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Alam M, Abser MN, Kumer A, Bhuiyan MMH, Akter P, Hossain ME, Chakma U. Synthesis, characterization, antibacterial activity of thiosemicarbazones derivatives and their computational approaches: Quantum calculation, molecular docking, molecular dynamic, ADMET, QSAR. Heliyon 2023; 9:e16222. [PMID: 37292281 PMCID: PMC10245008 DOI: 10.1016/j.heliyon.2023.e16222] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 05/04/2023] [Accepted: 05/10/2023] [Indexed: 06/10/2023] Open
Abstract
The thiosemicarbazones and their derivatives have been recognized as antimicrobial agents against human pathogenic bacteria and fungi. Regarding these prospective, this study was designed to address the new antimicrobial agents from thiosemicarbazones and their derivatives. These derivatives were synthesized by multi-step synthesis methods, such as alkylation, acidification, esterification, and formed the 4-(4'-alkoxybenzoyloxy) thiosemicarbazones and its derivatives (THS1, THS2, THS3, THS4, and THS5). Afterward the synthesis, compounds were characterized by 1H NMR, FTIR spectra, and melting point. Later, the computational tools were applied to evaluate the drug likeness properties, bioavailability score, Lipinski rule, absorption, distribution, metabolism, excretion, and toxicity (ADMET). Secondly, the quantum calculations, for instance HOMO, LUMO and chemical descriptors, were calculated by the density functional theory (DFT). Finally, the molecular docking was performed against seven human pathogenic bacteria, black fungus (Rhizomucor mieh, Mucor lusitanicus, Mycolicibacterium smegmatis) and white fungus strains (Candida Auris, Aspergillus luchuensis, Candida albicans). To check and validate of molecular docking procedure and stability of docked complex for ligand and protein, the molecular dynamic was performed of docked complex. From the docking score with calculating the binding affinity, these derivatives could show a higher affinity than standard drug against all pathogens. From the computational details, it could be decided to do in-vitro test as antimicrobial activity against Staphylococcus aurious, Staphylococcus homonis, Salmonella typhi, and Shigella flexneria. The obtained result of antibacterial activity compared to standard drugs, and it was found that the synthesized compounds were almost same value of standard drug. Finally, it could be said from the in-vitro and in-silico study that the thiosemicarbazones derivatives are good antimicrobial agents.
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Affiliation(s)
- Mahbub Alam
- Inorganic Research Laboratory, Department of Chemistry, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh
| | - Mohammed Nurul Abser
- Inorganic Research Laboratory, Department of Chemistry, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh
| | - Ajoy Kumer
- Laboratory of Computational Research for Drug Design and Material Science, Department of Chemistry, European University of Bangladesh, Dhaka, 1216, Bangladesh
| | | | - Parul Akter
- Department of Chemistry, Mirzapur Cadet College, Mirzapur, Tangail, 1942, Bangladesh
| | - Md Emdad Hossain
- Wazed Miah Science Research Centre, Jahangirnagar University, Savar, Dhaka, 134, Bangladesh
| | - Unesco Chakma
- Laboratory of Computational Research for Drug Design and Material Science, Department of Chemistry, European University of Bangladesh, Dhaka, 1216, Bangladesh
- School of Electronic Science and Engineering, Southeast University, Nanjing, PR China
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Schiffler B, Zöllner A, Bernhardt R. Kinetic and optical biosensor study of adrenodoxin mutant AdxS112W displaying an enhanced interaction towards the cholesterol side chain cleavage enzyme (CYP11A1). EUROPEAN BIOPHYSICS JOURNAL: EBJ 2011; 40:1275-82. [PMID: 21526428 DOI: 10.1007/s00249-011-0703-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2011] [Revised: 03/18/2011] [Accepted: 03/26/2011] [Indexed: 10/18/2022]
Abstract
In mammals, steroid hormones are synthesized from cholesterol that is metabolized by the mitochondrial CYP11A1 system leading to pregnenolone. The reduction equivalents for this reaction are provided by NADPH, via a small electron transfer chain, consisting of adrenodoxin reductase (AdR) and adrenodoxin (Adx). The reaction partners are involved in a series of transient interactions to realize the electron transfer from NADPH to CYP11A1. Here, we compared the ionic strength effect on the AdR/Adx and Adx/CYP11A1 interactions for wild-type Adx and mutant AdxS112W. Using surface plasmon resonance measurements, stopped flow kinetic investigations and analyses of the product formation, we were able to obtain new insights into the mechanism of these interactions. The replacement of serine 112 by tryptophan was demonstrated to lead to a dramatically decreased k (off) rate of the Adx/CYP11A1 complex, resulting in a four-fold decreased K (d) value and indicating a much higher stability of the complex involving the mutant. Stopped flow analysis at various ionic strengths and in different mixing modes revealed that the binding of reduced Adx to CYP11A1 seems to display the limiting step for electron transfer to CYP11A1 with pre-reduced AdxS112W being much more efficient than wild-type Adx. Finally, the dramatic increase in pregnenolone formation at higher ionic strength using the mutant demonstrates that the interaction of CYP11A1 with Adx is the rate-limiting step in substrate conversion and that hydrophobic interactions may considerably improve this interaction and the efficiency of product formation. The data are discussed using published structural data of the complexes.
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Affiliation(s)
- Burkhard Schiffler
- Naturwissenschaftlich-Technische Fakultät III, Lehrstuhl für Biochemie, Universität des Saarlandes, Saarbrücken, Germany
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Ewen KM, Kleser M, Bernhardt R. Adrenodoxin: the archetype of vertebrate-type [2Fe-2S] cluster ferredoxins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:111-25. [PMID: 20538075 DOI: 10.1016/j.bbapap.2010.06.003] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Revised: 05/28/2010] [Accepted: 06/01/2010] [Indexed: 11/15/2022]
Abstract
Adrenodoxin is probably the best characterized member of the vertebrate-type [2Fe-2S]-cluster ferredoxins. It has been in the spotlight of scientific interest for many years due to its essential role in mammalian steroid hormone biosynthesis, where it acts as electron mediator between the NADPH-dependent adrenodoxin reductase and several mitochondrial cytochromes P450. In this review we will focus on the present knowledge about protein-protein recognition in the mitochondrial cytochrome P450 system and the modulation of the electron transfer between Adx and its redox partners, AdR and CYP(s). We also intend to point out the potential biotechnological applications of Adx as a versatile electron donor to different cytochromes P450, both in vitro and in vivo. Finally we will address the comparison between the mammalian cytochrome P450-associated adrenodoxin and ferredoxins involved in iron-sulfur-cluster biosynthesis. Despite their different functions, these proteins display an amazing similarity regarding their primary sequence, tertiary structure and biophysical features.
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Affiliation(s)
- Kerstin Maria Ewen
- Department of Biochemistry, Saarland University, D-66041 Saarbrücken, Germany
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Xu X, Reinle W, Hannemann F, Konarev PV, Svergun DI, Bernhardt R, Ubbink M. Dynamics in a Pure Encounter Complex of Two Proteins Studied by Solution Scattering and Paramagnetic NMR Spectroscopy. J Am Chem Soc 2008; 130:6395-403. [DOI: 10.1021/ja7101357] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xingfu Xu
- Institute of Chemistry, Leiden University, P.O. Box 9502, NL-2300RA Leiden, The Netherlands, Naturwissenschaftlich-Technische Fakultat III, Institut für Biochemie, Universität des Saarlandes, P.O. Box 151150, D-66041, Saarbrucken, Germany, EMBL Hamburg, Notkestrasse 85, D-22603 Hamburg, Germany, and Institute of Crystallography, Russian Academy of Sciences, Leninsky pr. 59, 117333, Moscow, Russia
| | - Wolfgang Reinle
- Institute of Chemistry, Leiden University, P.O. Box 9502, NL-2300RA Leiden, The Netherlands, Naturwissenschaftlich-Technische Fakultat III, Institut für Biochemie, Universität des Saarlandes, P.O. Box 151150, D-66041, Saarbrucken, Germany, EMBL Hamburg, Notkestrasse 85, D-22603 Hamburg, Germany, and Institute of Crystallography, Russian Academy of Sciences, Leninsky pr. 59, 117333, Moscow, Russia
| | - Frank Hannemann
- Institute of Chemistry, Leiden University, P.O. Box 9502, NL-2300RA Leiden, The Netherlands, Naturwissenschaftlich-Technische Fakultat III, Institut für Biochemie, Universität des Saarlandes, P.O. Box 151150, D-66041, Saarbrucken, Germany, EMBL Hamburg, Notkestrasse 85, D-22603 Hamburg, Germany, and Institute of Crystallography, Russian Academy of Sciences, Leninsky pr. 59, 117333, Moscow, Russia
| | - Peter V. Konarev
- Institute of Chemistry, Leiden University, P.O. Box 9502, NL-2300RA Leiden, The Netherlands, Naturwissenschaftlich-Technische Fakultat III, Institut für Biochemie, Universität des Saarlandes, P.O. Box 151150, D-66041, Saarbrucken, Germany, EMBL Hamburg, Notkestrasse 85, D-22603 Hamburg, Germany, and Institute of Crystallography, Russian Academy of Sciences, Leninsky pr. 59, 117333, Moscow, Russia
| | - Dmitri I. Svergun
- Institute of Chemistry, Leiden University, P.O. Box 9502, NL-2300RA Leiden, The Netherlands, Naturwissenschaftlich-Technische Fakultat III, Institut für Biochemie, Universität des Saarlandes, P.O. Box 151150, D-66041, Saarbrucken, Germany, EMBL Hamburg, Notkestrasse 85, D-22603 Hamburg, Germany, and Institute of Crystallography, Russian Academy of Sciences, Leninsky pr. 59, 117333, Moscow, Russia
| | - Rita Bernhardt
- Institute of Chemistry, Leiden University, P.O. Box 9502, NL-2300RA Leiden, The Netherlands, Naturwissenschaftlich-Technische Fakultat III, Institut für Biochemie, Universität des Saarlandes, P.O. Box 151150, D-66041, Saarbrucken, Germany, EMBL Hamburg, Notkestrasse 85, D-22603 Hamburg, Germany, and Institute of Crystallography, Russian Academy of Sciences, Leninsky pr. 59, 117333, Moscow, Russia
| | - Marcellus Ubbink
- Institute of Chemistry, Leiden University, P.O. Box 9502, NL-2300RA Leiden, The Netherlands, Naturwissenschaftlich-Technische Fakultat III, Institut für Biochemie, Universität des Saarlandes, P.O. Box 151150, D-66041, Saarbrucken, Germany, EMBL Hamburg, Notkestrasse 85, D-22603 Hamburg, Germany, and Institute of Crystallography, Russian Academy of Sciences, Leninsky pr. 59, 117333, Moscow, Russia
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