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R D, S W, D P D, R S. Cracking a cancer code DNA methylation in epigenetic modification: an in-silico approach on efficacy assessment of Sri Lanka-oriented nutraceuticals. J Biomol Struct Dyn 2024:1-21. [PMID: 38425013 DOI: 10.1080/07391102.2024.2321235] [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: 08/02/2023] [Accepted: 02/14/2024] [Indexed: 03/02/2024]
Abstract
DNA methyltransferase (DNMTs) are essential epigenetic modifiers that play a critical role in gene regulation. These enzymes add a methyl group to cytosine's 5'-carbon, specifically within CpG dinucleotides, using S-adenosyl-L-methionine. Abnormal overexpression of DNMTs can alter the gene expression patterns and contribute to cancer development in the human body. Therefore, the inhibition of DNMT is a promising therapeutic approach to cancer treatment. This study was aimed to identify potential nutraceutical inhibitors from the Sri Lanka Flora database using computational methods, which provided an atomic-level description of the drug binding site and examined the interactions between nutraceuticals and amino acids of the DNMT enzyme. A series of nutraceuticals from Sri Lanka-oriented plants were selected and evaluated to assess their inhibitory effects on DNMT using absorption, distribution, metabolism, excretion and toxicity analysis, virtual screening, molecular docking, molecular dynamics simulation and trajectory analysis. Azacitidine, a DNMT inhibitor approved by the US Food and Drug Administration, was selected as a reference inhibitor. The complexes with more negative binding energies were selected and further assessed for their potency. Seven molecules were identified from 200 nutraceuticals, demonstrating significantly negative binding energies against the DNMT enzyme. Various trajectory analyses were conducted to investigate the stability of the DNMT enzyme. The results indicated that petchicine (NP#0003), ouregidione (NP#0011) and azacitidine increased the stability of the DNMT enzyme. Consequently, these two nutraceuticals showed inhibitory efficacies similar to azacitidine, making them potential candidates for therapeutic interventions targeting DNMT enzyme-related cancers. Additional bioassay testing is recommended to confirm the efficacies of these nutraceuticals and explore their applicability in clinical treatments.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dushanan R
- Department of Chemistry, Faculty of Natural Sciences, The Open University of Sri Lanka, Nawala, Sri Lanka
| | - Weerasinghe S
- Department of Chemistry, Faculty of Science, University of Colombo, Colombo, Sri Lanka
| | - Dissanayake D P
- Department of Chemistry, Faculty of Science, University of Colombo, Colombo, Sri Lanka
| | - Senthilnithy R
- Department of Chemistry, Faculty of Natural Sciences, The Open University of Sri Lanka, Nawala, Sri Lanka
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Taysi MR, Kirici M, Kirici M, Tuzun B, Poustforoosh A. Antioxidant enzyme activities, molecular docking studies, MM-GBSA, and molecular dynamic of chlorpyrifos in freshwater fish Capoeta umbla. J Biomol Struct Dyn 2024; 42:163-176. [PMID: 36974945 DOI: 10.1080/07391102.2023.2192807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 03/10/2023] [Indexed: 03/29/2023]
Abstract
Chlorpyrifos (CPF), which was started to be used in 1965, is a broad spectrum organophosphate insecticide that is used more and more day by day. Commonly used to control pests in farmland and homes, CPF is more toxic to fish than organochlorine compounds. CPF poses a serious threat to the health of humans and aquatic organisms. This paper studies the relationship between CPF exposure and antioxidant enzyme activities in gill, kidney and liver tissues of Capoeta umbla. Different time intervals (12, 24, 48, 72, and 96 h) and CPF doses (55 and 110 µg L-1) were used in the study. Spectrophotometrical measures were taken in all tissues for antioxidant enzyme activities and malondialdehyde (MDA) levels, as indices of the lipid peroxidation (LPO). A positive relationship between CPF and MDA levels was found in the study at a statistically significant level (p < 0.05). The study also found a negative relationship between CPF levels and catalase (CAT), superoxide dismutase (SOD), glutathione peroxidase (GPx), and glutathione reductase (GR) activity. Independent variables in the study can act as biomarkers of CPF exposure. The study recommends employing proper ecotoxicological risk evaluations in cases of CPF usage as a pesticide. The activities of the studied molecules against various proteins that are crystal structure of human peroxiredoxin 5 (PDB ID: 1HD2) has docking score value is -2.67, crystal structure of Bovine Xanthine Oxidase (PDB ID: 3NRZ) has docking score value is -3.76, and crystal structure of antibacterial FabH (PDB ID: 4Z8D) has docking score value is -3.16, were compared. Molecular dynamic (MD) calculations were made in 100 ns. MM/GBSA methods are calculated binding free energy. Afterwards, ADME/T analysis was performed to examine the some properties of the molecules.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mehmet Reşit Taysi
- Department of Fisheries, Faculty of Agriculture, Bingol University, Bingöl, Turkey
| | - Muammer Kirici
- Department of Veterinary Health, Food Agriculture and Livestock Vocational School, Bingöl University, Bingöl, Turkey
| | - Mahinur Kirici
- Department of Chemistry, Faculty of Arts and Science, Bingöl University, Bingöl, Turkey
| | - Burak Tuzun
- Plant and Animal Production Department, Technical Sciences Vocational School of Sivas, Sivas Cumhuriyet University, Sivas, Turkey
| | - Alireza Poustforoosh
- Chemical Engineering Department, Faculty of Engineering, Shahid Bahonar University of Kerman, Kerman, Iran
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Bostancı HE, Çevik UA, Kapavarapu R, Güldiken YC, Inan ZDŞ, Güler ÖÖ, Uysal TK, Uytun A, Çetin FN, Özkay Y, Kaplancıklı ZA. Synthesis, biological evaluation and in silico studies of novel thiadiazole-hydrazone derivatives for carbonic anhydrase inhibitory and anticancer activities. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2023; 34:543-567. [PMID: 37538028 DOI: 10.1080/1062936x.2023.2240698] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 07/05/2023] [Indexed: 08/05/2023]
Abstract
Thiadiazole and hydrazone derivatives (5a-5i) were synthesized and their chemical structures were verified and described by 1H NMR, 13C NMR, and HRMS spectra. Three cancer cell lines (MCF-7, MDA, and HT-29) and one healthy cell line (L929) were used to test the cytotoxicity activity of synthesized compounds as well as their inhibitory activity against carbonic anhydrase I, II and IX isoenzymes. Compound 5d (29.74 µM) had a high inhibitory effect on hCA I and compound 5b (23.18 µM) had a high inhibitory effect on hCA II. Furthermore, compound 5i was found to be the most potent against CA IX. Compounds 5a-5i, 5b and 5i showed the highest anticancer effect against MCF-7 cell line with an IC50 value of 9.19 and 23.50 µM, and compound 5d showed the highest anticancer effect against MDA cell line with an IC50 value of 10.43 µM. The presence of fluoro substituent in the o-position of the phenyl ring increases the effect on hCA II, while the methoxy group in the o-position of the phenyl ring increases the activity on hCA I as well as increase the anticancer activity. Cell death induction was evaluated by Annexin V assay and it was determined that these compounds cause cell death by apoptosis. Molecular docking was performed for compounds 5b and 5d to understand their biological interactions. The physical and ADME properties of compounds 5b and 5d were evaluated using SwissADME.
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Affiliation(s)
- H E Bostancı
- Department of Biochemistry, Faculty of Pharmacy, Cumhuriyet University, Sivas, Turkey
| | - U A Çevik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, Eskişehir, Turkey
| | - R Kapavarapu
- Department of Pharmaceutical Chemistry and Phytochemistry, Nirmala College of Pharmacy, Atmakur, India
| | - Y C Güldiken
- Department of Neurology, Kocaeli University Research and Application Hospital, İzmit, Turkey
| | - Z D Ş Inan
- Department of Histology and Embryology, Sivas Cumhuriyet University, Sivas, Turkey
| | - Ö Ö Güler
- Department of Medical Biology, Faculty of Medicine, Ankara Yildirim Beyazit University, Ankara, Turkey
| | - T K Uysal
- Department of Medical Biology, Faculty of Medicine, Ankara Yildirim Beyazit University, Ankara, Turkey
| | - A Uytun
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, Eskişehir, Turkey
| | - F N Çetin
- Department of Biochemistry, Faculty of Pharmacy, Cumhuriyet University, Sivas, Turkey
| | - Y Özkay
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, Eskişehir, Turkey
| | - Z A Kaplancıklı
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, Eskişehir, Turkey
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Mareş C, Udrea AM, Şuţan NA, Avram S. Bioinformatics Tools for the Analysis of Active Compounds Identified in Ranunculaceae Species. Pharmaceuticals (Basel) 2023; 16:842. [PMID: 37375790 DOI: 10.3390/ph16060842] [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: 05/15/2023] [Revised: 05/30/2023] [Accepted: 05/31/2023] [Indexed: 06/29/2023] Open
Abstract
The chemical compounds from extracts of three Ranunculaceae species, Aconitum toxicum Rchb., Anemone nemorosa L. and Helleborus odorus Waldst. & Kit. ex Willd., respectively, were isolated using the HPLC purification technique and analyzed from a bioinformatics point of view. The classes of compounds identified based on the proportion in the rhizomes/leaves/flowers used for microwave-assisted extraction and ultrasound-assisted extraction were alkaloids and phenols. Here, the quantifying of pharmacokinetics, pharmacogenomics and pharmacodynamics helps us to identify the actual biologically active compounds. Our results showed that (i) pharmacokinetically, the compounds show good absorption at the intestinal level and high permeability at the level of the central nervous system for alkaloids; (ii) regarding pharmacogenomics, alkaloids can influence tumor sensitivity and the effectiveness of some treatments; (iii) and pharmacodynamically, the compounds of these Ranunculaceae species bind to carbonic anhydrase and aldose reductase. The results obtained showed a high affinity of the compounds in the binding solution at the level of carbonic anhydrases. Carbonic anhydrase inhibitors extracted from natural sources can represent the path to new drugs useful both in the treatment of glaucoma, but also of some renal, neurological and even neoplastic diseases. The identification of natural compounds with the role of inhibitors can have a role in different types of pathologies, both associated with studied and known receptors such as carbonic anhydrase and aldose reductase, as well as new pathologies not yet addressed.
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Affiliation(s)
- Cătălina Mareş
- Department of Anatomy, Animal Physiology and Biophysics, University of Bucharest, 91-95 Splaiul Independentei, 050095 Bucharest, Romania
| | - Ana-Maria Udrea
- Laser Department, National Institute for Laser, Plasma and Radiation Physics, Atomistilor 409, 077125 Magurele, Romania
- Research Institute of the University of Bucharest-ICUB, University of Bucharest, 91-95 Splaiul Independentei, 050095 Bucharest, Romania
| | - Nicoleta Anca Şuţan
- Department of Natural Sciences, University of Piteşti, 1 Targul din Vale Str., 110040 Pitesti, Romania
| | - Speranţa Avram
- Department of Anatomy, Animal Physiology and Biophysics, University of Bucharest, 91-95 Splaiul Independentei, 050095 Bucharest, Romania
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Patel CN, Mall R, Bensmail H. AI-driven drug repurposing and binding pose meta dynamics identifies novel targets for Monkeypox virus. J Infect Public Health 2023; 16:799-807. [PMID: 36966703 PMCID: PMC10014505 DOI: 10.1016/j.jiph.2023.03.007] [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: 09/20/2022] [Revised: 02/28/2023] [Accepted: 03/05/2023] [Indexed: 03/17/2023] Open
Abstract
Monkeypox virus (MPXV) was confirmed in May 2022 and designated a global health emergency by WHO in July 2022. MPX virions are big, enclosed, brick-shaped, and contain a linear, double-stranded DNA genome as well as enzymes. MPXV particles bind to the host cell membrane via a variety of viral-host protein interactions. As a result, the wrapped structure is a potential therapeutic target. DeepRepurpose, an artificial intelligence-based compound-viral proteins interaction framework, was used via a transfer learning setting to prioritize a set of FDA approved and investigational drugs which can potentially inhibit MPXV viral proteins. To filter and narrow down the lead compounds from curated collections of pharmaceutical compounds, we used a rigorous computational framework that included homology modeling, molecular docking, dynamic simulations, binding free energy calculations, and binding pose metadynamics. We identified Elvitegravir as a potential inhibitor of MPXV virus using our comprehensive pipeline.
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Affiliation(s)
- Chirag N. Patel
- Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Science, Gujarat University, Ahmedabad-380009, India,Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institute of Health, Frederick, MD-21702, USA
| | - Raghvendra Mall
- Department of Immunology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee-38105, USA,Biotechnology Research Center, Technology Innovation Institute, Abu Dhabi-9639, United Arab Emirates,Corresponding author at: Department of Immunology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee-38105, USA
| | - Halima Bensmail
- Qatar Computing Research Institute, Hamad Bin Khalifa University, Doha-34110, Qatar,Corresponding author
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