1
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Zidar N, Onali A, Peršolja P, Benedetto Tiz D, Dernovšek J, Skok Ž, Durcik M, Cotman AE, Hrast Rambaher M, Cruz CD, Tammela P, Senerovic L, Jovanovic M, Szili PÉ, Czikkely MS, Pál C, Zega A, Peterlin Mašič L, Ilaš J, Tomašič T, Kikelj D. Improved N-phenylpyrrolamide inhibitors of DNA gyrase as antibacterial agents for high-priority bacterial strains. Eur J Med Chem 2024; 278:116823. [PMID: 39236496 DOI: 10.1016/j.ejmech.2024.116823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 08/29/2024] [Accepted: 08/30/2024] [Indexed: 09/07/2024]
Abstract
In this work, we describe an improved series of N-phenylpyrrolamide inhibitors that exhibit potent activity against DNA gyrase and are highly effective against high-priority gram-positive bacteria. The most potent compounds show low nanomolar IC50 values against Escherichia coli DNA gyrase, and in addition, compound 7c also inhibits E. coli topoisomerase IV in the nanomolar concentration range, making it a promising candidate for the development of potent dual inhibitors for these enzymes. All tested compounds show high selectivity towards the human isoform DNA topoisomerase IIα. Compounds 6a, 6d, 6e and 6f show MIC values between 0.031 and 0.0625 μg/mL against vancomycin-intermediate S. aureus (VISA) and Enterococcus faecalis strains. Compound 6g shows an inhibitory effect against the methicillin-resistant S. aureus strain (MRSA) with a MIC of 0.0625 μg/mL and against the E. faecalis strain with a MIC of 0.125 μg/mL. In a time-kill assay, compound 6d showed a dose-dependent bactericidal effect on the MRSA strain and achieved bactericidal activity at 8 × MIC after 8 h. The duration of the post-antibiotic effect (PAE) on the MRSA strain for compound 6d was 2 h, which corresponds to the PAE duration for ciprofloxacin. The compounds were not cytotoxic at effective concentrations, as determined in an MTS assay on the MCF-7 breast cancer cell line.
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Affiliation(s)
- Nace Zidar
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia.
| | - Alessia Onali
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Peter Peršolja
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Davide Benedetto Tiz
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Jaka Dernovšek
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Žiga Skok
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Martina Durcik
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Andrej Emanuel Cotman
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Martina Hrast Rambaher
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Cristina D Cruz
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, Viikinkaari 5E, Helsinki, 00014, Finland
| | - Päivi Tammela
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, Viikinkaari 5E, Helsinki, 00014, Finland
| | - Lidija Senerovic
- Laboratory for Microbial Molecular Genetics and Ecology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11 042, Belgrade, Serbia
| | - Milija Jovanovic
- Laboratory for Microbial Molecular Genetics and Ecology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11 042, Belgrade, Serbia
| | - Petra Éva Szili
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, H-6726, Hungary
| | - Márton Simon Czikkely
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, H-6726, Hungary; Doctoral School of Multidisciplinary Medical Sciences, University of Szeged, Szeged, HU-6722, Hungary; Department of Forensic Medicine, Albert-Szent-Györgyi Medical School, University of Szeged, Szeged, HU-6722, Hungary
| | - Csaba Pál
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, H-6726, Hungary
| | - Anamarija Zega
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Lucija Peterlin Mašič
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Janez Ilaš
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Tihomir Tomašič
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Danijel Kikelj
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
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2
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Cotman AE, Fulgheri F, Piga M, Peršolja P, Tiz DB, Skok Ž, Durcik M, Sterle M, Dernovšek J, Cruz CD, Tammela P, Szili PÉ, Daruka L, Pál C, Zega A, Mašič LP, Ilaš J, Tomašič T, Kikelj D, Zidar N. New N-phenylpyrrolamide inhibitors of DNA gyrase with improved antibacterial activity. RSC Adv 2024; 14:28423-28454. [PMID: 39247510 PMCID: PMC11378028 DOI: 10.1039/d4ra04802d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Accepted: 08/30/2024] [Indexed: 09/10/2024] Open
Abstract
This study presents the discovery of a new series of N-phenylpyrrolamide inhibitors of bacterial DNA gyrase with improved antibacterial activity. The most potent inhibitors had low nanomolar IC50 values against Escherichia coli DNA gyrase (IC50; 2-20 nM) and E. coli topoisomerase IV (22i, IC50 = 143 nM). Importantly, none of the compounds showed activity against human DNA topoisomerase IIα, indicating selectivity for bacterial targets. Among the tested compounds, 22e emerged as the most effective against Gram-positive bacteria with minimum inhibitory concentration (MIC) values of 0.25 μg mL-1 against Staphylococcus aureus ATCC 29213 and MRSA, and 0.125 μg mL-1 against Enterococcus faecalis ATCC 29212. For Gram-negative bacteria, compounds 23b and 23c showed the greatest efficacy with MIC values ranging from 4 to 32 μg mL-1 against E. coli ATCC 25922, Pseudomonas aeruginosa ATCC 27853, Acinetobacter baumannii ATCC 17978 and A. baumannii ATCC 19606. Notably, compound 23b showed promising activity against the clinically relevant Gram-negative pathogen Klebsiella pneumoniae ATCC 10031, with an MIC of 0.0625 μg mL-1. Furthermore, compounds 23a and 23c exhibited significantly lower susceptibility to resistance development compared to novobiocin in S. aureus ATCC 29213 and K. pneumoniae ATCC 10031. Overall, the most promising compounds of this series showed excellent on-target potency, marking a significant improvement over previous N-phenylpyrrolamide inhibitors.
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Affiliation(s)
- Andrej Emanuel Cotman
- University of Ljubljana, Faculty of Pharmacy Aškerčeva cesta 7 1000 Ljubljana Slovenia
| | - Federica Fulgheri
- University of Ljubljana, Faculty of Pharmacy Aškerčeva cesta 7 1000 Ljubljana Slovenia
| | - Martina Piga
- University of Ljubljana, Faculty of Pharmacy Aškerčeva cesta 7 1000 Ljubljana Slovenia
| | - Peter Peršolja
- University of Ljubljana, Faculty of Pharmacy Aškerčeva cesta 7 1000 Ljubljana Slovenia
| | - Davide Benedetto Tiz
- University of Ljubljana, Faculty of Pharmacy Aškerčeva cesta 7 1000 Ljubljana Slovenia
| | - Žiga Skok
- University of Ljubljana, Faculty of Pharmacy Aškerčeva cesta 7 1000 Ljubljana Slovenia
| | - Martina Durcik
- University of Ljubljana, Faculty of Pharmacy Aškerčeva cesta 7 1000 Ljubljana Slovenia
| | - Maša Sterle
- University of Ljubljana, Faculty of Pharmacy Aškerčeva cesta 7 1000 Ljubljana Slovenia
| | - Jaka Dernovšek
- University of Ljubljana, Faculty of Pharmacy Aškerčeva cesta 7 1000 Ljubljana Slovenia
| | - Cristina D Cruz
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki P.O. Box 56, Viikinkaari 5E Helsinki 00014 Finland
| | - Päivi Tammela
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki P.O. Box 56, Viikinkaari 5E Helsinki 00014 Finland
| | - Petra Éva Szili
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences Szeged H-6726 Hungary
| | - Lejla Daruka
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences Szeged H-6726 Hungary
| | - Csaba Pál
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences Szeged H-6726 Hungary
| | - Anamarija Zega
- University of Ljubljana, Faculty of Pharmacy Aškerčeva cesta 7 1000 Ljubljana Slovenia
| | - Lucija Peterlin Mašič
- University of Ljubljana, Faculty of Pharmacy Aškerčeva cesta 7 1000 Ljubljana Slovenia
| | - Janez Ilaš
- University of Ljubljana, Faculty of Pharmacy Aškerčeva cesta 7 1000 Ljubljana Slovenia
| | - Tihomir Tomašič
- University of Ljubljana, Faculty of Pharmacy Aškerčeva cesta 7 1000 Ljubljana Slovenia
| | - Danijel Kikelj
- University of Ljubljana, Faculty of Pharmacy Aškerčeva cesta 7 1000 Ljubljana Slovenia
| | - Nace Zidar
- University of Ljubljana, Faculty of Pharmacy Aškerčeva cesta 7 1000 Ljubljana Slovenia
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3
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Gutierrez L, Peršolja P, Tosso R, Zidar N, Kikelj D, Enriz RD. New ATP-competitive inhibitors of E. coli GyrB obtained from the mapping of the hydrophobic floor at the binding site: synthesis and biological evaluation. RSC Med Chem 2024:d4md00498a. [PMID: 39290385 PMCID: PMC11403825 DOI: 10.1039/d4md00498a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Accepted: 08/21/2024] [Indexed: 09/19/2024] Open
Abstract
We mapped the hydrophobic floor, an interesting subsite at the active site of DNA gyrase B (GyrB) from E. coli. We synthesized three new compounds with pendant groups targeting the hydrophobic floor and evaluated their inhibitory activities on DNA gyrase. A new benzothiazole derivative with a benzyl substituent at position 3 of the benzothiazole ring exhibited strong inhibitory activity against E. coli DNA gyrase (IC50 = 19 ± 3 nM). An exhaustive conformational study using potential energy surfaces (PESs) allowed us to map the new subsite evaluating all critical points on the surface and conformational interconversion pathways. We analyzed the molecular interactions using QTAIM calculations. Our data provide insights into the mechanism of action of these new ligands at the molecular level. Theoretical and experimental data suggest that new ligand optimization strategies should focus on strengthening interactions at the hydrophobic floor while preserving the binding mode of the main scaffold.
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Affiliation(s)
- Lucas Gutierrez
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL) Ejercito de los Andes 950 5700 San Luis Argentina
| | - Peter Peršolja
- Faculty of Pharmacy, University of Ljubljana Aškerčeva cesta 7 1000 Ljubljana Slovenia
| | - Rodrigo Tosso
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL) Ejercito de los Andes 950 5700 San Luis Argentina
| | - Nace Zidar
- Faculty of Pharmacy, University of Ljubljana Aškerčeva cesta 7 1000 Ljubljana Slovenia
| | - Danijel Kikelj
- Faculty of Pharmacy, University of Ljubljana Aškerčeva cesta 7 1000 Ljubljana Slovenia
| | - Ricardo D Enriz
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL) Ejercito de los Andes 950 5700 San Luis Argentina
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4
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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] [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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5
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Moghadam ES, Mireskandari K, Abdel-Jalil R, Amini M. An approach to pharmacological targets of pyrrole family from a medicinal chemistry viewpoint. Mini Rev Med Chem 2022; 22:2486-2561. [PMID: 35339175 DOI: 10.2174/1389557522666220325150531] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 01/12/2022] [Accepted: 01/30/2022] [Indexed: 11/22/2022]
Abstract
Pyrrole is one of the most widely used heterocycles in the pharmaceutical industry. Due to the importance of pyrrole structure in drug design and development, herein, we tried to conduct an extensive review of the bioactive pyrrole based compounds reported recently. The bioactivity of pyrrole derivatives varies, so in the review, we categorized them based on their direct pharmacologic targets. Therefore, readers are able to find the variety of biologic targets for pyrrole containing compounds easily. This review explains around seventy different biologic targets for pyrrole based derivatives, so, it is helpful for medicinal chemists in design and development novel bioactive compounds for different diseases. This review presents an extensive meaningful structure activity relationship for each reported structure as much as possible. The review focuses on papers published between 2018 and 2020.
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Affiliation(s)
- Ebrahim Saeedian Moghadam
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran14176, Iran.
- The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran.
- Department of Chemistry, College of Science, Sultan Qaboos University, Muscat, P.O. Box 36, P.C. 123, Sultanate of Oman
| | - Katayoon Mireskandari
- Department of Pharmaceutics, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran 1417614411, Iran
| | - Raid Abdel-Jalil
- Department of Chemistry, College of Science, Sultan Qaboos University, Muscat, P.O. Box 36, P.C. 123, Sultanate of Oman
| | - Mohsen Amini
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran14176, Iran.
- The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran
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6
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Bhuvaneswari S, Aakash VB, Ramalakshmi N, Arunkumar S. Quantitative Structure–Activity Relationship Analysis and Validation of New DNA Gyrase Inhibitors. Pharm Chem J 2022. [DOI: 10.1007/s11094-021-02513-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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7
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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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8
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Cotman A, Guérin T, Kovačević I, Benedetto Tiz D, Durcik M, Fulgheri F, Možina Š, Secci D, Sterle M, Ilaš J, Zega A, Zidar N, Mašič LP, Tomašič T, Leroux F, Hanquet G, Kikelj D. Practical Synthesis and Application of Halogen-Doped Pyrrole Building Blocks. ACS OMEGA 2021; 6:9723-9730. [PMID: 33869952 PMCID: PMC8047689 DOI: 10.1021/acsomega.1c00331] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/18/2021] [Indexed: 06/12/2023]
Abstract
A practical access to four new halogen-substituted pyrrole building blocks was realized in two to five synthetic steps from commercially available starting materials. The target compounds were prepared on a 50 mg to 1 g scale, and their conversion to nanomolar inhibitors of bacterial DNA gyrase B was demonstrated for three of the prepared building blocks to showcase the usefulness of such chemical motifs in medicinal chemistry.
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Affiliation(s)
- Andrej
Emanuel Cotman
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Thomas Guérin
- Université
de Strasbourg, CNRS, UMR 7042-LIMA, ECPM, 25 Rue Becquerel, Strasbourg 67087, France
| | - Ivana Kovačević
- Faculty
of Sciences, Department of Chemistry, Biochemistry and Environmental
Protection, University of Novi Sad, Trg Dositeja Obradovića 3, 21000 Novi Sad, Serbia
| | - Davide Benedetto Tiz
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Martina Durcik
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Federica Fulgheri
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Štefan Možina
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Daniela Secci
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Maša Sterle
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Janez Ilaš
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Anamarija Zega
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Nace Zidar
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Lucija Peterlin Mašič
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Tihomir Tomašič
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Frédéric
R. Leroux
- Université
de Strasbourg, CNRS, UMR 7042-LIMA, ECPM, 25 Rue Becquerel, Strasbourg 67087, France
| | - Gilles Hanquet
- Université
de Strasbourg, CNRS, UMR 7042-LIMA, ECPM, 25 Rue Becquerel, Strasbourg 67087, France
| | - Danijel Kikelj
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
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9
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Ibrahim TS, Almalki AJ, Moustafa AH, Allam RM, Abuo-Rahma GEDA, El Subbagh HI, Mohamed MFA. Novel 1,2,4-oxadiazole-chalcone/oxime hybrids as potential antibacterial DNA gyrase inhibitors: Design, synthesis, ADMET prediction and molecular docking study. Bioorg Chem 2021; 111:104885. [PMID: 33838559 DOI: 10.1016/j.bioorg.2021.104885] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/26/2021] [Accepted: 03/28/2021] [Indexed: 01/19/2023]
Abstract
New antibacterial drugs are urgently needed to tackle the rapid rise in multi-drug resistant bacteria. DNA gyrase is a validated target for the development of new antibacterial drugs. Thus, in the present investigation, a novel series of 1,2,4-oxadiazole-chalcone/oxime (6a-f) and (7a-f) were synthesized and characterized by IR, NMR (1H and 13C) and elemental analyses. The title compounds were evaluated for their in-vitro antimicrobial activity by the modified agar diffusion method as well as their E. coli DNA gyrase inhibitory activity. The minimum inhibitory concentration (MIC) and the structure activity relationships (SARs) were evaluated. Among all, compounds 6a, 6c-e, 7b and 7e were the most potent and proved to possess broad spectrum activity against the tested Gram-positive and Gram-negative organisms. Additionally, compounds 6a (against S. aureus), 6c (against B. subtilis and E. hirae), 6e (against E. hirae), 6f, 7a and 7c (against E. coli) and 7d (against B. subtilis), with MIC value of 3.12 μM were two-fold more potent than the standard ciprofloxacin (MIC = 6.25 μM). Mechanistically, compounds 6c, 7c, 7e and 7b had good inhibitory activity against E. coli gyrase with IC50 values of 17.05, 13.4, 16.9, and 19.6 µM, respectively, in comparison with novobiocin (IC50 = 12.3 µM) and ciprofloxacin (IC50 = 10.5 µM). The molecular docking results at DNA gyrase active site revealed that the most potent compounds 6c and 7c have binding mode and docking scores comparable to that of ciprofloxacin and novobiocin suggesting their antibacterial activity via inhibition of DNA gyrase. Finally, the predicted parameters of Lipinski's rule of five and ADMET analysis showed that 6c and 7c had good drug-likeness and acceptable physicochemical properties. Therefore, the hybridization of the chalcone and oxadiazole moieties could be promising lead as antibacterial candidate which merit further future structural optimizations.
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Affiliation(s)
- Tarek S Ibrahim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt.
| | - Ahmad J Almalki
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Amr H Moustafa
- Department of Chemistry, Faculty of Science, Sohag University, Sohag 82524, Egypt
| | - Rasha M Allam
- Pharmacology Department, National Research Centre, Cairo 12622 (ID: 60014618), Egypt
| | - Gamal El-Din A Abuo-Rahma
- Department of Medicinal Chemistry, Faculty of Pharmacy, Minia University, Minia 61519, Egypt; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Deraya University, New Minia, Minia, Egypt
| | - Hussein I El Subbagh
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, 35516 Mansoura, Egypt
| | - Mamdouh F A Mohamed
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Sohag University, 82524 Sohag, Egypt.
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10
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Mohi El-Deen EM, Abd El-Meguid EA, Karam EA, Nossier ES, Ahmed MF. Synthesis and Biological Evaluation of New Pyridothienopyrimidine Derivatives as Antibacterial Agents and Escherichia coli Topoisomerase II Inhibitors. Antibiotics (Basel) 2020; 9:antibiotics9100695. [PMID: 33066400 PMCID: PMC7602199 DOI: 10.3390/antibiotics9100695] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 09/30/2020] [Accepted: 10/07/2020] [Indexed: 11/16/2022] Open
Abstract
The growing resistance of bacteria to many antibiotics that have been in use for several decades has generated the need to discover new antibacterial agents with structural features qualifying them to overcome the resistance mechanisms. Thus, novel pyridothienopyrimidine derivatives (2a,b-a,b) were synthesized by a series of various reactions, starting with 3-aminothieno[2,3-b]pyridine-2-carboxamides (1a,b). Condensation of compounds 1a,b with cyclohexanone gave 1'H-spiro[cyclohexane-1,2'-pyrido[3',2':4,5]thieno[3,2-d]pyrimidin]-4'(3'H)-ones (2a,b), which in turn were utilized to afford the target 4-substituted derivatives (3a,b-8a,b). In vitro antibacterial activity evaluations of all the new compounds (2a,b-8a,b) were performed against six strains of Gram-negative and Gram-positive bacteria. The target compounds showed significant antibacterial activity, especially against Gram-negative strains. Moreover, the compounds (2a,b; 3a,b; 4a,b; and 5a,b) that exhibited potent activity against Escherichia coli were selected to screen their inhibitory activity against Escherichia coli topoisomerase II (DNA gyrase and topoisomerase IV) enzymes. Compounds 4a and 4b showed potent dual inhibition of the two enzymes with IC50 values of 3.44 µΜ and 5.77 µΜ against DNA gyrase and 14.46 µΜ and 14.89 µΜ against topoisomerase IV, respectively. In addition, docking studies were carried out to give insight into the binding mode of the tested compounds within the E. coli DNA gyrase B active site compared with novobiocin.
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Affiliation(s)
- Eman M. Mohi El-Deen
- Department of Therapeutic Chemistry, National Research Centre, Dokki, Cairo 12622, Egypt
- Correspondence: ; Tel.: +20-0106-385-3338
| | - Eman A. Abd El-Meguid
- Department of Chemistry of Natural and Microbial Products, National Research Centre, Dokki, Cairo 12622, Egypt;
| | - Eman A. Karam
- Microbial Chemistry Department, National Research Centre, Dokki, Cairo 12622, Egypt;
| | - Eman S. Nossier
- Department of Pharmaceutical Medicinal Chemistry, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo 11754, Egypt;
| | - Marwa F. Ahmed
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Taif University, Taif 21974, Saudi Arabia;
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Helwan University, Cairo 11795, Egypt
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11
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Tambe PM, Bhowmick S, Chaudhary SK, Khan MR, Wabaidur SM, Muddassir M, Patil PC, Islam MA. Structure-Based Screening of DNA GyraseB Inhibitors for Therapeutic Applications in Tuberculosis: a Pharmacoinformatics Study. Appl Biochem Biotechnol 2020; 192:1107-1123. [PMID: 32686004 DOI: 10.1007/s12010-020-03374-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 06/22/2020] [Indexed: 11/27/2022]
Abstract
Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis (MTB) and considered as serious public health concern worldwide which kills approximately five thousand people every day. Therefore, TB drug development efforts are in gigantic need for identification of new potential chemical agents to eradicate TB from the society. The bacterial DNA gyrase B (GyrB) protein as an experimentally widely accepted effective drug target for the development of TB chemotherapeutics. In the present study, advanced pharmacoinformatics approaches were used to screen the Mcule database against the GyrB protein. Based on a number of chemometric parameters, five molecules were found to be crucial to inhibit the GyrB. A number of molecular binding interactions between the proposed inhibitors and important active site residues of GyrB were observed. The predicted drug-likeness properties of all molecules were indicated that compounds possess characteristics to be the drug-like candidates. The dynamic nature of each molecule was explored through the molecular dynamics (MD) simulation study. Various analyzing parameters from MD simulation trajectory have suggested rationality of the molecules to be potential GyrB inhibitor. Moreover, the binding free energy was calculated from the entire MD simulation trajectories highlighted greater binding free energy values for all newly identified compounds also substantiated the strong binding affection towards the GyrB in comparison to the novobiocin. Therefore, the proposed molecules might be considered as potential anti-TB chemical agents for future drug discovery purposes subjected to experimental validation. Graphical Abstract.
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Affiliation(s)
- Pranjali Mahadeo Tambe
- Department of Bioinformatics, Rajiv Gandhi Institute of IT and Biotechnology, Bharati Vidyapeeth Deemed University, Pune-Satara Road, Pune, India
| | - Shovonlal Bhowmick
- Department of Chemical Technology, University of Calcutta, 92 A.P.C. Road, Kolkata, India
| | - Sushil K Chaudhary
- Faculty of Pharmacy, DIT University, Mussoorie-Diversion Road, Makkawala, Dehradun, Uttarakhand, 248009, India
| | - Mohammad Rizwan Khan
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Saikh M Wabaidur
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Mohd Muddassir
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Preeti Chunarkar Patil
- Department of Bioinformatics, Rajiv Gandhi Institute of IT and Biotechnology, Bharati Vidyapeeth Deemed University, Pune-Satara Road, Pune, India
| | - Md Ataul Islam
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, M13 9PL, UK. .,School of Health Sciences, University of Kwazulu-Natal, Westville Campus, Durban, South Africa. .,Department of Chemical Pathology, Faculty of Health Sciences, University of Pretoria and National Health Laboratory Service Tshwane Academic Division, Pretoria, South Africa.
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12
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Discovery of new ATP-competitive inhibitors of human DNA topoisomerase IIα through screening of bacterial topoisomerase inhibitors. Bioorg Chem 2020; 102:104049. [PMID: 32688116 DOI: 10.1016/j.bioorg.2020.104049] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 06/19/2020] [Accepted: 06/25/2020] [Indexed: 02/07/2023]
Abstract
Human DNA topoisomerase II is one of the major targets in anticancer therapy, however ATP-competitive inhibitors of this target have not yet reached their full potential. ATPase domain of human DNA topoisomerase II belongs to the GHKL ATPase superfamily and shares a very high 3D structural similarity with other superfamily members, including bacterial topoisomerases. In this work we report the discovery of a new chemotype of ATP-competitive inhibitors of human DNA topoisomerase IIα that were discovered through screening of in-house library of ATP-competitive inhibitors of bacterial DNA gyrase and topoisomerase IV. Systematic screening of this library provided us with 20 hit compounds. 1,2,4-Substituted N-phenylpyrrolamides were selected for a further exploration which resulted in 13 new analogues, including 52 with potent activity in relaxation assay (IC50 = 3.2 µM) and ATPase assay (IC50 = 0.43 µM). Cytotoxic activity of all hits was determined in MCF-7 cancer cell line and the most potent compounds, 16 and 20, showed an IC50 value of 8.7 and 8.2 µM, respectively.
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13
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Stokes SS, Vemula R, Pucci MJ. Advancement of GyrB Inhibitors for Treatment of Infections Caused by Mycobacterium tuberculosis and Non-tuberculous Mycobacteria. ACS Infect Dis 2020; 6:1323-1331. [PMID: 32183511 DOI: 10.1021/acsinfecdis.0c00025] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The prospect of ever increasing antibiotic resistance eroding currently available treatment options for bacterial infections underscores the need to continue to identify new antibiotics, preferably those that act on novel targets or with novel mechanisms of action. Bacterial gyrase B subunit (GyrB), an essential component of bacterial gyrase required for successful DNA replication, represents such a target. We describe recent examples of GyrB inhibitors and point out their potential utility for treatment of mycobacterial diseases caused by Mycobacterium tuberculosis (TB) and non-tuberculous mycobacteria (NTM). Current therapeutic options for these diseases are often suboptimal due to resistance to current standard of care antibiotics. A future GyrB inhibitor-based antibiotic could offer a new and effective addition to the armamentarium for treatment of mycobacterial diseases and possibly for infections caused by other bacterial pathogens. One GyrB inhibitor, SPR720, has recently completed a first-in-human clinical trial and is in clinical development for the treatment of NTM and TB infections.
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Affiliation(s)
- Suzanne S. Stokes
- Spero Therapeutics, 675 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Rajender Vemula
- Spero Therapeutics, 675 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Michael J. Pucci
- Spero Therapeutics, 675 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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