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Dobričić V, Marodi M, Marković B, Tomašič T, Durcik M, Zidar N, Mašič LP, Ilaš J, Kikelj D, Čudina O. Estimation of passive gastrointestinal absorption of new dual DNA gyrase and topoisomerase IV inhibitors using PAMPA and biopartitioning micellar chromatography and quantitative structure-retention relationship analysis. J Chromatogr B Analyt Technol Biomed Life Sci 2024; 1240:124158. [PMID: 38776787 DOI: 10.1016/j.jchromb.2024.124158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 04/09/2024] [Accepted: 05/16/2024] [Indexed: 05/25/2024]
Abstract
DNA gyrase and topoisomerase IV play significant role in maintaining the correct structure of DNA during replication and they have been identified as validated targets in antibacterial drug discovery. Inadequate pharmacokinetic properties are responsible for many failures during drug discovery and their estimation in the early phase of this process maximizes the chance of getting useful drug candidates. Passive gastrointestinal absorption of a selected group of thirteen dual DNA gyrase and topoisomerase IV inhibitors was estimated using two in vitro tests - parallel artificial membrane permeability assay (PAMPA) and biopartitioning micellar chromatography (BMC). Due to good correlation between obtained results, passive gastrointestinal absorption of remaining ten compounds was estimated using only BMC. With this experimental setup, it was possible to identify compounds with high values of retention factors (k) and highest expected passive gastrointestinal absorption, and compounds with low values of k for which low passive gastrointestinal absorption is predicted. Quantitative structure-retention relationship (QSRR) modelling was performed by creating multiple linear regression (MLR), partial least squares (PLS) and support vector machines (SVM) models. Descriptors with the highest influence on retention factor were identified and their interpretation can be used for the design of new compounds with improved passive gastrointestinal absorption.
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Affiliation(s)
- Vladimir Dobričić
- Department of Pharmaceutical Chemistry, University of Belgrade - Faculty of Pharmacy, Vojvode Stepe 450, 11000 Belgrade, Serbia.
| | - Marko Marodi
- Department of Pharmaceutical Chemistry, University of Belgrade - Faculty of Pharmacy, Vojvode Stepe 450, 11000 Belgrade, Serbia
| | - Bojan Marković
- Department of Pharmaceutical Chemistry, University of Belgrade - Faculty of Pharmacy, Vojvode Stepe 450, 11000 Belgrade, Serbia
| | - Tihomir Tomašič
- University of Ljubljana, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Martina Durcik
- University of Ljubljana, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Nace Zidar
- University of Ljubljana, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Lucija Peterlin Mašič
- University of Ljubljana, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Janez Ilaš
- University of Ljubljana, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Danijel Kikelj
- University of Ljubljana, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Olivera Čudina
- Department of Pharmaceutical Chemistry, University of Belgrade - Faculty of Pharmacy, Vojvode Stepe 450, 11000 Belgrade, Serbia
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2
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Zhou G, Li Y. Investigation of bacterial DNA gyrase Inhibitor classification models and structural requirements utilizing multiple machine learning methods. Mol Divers 2024:10.1007/s11030-024-10806-y. [PMID: 38372837 DOI: 10.1007/s11030-024-10806-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 01/04/2024] [Indexed: 02/20/2024]
Abstract
Infections from multidrug-resistant (MDR) bacteria have emerged as a paramount global health concern, and the therapeutic effectiveness of current treatments is swiftly diminishing. An urgent need exists to explore innovative strategies for countering drug-resistant bacteria. Bacterial DNA gyrase, functioning as an ATP-dependent enzyme, plays a pivotal role in the intricate processes of transcription, replication, and chromosome segregation within bacterial DNA. This renders it a prime target for the development of innovative antibacterial agents. However, the experimental identification of bacterial DNA gyrase inhibitors faces multifaceted challenges due to current methodological constraints. Recognizing its significance, this study developed 56 computational models designed for predicting bacterial DNA gyrase inhibitors. These models employed seven distinct molecular fingerprints and eight machine learning algorithms. Among these models, Model_2D, created using KlekotaRoth fingerprints and the SVM algorithm, stands out as the most robust performer (ACC = 0.86, MCC = 0.63, G-mean = 0.82). Moreover, given the limited exploration of structural fragments required for DNA Gyrase B inhibitors, crucial structural fingerprints influencing DNA Gyrase B inhibitors were identified through Bayesian classification. Subsequently, we conducted molecular docking to reveal the binding modes between these crucial structural fingerprints and the active site of DNA gyrase B. In conclusion, the present study aimed to develop the optimal classification model for bacterial DNA gyrase inhibitors, offering invaluable support to medicinal chemists creating innovative DNA gyrase inhibitors.
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Affiliation(s)
- Guozheng Zhou
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian, 116024, Liaoning, China
| | - Yan Li
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian, 116024, Liaoning, China.
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3
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Zheng WF, Chen J, Qi X, Huang Z. Modular and diverse synthesis of amino acids via asymmetric decarboxylative protonation of aminomalonic acids. Nat Chem 2023; 15:1672-1682. [PMID: 37973941 DOI: 10.1038/s41557-023-01362-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 10/06/2023] [Indexed: 11/19/2023]
Abstract
Stereoselective protonation is a challenge in asymmetric catalysis. The small size and high rate of transfer of protons mean that face-selective delivery to planar intermediates is hard to control, but it can unlock previously obscure asymmetric transformations. Particularly, when coupled with a preceding decarboxylation, enantioselective protonation can convert the abundant acid feedstocks into structurally diverse chiral molecules. Here an anchoring group strategy is demonstrated as a potential alternative and supplement to the conventional structural modification of catalysts by creating additional catalyst-substrate interactions. We show that a tailored benzamide group in aminomalonic acids can help build a coordinated network of non-covalent interactions, including hydrogen bonds, π-π interactions and dispersion forces, with a chiral acid catalyst. This allows enantioselective decarboxylative protonation to give α-amino acids. The malonate-based synthesis introduces side chains via a facile substitution of aminomalonic esters and thus can access structurally and functionally diverse amino acids.
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Affiliation(s)
- Wei-Feng Zheng
- State Key Laboratory of Synthetic Chemistry, Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Jingdan Chen
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, China
| | - Xiaotian Qi
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, China.
| | - Zhongxing Huang
- State Key Laboratory of Synthetic Chemistry, Department of Chemistry, The University of Hong Kong, Hong Kong, China.
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4
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Russo CM, Howey KG, O'Reilly MC. Scalable and Chromatography-Free Synthesis of Efflux Pump Inhibitor Phenylalanine Arginine β-Naphthylamide for Its Validation in Wild-Type Bacterial Strains. ChemMedChem 2023; 18:e202300128. [PMID: 37126222 PMCID: PMC10524873 DOI: 10.1002/cmdc.202300128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/27/2023] [Accepted: 04/28/2023] [Indexed: 05/02/2023]
Abstract
Phenylalanine arginine β-naphthylamine, or PAβN, is a C-terminus capped dipeptide discovered in 1999 as an RND-type efflux pump inhibitor (EPI). Since then, PAβN has become a standard tool compound in EPI research and development. Despite this, PAβN lacks a detailed or efficient synthesis, and standard parameters for its use in wild-type bacterial strains are inconsistent or non-existent. Therefore, a scalable and chromatography-free synthesis of PAβN was developed using streamlined traditional solution-phase peptide coupling chemistry. With this procedure, gram scale quantities of PAβN were synthesized alongside analogues and stereoisomers to build a focused library to evaluate simple structure activity relationships. While most analogues were less active than the broadly utilized L,L-PAβN itself, we identified that its enantiomer, D,D-PAβN, also provided 8- to 16-fold potentiation of the antibiotic levofloxacin at 40 to 50 μg/mL concentrations of EPI in various wild-type Pseudomonas aeruginosa strains. Additionally, D,D-PAβN was shown to be significantly more hydrolytically stable than L,L-PAβN, indicating that it may be a useful, and now readily synthesized, tool compound facilitating future EPI research.
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Affiliation(s)
| | - Kelsey G Howey
- Department of Chemistry, Villanova University, Villanova, PA 19085, USA
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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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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] [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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7
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Pudipeddi A, Vasudevan S, Shanmugam K, Mohan S S, Vairaprakash P, Neelakantan P, Balraj AS, Solomon AP. Design, dynamic docking, synthesis, and in vitro validation of a novel DNA gyrase B inhibitor. J Biomol Struct Dyn 2022:1-14. [PMID: 35924774 DOI: 10.1080/07391102.2022.2107073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-intermediate-resistant Staphylococcus aureus (VRSA) are among the WHO's high priority pathogens. Among these two, MRSA is the most globally documented pathogen that necessitates the pressing demand for new classes of anti-MRSA drugs. Bacterial gyrase targeted therapeutics are unique strategies to overcome cross-resistance as they are present only in bacteria and absent in higher eukaryotes. The GyrB subunit is essential for the catalytic functions of the bacterial enzyme DNA Gyrase, thereby constituting a promising druggable target. The current study performed a structure-based virtual screening to designing GyrB target-specific candidate molecules. The de novo ligand design of novel hit molecules was performed using a rhodanine scaffold. Through a systematic in silico screening process, the hit molecules were screened for their synthetic accessibility, drug-likeness and pharmacokinetics properties in addition to its target specific interactions. Of the 374 hit molecules obtained through de novo ligand design, qsl-304 emerged as the most promising ligand. The molecular dynamic simulation studies confirmed the stable interaction between the key residues and qsl-304. qsl-304 was synthesized through a one-step chemical synthesis procedure, and the in vitro activity was proven, with an IC50 of 31.23 µg/mL against the novobiocin resistant clinical isolate, Staphylococcus aureus sa-P2003. Further studies on time-kill kinetics showed the bacteriostatic nature with the diminished recurrence of resistance. The on-target gyrB inhibition further proved the efficacy of qsl-304.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Akhila Pudipeddi
- Quorum Sensing Laboratory, Centre of Research in Infectious Diseases, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India.,Faculty of Dentistry, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Sahana Vasudevan
- Quorum Sensing Laboratory, Centre of Research in Infectious Diseases, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Karthi Shanmugam
- Quorum Sensing Laboratory, Centre of Research in Infectious Diseases, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India.,Department of Bioinformatics, School of Chemical & Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Suma Mohan S
- Department of Bioinformatics, School of Chemical & Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Pothiappan Vairaprakash
- Department of Chemistry, School of Chemical & Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | | | - Alex Stanley Balraj
- Quorum Sensing Laboratory, Centre of Research in Infectious Diseases, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India.,Department of Bioinformatics, School of Chemical & Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Adline Princy Solomon
- Quorum Sensing Laboratory, Centre of Research in Infectious Diseases, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
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8
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Bagra N, Jain R. Synthesis of 4-(1,2,3-triazol-1-yl)-L-phenylalanines. SYNTHETIC COMMUN 2022. [DOI: 10.1080/00397911.2022.2077114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Nitin Bagra
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Punjab, India
| | - Rahul Jain
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Punjab, India
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9
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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: 0] [Impact Index Per Article: 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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10
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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] [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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11
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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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12
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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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13
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Design, Synthesis, Characterization of New Carbamates of 4-Nitrophenylchloroformate and Their Antimicrobial and Antioxidant Activities: an In Vitro and In Silico Approach. CHEMISTRY AFRICA 2021. [DOI: 10.1007/s42250-020-00211-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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14
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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] [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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15
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Jaswal S, Nehra B, Kumar S, Monga V. Recent advancements in the medicinal chemistry of bacterial type II topoisomerase inhibitors. Bioorg Chem 2020; 104:104266. [PMID: 33142421 DOI: 10.1016/j.bioorg.2020.104266] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/14/2020] [Accepted: 08/31/2020] [Indexed: 02/06/2023]
Abstract
Replication proteins are sought as a potential targets for antimicrobial agents. Despite their promising target characteristics, only topoisomerase II inhibitors targeting DNA gyrase and/or topoisomerase IV have reached clinical use. Topoisomerases are the enzymes that are essential for cellular functions and various biological activities. A wide range of natural and synthetic compounds have been identified as potential topoisomerase inhibitors but the resistance is most commonly found in these drugs. The emergence of FQ resistance has increased the need for the development of novel topoisomerase inhibitors with efficacy and high potency against FQ-resistant strains. Besides structural modifications of existing FQ scaffolds, novel non-quinolone topoisomerase II inhibitors, known as novel bacterial topoisomerase inhibitors, have been developed which showed remarkable inhibitory activity against DNA gyrase/topoisomerase IV or both with an improved spectrum of antibacterial potency including drug-resistant strains. This review aims to summarize various recent advancements in the medicinal chemistry of topoisomerase inhibitors with the following objectives: (1) To represent inclusive data on types of topoisomerases and various marketed topoisomerase inhibitors as drugs; (2) To discuss the recent advances in the medicinal chemistry of various topoisomerase inhibitors (DNA gyrase and topo IV) belonging to different structural classes as potential antibacterial agents; (3) To summarizes the structure activity relationship (SAR) including in silico and mechanistic studies to afford ideas and to provide focused direction for the development of new chemical entities which are effective against drug-resistant bacterial pathogens and biofilms.
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Affiliation(s)
- Shalini Jaswal
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, GT Road, Ghal Kalan, Moga 142001, Punjab, India
| | - Bhupender Nehra
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, GT Road, Ghal Kalan, Moga 142001, Punjab, India
| | - Shubham Kumar
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, GT Road, Ghal Kalan, Moga 142001, Punjab, India
| | - Vikramdeep Monga
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, GT Road, Ghal Kalan, Moga 142001, Punjab, India.
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16
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Huang Z, Liu Y, Wang L, Ali A, Yao Q, Jiang X, Gao Y. Supramolecular assemblies mimicking neutrophil extracellular traps for MRSE infection control. Biomaterials 2020; 253:120124. [DOI: 10.1016/j.biomaterials.2020.120124] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 05/13/2020] [Accepted: 05/14/2020] [Indexed: 01/20/2023]
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17
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Recent advances in DNA gyrase-targeted antimicrobial agents. Eur J Med Chem 2020; 199:112326. [DOI: 10.1016/j.ejmech.2020.112326] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 04/07/2020] [Accepted: 04/08/2020] [Indexed: 12/16/2022]
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18
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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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19
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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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20
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Khalil HH, Khattab SN, Toughan MM, El‐Saghier AMM, El‐Wakil MH. Identification of a Novel DNA Gyrase Inhibitor via Design and Synthesis of New Antibacterial Pyrido[1′,2′:1,2]pyrimido[4,5‐
e
][1,3,4]thiadiazin‐5‐ol Derivatives. ChemistrySelect 2020. [DOI: 10.1002/slct.202000886] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Hosam H. Khalil
- Department of ChemistryFaculty of ScienceAlexandria University Alexandria 21321 Egypt
| | - Sherine N. Khattab
- Department of ChemistryFaculty of ScienceAlexandria University Alexandria 21321 Egypt
- Cancer Nanotechnology Research Laboratory (CNRL)Faculty of PharmacyAlexandria University Alexandria 21521 Egypt
| | - Mayada M. Toughan
- Department of ChemistryFaculty of ScienceAlexandria University Alexandria 21321 Egypt
| | | | - Marwa H. El‐Wakil
- Department of Pharmaceutical ChemistryFaculty of PharmacyAlexandria University Alexandria 21521 Egypt
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21
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Second-generation 4,5,6,7-tetrahydrobenzo[ d]thiazoles as novel DNA gyrase inhibitors. Future Med Chem 2020; 12:277-297. [PMID: 32043377 DOI: 10.4155/fmc-2019-0127] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Aim: DNA gyrase and topoisomerase IV are essential bacterial enzymes, and in the fight against bacterial resistance, they are important targets for the development of novel antibacterial drugs. Results: Building from our first generation of 4,5,6,7-tetrahydrobenzo[d]thiazole-based DNA gyrase inhibitors, we designed and prepared an optimized series of analogs that show improved inhibition of DNA gyrase and topoisomerase IV from Staphylococcus aureus and Escherichia coli, with IC50 values in the nanomolar range. Importantly, these inhibitors also show improved antibacterial activity against Gram-positive strains. Conclusion: The most promising inhibitor, 29, is active against Enterococcus faecalis, Enterococcus faecium and S. aureus wild-type and resistant strains, with minimum inhibitory concentrations between 4 and 8 μg/ml, which represents good starting point for development of novel antibacterials.
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22
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Ghannam IA, Abd El-Meguid EA, Ali IH, Sheir DH, El Kerdawy AM. Novel 2-arylbenzothiazole DNA gyrase inhibitors: Synthesis, antimicrobial evaluation, QSAR and molecular docking studies. Bioorg Chem 2019; 93:103373. [DOI: 10.1016/j.bioorg.2019.103373] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 10/06/2019] [Accepted: 10/16/2019] [Indexed: 11/29/2022]
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23
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Yang SC, Tang KW, Lin CH, Alalaiwe A, Tseng CH, Fang JY. Discovery of Furanoquinone Derivatives as a Novel Class of DNA Polymerase and Gyrase Inhibitors for MRSA Eradication in Cutaneous Infection. Front Microbiol 2019; 10:1197. [PMID: 31191504 PMCID: PMC6549599 DOI: 10.3389/fmicb.2019.01197] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 05/13/2019] [Indexed: 11/26/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is the primary microbe responsible for skin infections that are particularly difficult to eradicate. This study sought to inhibit planktonic and biofilm MRSA using furanoquinone-derived compounds containing imine moiety. A total of 19 furanoquinone analogs were designed, synthesized, and assessed for anti-MRSA potency. Among 19 compounds, (Z)-4-(hydroxyimino)naphtho[1,2-b]furan-5(4H)-one (HNF) and (Z)-4-(acetoxyimino)naphtho[1,2-b]furan-5(4H)-one (ANF) showed antibacterial activity superior to the others based on an agar diffusion assay. HNF and ANF exerted a bactericidal effect with a minimum inhibitory concentration (MIC) of 9.7 ∼ 19.5 and 2.4 ∼ 9.7 μg/ml, respectively. Both compounds were able to reduce the MRSA count by 1,000-fold in biofilm as compared to the control. In vivo efficacy was evaluated using a mouse model of skin infection. Topical application of lead compounds significantly suppressed abscess occurrence and the MRSA burden, and also ameliorated the skin-barrier function. The biochemical assay indicated the compounds’ inhibition of DNA polymerase and gyrase. In silico docking revealed a favorable interaction of the compounds with DNA polymerase and gyrase although the binding was not very strong. The total DNA analysis and proteomic data suggested a greater impairment of some proteins by HNF than ANF. In general, HNF and ANF were similarly potent in MRSA inhibition in vitro and in vivo. The findings demonstrated that there was room for structural modification of furanoquinone compounds that could be used to identify anti-MRSA agent candidates.
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Affiliation(s)
- Shih-Chun Yang
- Department of Cosmetic Science, Providence University, Taichung, Taiwan
| | - Kai-Wei Tang
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chih-Hung Lin
- Center for General Education, Chang Gung University of Science and Technology, Taoyuan, Taiwan
| | - Ahmed Alalaiwe
- Department of Pharmaceutics, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al Kharj, Saudi Arabia
| | - Chih-Hua Tseng
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Fragrance and Cosmetic Science, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.,Department of Pharmacy, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung, Taiwan
| | - Jia-You Fang
- Pharmaceutics Laboratory, Graduate Institute of Natural Products, Chang Gung University, Taoyuan, Taiwan.,Chinese Herbal Medicine Research Team, Healthy Aging Research Center, Chang Gung University, Taoyuan, Taiwan.,Research Center for Food and Cosmetic Safety and Research Center for Chinese Herbal Medicine, Chang Gung University of Science and Technology, Taoyuan, Taiwan.,Department of Anesthesiology, Chang Gung Memorial Hospital, Taoyuan, Taiwan
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24
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Islam MA, Pillay TS. Identification of promising anti-DNA gyrase antibacterial compounds using de novo design, molecular docking and molecular dynamics studies. J Biomol Struct Dyn 2019; 38:1798-1809. [PMID: 31084271 DOI: 10.1080/07391102.2019.1617785] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The rapidly increasing rate of antibiotic resistance is of great concern. Approximately two million deaths result annually from bacterial infections worldwide. Therefore, there is a paramount requirement to develop innovative and novel antibacterial agents with new mechanisms of action and activity against resistant bacterial strains. For this purpose, a set of benzothiazole and N-phenylpyrrolamides derivatives reported as DNA Gyrase B (GyrB) inhibitors were collected from the literature and docked inside the receptor cavity of DNA Gyrase B (PDB ID: 5L3J). The best 10 docked complexes were used to identify novel antibacterial chemical agents through a de novo design approach. Out of initial 300 chemical analogues, the best six analogues were identified using screening with a set of criteria followed by pharmacokinetic analysis. The binding interactions of the best six analogues revealed that all molecules formed a number of critical interactions with catalytic amino residues of DNA Gyrase B with high binding energy. The predicted inhibitory constant biological activity based on binding energy supported the potential of the molecules as DNA Gyrase B ligands. The RMSD, RMSF, and radius of gyration parameters obtained from the 100 ns molecular dynamics simulation study clearly demonstrated that all six analogues were efficient enough to form stable complexes with DNA Gyrase B. High negative binding energy of all ligands obtained from MM-GBSA approach undoubtedly explained the strong affinity toward the DNA Gyrase B. Therefore, the proposed de novo designed molecules can be considered as promising antibacterial chemical agents subject to experimental validation, in vitro.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Md Ataul Islam
- Department of Chemical Pathology, Faculty of Health Sciences, University of Pretoria and National Health Laboratory Service Tshwane Academic Division, Pretoria, South Africa.,School of Health Sciences, University of Kwazulu-Natal, Durban, South Africa.,Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Tahir S Pillay
- Department of Chemical Pathology, Faculty of Health Sciences, University of Pretoria and National Health Laboratory Service Tshwane Academic Division, Pretoria, South Africa.,Division of Chemical Pathology, University of Cape Town, Cape Town, South Africa
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Zidar N, Macut H, Tomašič T, Peterlin Mašič L, Ilaš J, Zega A, Tammela P, Kikelj D. New N-phenyl-4,5-dibromopyrrolamides as DNA gyrase B inhibitors. MEDCHEMCOMM 2019; 10:1007-1017. [PMID: 31303999 DOI: 10.1039/c9md00224c] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 05/18/2019] [Indexed: 11/21/2022]
Abstract
Due to the rapid development of antimicrobial resistance, the discovery of new antibacterials is essential in the fight against potentially lethal infections. The DNA gyrase B (GyrB) subunit of bacterial DNA gyrase is an excellent target for the design of antibacterials, as it has been clinically validated by novobiocin. However, there are currently no drugs in clinical use that target GyrB. We prepared a new series of N-phenyl-4,5-dibromopyrrolamides and evaluated them against DNA gyrase and against the structurally and functionally similar enzyme, topoisomerase IV. The most active compound, 28, had an IC50 of 20 nM against Escherichia coli DNA gyrase. The IC50 values of 28 against Staphylococcus aureus DNA gyrase, and E. coli and S. aureus topoisomerase IV were in the low micromolar range. However, the compounds evaluated did not show significant antibacterial activities against selected Gram-positive and Gram-negative bacteria. Our results indicate that for potent inhibition of DNA gyrase, a combination of polar groups on the carboxylic end of the molecule and substituents that reach into the 'lipophilic floor' of the enzyme is required.
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Affiliation(s)
- Nace Zidar
- University of Ljubljana , Faculty of Pharmacy , Aškerčeva cesta 7 , 1000 Ljubljana , Slovenia . ; ; Tel: +386 1 4769578
| | - Helena Macut
- University of Ljubljana , Faculty of Pharmacy , Aškerčeva cesta 7 , 1000 Ljubljana , Slovenia . ; ; Tel: +386 1 4769578
| | - Tihomir Tomašič
- University of Ljubljana , Faculty of Pharmacy , Aškerčeva cesta 7 , 1000 Ljubljana , Slovenia . ; ; Tel: +386 1 4769578
| | - Lucija Peterlin Mašič
- University of Ljubljana , Faculty of Pharmacy , Aškerčeva cesta 7 , 1000 Ljubljana , Slovenia . ; ; Tel: +386 1 4769578
| | - Janez Ilaš
- University of Ljubljana , Faculty of Pharmacy , Aškerčeva cesta 7 , 1000 Ljubljana , Slovenia . ; ; Tel: +386 1 4769578
| | - Anamarija Zega
- University of Ljubljana , Faculty of Pharmacy , Aškerčeva cesta 7 , 1000 Ljubljana , Slovenia . ; ; Tel: +386 1 4769578
| | - Päivi Tammela
- Drug Research Program , Division of Pharmaceutical Biosciences , Faculty of Pharmacy , University of Helsinki , P.O. Box 56 (Viikinkaari 5 E) , Helsinki FI-00014 , Finland
| | - Danijel Kikelj
- University of Ljubljana , Faculty of Pharmacy , Aškerčeva cesta 7 , 1000 Ljubljana , Slovenia . ; ; Tel: +386 1 4769578
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Tiz DB, Skok Ž, Durcik M, Tomašič T, Mašič LP, Ilaš J, Zega A, Draskovits G, Révész T, Nyerges Á, Pál C, Cruz CD, Tammela P, Žigon D, Kikelj D, Zidar N. An optimised series of substituted N-phenylpyrrolamides as DNA gyrase B inhibitors. Eur J Med Chem 2019; 167:269-290. [PMID: 30776691 DOI: 10.1016/j.ejmech.2019.02.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 01/18/2019] [Accepted: 02/01/2019] [Indexed: 10/27/2022]
Abstract
ATP competitive inhibitors of DNA gyrase and topoisomerase IV have great therapeutic potential, but none of the described synthetic compounds has so far reached the market. To optimise the activities and physicochemical properties of our previously reported N-phenylpyrrolamide inhibitors, we have synthesized an improved, chemically variegated selection of compounds and evaluated them against DNA gyrase and topoisomerase IV enzymes, and against selected Gram-positive and Gram-negative bacteria. The most potent compound displayed IC50 values of 6.9 nM against Escherichia coli DNA gyrase and 960 nM against Staphylococcus aureus topoisomerase IV. Several compounds displayed minimum inhibitory concentrations (MICs) against Gram-positive strains in the 1-50 μM range, one of which inhibited the growth of Enterococcus faecalis, Enterococcus faecium, S. aureus and Streptococcus pyogenes with MIC values of 1.56 μM, 1.56 μM, 0.78 μM and 0.72 μM, respectively. This compound has been investigated further on methicillin-resistant S. aureus (MRSA) and on ciprofloxacin non-susceptible and extremely drug resistant strain of S. aureus (MRSA VISA). It exhibited the MIC value of 2.5 μM on both strains, and MIC value of 32 μM against MRSA in the presence of inactivated human blood serum. Further studies are needed to confirm its mode of action.
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Affiliation(s)
- Davide Benedetto Tiz
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Žiga Skok
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Martina Durcik
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Tihomir Tomašič
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Lucija Peterlin Mašič
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Janez Ilaš
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Anamarija Zega
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Gábor Draskovits
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, H-6726, Hungary
| | - Tamás Révész
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, H-6726, Hungary
| | - Ákos Nyerges
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, H-6726, Hungary
| | - Csaba Pál
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), Helsinki, FI-00014, Finland
| | - Cristina D Cruz
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), Helsinki, FI-00014, Finland
| | - Päivi Tammela
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), Helsinki, FI-00014, Finland
| | - Dušan Žigon
- Jožef Stefan Institute, Department of Environmental Science, Jamova cesta 39, 1000, Ljubljana, Slovenia
| | - Danijel Kikelj
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Nace Zidar
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia.
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