1
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Sterle M, Habjan E, Piga M, Peršolja P, Durcik M, Dernovšek J, Szili P, Czikkely MS, Zidar N, Janez I, Pal C, Accetto T, Pardo LA, Kikelj D, Peterlin Mašič L, Tomašič T, Bitter W, Cotman AE, Speer A, Zega A. Development of narrow-spectrum topoisomerase-targeting antibacterials against mycobacteria. Eur J Med Chem 2024; 276:116693. [PMID: 39053193 DOI: 10.1016/j.ejmech.2024.116693] [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: 04/26/2024] [Revised: 06/21/2024] [Accepted: 07/17/2024] [Indexed: 07/27/2024]
Abstract
New 2-pyrrolamidobenzothiazole-based inhibitors of mycobacterial DNA gyrase were discovered. Among these, compounds 49 and 51, show excellent antibacterial activity against Mycobacterium tuberculosis and Mycobacterium abscessus with a notable preference for mycobacteria. Both compounds can penetrate infected macrophages and reduce intracellular M. tuberculosis load. Compound 51 is a potent inhibitor of DNA gyrase (M. tuberculosis DNA gyrase IC50 = 4.1 nM, Escherichia coli DNA gyrase IC50 of <10 nM), selective for bacterial topoisomerases. It displays low MIC90 values (M. tuberculosis: 0.63 μM; M. abscessus: 2.5 μM), showing specificity for mycobacteria, and no apparent toxicity. Compound 49 not only displays potent antimycobacterial activity (MIC90 values of 2.5 μM for M. tuberculosis and 0.63 μM for M. abscessus) and selectivity for mycobacteria but also exhibits favorable solubility (kinetic solubility = 55 μM) and plasma protein binding (with a fraction unbound of 2.9 % for human and 4.7 % for mouse). These findings underscore the potential of fine-tuning molecular properties to develop DNA gyrase B inhibitors that specifically target the mycobacterial chemical space, mitigating the risk of resistance development in non-target pathogens and minimizing harm to the microbiome.
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Affiliation(s)
- Maša Sterle
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Eva Habjan
- Department of Medical Microbiology and Infection Control, Amsterdam UMC, Location VU Medical Center, De Boelelaan 1108, 1081 HZ, Amsterdam, the Netherlands
| | - 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
| | - Martina Durcik
- 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
| | - Petra Szili
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged, H-6726, Hungary
| | - Marton Simon Czikkely
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, 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
| | - Nace Zidar
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Ilaš Janez
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Csaba Pal
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged, H-6726, Hungary
| | - Tomaž Accetto
- University of Ljubljana, Biotechnical Faculty, Department of Microbiology, Groblje 3, 1230, Domžale, Slovenia
| | - Luis A Pardo
- Max Planck Institute for Multidisciplinary Sciences, Oncophysiology, Hermann-Rein-Str. 3, 37075, Göttingen, Germany
| | - Danijel Kikelj
- 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
| | - Tihomir Tomašič
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Wilbert Bitter
- Department of Medical Microbiology and Infection Control, Amsterdam UMC, Location VU Medical Center, De Boelelaan 1108, 1081 HZ, Amsterdam, the Netherlands
| | - Andrej Emanuel Cotman
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Alexander Speer
- Department of Medical Microbiology and Infection Control, Amsterdam UMC, Location VU Medical Center, De Boelelaan 1108, 1081 HZ, Amsterdam, the Netherlands.
| | - Anamarija Zega
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia.
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2
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Dinh Thanh N, Son Hai D, Ngoc Toan V, Thi Kim Van H, Thi Kim Giang N, Minh Tri N. Sulfonyl thioureas with a benzo[d]thiazole ring as dual acetylcholinesterase/butyrylcholinesterase and human monoamine oxidase A and B inhibitors: An in vitro and in silico study. Arch Pharm (Weinheim) 2024; 357:e2300557. [PMID: 38321839 DOI: 10.1002/ardp.202300557] [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: 10/01/2023] [Revised: 12/30/2023] [Accepted: 01/12/2024] [Indexed: 02/08/2024]
Abstract
A series of sulfonyl thioureas 6a-q containing a benzo[d]thiazole ring with an ester functional group was synthesized from corresponding substituted 2-aminobenzo[d]thiazoles 3a-q and p-toluenesulfonyl isothiocyanate. They had remarkable inhibitory activity against acetylcholinesterase (AChE), butyrylcholinesterase (BChE), monoamine oxidase (MAO)-A, and MAO-B. Among thioureas, several compounds had notable activity in the order of 6k > 6 h > 6c (AChE), 6j > 6g > 6k (BChE), 6k > 6g > 6f (MAO-A), and 6i > 6k > 6h (MAO-B). Compound 6k was an inhibitor of interest due to its potent or good activity against all studied enzymes, with IC50 values of 0.027 ± 0.008 μM (AChE), 0.043 ± 0.004 μM (BChE), 0.353 ± 0.01 μM (MAO-A), and 0.716 ± 0.02 μM (MAO-B). This inhibitory capacity was comparable to that of the reference drugs for each enzyme. Kinetic studies of two compounds with potential activity, 6k (against AChE) and 6j (against BChE), had shown that both 6k and 6j followed competitive-type enzyme inhibition, with Ki constants of 24.49 and 12.16 nM, respectively. Induced fit docking studies for enzymes 4EY7, 7BO4, 2BXR, and 2BYB showed active interactions between sulfonyl thioureas of benzo[d]thiazoles and the residues in the active pocket with ligands 6k, 6i, and 6j, respectively. The stability of the ligand-protein complexes while each ligand entered the active site of each enzyme (4EY7, 7BO4, 2BXR, or 2BYB) was confirmed by molecular dynamics simulations.
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Affiliation(s)
- Nguyen Dinh Thanh
- Department of Organic Chemistry, Faculty of Chemistry, University of Science (Vietnam National University, Ha Noi), Ha Noi, Hoan Kiem, Viet Nam
| | - Do Son Hai
- Department of Organic Chemistry, Faculty of Chemistry, University of Science (Vietnam National University, Ha Noi), Ha Noi, Hoan Kiem, Viet Nam
- Institute of Science and Technology, Ministry of Public Security of Vietnam, Ha Noi, Cau Giay, Viet Nam
| | - Vu Ngoc Toan
- Department of Organic Chemistry, Faculty of Chemistry, University of Science (Vietnam National University, Ha Noi), Ha Noi, Hoan Kiem, Viet Nam
- Institute of New Technology, Military Institute of Science and Technology, Ha Noi, Cau Giay, Viet Nam
| | - Hoang Thi Kim Van
- Department of Organic Chemistry, Faculty of Chemistry, University of Science (Vietnam National University, Ha Noi), Ha Noi, Hoan Kiem, Viet Nam
- Faculty of Chemical Technology, Viet Tri University of Industry, Tien Kien, Lam Thao, Phu Tho, Viet Nam
| | - Nguyen Thi Kim Giang
- Department of Organic Chemistry, Faculty of Chemistry, University of Science (Vietnam National University, Ha Noi), Ha Noi, Hoan Kiem, Viet Nam
- Institute of Science and Technology, Ministry of Public Security of Vietnam, Ha Noi, Cau Giay, Viet Nam
| | - Nguyen Minh Tri
- Department of Organic Chemistry, Faculty of Chemistry, University of Science (Vietnam National University, Ha Noi), Ha Noi, Hoan Kiem, Viet Nam
- Institute of New Technology, Military Institute of Science and Technology, Ha Noi, Cau Giay, Viet Nam
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3
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Durcik M, Cruz CD, Scorciapino MA, Ilaš J, Tammela P, Ceccarelli M, Mašič LP, Tomašič T. Benzothiazole DNA gyrase inhibitors and their conjugates with siderophore mimics: design, synthesis and evaluation. RSC Adv 2024; 14:2905-2917. [PMID: 38239435 PMCID: PMC10794952 DOI: 10.1039/d3ra08337c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 01/11/2024] [Indexed: 01/22/2024] Open
Abstract
Benzothiazole-based bacterial DNA gyrase and topoisomerase IV inhibitors are promising new antibacterial agents with potent activity against Gram-positive and Gram-negative bacterial strains. The aim of this study was to improve the uptake of these inhibitors into the cytoplasm of Gram-negative bacteria by conjugating them to the small siderophore mimics. The best conjugate 18b displayed potent Escherichia coli DNA gyrase and topoisomerase IV inhibition. The interaction analysis of molecular dynamics simulation trajectory showed the important contribution of the siderophore mimic moiety to binding affinity. By NMR spectroscopy, we demonstrated that the hydroxypyridinone moiety alone was responsible for the chelation of iron(iii). Moreover, 18b showed an enhancement of antibacterial activity against E. coli JW5503 in an iron-depleted medium, clearly indicating an increased uptake of 18b in this bacterial strain.
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Affiliation(s)
- Martina Durcik
- 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
| | - Mariano Andrea Scorciapino
- Department of Chemical and Geological Sciences, University of Cagliari, Cittadella Universitaria di Monserrato - S. P. 8 km 0.700 09042 - Monserrato (CA) Italy
| | - 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
| | - Matteo Ceccarelli
- Department of Physics and IOM/CNR, Sezione di Cagliari, University of Cagliari, Cittadella Universitaria di Monserrato - S. P. 8 km 0700 09042 - Monserrato (CA) Italy
| | - Lucija Peterlin Mašič
- 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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4
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Sterle M, Durcik M, Stevenson CEM, Henderson SR, Szili PE, Czikkely M, Lawson DM, Maxwell A, Cahard D, Kikelj D, Zidar N, Pal C, Mašič LP, Ilaš J, Tomašič T, Cotman AE, Zega A. Exploring the 5-Substituted 2-Aminobenzothiazole-Based DNA Gyrase B Inhibitors Active against ESKAPE Pathogens. ACS OMEGA 2023; 8:24387-24395. [PMID: 37457471 PMCID: PMC10339456 DOI: 10.1021/acsomega.3c01930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 06/16/2023] [Indexed: 07/18/2023]
Abstract
We present a new series of 2-aminobenzothiazole-based DNA gyrase B inhibitors with promising activity against ESKAPE bacterial pathogens. Based on the binding information extracted from the cocrystal structure of DNA gyrase B inhibitor A, in complex with Escherichia coli GyrB24, we expanded the chemical space of the benzothiazole-based series to the C5 position of the benzothiazole ring. In particular, compound E showed low nanomolar inhibition of DNA gyrase (IC50 < 10 nM) and broad-spectrum antibacterial activity against pathogens belonging to the ESKAPE group, with the minimum inhibitory concentration < 0.03 μg/mL for most Gram-positive strains and 4-16 μg/mL against Gram-negative E. coli, Acinetobacter baumannii, Pseudomonas aeruginosa, and Klebsiella pneumoniae. To understand the binding mode of the synthesized inhibitors, a combination of docking calculations, molecular dynamics (MD) simulations, and MD-derived structure-based pharmacophore modeling was performed. The computational analysis has revealed that the substitution at position C5 can be used to modify the physicochemical properties and antibacterial spectrum and enhance the inhibitory potency of the compounds. Additionally, a discussion of challenges associated with the synthesis of 5-substituted 2-aminobenzothiazoles is presented.
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Affiliation(s)
- Maša Sterle
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, Ljubljana 1000, Slovenia
| | - Martina Durcik
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, Ljubljana 1000, Slovenia
| | - Clare E. M. Stevenson
- Department
of Biochemistry and Metabolism, John Innes
Centre, Norwich Research Park, Norwich NR4 7UH, U.K.
| | - Sara R. Henderson
- Institute
of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, U.K.
| | - Petra Eva Szili
- Synthetic
and Systems Biology Unit, Biological Research Centre, Institute of Biochemistry, Szeged H-6726, Hungary
| | - Marton Czikkely
- Synthetic
and Systems Biology Unit, Biological Research Centre, Institute of Biochemistry, Szeged H-6726, Hungary
| | - David M. Lawson
- 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.
| | - Dominique Cahard
- CNRS
UMR 6014 COBRA, Normandie Université, Mont Saint Aignan 76821, France
| | - Danijel Kikelj
- 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
| | - Csaba Pal
- Synthetic
and Systems Biology Unit, Biological Research Centre, Institute of Biochemistry, Szeged H-6726, Hungary
| | - Lucija Peterlin Mašič
- 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
| | - Tihomir Tomašič
- 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
| | - Anamarija Zega
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, Ljubljana 1000, Slovenia
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5
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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] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [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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6
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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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7
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Bhagat DS, Chawla PA, Gurnule WB, Shejul SK, Bumbrah GS. An Insight into Synthesis and Anticancer Potential of Thiazole and 4-thiazolidinone Containing Motifs. CURR ORG CHEM 2021. [DOI: 10.2174/1385272825999210101234704] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Over the years, the branch of oncology has reached a mature stage, and substantial
development and advancement have been achieved in this dimension of medical science. The
synthesis and isolation of numerous novel anticancer agents of natural and synthetic origins
have been reported. Thiazole and 4-thiazolidinone containing heterocyclic compounds, having
a broad spectrum of pharmaceutical activities, represent a significant class of medicinal
chemistry. Thiazole and 4-thiazolidinone are five-membered unique heterocyclic motifs containing
S and N atoms as an essential core scaffold and have commendable medicinal significance.
Thiazoles and 4-thiazolidinones containing heterocyclic compounds are used as building
blocks for the next generation of pharmaceuticals. Thiazole precursors have been frequently
used due to their capabilities to bind to numerous cancer-specific protein targets.
Suitably, thiazole motifs have a biological suit via inhibition of different signaling pathways involved in cancer
causes. The scientific community has always tried to synthesize novel thiazole-based heterocycles by carrying out
different replacements of functional groups or skeleton around thiazole moiety. Herein, we report the current trend of
research and development in anticancer activities of thiazoles and 4-thiazolidinones containing scaffolds. In the current
study, we have also highlighted some other significant biological properties of thiazole, novel protocols of synthesis
for the synthesis of the new candidates, along with a significant broad spectrum of the anticancer activities of
thiazole containing scaffolds. This study facilitates the development of novel thiazole and 4-thiazolidinone containing
candidates with potent, efficient anticancer activity and less cytotoxic property.
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Affiliation(s)
- Devidas S. Bhagat
- Department of Forensic Chemistry and Toxicology, Government Institute of Forensic Science, Aurangabad 431 004, (MS), India
| | - Pooja A. Chawla
- Department of Pharmaceutical Chemistry and Analysis, ISF College of Pharmacy, Moga 142001, Punjab, India
| | - Wasudeo B. Gurnule
- Department of Chemistry, Kamla Nehru Mahavidyalaya, Nagpur-440024, (MS), India
| | - Sampada K. Shejul
- Department of Life Science, Vivekanand Arts, Sardar Dalipsingh Commerce and Science College, Aurangabad 431 001, (MS), India
| | - Gurvinder S. Bumbrah
- Department of Chemistry, Biochemistry and Forensic Science, Amity School of Applied Sciences, Amity University, 122413, Haryana, India
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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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New dual ATP-competitive inhibitors of bacterial DNA gyrase and topoisomerase IV active against ESKAPE pathogens. Eur J Med Chem 2021; 213:113200. [PMID: 33524686 DOI: 10.1016/j.ejmech.2021.113200] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/10/2020] [Accepted: 01/12/2021] [Indexed: 11/21/2022]
Abstract
The rise in multidrug-resistant bacteria defines the need for identification of new antibacterial agents that are less prone to resistance acquisition. Compounds that simultaneously inhibit multiple bacterial targets are more likely to suppress the evolution of target-based resistance than monotargeting compounds. The structurally similar ATP binding sites of DNA gyrase and topoisomerase Ⅳ offer an opportunity to accomplish this goal. Here we present the design and structure-activity relationship analysis of balanced, low nanomolar inhibitors of bacterial DNA gyrase and topoisomerase IV that show potent antibacterial activities against the ESKAPE pathogens. For inhibitor 31c, a crystal structure in complex with Staphylococcus aureus DNA gyrase B was obtained that confirms the mode of action of these compounds. The best inhibitor, 31h, does not show any in vitro cytotoxicity and has excellent potency against Gram-positive (MICs: range, 0.0078-0.0625 μg/mL) and Gram-negative pathogens (MICs: range, 1-2 μg/mL). Furthermore, 31h inhibits GyrB mutants that can develop resistance to other drugs. Based on these data, we expect that structural derivatives of 31h will represent a step toward clinically efficacious multitargeting antimicrobials that are not impacted by existing antimicrobial resistance.
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