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- 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.
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İncele - 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.
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İncele - 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.
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