10/25/2022]
Abstract
Bacterial DNA gyrase is an important target for the development of novel antibacterial drugs, which are urgently needed because of high level of antibiotic resistance worldwide. We designed and synthesized new 4,5,6,7-tetrahydrobenzo[d]thiazole-based DNA gyrase B inhibitors and their conjugates with siderophore mimics, which were introduced to increase the uptake of inhibitors into the bacterial cytoplasm. The most potent conjugate 34 had an IC50 of 58 nM against Escherichia coli DNA gyrase and displayed MIC of 14 µg/mL against E. coli ΔtolC strain. Only minor improvements in the antibacterial activities against wild-type E. coli in low-iron conditions were seen for DNA gyrase inhibitor - siderophore mimic conjugates.
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Affiliation(s)
- Andraž Lamut
- 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 5 E), FI-00014 Helsinki, Finland
| | - 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
| | - Nace Zidar
- 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
| | - 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
| | - Päivi Tammela
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), FI-00014 Helsinki, Finland
| | - Danijel Kikelj
- 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.
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11
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Fois B, Skok Ž, Tomašič T, Ilaš J, Zidar N, Zega A, Peterlin Mašič L, Szili P, Draskovits G, Nyerges Á, Pál C, Kikelj D. Dual
Escherichia coli
DNA Gyrase A and B Inhibitors with Antibacterial Activity. ChemMedChem 2019; 15:265-269. [DOI: 10.1002/cmdc.201900607] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Indexed: 01/11/2023]
Affiliation(s)
- Benedetta Fois
- Faculty of Pharmacy University of Ljubljana Aškerčeva cesta 7 1000 Ljubljana Slovenia
- Faculty of Biology and Pharmacy University of Cagliari Via Ospedale 72 09124 Cagliari Italy
| | - Žiga Skok
- 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
| | - Janez Ilaš
- 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
| | - Anamarija Zega
- 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
| | - Petra Szili
- Synthetic and Systems Biology Unit Hungarian Academy of Sciences Szeged 6726 Hungary
- Doctoral School of Multidisciplinary Medical Sciences University of Szeged Szeged 6720 Hungary
| | - Gábor Draskovits
- Synthetic and Systems Biology Unit Hungarian Academy of Sciences Szeged 6726 Hungary
| | - Ákos Nyerges
- Synthetic and Systems Biology Unit Hungarian Academy of Sciences Szeged 6726 Hungary
| | - Csaba Pál
- Synthetic and Systems Biology Unit Hungarian Academy of Sciences Szeged 6726 Hungary
| | - Danijel Kikelj
- Faculty of Pharmacy University of Ljubljana Aškerčeva cesta 7 1000 Ljubljana Slovenia
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12
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Affiliation(s)
- Žiga Skok
- Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Nace Zidar
- Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Danijel Kikelj
- Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Janez Ilaš
- Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia
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13
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Fedorowicz J, Sączewski J, Konopacka A, Waleron K, Lejnowski D, Ciura K, Tomašič T, Skok Ž, Savijoki K, Morawska M, Gilbert-Girard S, Fallarero A. Synthesis and biological evaluation of hybrid quinolone-based quaternary ammonium antibacterial agents. Eur J Med Chem 2019; 179:576-590. [PMID: 31279292 DOI: 10.1016/j.ejmech.2019.06.071] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 06/25/2019] [Accepted: 06/26/2019] [Indexed: 11/18/2022]
Abstract
A series of novel fluoroquinolone-Safirinium dye hybrids was synthesized by means of tandem Mannich-electrophilic amination reactions from profluorophoric isoxazolones and antibiotics bearing a secondary amino group at position 7 of the quinoline ring. The obtained fluorescent spiro fused conjugates incorporating quaternary nitrogen atoms were characterized by 1H NMR, IR, MS, and elemental analysis. All the synthetic analogues (3a-h and 4a-h) were evaluated for their in vitro antimicrobial, bactericidal, and antibiofilm activities against a panel of Gram positive and Gram-negative pathogenic bacteria. The most active Safirinium Q derivatives of lomefloxacin (4d) and ciprofloxacin (4e) exhibited molar-based antibacterial activities comparable to the unmodified drugs and displayed considerable inhibitory potencies in E. coli DNA gyrase supercoiling assays with IC50 values in the low micromolar range. Zwiterionic hybrids were noticeably less lipophilic than the parent quinolones in micellar electrokinetic chromatography (MECK) experiments. The tests performed in the presence of phenylalanine-arginine β-naphthylamide (PAβN) or carbonyl cyanide m-chlorophenylhydrazone (CCCP) revealed that the conjugates are to some extent subject to bacterial efflux and cellular accumulation, respectively. Moreover, the hybrids did not exhibit notable cytotoxicity towards the HEK 293 control cell line and demonstrated low propensity for resistance development, as exemplified for compounds 3g and 4b. Finally, molecular docking experiments revealed that the synthesized compounds were able to bind in the fluoroquinolone-binding mode at S. aureus DNA gyrase and S. pneumoniae topoisomerase IV active sites.
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Affiliation(s)
- Joanna Fedorowicz
- Department of Chemical Technology of Drugs, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416, Gdańsk, Poland.
| | - Jarosław Sączewski
- Department of Organic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416, Gdańsk, Poland.
| | - Agnieszka Konopacka
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416, Gdańsk, Poland
| | - Krzysztof Waleron
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416, Gdańsk, Poland
| | - Dawid Lejnowski
- Department of Biology and Pharmaceutical Botany, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416, Gdańsk, Poland
| | - Krzesimir Ciura
- Department of Physical Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416, Gdańsk, Poland
| | - Tihomir Tomašič
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Žiga Skok
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Kirsi Savijoki
- Faculty of Pharmacy, University of Helsinki, Yliopistonkatu 4, 00100, Helsinki, Finland
| | - Małgorzata Morawska
- Department of Chemical Technology of Drugs, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416, Gdańsk, Poland; Department of Organic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416, Gdańsk, Poland; Faculty of Pharmacy, University of Helsinki, Yliopistonkatu 4, 00100, Helsinki, Finland
| | - Shella Gilbert-Girard
- Faculty of Pharmacy, University of Helsinki, Yliopistonkatu 4, 00100, Helsinki, Finland
| | - Adyary Fallarero
- Faculty of Pharmacy, University of Helsinki, Yliopistonkatu 4, 00100, Helsinki, Finland
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14
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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