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Journals / Turkish Computational and Theoretical Chemistry / 2026 / Volume: 10 Issue: 3

Computational Exploration of Amino Acids and Endogenous Bioactive Molecules as Potential Caspase-3 Modulators: DFT, Molecular Docking, Diamagnetic Susceptibility and ADME Studies

Kağan Girgin(SIVAS CUMHURIYET UNIVERSITY)0009-0007-0493-4889
Kübra Nur Menekşe(SIVAS CUMHURIYET UNIVERSITY)0009-0001-3402-4735
Gamze Tüzün(SIVAS CUMHURIYET UNIVERSITY)0000-0002-5876-2046
Burak Tüzün(SİVAS CUMHURİYET ÜNİVERSİTESİ, SİVAS TEKNİK BİLİMLER MESLEK YÜKSEKOKULU)0000-0002-0420-2043
Pages
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Publication Date
2026-09-29
DOI
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AI Summary & Key Takeaways

AI Insight
⚡ TL;DR(Too Long; Didn't Read)

Results of both theoretical and molecular docking indicate that serotonin, melatonin, progesterone, histidine, and tryptophan may serve as promising molecular candidates for future studies directed at caspase-3-mediated biological pathways.

📌 3 Key Takeaways

🎯
Objective & Hypothesis:Caspase-3 is an executioner enzyme associated with apoptosis and is an important therapeutic target in cancer, neurodegenerative diseases, and inflammatory disorders.
📊
Key Findings & Data:Twenty amino acids in combination with five biologically active endogenous molecules (adrenaline, noradrenaline, serotonin, melatonin, and progesterone) were investigated in detail by density functional theory (DFT), Hartree–Fock (HF) and M06-2X methods with the 6-31++G(d,p) basis set in that study.
💡
Conclusion & Impact:Results of both theoretical and molecular docking indicate that serotonin, melatonin, progesterone, histidine, and tryptophan may serve as promising molecular candidates for future studies directed at caspase-3-mediated biological pathways.
🔬Design:Research Article
📍Scope:Comprehensive Sample
⚙️Variables:Caspase-3 · Density Functional Theory · Molecular Docking

Abstract

Caspase-3 is an executioner enzyme associated with apoptosis and is an important therapeutic target in cancer, neurodegenerative diseases, and inflammatory disorders. Twenty amino acids in combination with five biologically active endogenous molecules (adrenaline, noradrenaline, serotonin, melatonin, and progesterone) were investigated in detail by density functional theory (DFT), Hartree–Fock (HF) and M06-2X methods with the 6-31++G(d,p) basis set in that study. The electronic features including frontier molecular orbital energies, HOMO–LUMO energy gaps, global reactivity descriptors, molecular electrostatic potential distributions, and molar diamagnetic susceptibilities were assessed. Molecular docking studies were conducted with 3 caspase-3 crystal configurations (PDB IDs: 3DEI, 3GJQ, and 5I9B) by the Glide protocol; ADME analyses in order to evaluate the pharmacokinetic behaviors were performed. Quantum chemical analyses confirmed that serotonin, melatonin, and progesterone showed significantly lower HOMO–LUMO energy gaps, signifying higher chemical reactivity and organic intermolecular potential. Progesterone was the most electrophilic and electronegative compound of the compounds explored. Molar diamagnetic susceptibility analyses showed that aromatic amino acids such as tryptophan and tyrosine showed a significantly higher diamagnetic response compared to aliphatic amino acids. Docking studies showed the same interactions were favorable for serotonin for 3DEI (−6.31 kcal/mol), histidine for 5I9B (−6.92 kcal/mol) and tryptophan for 3GJQ (−5.60 kcal/mol). ADME analyses showed that the most balanced pharmacokinetic profile was established for serotonin, i.e., its relatively favorable oral penetration and physicochemical properties. Results of both theoretical and molecular docking indicate that serotonin, melatonin, progesterone, histidine, and tryptophan may serve as promising molecular candidates for future studies directed at caspase-3-mediated biological pathways.

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Cite This Article

Girgin, K., Menekşe, K. N., Tüzün, G., Tüzün, B. (2026). Computational Exploration of Amino Acids and Endogenous Bioactive Molecules as Potential Caspase-3 Modulators: DFT, Molecular Docking, Diamagnetic Susceptibility and ADME Studies. Turkish Computational and Theoretical Chemistry, Volume: 10 Issue: 3. https://ajindex.com/articles/1554732

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