Browsing by Author "Karakus, Fuat"

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Design, Synthesis, and Antiproliferative Activities of Novel Thiazolyl-Pyrazole Hybrid Derivatives
(Springer Birkhauser, 2023) Kuzu, Burak; Erguc, Ali; Karakus, Fuat; Arzuk, Ege
In this study, a series of derivatives of thiazolyl-pyrazole hybrid structures were designed to search for new heterocyclic compound-based antitumor agents. The designed target structures were synthesized with easy, practical, and efficient procedures. The antiproliferative effect of the synthesized compounds against cancer cell lines A549, MCF-7, and HepG2 was evaluated regarding inhibition concentration and selectivity index against healthy cell line CCD-34Lu. The results overall showed that the compounds had high antiproliferation against cancer cells compared to the doxorubicin-positive control. In particular, compound 11 A549 (SI: 3.58) and HepG2 (SI: 12.36) had high selectivity in cancer cell lines, while compounds 10h and 10o had high selectivity (SI: 10.74 for both) in MCF-7 cancer cell lines. The calculated theoretical pharmacokinetic properties revealed that they could be suitable drug candidates. In addition, in vitro test results indicate a correlation between the structure-activity relationships of the compounds. The various molecular modifications of thiazolyl-pyrazole hybrid compounds are promising for developing new anticancer drug candidates.
Design, Synthesis, and Evaluation of Pyrrolopyrazine-Substituted Benzoxazole/Benzothiazole Derivatives Targeting Aurora Kinase a in Mcf-7 Cells
(Wiley-V C H Verlag Gmbh, 2025) Kuzu, Burak; Kostekci, Sedat; Karakus, Fuat; Tuluce, Yasin
This study reports the synthesis, characterization, and biological evaluation of 19 benzoxazole/benzothiazole hybrids (19a-s). The compounds were synthesized through a multi-step process and structurally confirmed via NMR, elemental, and MS analyzes. Their antiproliferative effects were assessed on MCF-7 breast cancer and HME1 healthy epithelial cells. MTT assays identified 15 compounds with significant cytotoxic activity, among which 19e, 19g, 19i, 19j, and 19k exhibited high selectivity for MCF-7 cells. ELISA results demonstrated that 19g, 19i, 19j, and 19k significantly reduced AURKA protein levels in MCF-7 cells, while sparing healthy cells, suggesting their role in inhibiting cancer cell proliferation. These findings highlight 19g, 19i, 19j, and 19k as promising selective AURKA-targeted agents for breast cancer therapy.
Exploring the Role of Quercetin on Doxorubicin and Lapatinib-Mediated Cellular and Mitochondrial Responses Using in Vitro and in Silico Studies
(Taylor & Francis Ltd, 2025) Erguc, Ali; Albayrak, Gokay; Muhammed, Muhammed Tilahun; Karakus, Fuat; Arzuk, Ege; Ince-Erguc, Elif
Doxorubicin (DOX) and lapatinib (LAP) have been reported to cause liver toxicity. The roles of mitochondrial and cellular responses in DOX and LAP mediated-hepatotoxicity have not been investigated with or without quercetin (QUE) in HepG2 cells sensitive to mitochondrial damage (high-glucose or galactose media) in addition to in silico studies. Our results revealed that cytosolic pathways might play role a in DOX-induced cytotoxicity rather than mitochondria. QUE exacerbated DOX-induced ATP depletion in both environments. Our data also indicated that cytosolic and mitochondrial pathways might play a role in LAP-induced cytotoxicity. Incubating QUE with LAP increased ATP levels in high-glucose media. Therefore, QUE might have protective effect against LAP-induced cytotoxicity resulting from cytosolic pathways. The findings from in vitro experiments that QUE increased DOX or LAP-induced mitochondrial dysfunction were confirmed by the results from in silico studies indicating that QUE incubated with LAP or DOX might increase mitochondrial dysfunction.
An in Silico Analysis of Dicofol-Induced Neurotoxicity Mechanisms in Humans
(Pergamon-elsevier Science Ltd, 2025) Karakus, Fuat; Kuzu, Burak
Dicofol (DCF) is an organochlorine pesticide that has recently been recognized as a persistent organic pollutant. This study begins by investigating the neurotoxicity of DCF and its metabolites through in silico tools. It subsequently explores the molecular mechanisms and key targets associated with DCF-induced neurotoxicity in humans by employing network toxicology, multi-level bioinformatics approaches, and molecular docking analyses. The prediction results indicate that both DCF and its metabolites can traverse the blood-brain barrier, penetrating the central nervous system, and inducing neurotoxicity. A thorough analysis has identified 56 potential targets linked to DCF-induced neurotoxicity. Gene Ontology enrichment analysis revealed significant associations with pathways related to sodium ion transmembrane transport, sodium/potassium-exchanging ATPase complexes, and P-type calcium transporter activity. Pathway enrichment analysis suggests that DCFinduced neurotoxicity arises from disruptions in ion transport via P-type ATPases. Further examination of gene-gene and protein-protein interactions, along with centrality analysis, identified 11 hub targets, including ATP1A1, ATP1A2, ATP1A3, ATP1A4, ATP1B1, ATP1B2, and MAPK1, as key players. Notably, six of these targets are subunits of the Na+/K+-ATPase, a P-type ATPase. Molecular docking results demonstrated that DCF binds more effectively to the ATP1A3-ATP1B1 protein complex than to its natural ligand, ATP. These findings suggest that DCF may inhibit Na+/K+-ATPase through ATP1A3, resulting in an imbalance of sodium and potassium gradients and ultimately leading to neurotoxicity.
In Silico Network Toxicology, Molecular Docking, and Multi-Level Bioinformatics Reveal Methyl Eugenol-Induced Hepatocellular Carcinoma Mechanisms in Humans
(Wiley, 2025) Karakus, Fuat; Tanriverdi, Zuebeyde; Kuzu, Burak
BackgroundMethyl eugenol (ME), a natural compound found in various essential oils, has recently been classified as a Group 2A carcinogen by the International Agency for Research on Cancer.MethodsThis study aims to investigate the potential molecular mechanisms and underlying ME-induced hepatocellular carcinoma (HCC) in humans using network toxicology, molecular docking, and integrative bioinformatics approaches, including transcriptomic and survival analyses of human HCC datasets.ResultsEnrichment analysis highlighted significant associations with pathways related to steroid metabolic processes, extracellular exosomes, and diverse binding activities. KEGG pathway enrichment further implicated metabolic pathways in ME-induced HCC development. Integration of STRING and Cytoscape analyses identified 14 hub targets, including key proteins such as AURKB, CCNB1, CDK1, and PLK1. Molecular docking studies demonstrated weak binding affinities of ME to these targets compared to their specific inhibitors. However, microarray data and survival analyses of human HCC samples revealed that AURKB, CCNB1, CDK1, and PLK1 are upregulated in HCC, with higher expression levels correlating with poorer overall survival, particularly for CCNB1.ConclusionsThese findings suggest that ME exposure may enhance the expression of these genes in hepatocytes, disrupting the cell cycle and promoting proliferation. This study provides valuable insights into the molecular mechanisms of ME-induced HCC in humans and highlights potential therapeutic targets, such as CCNB1, for further investigation.
Investigation of Potential Anti-Metastatic Effect of Metformin and Caffeic Acid Combination Therapy in Breast Cancer Cell Line in In-Vitro Culture Model
(Humana Press inc, 2025) Yavuz, Halil; Tuluce, Yasin; Karakus, Fuat; Kostekci, Sedat; Tuncyurekli, Merve; Keles, Ahmet Yasin
The invasion and metastasis of cancer cells transform localized cancers into systemic and life-threatening diseases, posing one of the most significant challenges in cancer treatment. This study tested the hypothesis that combined treatment with Caffeic acid (CA) and metformin (MTF) could inhibit or reduce effective signaling pathways involved in the proliferation, survival, and metastasis of MCF-7 breast cancer cells. Anti-proliferation analysis determined the IC50 values for MTF (4.5 mM) and CA (163 mu M) after 72 h. Cell migration analysis showed that MTF and CA significantly inhibited MCF-7 cell migration by the 72nd hour, both alone and in combination, without affecting HME1 healthy cell migration from the 48th hour. Colony formation analysis revealed that CA completely inhibited colony formation in MCF-7 cells, while MTF reduced it by 19%. ELISA results indicated that neither CA nor MTF affected the levels of VEGF-A, E-cadherin, or TINAGL-1 proteins, which are involved in MCF-7 cell migration and invasion. However, MTF significantly reduced IL-1 beta protein levels, and CA significantly reduced IL-4 protein levels in MCF-7 cells. RT-qPCR results largely supported the ELISA findings. Overall, CA and MTF exhibited potential to inhibit MCF-7 cell apoptosis, migration, tumor microenvironment modulation, and metastasis.
Investigation the Immunotherapeutic Potential of Mir-4477a Targeting Pd-1/Pd-l1 in Breast Cancer Cell Line Using a Cd8+ Co-Culture Model
(Springer, 2025) Tuluce, Yasin; Kostekci, Sedat; Karakus, Fuat; Keles, Ahmet Yasin; Tuncyurekli, Merve
BackgroundIn the present study, we investigated the immunotherapeutic and anticancer activities of microRNA-4477a (miR-4477a) as a PD-L1 inhibitor in breast cancer cells (MCF-7).MethodsTo this end, a series of analytical procedures were conducted, including bioinformatic analysis, RT-PCR analysis, PD-L1 ELISA, in vitro co-culture analysis, cytotoxicity assays, cell migration assays, and colony formation assays, with the objective of determining the anticancer activity of the compound in question.ResultsThe results demonstrated that miR-4477a can bind to three distinct regions of PD-L1 mRNA with high scores (94%, 88% and 80%), effectively targeting and suppressing the crucial regulatory pathways of cancer cells. In vitro studies demonstrated that a 25 nM dose of miR-4477a caused relatively high cytotoxicity in the MCF-7 cell line, suppressed PD-L1 gene expression, and decreased sPD-L1 protein levels, strongly inhibited cell migration, and significantly reduced colony formation. The in vitro co-culture analysis revealed that cancer cells were unable to evade the surveillance and cytotoxic activity of T cells (CD8+) due to the blockade of PD-L1 expression by miR-4477a.ConclusionsIn conclusion, miRNA-4477a has the capacity to regulate immune responses in breast cancer cells and may therefore be a promising candidate for use in cancer immunotherapy as a therapeutic agent.
Mechanisms of Developmental Neurotoxicity of Dechlorane Plus, a Recently Identified Persistent Organic Pollutant: An in Silico Study
(Elsevier, 2025) Karakus, Fuat; Tanriverdi, Zubeyde; Kuzu, Burak
Dechlorane Plus (DP), a polychlorinated flame retardant, has recently been recognized as a persistent organic pollutant. In this study, the molecular mechanisms and targets associated with DP-induced developmental neurotoxicity (DNT) in humans were investigated through network toxicology, multi-level bioinformatics approaches, and molecular docking. Through comprehensive database analysis, 32 potential targets associated with DP-induced DNT were identified. Gene Ontology terms enrichment analysis revealed significant enrichment in pathways related to the nervous system processes, GABA-A receptor complex, and various binding and channel activities. KEGG pathway enrichment analysis indicated that DP-induced DNT is mediated through complex interactions involving neuroactive ligand-receptor interaction pathways. Further analysis using GeneMANIA, STRING, Cytoscape tools, and MCODE identified 11 hub targets, including GABRA1, GABRB1, GABRB3, and GABRG2 as key targets. Molecular docking revealed that DP binds to the GABRB3-GABRA1-GABRG2 protein complex to a degree comparable to the control bicuculline, a potent and selective antagonist of the GABA-A receptor. These findings suggest that DP may have antagonistic effects on the GABA-A receptor, potentially increasing neuronal excitability. This study offers valuable insights into the molecular mechanisms underlying DP-induced DNT and provides data for in vitro or in vivo studies.
Mechanistic Analysis of Decabromodiphenyl Ether-Induced Neurotoxicity in Humans Using Network Toxicology and Molecular Docking
(Springer, 2025) Karakus, Fuat; Kuzu, Burak
Commercial decabromodiphenyl ether (c-decaBDE) is a widely used additive flame retardant in textiles and plastics. This formulation predominantly consists of the congener BDE-209, with trace amounts of other brominated diphenyl ether congeners, such as nonabromodiphenyl ether and octabromodiphenyl ether. Recognized as a persistent organic pollutant due to its potential for long-range environmental transport, c-decaBDE poses significant environmental threats and serious human health risks, including endocrine, reproductive, developmental, and neurotoxic effects. The mechanisms underlying its neurotoxicity remain largely undefined. This study investigates the neurotoxic effects of BDE-209 in humans through network toxicology, multi-level bioinformatics approaches, and molecular docking analyses. Prediction results indicate that BDE-209 can cross the blood-brain barrier, entering the central nervous system and inducing neurotoxic effects. A comprehensive analysis has identified 294 potential targets linked to the neurotoxicity induced by BDE-209. Gene-gene interaction and pathway enrichment analyses revealed significant associations related to cellular responses to chemical stress and synaptic transmission. Further investigation of protein-protein interactions, combined with centrality analysis, identified 14 hub targets, including CaMK-II alpha, PSD-95, GluR-1, and GluN2B, as key proteins in this process. Molecular docking results indicate that BDE-209 exhibits a stronger binding affinity to GluN2B, a subunit of the N-methyl-D-aspartate (NMDA) receptors, compared to other key targets. These findings suggest that BDE-209 may disrupt the function of GluN2B-containing NMDA receptors, potentially leading to their inhibition. Such inhibition could result in reduced excitatory neurotransmission, impairing synaptic potentiation and plasticity, and ultimately contributing to neurotoxicity.
Mitochondrial Impact of Organophosphate Pesticide-Induced Cardiotoxicity: an in Silico and in Vitro Study
(Sage Publications inc, 2024) Karakus, Fuat; Arzuk, Ege; Erguc, Ali
Organophosphate pesticides are widely used; however, their use is limited due to neurotoxicity and, to a lesser extent, cardiotoxicity in humans. Given the high energy demands of cardiac muscle, which is characterized by a dense population of mitochondria, any damage to these organelles can exacerbate cardiotoxicity. This study aims to elucidate whether the cardiotoxic effects of organophosphate pesticides originate from mitochondrial dysfunction. To investigate this, in silico toxicogenomic analyses were performed using various tools, such as the Comparative Toxicogenomic Database, GeneMANIA, STRING, and Cytoscape. Results revealed that 11 out of the 13 WHO-recommended Class Ia organophosphate pesticides target genes associated with cardiotoxicity. Notably, three of these genes were mitochondrial, with catalase (CAT) being the common differentially expressed gene among parathion, methyl parathion, and phorate. Furthermore, protein-protein interaction analysis indicated a strong association between CAT and superoxide dismutase 2, mitochondrial (SOD2). Subsequently, isolated heart mitochondria were utilized to assess CAT and superoxide dismutase (SOD) activities in vitro. The findings demonstrated that at a concentration of 7.5 ng/mu L, both methyl parathion and phorate significantly decreased CAT activity by approximately 35%. Moreover, phorate reduced total SOD and SOD2 activities by 17% and 19%, respectively, at the same concentration. In contrast, none of the three organophosphate pesticides induced the opening of the mitochondrial permeability transition pore. These results suggest that the reduction in CAT and SOD2 activities, critical antioxidant enzymes, leads to the accumulation of reactive oxygen species within mitochondria, ultimately resulting in mitochondrial damage. This mechanism likely underlies the observed cardiotoxicity induced by these organophosphate pesticides.
Mitochondrial Toxicity of Selected Natural Compounds: in Vitro Assessment and in Silico Molecular Docking and Dynamics Simulation
(Taylor & Francis Ltd, 2025) Erguc, Ali; Albayrak, Gokay; Muhammed, Muhammed Tilahun; Karakus, Fuat; Arzuk, Ege
Prangos uechtritzii Boiss & Hausskn stands out for its rich bioactive constituents including prantschimgin (PRA), imperatorin (IMP), suberosin (SUB), adicardin (ADI), and oxypeucedanin hydrate (OPH) in the Apiaceae family. Although these molecules contribute to several biological activities, their mitochondrial toxicity were not illuminated in depth with the appropriate in vitro and in silico models. Cell viability studies investigated the cytotoxic activities of molecules in HepG2 cells by replacing glucose with galactose due to Warburg effects. Mitochondrial toxicity (mitotoxicity) parameters such as cellular adenosine triphosphate (ATP) and mitochondrial membrane potential (MMP) levels were assessed with cytotoxic concentrations of selected molecules. Molecular docking and dynamics studies were also conducted against mitochondrial electron transport chain (ETC) complexes (I-V) with selected compounds. In vitro results showed that PRA, SUB, and IMP reduced cell viability more in galactose media compared to high glucose media in a dose-dependent manner. PRA, IMP, and SUB decreased ATP levels and MMP, especially in the galactose medium. The in silico study revealed that PRA, IMP, and SUB might bind to complexes I-V at different levels. The docking study demonstrated that PRA had the highest binding potential with the complexes, higher than the standard ligands in some cases. The molecular dynamics (MD) simulation study showed that PRA formed stable complexes with complexes II, III, and IV. In addition, PRA was anticipated to remain inside the binding site of complex II most stably during the 230 ns simulation period. Our study suggests that PRA, IMP, and SUB exhibit mitotoxicity.
New Targets and Biomarkers for Doxorubicin-Induced Cardiotoxicity in Humans: Implications Drawn From Toxicogenomic Data and Molecular Modelling
(Taylor & Francis inc, 2024) Karakus, Fuat; Ece, Abdulilah; Kuzu, Burak
The doxorubicin-induced cardiotoxicity continues to be a life-threatening adverse effect in the clinic. Doxorubicin-induced acute cardiotoxicity is reversible, whereas chronic cardiotoxicity is irreversible, leading to dilated cardiomyopathy and heart failure. The aim of this study was to identify the molecular mechanisms associated with doxorubicin metabolites in doxorubicin-induced chronic cardiotoxicity. For this purpose, literature searches and in silico toxicogenomic analyses were conducted using various tools, including the Comparative Toxicogenomic Database, GeneMANIA, Metascape, MIENTURNET, ChEA3, and AutoDock. Additionally, molecular dynamics simulations were performed for 500 ns using Schr & ouml;dinger software to assess the stability and dynamics of the representative docked complexes. We observed that doxorubicin biotransformed into five metabolites in the human heart and identified 11 common genes related to doxorubicin, its metabolites, dilated cardiomyopathy, and heart failure. Our findings revealed that doxorubicin and its metabolites primarily exhibited binding affinity to the beta-1 adrenergic receptor and fatty acid synthase. Furthermore, we identified several key transcription factors, especially the Homeobox protein Nkx-2.6, and hsa-miR-183-3p associated with this cardiotoxicity. Finally, we observed that, in addition to doxorubicinol, 7-deoxidoxorubicinone, another metabolite of doxorubicin, may also contribute to this cardiotoxicity. These findings contribute to our understanding of the processes underlying doxorubicin-induced chronic cardiotoxicity.
Novel Pyrazole Derivatives Bearing Carbonitrile and Substituted Thiazole Moiety for Selective Cox-2 Inhibition
(Wiley-v C H verlag Gmbh, 2024) Arzuk, Ege; Karakus, Fuat; Erguc, Ali; Kuzu, Burak
In this study, a series of derivatives of pyrazole hybrid structures containing carbonitrile and substituted thiazole moiety were designed to search for selective COX-2 inhibition. The designed target structures were synthesized with easy, practical, and efficient procedures. COX-1/2 inhibition and cytotoxic effects of the synthesized compounds were evaluated in NIH/3T3 and MDA-MD-231 cell lines for inhibition concentration and selectivity index. The results showed that the compounds have an inhibitory effect with higher selectivity towards COX-2 overall in both cell lines and moderate antiproliferative activity by targeting the breast cancer cell line MDA-MB-231. Among the 19 compounds synthesized (19 a-t), especially compound 19 m was found to be highly effective with COX-2 inhibition of 5.63 mu M in the NIH/3T3 cell line and 4.12 mu M in the MDA-MB-231 cell line. Moreover, molecular docking studies showed that the compounds indeed exhibited higher affinity for the COX-2 active site. The theoretical ADMET properties of the presented compounds were calculated, and the results showed that the compounds may have a more favorable pharmacokinetic effect profile than the selective COX-2 inhibitor Celecoxib, thus promising COX-2 inhibitor drug candidates for the future. A series of derivatives of pyrazole hybrid structures were designed to search for selective COX-2 inhibition. COX-1/2 inhibition and cytotoxic effects of the synthesized compounds were evaluated in NIH/3T3 and MDA-MD-231 cell lines. Moreover, molecular docking, SAR, and ADMET studies showed that the compounds may have a more favorable pharmacokinetic profile, thus promising COX-2 inhibitor drug candidates for the future.image
Potential Inhibitors of Extra-Synaptic Nmdar/Trpm4 Interaction: Screening, Molecular Docking, and Structure-Activity Analysis
(Elsevier, 2023) Deniz, Elif; Karakus, Fuat; Kuzu, Burak
Over-activation of extra-synaptic NMDARs by excessive glutamate is known to cause excitotoxicity. The molecular mechanism of how this excitotoxicity occurs was revealed recently. This paper presents the results of in silico studies aimed at finding potential small-molecule inhibitors that can block this mechanism, namely the extra-synaptic NMDAR/TRPM4 interaction. We screened for small molecules according to 2D (at least Tanimoto threshold was 90%) and/or 3D similarity, molecular weight, lipophilicity using control compounds (C8 and C19) targeting this interaction. We then pre-filtered these molecules according to their drug-likeness and toxicity profiles. After pre-filtering, we performed a docking study against the extra-synaptic NMDAR/TRPM4 interaction with the remaining 26 compounds. In addition, we determined that selected compounds exhibit low affinity for classical NMDAR ligand binding sites. Ultimately, we identified four novel compounds (C8-12, C8-15, C19-3, C19-4) that could block the extra-synaptic NMDAR/TRPM4 interaction without inhibiting the normal function of synaptic NMDARs.
Predicting the Molecular Mechanisms of Cardiovascular Toxicity Induced by Per- and Polyfluoroalkyl Substances: an in Silico Network Toxicology Perspective
(Oxford Univ Press, 2024) Karakus, Fuat; Kuzu, Burak
Background: Per- and polyfluoroalkyl substances (PFAS) are human-made chemicals that accumulate in the human body and the environment over time. Humans are primarily exposed to PFAS through drinking water, food, consumer products, and dust. These exposures can have many adverse health effects, including cardiovascular diseases (CVDs) and factors contributing to CVDs. This study identified the molecular mechanisms of CVDs caused by PFAS. Methods: For this purpose, various computational tools, such as the Comparative Toxicogenomic Database, ShinyGO, ChEA3, MIENTURNET, GeneMANIA, STRING, and Cytoscape, were used to conduct in silico analyses. Results: The results showed that 10 genes were common between PFAS and CVDs, and among these common genes, the PPAR signaling pathway, fatty acid metabolic processes, and lipid binding were the most significantly associated gene ontology terms. Among the top 10 transcription factors (TFs) related to these common genes, peroxisome proliferator-activated receptor gamma and androgen receptor were the most prominent. Additionally, hsa-miR-130b-3p, hsa-miR-130a-3p, and hsa-miR-129-5p were featured microRNAs involved in PFAS-induced CVDs. Finally, PPARA and PPARG were identified as core genes involved in PFAS-induced CVDs. Conclusion: These findings may contribute to a better understanding of the molecular mechanisms and reveal new potential targets in PFAS-induced CVDs.
Role of Oxidative Stress and Reactive Metabolites in Cytotoxicity & Mitotoxicity of Clozapine, Diclofenac and Nifedipine in Cho-K1 Cells in Vitro
(Bentham Science Publ Ltd, 2023) Erguec, Ali; Karakus, Fuat; Arzuk, Ege; Mutlu, Neliye; Orhan, Hilmi
Background CHO-K1 cells were used as in vitro model to explore mechanisms of cytotoxicity of the test drugs. Aim To provide in vitro data on toxicity mechanisms of clozapine, diclofenac and nifedipine. Objective Cytotoxic mechanisms of clozapine (CLZ), diclofenac (DIC) and nifedipine (NIF) were studied in CHO-K1 cells in vitro. All three drugs induce adverse reactions in some patients with partially unknown mechanisms. Methods Following the determination of time- and dose-dependency of cytotoxicity by the MTT test, cytoplasmic membrane integrity was explored by the LDH leakage test. Both end-points were further examined in the presence of soft and hard nucleophilic agents, glutathione (GSH) and potassium cyanide (KCN), respectively, and either individual or general cytochrome P450 (CYP) inhibitors, whether CYP-catalysed formation of electrophilic metabolites play a role in the observed cytotoxicity and membrane damage. The generation of reactive metabolites during the incubations was also explored. Formation of malondialdehyde (MDA) and oxidation of dihydrofluorescein (DCFH) were monitored whether peroxidative membrane damage and oxidative stress take place in cytotoxicity. Incubations were also conducted in the presence of chelating agents of EDTA or DTPA to explore any possible role of metals in cytotoxicity by facilitating electron transfer in redox reactions. Finally, mitochondrial membrane oxidative degradation and permeability transition pore (mPTP) induction by the drugs were tested as markers of mitochondrial damage. Results The presence of an individual or combined nucleophilic agents significantly diminished CLZ- and NIF-induced cytotoxicities, while the presence of both agents paradoxically increased DIC-induced cytotoxicity by a factor of three with the reason remaining unknown. The presence of GSH significantly increased DIC-induced membrane damage too. Prevention of membrane damage by the hard nucleophile KCN suggests the generation of a hard electrophile upon DIC and GSH interaction. The presence of CYP2C9 inhibitor sulfaphenazole significantly diminished DIC-induced cytotoxicity, probably by preventing the formation of 4-hydroxylated metabolite of DIC, which further converts to an electrophilic reactive intermediate. Among the chelating agents, EDTA caused a marginal decrease in CLZ-induced cytotoxicity, while DIC-induced cytotoxicity was amplified by a factor of five. Both reactive and stable metabolites of CLZ could be detected in the incubation medium of CLZ with CHO-K1 cells, which are known to have low metabolic capacity. All three drugs caused a significant increase in cytoplasmic oxidative stress by means of DCFH oxidation, which was confirmed by increased MDA from cytoplasmic as well as mitochondrial membranes. The addition of GSH paradoxically and significantly increased DIC-induced MDA formation, in parallel with the increase in membrane damage when DIC and GSH combined. Conclusion Our results suggested that the soft electrophilic nitrenium ion of CLZ is not responsible for the observed in vitro toxicities, and this may originate from a relatively low amount of the metabolite due to the low metabolic capacity of CHO-K1. A hard electrophilic intermediate may contribute to cellular membrane damage incubated with DIC, while a soft electrophilic intermediate seems to exacerbate cell death by a mechanism other than membrane damage. A significant decrease in cytotoxicity of NIF by GSH and KCN suggested that both soft and hard electrophiles contribute to NIF-induced cytotoxicity. All three drugs induced peroxidative cytoplasmic membrane damage, while only DIC and NIF induced peroxidative mitochondrial membrane damage, which suggested mitochondrial processes may contribute to adverse effects of these drugs in vivo.
Screening and Toxicity Evaluation of Natural Compounds as Adenosine 2a and 2b Receptor Ligands: Insights From Molecular Docking, Dynamics, and Admet Analysis
(Taylor & Francis Ltd, 2024) Karakus, Fuat; Alagoz, Mehmet Abdullah; Kuzu, Burak
Recent studies suggest that immunological and inflammatory responses in cardiovascular disorders, such as hypertension, myocardial infarction, ischemia injury, heart failure, arrhythmias, and atherosclerosis, may be affected by changes in the adenosine system. Pharmacological modulation of adenosine occurs through its receptor subtypes. In numerous preclinical studies, the activation of adenosine receptor 2A (A2AR) or the blockade of adenosine receptor 2B (A2BR) has shown promising results against cardiovascular diseases. This in silico study aimed to identify potential natural compounds that can activate A2AR or block A2BR without causing toxicity. Natural compounds were screened using COlleCtion of Open Natural ProdUcTs (COCONUT) or Natural Product Activity and Species Source Database (NPASS) databases to find agonists for A2AR or an antagonists/inverse agonists for A2BR. These compounds were then pre-filtered based on their toxicity profiles. The remaining compounds were subjected to molecular docking against A2AR and A2BR followed by molecular dynamics simulations were conducted. Finally, selected compounds' ADMET properties were determined using ADMETlab 2.0 web tool. Ultimately, one novel natural compound with potential agonistic activity (COCONUT IDs: CNP0450901) for A2AR and one antagonist/inverse agonist (rauwolscine) for A2BR were identified.
Synthesis of Thiazole-Integrated Pyrrolotriazinones: Evaluations of Cytotoxicity and Effects on P3ik Levels in Cancer Cells
(Tubitak Scientific & Technological Research Council Turkey, 2025) Kuzu, Eylem; Arzuk, Ege; Karakus, Fuat; Kuzu, Burak; Genc, Hasan
The synthesis of novel heterocyclic compounds, particularly those targeting critical signaling pathways in cancer, represents a promising approach to drug development. In this study, we designed and synthesized a series of thiazole-integrated pyrrolotriazinone derivatives, aiming to combine the antiproliferative properties of thiazole with the PI3K inhibitory activity of pyrrolotriazinones. The PI3K pathway, which plays a critical role in regulating cell growth, proliferation, and survival, is frequently dysregulated in cancer, making it an attractive target for therapeutic intervention. The synthesized derivatives were evaluated for their cytotoxic activities against MCF-7, A549, and HepG2 cancer cell lines. Their effect on PI3K protein levels was assessed to evaluate their potential as PI3K inhibitors. Preliminary results indicate that these thiazole-pyrrolotriazinone hybrids exhibit significant cytotoxic effects and may reduce PI3K protein levels in cancer cells. Furthermore, drug-likeness assessments and pre-ADMET evaluations demonstrated that the compounds exhibited promising characteristics, supporting their potential as viable drug candidates. Overall, this study highlights the potential of these novel compounds in cancer therapy and provides valuable insights into the design of small molecules that can target key regulatory pathways involved in cancer progression.