Scopus İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/395
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Article Identification of Potential Dual HDAC6 and HSP90 Inhibitors for the Treatment of Cancer Using Molecular Docking, Molecular Dynamics and MM/PBSA Studies: A Comprehensive In Silico Study(Bentham Science Publ Ltd, 2026) Yucel, Muhsin Samet; Akcok, IsmailBackground Histone deacetylase 6 (HDAC6) and heat shock protein 90 (Hsp90) are crucial therapeutic targets in cancer research with their interconnected roles in regulating protein homeostasis and cellular processes. The interaction of these proteins within the cytosolic complex plays a critical role in regulating cancer cell survival and progression. Notably, current studies highlight that the simultaneous inhibition of HDAC6 and Hsp90 can produce synergistic effects and offer a promising therapeutic potential for combating malignant cancers.Objective The objective of this study was to explore potential compounds that can inhibit both HDAC6 and Hsp90 proteins.Methods In this study, a number of in-silico computational techniques were employed. A total of 791 molecules, sharing at least 30% similarity with previously identified four HDAC inhibitors, were obtained from the ZINC15 database and subjected to docking on HDAC6 and Hsp90 proteins. The top eight ligands demonstrating the best binding scores against both targets, with panobinostat and ganetespib serving as reference compounds for HDAC6 and Hsp90, respectively, were selected for further analysis. Subsequently, ADME prediction and molecular dynamics simulations were conducted on the selected ligands.Results A detailed molecular docking, molecular dynamics simulations and ADME studies have revealed that ZINC27653366 exhibited the highest inhibitory potential against both Hsp90 and HDAC6 target proteins, making it the most promising inhibitor.Conclusion In conclusion, although additional in vitro and in vivo studies are required for the validation, in silico evaluation of ZINC27653366 may position it as a promising candidate for the treatment of different types of cancers.Article A Small Indole Derivative Isolated From Caper (Capparis Ovata) as an Inducer of P53-Mediated Apoptosis in Prostate Cancer: Comprehensive In Vitro and In Silico Studies(Wiley, 2025-12-31) Acar, Ozden Ozgun; Gazioglu, Isil; Oruc, Hatice; Kale, Elif; Senol, Halil; Topcu, Gulacti; Sen, AlaattinNatural products with stunning chemical diversity have been extensively researched for their anticancer potential for more than fifty years. This study aimed to determine the effect of indole derivative 1H-indole-2-hydroxy-3-carboxylic acid (IHCA), isolated as a novel alkaloid from Capparis ovata, on selected tumor suppressor, apoptotic, and cell cycle regulatory genes, which are known to be important in cancer pathophysiology, on Caco-2 and LNCaP cells in comparison with Taxol. The molecular mechanism of IHCA's anticancer activity is essentially undefined. Different concentrations of IHCA increased the expression levels of apoptosis-related genes, including BCL-2 and TNF-alpha. In addition, the tumor suppressor genes PTEN, P53, and RB were increased in LNCaP and Caco-2 cells. KRAS, an oncogenic gene, was significantly downregulated by IHCA in LNCaP cells. Western blot results showed that the protein expression levels of P53 and PTEN in LNCaP cells were increased when treated with IHCA, whereas CDK4 and TNF-alpha were decreased. Finally, IHCA and doxorubicin significantly increased P53-driven luciferase activity compared to the control. The results strongly suggest that the novel natural compound IHCA has an anticancer effect involving the regulation of the P53 gene and its networks in vitro. The molecular docking and MD simulation analyses reveal that IHCA exhibits superior binding potential to the MDM2 protein compared to Nutlin-3a. MD simulations further confirm that IHCA maintains a more stable and consistent interaction with MDM2, as indicated by lower RMSD values and reduced ligand fluctuation. These results highlight IHCA's potential as a more effective MDM2 inhibitor, suggesting its promise as a lead compound for anticancer drug development.Clinical Trial Registration: Not applicable.Article Toward the Design of New Α-Carboline Derivatives Against Anaplastic Lymphoma Kinase (Alk): A Comprehensive in Silico Approach(Wiley-VCH Verlag GmbH, 2025-11) Sari, Ceyhun; Akcok, IsmailAfter the first description of anaplastic lymphoma kinase (ALK) in an anaplastic large cell lymphoma cell line as a nucleophosmin (NPM) fusion partner, ALK and its various fusion partners have been implicated in numerous cancers such as non-small cell lung cancer (NSCLC), anaplastic large cell lymphoma (ALCL), neuroblastoma, and rhabdomyosarcoma. In the last decade, several compounds targeting ALK have been developed and approved by the Food and Drug Administration (FDA). Despite the advances of generations of ALK inhibitors, a recent study highlighted that around half of the ALK-positive NSCLC patients will go through disease progression in response to first-line alectinib, which is a second-generation ALK inhibitor. In this study, we aimed to propose a novel alpha-carboline compound targeting the ALK tyrosine kinase domain to be used against various types of cancer in which ALK fusion proteins may be involved. In this regard, we designed more than 200 alpha-carboline derivatives and investigated their binding properties against ALK tyrosine kinase by using in silico protocols consisting of molecular docking studies, molecular dynamics simulations, MM/PBSA binding free energy calculation, and essential dynamics analysis. Considering the obtained results, we developed two promising candidates, compounds 208 & 209 with -9.05 and -9.80 binding energies, respectively, which demonstrated improved binding profiles over the course of a 300 ns simulation.Article Citation - WoS: 40Citation - Scopus: 43The Role of Hydrogen in the Edge Dislocation Mobility and Grain Boundary-Dislocation Interaction in Α-Fe(Pergamon-Elsevier Science Ltd, 2021-09) Kapci, Mehmet Fazil; Schoen, J. Christian; Bal, Burak; Schön, J. ChristianThe atomistic mechanisms of dislocation mobility depending on the presence of hydrogen were investigated for two edge dislocation systems that are active in the plasticity of alpha-Fe, specifically 1/2<111>{110} and 1/2<111>{112}. In particular, the glide of the dislocation pile-ups through a single crystal, as well as transmission of the pile-ups across the grain boundary were evaluated in bcc iron crystals that contain hydrogen concentrations in different amounts. Additionally, the uniaxial tensile response under a constant strain rate was analyzed for the aforementioned structures. The results reveal that the presence of hydrogen decreases the velocity of the dislocations -in contrast to the commonly invoked HELP (Hydrogen-enhanced localized plasticity) mechanism-, although some localization was observed near the grain boundary where dislocations were pinned by elastic stress fields. In the presence of pre-exisiting dislocations, hydrogen-induced hardening was observed as a consequence of the restriction of the dislocation mobility under uniaxial tension. Furthermore, it was observed that hydrogen accumulation in the grain boundary suppresses the formation of new grains that leads to a hardening response in the stress-strain behaviour which can initiate brittle fracture points. (C) 2021 Hydrogen Energy Publications LLC. Published by Elsevier Ltd. All rights reserved.Article Citation - Scopus: 1Possible Drug-Drug Interactions Between Mesalamine and Tricyclic Antidepressants Through CYP2D6 Metabolism - in Silico and in Vitro Analyses(Georg Thieme Verlag, 2025-04-01) Ozen, Melek B.; Gazioğlu, Işil; Ozgun-Acar, Özden; Guner, Hüseyin; Semiz, Gürkan; Sen, Alaattin; Ozgun Acar, OzdenMesalamine (mesalazine, 5-aminosalicylic acid, 5-ASA) is an essential anti-inflammatory agent both used for therapy and as a remission control in patients with inflammatory bowel diseases (IBD) such as ulcerative colitis (UC). Tricyclic antidepressants (TCAs) are used to alleviate remaining symptoms in patients already receiving IBD therapy or with quiescent inflammation. The cytochrome P4502D6 enzyme is involved in the metabolism of TCAs. Hence, it is crucial to investigate the role of CYP2D6 in 5-ASA metabolism. Initially, in silico analysis involving the docking of 5-ASA to CYP2D6 and molecular dynamics simulations was conducted. Next, the rate of O-demethylation of a nonfluorescent probe 3-[2-(N,N-diethyl-N-methylammonium)-ethyl]-7-methoxy-4-methylcoumarin (AMMC) into a fluorescent metabolite AMHC (3-[2-(N,N-diethyl-N-methylammonium)ethyl]-7-hydroxy-4-methylcoumarin) was optimized with baculosomes co-expressing human CYP2D6 and human P450 oxidoreductase (hCPR) to monitor CYP2D6 activity in a microtiter plate assay. The apparent Km and Vmax were found to be 1.30 μM and 32.68 pmol/min/mg of protein for the O-demethylation of AMMC to AMHC, and the reaction was linear for 40 min. Then, nonselective inhibition of CYP2D6 activity with various concentrations of 5-ASA was detected. Finally, the conversion of AMMC to metabolites was analyzed by HPLC-ESI-MS/MS spectrometry, and none were identified. Thus, this study suggests that concurrent use of mesalamine with TCA may lead to adverse effects, and CYP2D6 genotyping should be routinely performed on these patients to eliminate possible threats. © 2025 Elsevier B.V., All rights reserved.Conference Object Investigation of Temperature and Pressure Effect on the Hydrogen Sorption Kinetics in the Interface of Mg/MgH2 by Molecular Dynamics(International Association for Hydrogen Energy, IAHE, 2022) Kapci, Mehmet Fazil; Wu, Zhen; Bal, BurakMolecular dynamics simulations were performed in order to analyze the hydrogen sorption kinetics between αMgH<inf>2</inf> and hcp Mg structures under different temperatures and pressures. Results showed that hydrogen desorption from magnesium hydride and absorption by hcp magnesium increase at the higher temperatures. During the hydrogen desorption from magnesium hydride and absorption into hcp magnesium, crystallographic orientation change in the magnesium atoms was observed. At 400 °C, the pressure was found to have a negative impact during the hydrogen desorption from magnesium hydride due to the prevention of recrystallization. © 2023 Elsevier B.V., All rights reserved.Article Citation - WoS: 5Citation - Scopus: 7Experimental and Molecular Dynamics Simulation-Based Investigations on Hydrogen Embrittlement Behavior of Chromium Electroplated 4340 Steel(ASME, 2021-06-17) Dogan, Ozge; Kapci, Mehmet Fazil; Esat, Volkan; Bal, BurakIn this study, chromium electroplating process, corresponding hydrogen embrittlement, and the effects of baking on hydrogen diffusion are investigated. Three types of materials in the form of Raw 4340 steel, Chromium electroplated 4340 steel, and Chromium electroplated and baked 4340 steel are used in order to shed light on the aforementioned processes. Mechanical and microstructural analyses are carried out to observe the effects of hydrogen diffusion. Mechanical analyses show that the tensile strength and hardness of the specimens deteriorate after the chrome-electroplating process due to the presence of atomic hydrogen. X-ray diffraction (XRD) analyses are carried out for material characterization. Microstructural analyses reveal that hydrogen enters into the material with chromium electroplating process, and baking after chromium electroplating process is an effective way to prevent hydrogen embrittlement. Additionally, the effects of hydrogen on the tensile response of alpha-Fe-based microstructure with a similar chemical composition of alloying elements are simulated through molecular dynamics (MD) method.Article Citation - WoS: 12Citation - Scopus: 12Edge Dislocation Depinning From Hydrogen Atmosphere in Α-Iron(Pergamon-Elsevier Science Ltd, 2024-07) Kapci, Mehmet Fazil; Yu, Ping; Marian, Jaime; Liu, Guisen; Shen, Yao; Li, Yang; Bal, BurakUnderstanding the dislocation motion in hydrogen atmosphere is essential for revealing the hydrogen-related degradation in metallic materials. Atomic simulations were adopted to investigate the interaction between dislocations and hydrogen atoms, where the realistic hydrogen distribution in the vicinity of the dislocation core was emulated from the Grand Canonical Monte Carlo computations. The depinning of edge dislocations in alpha-Fe at different temperatures and hydrogen concentrations was then studied using Molecular Dynamics simulations. The results revealed that an increase in bulk hydrogen concentration increases the flow stress due to the pinning effect of solute hydrogen. The depinning stress was found to decrease due to the thermal activation of the edge dislocation at higher temperatures. In addition, prediction of the obtained results was performed by an elastic model that can correlate the bulk hydrogen concentration to depinning stress.Article Citation - WoS: 3Citation - Scopus: 3Dual Targeting of DNA Damage Response Proteins Implicated in Cancer Radioresistance(MDPI, 2023-12-17) Vasilopoulos, Spyridon N.; Guner, Hueseyin; Apaydin, Merve Uca; Pavlopoulou, Athanasia; Georgakilas, Alexandros G.; Uça Apaydın, MerveIonizing radiation can induce different types of DNA lesions, leading to genomic instability and ultimately cell death. Radiation therapy or radiotherapy, a major modality in cancer treatment, harnesses the genotoxic potential of radiation to target and destroy cancer cells. Nevertheless, cancer cells have the capacity to develop resistance to radiation treatment (radioresistance), which poses a major obstacle in the effective management of cancer. It has been shown that administration of platinum-based drugs to cancer patients can increase tumor radiosensitivity, but despite this, it is associated with severe adverse effects. Several lines of evidence support that activation of the DNA damage response and repair machinery in the irradiated cancer cells enhances radioresistance and cellular survival through the efficient repair of DNA lesions. Therefore, targeting of key DNA damage repair factors would render cancer cells vulnerable to the irradiation effects, increase cancer cell killing, and reduce the risk of side effects on healthy tissue. Herein, we have employed a computer-aided drug design approach for generating ab initio a chemical compound with drug-like properties potentially targeting two proteins implicated in multiple DNA repair pathways. The findings of this study could be taken into consideration in clinical decision-making in terms of co-administering radiation with DNA damage repair factor-based drugs.Article Discovery of New Candidates Targeting the SH2 Domains of Spleen Tyrosine Kinase (Syk) Through in Silico Studies(Wiley-VCH Verlag GmbH, 2025-06) Sansacar, Merve; Sari, Ceyhun; Yucel, Muhsin Samet; Akcok, Emel Basak Gencer; Akcok, Ismail; Gencer Akçok, Emel BaşakSrc homology 2 (SH2) domains have become an increasingly popular candidate for researchers to search for novel therapeutics to target different diseases. Spleen tyrosine kinase (Syk) is one of the proteins with two SH2 domains that has a role in the pathogenesis of many diseases. Here, we report the discovery of a promising natural product (NP) inhibitor that targets the N-terminal SH2 (N-SH2) and C-terminal SH2 (C-SH2) domains of Syk simultaneously, through structure-based drug discovery approach. Molecular docking studies, followed by molecular dynamics (MD) simulations and molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) calculations, were utilized to reveal the interactions between NPs from "the COlleCtion of Open NatUral producTs (COCONUT)" database and Syk enzyme. Five natural products that have lowest Scoring and Minimization with AutoDock Vina (SMINA) scores against both SH2 domains of Syk were selected for further studies and compound CNP0265345 has the best binding free energies toward both C-SH2 and N-SH2 of Syk enzyme with -44.54 and -55.98 kcal/mol, respectively. Drug-likeness properties, absorption, distribution, metabolism, and excretion (ADME) and carcinogenicity predictions were also studied. In conclusion, our work highlights a novel drug candidate to target the Syk enzyme of SH2 domains using in silico methods.