Sürdürülebilir Kalkınma Amaçları
Yayınlar
- MakaleAçık Erişim2026In silico biochemical de novo drug design of valproic acid derivatives to suppress cancerous dna: comprehensive molecular docking, molecular dynamics, 1 h nmr, adme
Acar, Esra; Issa, Ghassan; Agar, Soykan; Gökoluk, Erkan; Giglou, Erfan Akhavan; Şimşek, Dilruba
Objective: This comprehensive in silico computational and theoretical biochemistry/organic chemistry research study covers the inhibition methodologies of 1-BNA, which is an essential template for cancer- suppressing research. By disrupting the minor groove domain binding site of the DNA template 1-BNA dodecamer, three de novo drug candidate molecules via derivatization of anti-epileptic valproic acid (VPA) drug were designed. Methods: Calf thymus DNA (ct-DNA) sequence d(CGCGAATTCGCG)2 dodecamer (PDB ID: 1BNA) was obtained from the Protein Data Bank to study. Molecular docking simulations, the most updated docking programs of AutoDock Vina and PyRx were utilized. Molecular dynamics (MD) simulations and Absorption, distribution, metabolism and excretion (ADME) analyses were employed by Schrödinger’s Desmond software. Results: Thorough in silico results of three new derivatized analogues of VPA showed that chloro-derivatized analogue with its -9.6 kcal/mol docking score and 297.2 µM inhibition constant (IC) has a much better indication in the suppression where isopropyl and fluoro derivatized analogues possess -9.1 kcal/mol docking score with 483.8 µM IC and - 8.3 kcal/mol docking score with 896.2 µM IC respectively compared to the results of pristine VPA’s -8.2 kcal/mol docking score with 863.6 µM IC. Along with the detailed ADME results, isopropyl and chloro- derivatized ligands prove their worth of being a new drug candidate. Conclusion: All results proved that the de novo derivatives of VPA illustrate better docking scores (better suppression) along with better ICs and oral absorption percentage values, meaning that the analogues possess better indications compared to pristine VPA toward the suppression of cancerous cell template DNA.
- MakaleAçık Erişim2026Suppressing breast cancer via 2KS1 protein using biochemical de novo drug design and repurposing of valproic acid derivatives with better indications: comprehensive molecular docking, molecular dynamics simulations, 1H nmr, and admet estimations
Agar, Soykan
Objective: This comprehensive in silico computational and theoretical biochemistry/organic chemistry research study covers the inhibition methodologies of 2KS1, which is an essential template for breast cancer-suppressing research. Methods: To block the active site domain binding site of this protein, three de novo designed organic molecules by derivatizing Valproic Acid (VPA) were studied. Pharmacological organic chemistry effects of these analogues were enhanced to suppress 2KS1 better. The most recent molecular docking, molecular dynamics (MD), Proton Nuclear Magnetic Resonance (1H NMR), and Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) values showed that the derivatives of VPA exhibit better docking scores along with lower (better) inhibition constants and higher oral absorption percentage values compared to pristine VPA, meaning that the analogues possess better indications/pharmacological profiles. Results: The new drug candidate derivatives showed approximately 50 to 200 times inhibition constant efficiency (1/50th to 1/200th of the dose usage) in the affinity and suppression capability compared to pristine VPA. Conclusion: Being able to conduct such a crucial cancer study proves the fact that this study sheds light on the potential of new highly efficient drug molecules for future studies in terms of in vitro and in vivo for the suppression of breast cancer disease.
- MakaleYalnız künye2026Inhibiting liver cancer via the VEGFR1 receptor protein using in silico biochemistry de novo drug analogues of ellagic acid: comprehensive admet, rmsd, molecular docking, and molecular dynamics simulations
Agar, Soykan
Objective: Ellagic Acid, one of the well-known Pharmacognostic molecules, has been discovered to have great potential in its new derivatives to be used as drug candidates to suppress liver cancer via the VEGFR1 receptor mechanism. This study aimed to simulate (in silico biochemistry) design two novel derivatives of Ellagic Acid, a hydroxylated analogue and an Ellagic Acid–Quercetin co-drug, to improve inhibitory binding against the VEGFR1 receptor implicated in liver cancer angiogenesis. Methods: Three-dimensional ligand structures were built and optimized using density functional theory (DFT) with the B3LYP/6-31G(d,p) basis set. Molecular docking simulations were performed using AutoDock Vina 1.2.0. The most favorable poses were subjected to molecular dynamics (MD) simulations in Desmond Maestro 2024-2 under NPT conditions (310 K, 1.01 bar) with the OPLS 3.0 force field. Binding free energies were assessed using MM/GBSA calculations. Results: The pristine Ellagic Acid possesses -89.236 kJ/mol of binding energy in Molecular Dynamics, where its de novo Hydroxylated analogue and Ellagic Acid-Quercetin co-drug possess -105.319 kJ/mol, -147.214 kJ/mol, respectively. The inhibition constant values of the two new drugs are nine times higher compared to pristine Ellagic Acid, proving their efficacy with much less dosage usage in the binding of VEGFR1 receptor’s active site. Conclusion: In two analogues of Ellagic Acid, results are so much better that they prove their worth from the perspective of in silico simulation studies in terms of being used as a VEGFR1 liver cancer transmembrane receptor inhibitor. Thus, these new molecules shed light on further in vitro cell line toxicity and in vivo studies for the future.
- Derleme MakaleYalnız künye2026Scopus SJRQ2Indomethacin as a Multi-target Anticancer Agent via Transmembrane Receptor-mediated Tumor Suppression: The Need for de novo Drug Derivatization
Ozturk, Ebru; Issa, Ghassan; Agar, Soykan
Introduction: Indomethacin, a non-steroidal anti-inflammatory drug (NSAID), has attracted increasing attention for its promising anticancer properties, particularly regarding its crucial effect on transmembrane receptor-mediated signal transduction in different cancers. Besides COX-inhibitory activities, other mechanisms underlying indomethacin's potential as an anticancer agent are being explored, including those related to the mediation of prostaglandin signaling through transmembrane receptors in solid tumors. Methods: In this mini-review, we summarize available information about modulation of transmembrane receptor signaling by indomethacin, including death receptors, EP receptors, receptor tyrosine kinases (RTKs), chemokine receptors, cannabinoid receptors, ACE2, P2X7, IP, and FZD/LRP5/6 receptors associated with Wnt pathways. Results: The presented data indicate that indomethacin may inhibit PGE₂-induced EP signaling, affect EGFR/FGFR and CXCR3 signaling pathways, increase death receptor-mediated apoptosis, and influence various types of receptor cross-talk involved in proliferation, angiogenesis, immune evasion, invasion, and metastasis. However, the most consistent results were obtained in colorectal cancer cells, while the role of indomethacin in breast, ovarian, and prostate cancers appears to be more contextual and receptor-profile dependent. Discussion: Overall, our review suggests that indomethacin functions mainly as a receptor signaling modulator rather than a selective receptor antagonist. The potential clinical application of indomethacin for cancer treatment is hindered by its poor selectivity towards COX enzymes, toxicity, and lack of specificity. Conclusion: Despite the possibility of using indomethacin as a template structure for creating more selective drugs, it seems that indomethacin cannot serve as a drug for anticancer therapy alone. This conclusion specifically positions parent indomethacin as a chemically modifiable scaffold for rational derivative development rather than as a final therapeutic endpoint. 2026, Bentham Science Publishers
- MakaleYalnız künye2026Scopus SJRQ3Investigating the interactions of Axitinib, a tyrosine kinase inhibitor, with DNA: experimental studies, molecular docking, and molecular dynamics simulations
Şenel, Pelin; Faysal, Abdullah Al; Agar, Soykan; Yurtsever, Mine; Gölcü, Ayşegül
Axitinib is an oral medication classified as a second-generation tyrosine kinase inhibitor. It serves as a primary treatment for metastatic renal cell carcinoma (RCC) due to its strong affinity for DNA, which leads to the disruption of the double helix structure. This disruption ultimately halts the cell cycle and induces senescence and mitotic catastrophe in RCC cells. Consequently, investigating the mechanism by which Axitinib binds to DNA is essential for comprehending its pharmacodynamic properties and for the advancement of more effective DNA-binding therapeutics. The present study aimed to examine the interaction between Axitinib and DNA through various analytical techniques, including UV-Vis spectroscopy, thermal denaturation assays, electrochemical methods, and fluorescence emission spectroscopy. According to the electrochemical studies, the binding constant (Kb) for Axitinib was calculated to be (5.13 ± 0.28) × 104, suggesting the potential for groove binding. This finding was further supported by in-silico analyses, where molecular docking and molecular dynamics simulations indicated that the drug selectively binds to the DNA minor groove through partial intercalation, forming new hydrogen bonds with its functional groups while separating the guanine and cytosine base pairs.
AtıfScopus1WoS1OpenAlex2
İncele - MakaleYalnız künye2026Scopus SJRQ2Transition-metal coordination modulates predicted DNA groove recognition and nucleobase contacts in oligohistidine complexes
Agar, Soykan; Yildiz, Alparslan Numan; Yurtsever, Mine
Histidine-rich peptides are widely used in affinity-based purification because imidazole donors can coordinate transition-metal ions. To examine how fixed metal-coordination models may alter the predicted DNA-contacting behavior of a histidine hexamer, a fully in silico comparison was performed using metal-free His6 and the tri-metal model complexes [Zn3(His6)]6+, [Ni3(His6)]6+, and [Cu3(His6)]6+ against the canonical B-DNA dodecamer 1BNA [d(CGCGAATTCGCG)]. The formulas denote the neutral-terminal/neutral-imidazole computational representation used for docking and molecular dynamics (MD), rather than a claim concerning the dominant solution-phase species. Molecular docking and MD simulations were used to compare predicted groove localization, recurrent nucleobase-associated contacts, hydrogen-bond patterns, relative docking scores, and trajectory-based structural persistence. Within the examined 1BNA model, metal-free His6 produced a dominant major-groove pose with adenine-associated contacts and a Vina docking score of −8.9 kcal/mol. The tri-metal coordination models produced dominant minor-groove poses with guanine-associated contacts, with relative docking scores of −9.5, −13.5, and −10.8 kcal/mol for the Zn(II), Ni(II), and Cu(II) models, respectively. The Ni(II)- and Cu(II)-containing models also displayed lower RMSD levels than the metal-free complex over the sampled trajectories. These observations are restricted to the defined computational models and the 1BNA sequence; they do not establish experimental binding affinities, universal nucleobase selectivity, or solution-phase metal speciation. The work provides a hypothesis-generating comparison that may guide future experimental investigation of metal-coordinated oligohistidine-DNA interactions.
- MakaleYalnız künye2025Scopus SJRQ2An in-depth study of clofarabine's binding mechanism to DNA: A thorough experimental and theoretical investigation
Agar, Soykan; Senel, Pelin; Al Faysal, Abdullah; Gölcü, Aysegul; Yurtsever, Mine
The interaction of medicinal compounds with nucleic acids is a critical challenge in drug development. This research focused on the binding dynamics of clofarabine (CLO), an antineoplastic agent, with fish sperm DNA (dsDNA) under conditions that simulate the physiological environment at a pH of 7.4. The investigations employed multiple techniques, including fluorescence and UV spectroscopy, thermal denaturation analysis, viscosity measurements, electrochemical assessments, and molecular docking studies to elucidate these binding interactions. The binding constant (Kb) for the interaction between CLO and dsDNA, as determined from the Benesi-Hildebrand plot, was found to be 2.74 x 104 at a temperature of 298 K. The entropy (Delta S) and enthalpy (Delta H) changes associated with this binding interaction were measured as + 43.08 J mol- 1 K- 1 and -12.44 kJ mol-1, respectively. These values indicate that the predominant forces driving the binding interaction are primarily due to hydrogen bonding. Studies using the ethidium bromide and the Hoechst probe showed that CLO does not bind to dsDNA intercalatively. Findings obtained through UV-Vis absorption spectroscopy, competitive binding assays, and viscosity assessments indicated that CLO associates with dsDNA by binding within the minor groove. Molecular docking analyses demonstrated that CLO is accommodated within the ATrich segment of the minor groove, with significant hydrogen bonding interactions occurring between CLO and dsDNA. These findings may offer valuable perspectives for elucidating the mechanisms underlying the toxicity, resistance, and adverse effects associated with CLO.
AtıfWoS3OpenAlex4İncele - MakaleYalnız künye2025Scopus SJRQ3De novo Drug Design and Repurposing to Suppress Liver Cancer via VEGF-R1 Mechanism: Comprehensive Molecular Docking, Molecular Dynamics Simulations and ADME Estimation
Agar, Soykan
Aim: The aim is to halt the progression of liver cancer (Hepatocellular carcinoma) by suppressing the VEGF-R1 receptor using Myricetin and its de novo-designed analogues. Background: VEGF/VEGFR autocrine signalling promotes the growth, progression, and metastasis of Hepatocellular carcinoma, making the development of molecularly targeted therapies highly feasible. Invasive and metastatic behaviours in various cancers, including hepatocellular carcinoma (HCC), are closely monitored through the use of VEGF signalling pathway inhibitors. Specifically in HCC, VEGFR-1 facilitates the invasive capabilities of cancer cells primarily by triggering the epithelial-mesenchymal transition (EMT) process. VEGFR-1 significantly influences the activity of proteolytic enzymes that are critical for the invasive behaviour of HCC cells. Notably, a novel mechanism has been discovered where VEGFR-1 activation leads to the upregulation of MMP-9, thereby enhancing the invasiveness of HCC cells. The scientists, in their study, have elaborated on the various antiangiogenic agents developed for the treatment of HCC. They have highlighted clinical trials that explore the efficacy of these treatments, which include the application of monoclonal antibodies and small-molecule kinase inhibitors designed to target specific pathways involved in tumour angiogenesis and growth. Objective: Creating a pharmaceutical chemistry table regarding “Structure-Activity Relationship of New Compounds on anticancer”. To do so, Myricetin and its de novo designed structured variants were used in molecular docking, molecular dynamics, cluster analyses, and 1H NMR estimation to specifically understand and enhance the mechanism of suppressing the VEGF-R1 receptor. Methods: Proper ligands (Myricetin and its analogues) and receptor (VEGF-R1) preparations, and optimizations were done using the density functional theory (DFT)/B3LYP function along with the 6-31G(d,p) basis set principle in the latest software programs such as Gaussian 09, Gauss View 6.0 and Avogadro. Then using PyRx and Autodock Vina 1.1.2., many molecular docking trials were achieved with 100 posed simulations in each run. An extensive cluster analysis was performed to identify the most optimal docking poses with the highest accumulation and most favourable binding interactions, ensuring the accuracy of the study. The docking configurations that exhibited the most precise and accurate poses with lowest inhibition constants were chosen as initial structured data for subsequent Molecular Dynamics (MD) simulations for each drug candidate. To verify the molecular docking results, MD runs were achieved in our supercomputers and the trajectory analyses were made. The data confirmed what was found in molecular docking results, verifying the high efficiency of the druggable molecules’ inhibition towards VEGF-R1. Results: Amine-derivatized Myricetin has a significantly high docking score (-10.56 kcal/mol) and great inhibition constant compared to pristine Myricetin (-4.77 kcal/mol) itself while Fluorine-derivatized Myricetin (-6.45 kcal/mol) has an affinity towards VEGF-R1 between the first two molecules. Thus, the structure-activity relationship concerning pharmaceutical chemistry aspects of all the molecules studied, yielded us a great insight into what Myricetin’s organic structure possesses towards inhibiting the progression of Liver Cancer. Also, ADME studies showed that both Amine and Fluorined-derivatized Myricetin molecules are good drug candidates. Conclusion: This study highlighted the significant potential of Myricetin as an anti-cancer drug when modified with specific functional groups. Through comprehensive in silico computational analyses, our research group enhanced Myricetin's inhibitory capabilities by derivatizing its Hydroxyl group with Amine and Fluorine, resulting in improved docking scores and inhibition constants. The findings from molecular docking and MD simulations provide a promising foundation for future in vitro and in vivo investigations of these molecules as potential drugs in cancer research.
AtıfScopus3WoS5OpenAlex8İncele - DüzeltmeAçık Erişim2025Scopus SJRQ3Erratum to: CORRECTION TO: The Inhibition Mechanism of Pancreatic Ductal Adenocarcinoma via LXR Receptors: A Multifaceted Approach Integrating Molecular Docking, Molecular Dynamics and Post-MD Inter-Molecular Contact Analysis (Asian Pacific Journal of Cancer Prevention, (2023), 24(12), (4103), (10.31557/APJCP.2023.24.12.4103))
Demirag, Aliye Demet; Agar, Soykan
- MakaleAçık Erişim2024High Performance Liquid Chromatography-Tandem Mass Spectrometric determination of carcinogen nitrosamine impurities from pharmaceuticals and DNA binding confirmation aided by molecular docking application
Danie, Ibrahim; Agar, Soykan; Yurtsever, Mine; Uenal, Durieehvar oezer
Background and Aims: Nitrosamines are amine compounds attached to a nitroso group. The reaction of amines and nitrosating agents forms nitrosamines. Nitrosamine impurities are classified as Class 1 based on the carcinogenicity and mutagenicity data by ICH M7 (R1). The recent discovery of nitrosamines in some pharmaceutical products has caused concern. Nitrosamines are carcinogenic, so it is necessary to determine the possible nitrosamines in pharmaceutical products. Methods: An Inertsil ODS-3, (4.6x250 mm, 5 mu m) column was used for separation. A triple quadrupole mass detector with electrospray Ionisation (ESI) was used for detection. Multiple reaction monitoring (MRM) was used for quantification. The transition ions are 75.1 > 43.3 for NDMA and 103.0 > 75.1 for NDEA. The calibration curves consist of 5 concentration levels, including NDMA and NDEA (5, 10, 50, 100, 150 ng/mL). The mean r2 value was 0.997 for NDMA and 0.999 for NDEA. For NDMA and NDEA, LOD: 2 ng/mL, LOQ: 5 ng/mL. Results: Comprehensive in silico and in vitro results indicate that the method has good accuracy and precision. Conclusion: DNA binding interactions of the molecules NDMA and NDEA, were investigated through the molecular docking and molecular dynamics methods. Molecular Docking simulations showed that these small organic molecules have high-affinity scores and strongly bind to the minor groove of the hDNA via strong hydrogen bonds.
AtıfWoS1OpenAlex2TR Dizin1
İncele - MakaleAçık Erişim2024Scopus SJRQ2The Inhibition of RXRα and RXRβ Receptors Provides Valuable Insights for Potential Prostate Cancer Treatment, in silico Molecular Docking and Molecular Dynamics Studies
Agar, Soykan; Akkurt, Barbaros; Ulukaya, Engin
Introduction: Prostate cancer has emerged as a widespread health concern, with systemic inflammation believed to substantially contribute to its development and progression. The presence of systemic inflammatory responses has been established as an independent predictor of unfavorable long-term outcomes in prostate cancer patients. The goal of this study is to inhibit RXRα and RXRβ receptors, which are involved in prostate cancer, with Luteolin, Formononetin, and Kaempferol, with varying success. Methods: Retinoid X receptors (RXRs) hold crucial roles within the nuclear receptor (NR) superfamily, and compelling evidence from preclinical studies underscores the therapeutic potential of targeting RXRs for treating neurodegenerative and inflammatory conditions. Consequently, the ability to regulate and modulate RXRs using phytoestrogen ligands, Formononetin, Kaempferol, and Luteolin, assume paramount importance in treatment strategies. Results: The comprehensive in silico findings of this study vividly demonstrate the remarkable efficacy of Luteolin in inhibiting and modulating RXRα and RXRβ, while Formononetin emerges as a notably potent suppressor of RXRβ. Kaempferol, as the third compound, also exhibits commendable inhibitory attributes, although its impact is slightly less pronounced compared to the other two. Discussion: These findings highlight the notable binding and inhibition capabilities to RXRα and RXRβ, offering valuable insights for potential prostate cancer treatment avenues warranting further exploration through in vitro and in vivo analyses.
AtıfScopus2İncele - MakaleAçık Erişim2024Scopus SJRQ3Inhibition of pancreatic cancer via LPAR4 receptor with a de novo drug complex design using theoretical organic chemistry: Comprehensive molecular docking, molecular dynamics
Agar, Soykan; Arasan, Yaren; Akkurt, Barbaros; Ulukaya, Engin
The present work relates to a de novo organic chemistry involved drug design and repurposing discovery of a Quercetin and Ascorbic Acid complex formation with the IUPAC nomenclature of ‘’3-((2S)-2-(3,4-dihydroxy-5-oxo-2,5-dihydrofuran-2-yl)-2-hydroxyethoxy)-2-(3,4-dihydroxyphenyl)-3,5,7-trihydroxychroman-4-one’’ to suppress pancreatic cancer via the inhibition of LPAR4 receptor. This was achieved with molecular docking and molecular dynamics studies and found that Ascorbic Acid is docking manoeuvre assistant for Quercetin to form Hydrogen bonds and Covalent bonds to shut down LPAR4 receptor with excellent inhibition constant. This study may very well lead to further in vitro organic synthesis, characterization and cell line results and in vivo/ex ovo animal testing for etherical bound Quercetin and Ascorbic Acid complex.
AtıfScopus1OpenAlex3TR Dizin3İncele - MakaleAçık Erişim2024Scopus SJRQ2De novo Antineoplastic Drug Design to Suppress Head, Neck and Oral Cancer using Theoretical Organic and Biochemistry via Comprehensive Molecular Docking and Dynamics
Agar, Soykan; Mokhtari, Mohaddeseh; Yanik, Muhammed; Akkurt, Barbaros; Ulukaya, Engin; Terzi, Rabia
Objective: A de novo antineoplastic drug was planned to suppress and modulate the Head, Neck, and Oral Cancer. Methods: Using the computational software tools including molecular docking, molecular dynamics (MD), and post-molecular dynamics bond contact analyses, it has been shown that the new drug called ‘’Innovative Head, Neck, and Oral Cancer Suppressor’’, or simply abbreviated as “IHNOCS” is very effective in terms of suppressing and co-modulating TGF-β and KRTAP2-3 together. Result: The drug suppresses the KRTAP2-3 protein activity while also holding onto TGF-β and modulating it to slow down and halt the metastasis. Conclusion: We have effectively created a novel medication using principles of theoretical chemistry, biochemistry, pharmaceutical chemistry and organic chemistry and organic chemistry to inhibit Head, Neck, and Oral Cancer. This medication should further undergo experimental testing in various stages, including in vitro, in vivo, and human clinical phases. It exhibits significant effectiveness in inhibiting the progression of cancer by simultaneously targeting TGF-β and KRTAP2-3, thereby impeding metastasis and suppressing the disease. This work is licensed under a Creative Commons Attribution-Non Commercial 4.0 International License.
AtıfScopus4OpenAlex4İncele - MakaleAçık Erişim2024Scopus SJRQ3De novo Drug Design to Suppress Coronavirus RNA-Glycoprotein via PNA-Calcitonin
Agar, Soykan; Akkurt, Barbaros; Alparslan, Levent
De novo drug design has been studied utilizing the organic chemical structures of Salmon Calcitonin 9-19 and Peptide Nucleic Acid (PNA) to suppress Coronavirus Ribonucleic Acid (RNA)-Glycoprotein complex. PNA has a polyamide backbone and thymine pendant groups to bind and selectively inhibit adenine domains of the RNA-Glycoprotein complex. While doing so, molecular docking and molecular dynamics studies revealed that there is great inhibition docking energy (-12.1 kcal/mol) with significantly good inhibition constant (124.1 µM) values confirming the efficient nucleotide-specific silencing of Coronavirus RNA-Glycoprotein complex.
AtıfScopus1OpenAlex3TR Dizin2İncele - MakaleAçık Erişim2024Scopus SJRQ3New Drug Design to Suppress Nonalcoholic Steatohepatitis
Agar, Soykan; Akkurt, Barbaros; Ulukaya, Engin
A de novo designed biomolecule called INASHD was utilized through computer-aided drug design techniques to specifically target β2-spectrin, effectively suppressing and preventing NASH disease. Advanced computational software tools concerning the technologies of molecular docking and molecular dynamics (MD), were employed to showcase the drug's remarkable ability to efficiently suppress and control the α-helical topology of β2-spectrin. This protein is a vital component within the disease pathway. We successfully devised an effective design suppressing β2-spectrin, exhibiting an inhibition score surpassing any other molecule documented in scientific literature. With robust support from validated computational software, this bioorganic structure holds significant value and can be applied for a patent due to its innovative design. It shows promising potential for delivering positive outcomes in various stages, including in vitro, in vivo, ex vivo, and human phase studies.
AtıfScopus2OpenAlex4TR Dizin3İncele - MakaleAçık Erişim2024Scopus SJRQ4AI Integrated Theoretical/Organic Chemistry is Set to Revolutionize the Future of Education and De Novo Drug Discovery
Agar, Soykan; Tokay, Ilgaz; Akkurt, Barbaros; Gokoluk, Erkan; Akbulut, M. Berk; Ozler, Berin Damla; Elmas, Muzaffer
This article discusses the rapidly expanding artificial intelligence (AI) tools combined with theoretical and organic chemistry software to point out the fact that near future is being reborn with a new education system and research system in drug discovery. The integration of AI into the field of chemistry and pharmacy has expanded rapidly in recent years. There has been a significant surge in both journal articles and patents, particularly from 2015 onward. Analyzing the distribution of these publications across various pharmaceutical and chemical research domains reveal that theoretical chemistry, organic chemistry and biochemistry have embraced AI most extensively, showing the highest growth rates. Utilizing such new software tools in educational research centers and academia, students and scholars can learn and apply much more long-durational and larger techniques in shorter times to yield massive results for the sake of humankind’s future with no diseases. This new type of educational and research-oriented technique integrating the control and check mechanism of AI is being used today for the design of new drugs which are essential for the longevity. The utilization of AI with in-silico studies and education increases the ability to stop diseases with a logarithmic increase while the old-fashioned ways of chemistry will be no more in the near future. Overall, this research paper offers a comprehensive overview of AI's advancement in pharmaceutical and chemical area and sheds light on its potential future trajectories.
- MakaleAçık Erişim2023Scopus SJRQ3The Inhibition Mechanism of Pancreatic DuctalAdenocarcinoma via LXR Receptors: A Multifaceted Approach Integrating Molecular Docking, Molecular Dynamics and Post-MD InterMolecular Contact Analysis
Agar, Soykan; Akkurt, Barbaros; Ulukaya, Engin
Objective: Pancreatic ductal adenocarcinoma (PDAC) has an unfavorable outlook due to its aggressive characteristics, delayed diagnosis, and limited effective treatment options for advanced stages of the disease. The significant mortality rate has prompted investigations into additional factors that could aid in managing this type of cancer. Liver X receptors, specifically LXRα and LXRβ, are nuclear receptors that oversee the expression of genes related to cholesterol, glucose, lipid metabolism, and inflammatory responses. LXRs have also emerged as potential targets for addressing PDAC, and recent findings have demonstrated that LXR ligands can impede cell proliferation in various cancer forms, notably pancreatic cancer. This comprehensive computational research study involving oncological in silico mechanism discovery explored inhibitory ligands for Liver X receptors (LXRα and LXRβ), which are believed to have prognostic significance in PDAC. Methods: The study utilized Baicalein, Beta-Sitosterol, Polydatin ligands in molecular docking and dynamics and post-molecular Hydrogen bonding contact analyses dynamics to characterize receptor inhibition. Result: The outcomes suggest that Baicalein exhibits versatile inhibitory effects on both receptors, while Beta-Sitosterol emerges as a highly effective inhibitor of LXRβ. Conclusion: Further in vitro and in vivo investigations will be beneficial and would shed light onto the mechanism to decipher the suppression of PDAC evaluating the potential of Baicalein, Beta-Sitosterol, Polydatin natural ligand compounds.
AtıfScopus6OpenAlex6İncele