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    De novo antineoplastic drug design to suppress head, neck and oral cancer using theoretical organic and biochemistry via comprehensive molecular docking and dynamics
    (Asian pacific organization for cancer prevention, 2024) Agar, Soykan; Mokhtari, Mohaddeseh; Yanık, 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.
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    De novo drug design to suppress coronavirus RNA-Glycoprotein via PNA-Calcitonin
    (Turkish Chemical Society, 15 Mayıs 2024) Alparslan, Levent; Akkurt, Barbaros; Agar, Soykan
    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 selectively bind and 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.
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    De novo drug design to suppress coronavirus RNA-glycoprotein via PNA-calcitonin
    (Turkish chemical society, 2024) 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.
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    Inhibition of pancreatic cancer via LPAR4 receptor with a de novo drug complex design using theoretical organic chemistry: Comprehensive molecular docking, molecular dynamics
    (Marmara University, 2024) 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. © 2024 Marmara University Press.
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    The inhibition of RXRα and RXRβ receptors provides valuable insights for potential prostate cancer treatment, in silico molecular docking and molecular dynamics studies
    (Asian pacific organization for cancer prevention, 2024) 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.