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Weyesa A, Eswaramoorthy R, Melaku Y, Mulugeta E. Antibacterial, Docking, DFT and ADMET Properties Evaluation of Chalcone-Sulfonamide Derivatives Prepared Using ZnO Nanoparticle Catalysis. Adv Appl Bioinform Chem 2021; 14:133-144. [PMID: 34924761 PMCID: PMC8674577 DOI: 10.2147/aabc.s336450] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/18/2021] [Indexed: 12/23/2022] Open
Abstract
INTRODUCTION In the present work, two novel compounds were synthesized using zinc oxide nanoparticles through green synthesis protocol. The zinc oxide nanoparticles catalyzed reactions were afforded good to excellent yields of the target compounds 76.3-98.6%. METHODOLOGY The synthesized compounds were characterized by UV-Vis, IR and NMR. The antibacterial activity of the synthesized compounds was screened against two Gram-positive bacteria (Bacillus cereus and Staphylococcus aureus) and two Gram-negative bacteria (Escherichia coli and Salmonella typhimurium). RESULTS AND DISCUSSION The synthesized compounds displayed potent activity against the bacterial strains. Among them, compound 8 showed strong activity against Bacillus cereus relative to the standard drug. On the other hand, compound 9 exhibited strong activity against Escherichia coli. The molecular docking study of the synthesized compounds was conducted to investigate their binding pattern with DNA gyrase and E. coli dihydropteroate synthase and all of them were found to have minimum binding energy ranging from -6.0 to -7.3 kcal/mol, and the best result achieved with compound 8 and 9. CONCLUSION The findings of the in vitro antibacterial and molecular docking analysis demonstrated that the synthesized compounds have potential of antibacterial activity and can be further optimized to serve as a lead compound.
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Affiliation(s)
- Abdanne Weyesa
- Department of Applied Chemistry, School of Applied Natural Science, Adama Science and Technology University, Adama, Ethiopia
| | - Rajalakshmanan Eswaramoorthy
- Department of Applied Chemistry, School of Applied Natural Science, Adama Science and Technology University, Adama, Ethiopia
- Department of Biomaterials, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
| | - Yadessa Melaku
- Department of Applied Chemistry, School of Applied Natural Science, Adama Science and Technology University, Adama, Ethiopia
| | - Endale Mulugeta
- Department of Applied Chemistry, School of Applied Natural Science, Adama Science and Technology University, Adama, Ethiopia
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Hirsch J, Klostermeier D. What makes a type IIA topoisomerase a gyrase or a Topo IV? Nucleic Acids Res 2021; 49:6027-6042. [PMID: 33905522 PMCID: PMC8216471 DOI: 10.1093/nar/gkab270] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/26/2021] [Accepted: 04/01/2021] [Indexed: 12/14/2022] Open
Abstract
Type IIA topoisomerases catalyze a variety of different reactions: eukaryotic topoisomerase II relaxes DNA in an ATP-dependent reaction, whereas the bacterial representatives gyrase and topoisomerase IV (Topo IV) preferentially introduce negative supercoils into DNA (gyrase) or decatenate DNA (Topo IV). Gyrase and Topo IV perform separate, dedicated tasks during replication: gyrase removes positive supercoils in front, Topo IV removes pre-catenanes behind the replication fork. Despite their well-separated cellular functions, gyrase and Topo IV have an overlapping activity spectrum: gyrase is also able to catalyze DNA decatenation, although less efficiently than Topo IV. The balance between supercoiling and decatenation activities is different for gyrases from different organisms. Both enzymes consist of a conserved topoisomerase core and structurally divergent C-terminal domains (CTDs). Deletion of the entire CTD, mutation of a conserved motif and even by just a single point mutation within the CTD converts gyrase into a Topo IV-like enzyme, implicating the CTDs as the major determinant for function. Here, we summarize the structural and mechanistic features that make a type IIA topoisomerase a gyrase or a Topo IV, and discuss the implications for type IIA topoisomerase evolution.
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Affiliation(s)
- Jana Hirsch
- University of Muenster, Institute for Physical Chemistry, Corrensstrasse 30, 48149 Muenster, Germany
| | - Dagmar Klostermeier
- University of Muenster, Institute for Physical Chemistry, Corrensstrasse 30, 48149 Muenster, Germany
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Synthesis, Antibacterial, Antioxidant, and Molecular Modeling Studies of Novel [2,3′-Biquinoline]-4-Carboxylic Acid and Quinoline-3-Carbaldehyde Analogs. J CHEM-NY 2021. [DOI: 10.1155/2021/9939506] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Currently, it has been common to see people being affected and dying from untreatable infections caused by multidrug-resistant (MDR) germs. To tackle this problem, developing new effective chemotropic agents is urgently needed. Hence, this project aims to design, synthesize, and evaluate their antibacterial and antioxidant activities of new series of [2,3′-biquinoline]-4-carboxylic acid and quinoline-3-carbaldehyde analogs. The molecular docking analysis of the compounds against E. coli DNA gyrase was computed to investigate the binding mode of the compounds within the active site of the enzyme. In this regard, a new series of [2,3′-biquinoline]-4-carboxylic acid and quinoline-3-carbaldehyde analogs were synthesized by utilization of Vilsmeier–Haack, Doebner, nucleophilic substitution, and hydrolysis reactions. The structures of the synthesized compounds were determined using UV-Vis, FT-IR, and NMR. The synthesized compounds were screened for their antibacterial activity against four bacterial strains using disc diffusion methods. The findings of the study revealed that seven of synthetic compounds possess good antibacterial activity compared to ciprofloxacin which was used as a positive control in the experiment. Among them, compounds 4, 9, and 10 displayed the highest mean inhibition zone of 13.7 ± 0.58, 16.0 ± 1.7, and 20.7 ± 1.5 mm, respectively, at 0.1 μg/μL. The radical scavenging property of these compounds was evaluated using DPPH radical assay where compounds 9 and 20 showed the strongest activity with IC50 values of 1.25 and 1.75 μg/mL, respectively. At the same concentration, the IC50 value of ascorbic acid was 4.5 μg/mL. The synthesized compounds were also assessed for their in silico molecular docking analysis. Compounds 4 (−6.9 kcal/mol), 9 (−6.9 kcal/mol), and 10 (−7.9 kcal/mol) showed the maximum binding affinity close to ciprofloxacin (−7.2 kcal/mol) used as a positive control. Thus, compounds 4, 9, and 10 showed the best antibacterial activities in both in vitro and molecular docking analyses among the synthetic compounds. The results of in silico molecular docking evaluation of the synthetic compounds against E. coli DNA gyrase B were in good agreement with the in vitro antibacterial analysis. Therefore, the antibacterial activity displayed by these compounds is encouraging for further investigation to improve the activities of [2,3′-biquinoline]-4-carboxylic acid by incorporating various bioisosteric groups in either of the quinoline rings.
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Piton J, Petrella S, Delarue M, André-Leroux G, Jarlier V, Aubry A, Mayer C. Structural insights into the quinolone resistance mechanism of Mycobacterium tuberculosis DNA gyrase. PLoS One 2010; 5:e12245. [PMID: 20805881 PMCID: PMC2923608 DOI: 10.1371/journal.pone.0012245] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Accepted: 07/21/2010] [Indexed: 12/04/2022] Open
Abstract
Mycobacterium tuberculosis DNA gyrase, an indispensable nanomachine involved in the regulation of DNA topology, is the only type II topoisomerase present in this organism and is hence the sole target for quinolone action, a crucial drug active against multidrug-resistant tuberculosis. To understand at an atomic level the quinolone resistance mechanism, which emerges in extensively drug resistant tuberculosis, we performed combined functional, biophysical and structural studies of the two individual domains constituting the catalytic DNA gyrase reaction core, namely the Toprim and the breakage-reunion domains. This allowed us to produce a model of the catalytic reaction core in complex with DNA and a quinolone molecule, identifying original mechanistic properties of quinolone binding and clarifying the relationships between amino acid mutations and resistance phenotype of M. tuberculosis DNA gyrase. These results are compatible with our previous studies on quinolone resistance. Interestingly, the structure of the entire breakage-reunion domain revealed a new interaction, in which the Quinolone-Binding Pocket (QBP) is blocked by the N-terminal helix of a symmetry-related molecule. This interaction provides useful starting points for designing peptide based inhibitors that target DNA gyrase to prevent its binding to DNA.
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Affiliation(s)
- Jérémie Piton
- Unité de Dynamique Structurale des Macromolécules, Département de Biologie Structurale et Chimie, Institut Pasteur, Paris, France
- URA 2185, CNRS, Paris, France
- UPMC Univ Paris 06, Paris, France
| | | | - Marc Delarue
- Unité de Dynamique Structurale des Macromolécules, Département de Biologie Structurale et Chimie, Institut Pasteur, Paris, France
- URA 2185, CNRS, Paris, France
| | - Gwénaëlle André-Leroux
- URA 2185, CNRS, Paris, France
- Unité de Biochimie Structurale, Département de Biologie Structurale et Chimie, Institut Pasteur, Paris, France
| | - Vincent Jarlier
- UPMC Univ Paris 06, EA1541, Bactériologie-Hygiène, Paris, France
| | - Alexandra Aubry
- UPMC Univ Paris 06, EA1541, Bactériologie-Hygiène, Paris, France
| | - Claudine Mayer
- Unité de Dynamique Structurale des Macromolécules, Département de Biologie Structurale et Chimie, Institut Pasteur, Paris, France
- URA 2185, CNRS, Paris, France
- Université Paris Diderot Paris 7, Paris, France
- * E-mail:
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Sohi MK, Veselkov DA, Laponogov I, Pan XS, Fisher LM, Sanderson MR. The difficult case of crystallization and structure solution for the ParC55 breakage-reunion domain of topoisomerase IV from Streptococcus pneumoniae. PLoS One 2008; 3:e3201. [PMID: 18787651 PMCID: PMC2527675 DOI: 10.1371/journal.pone.0003201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2008] [Accepted: 07/08/2008] [Indexed: 11/19/2022] Open
Abstract
Background Streptococcus pneumoniae is the major cause of community-acquired pneumonia and is also associated with bronchitis, meningitis, otitis and sinusitis. The emergence and increasing prevalence of resistance to penicillin and other antibiotics has led to interest in other anti-pneumonococcal drugs such as quinolones that target the enzymes DNA gyrase and topoisomerase IV. During crystallization and in the avenues to finding a method to determine phases for the structure of the ParC55 breakage-reunion domain of topoisomerase IV from Streptococcus pneumoniae, obstacles were faced at each stage of the process. These problems included: majority of the crystals being twinned, either non-diffracting or exhibiting a high mosaic spread. The crystals, which were grown under conditions that favoured diffraction, were difficult to flash-freeze without loosing diffraction. The initial structure solution by molecular replacement failed and the approach proved to be unviable due to the complexity of the problem. In the end the successful structure solution required an in-depth data analysis and a very detailed molecular replacement search. Methodology/Principal Findings Crystal anti-twinning agents have been tested and two different methods of flash freezing have been compared. The fragility of the crystals did not allow the usual method of transferring the crystals into the heavy atom solution. Consequently, it was necessary to co-crystallize in the presence of the heavy atom compound. The multiple isomorphous replacement approach was unsuccessful because the 7 cysteine mutants which were engineered could not be successfully derivatized. Ultimately, molecular replacement was used to solve the structure by sorting through a large number of solutions in space group P1 using CNS. Conclusions/Significance The main objective of this paper is to describe the obstacles which were faced and overcome in order to acquire data sets on such difficult crystals and determine phases for successful structure solution.
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Affiliation(s)
- Maninder K. Sohi
- Randall Division of Cell and Molecular Biophysics, School of Biomedical and Health Sciences, King's College London, London, United Kingdom
| | - Dennis A. Veselkov
- Randall Division of Cell and Molecular Biophysics, School of Biomedical and Health Sciences, King's College London, London, United Kingdom
| | - Ivan Laponogov
- Randall Division of Cell and Molecular Biophysics, School of Biomedical and Health Sciences, King's College London, London, United Kingdom
| | - Xiao-Su Pan
- Molecular Genetics Group, Molecular and Metabolic Signalling Centre, Division of Basic Medical Sciences, St. George's, University of London, London, United Kingdom
| | - L. Mark Fisher
- Molecular Genetics Group, Molecular and Metabolic Signalling Centre, Division of Basic Medical Sciences, St. George's, University of London, London, United Kingdom
- * E-mail: (LMF); (MRS)
| | - Mark R. Sanderson
- Randall Division of Cell and Molecular Biophysics, School of Biomedical and Health Sciences, King's College London, London, United Kingdom
- * E-mail: (LMF); (MRS)
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