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Formononetinin Potansiyel Bir Anti-Obezite Ajanı Olarak Hesaplamalı (In Silico) Değerlendirilmesi: Kuantum Kimyasal ve Doking Analizleri

Year 2025, Volume: 8 Issue: 2, 61 - 70, 29.12.2025
https://doi.org/10.46239/ejbcs.1807471

Abstract

Formononetin, doğal bir polifenolik bileşik, obezite tedavisi için umut verici bir aday olarak ortaya çıkmıştır. Bu çalışma, formononetinin elektronik yapısını, protein-ligand etkileşimlerini ve farmakokinetik özelliklerini araştırmak için çok katmanlı bir hesaplamalı yaklaşım kullanmıştır. PM3 yöntemi kullanılarak yapılan kuantum kimyasal hesaplamalar, formononetinin yüksek kimyasal stabiliteye ve düşük reaktiviteye sahip olduğunu, geniş bir HOMO-LUMO enerji aralığı (ΔE = 8.319 eV), yüksek elektronegatiflik (4.748 eV) ve kimyasal sertlik (4.160 eV) gösterdiğini ortaya koymuştur. Yağ kütlesi ve obezite ile ilişkili protein (FTO) üzerinde yapılan moleküler yerleştirme simülasyonları, −7.70 kcal/mol'lük bir bağlanma afinitesi göstermiş, hidrofobik etkileşimler, hidrojen bağları ve π-katyon etkileşimleri kararlı ligand-protein kompleksine katkıda bulunmuştur. ADME analizi, formononetinin yüksek gastrointestinal emilim, orta düzeyde lipofilite ve ilaç benzeri kurallara uyum gibi olumlu ilaç benzeri özellikler sergilediğini göstermiştir. Ancak, düşük suda çözünürlüğü ve P-glikoprotein efflüksü potansiyeli daha fazla optimizasyon gerektirebilir. Genel olarak, bu çalışma formononetinin anti-obezite ajanı olarak potansiyelini vurgulamakta ve hesaplamalı yaklaşımlar kullanarak doğal ürün bazlı obezite terapötiklerinin keşfi için teorik olarak temellendirilmiş bir çerçeve sunmaktadır.

References

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In Silico Evaluation of Formononetin as a Potential Anti-Obesity Agent: Quantum Chemical and Docking Insights

Year 2025, Volume: 8 Issue: 2, 61 - 70, 29.12.2025
https://doi.org/10.46239/ejbcs.1807471

Abstract

Obesity is a growing global health concern and a major risk factor for various chronic diseases. This study employed a range of in silico computational approaches to evaluate the potential anti-obesity effects of formononetin, a natural bioactive compound. Quantum chemical analyses indicated that formononetin possesses a stable electronic structure and is well-suited for interactions with biological targets. Molecular docking results revealed that formononetin exhibits strong and favourable binding interactions with the ALKBH5 enzyme, which plays a role in epigenetic mechanisms associated with obesity. Additionally, the ADME assessment revealed that formononetin exhibits drug-like properties and high gastrointestinal absorption, although certain limitations related to solubility and transport mechanisms may impact its bioavailability. Overall, the findings suggest that formononetin is a promising candidate for managing metabolic disorders and reinforce the therapeutic potential of natural compounds in multi-targeted obesity treatments.

References

  • Adasme MF, Linnemann KL, Bolz SN, Kaiser F, Salentin S, Haupt VJ, Schroeder M. 2021. PLIP 2021: expanding the scope of the protein-ligand interaction profiler to DNA and RNA. Nucleic Acids Res. 49:W530–W534. doi:10.1093/nar/gkab294
  • BIOVIA Discovery Studio Visualizer, version 21.1.0.20298. Dassault Systèmes, San Diego, CA. 2021.
  • Chattaraj PK, Maiti B, Sarkar U. 2003. Philicity: a unified treatment of chemical reactivity and selectivity. J Phys Chem A. 107:4973–4975.
  • Choudhari S, Patil SK, Rathod S. 2024. Identification of hits as anti-obesity agents against human pancreatic lipase via docking, drug-likeness, in-silico ADME(T), pharmacophore, DFT, molecular dynamics, and MM/PB(GB)SA analysis. J Biomol Struct Dyn. 42:10688–10710. doi:10.1080/07391102.2023.2258407
  • Çakmak Ş, Aycan T, Yakan H, Veyisoğlu A, Tanak H, Evecen M. 2023. Preparation, spectroscopic, X-ray crystallographic, DFT, antimicrobial and ADMET studies of N-[(4-fluorophenyl)sulfanyl]phthalimide. Cryst Struct Commun. 79:249–256.
  • Daina A, Michielin O, Zoete V. 2017. SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci Rep. 7(1):42717.
  • Dewar MJS, Zoobisch EG, Healy EF, Stewart JJP. 1985. AM1: A new general purpose quantum mechanical molecular model. J Am Chem Soc. 107:3902–3910.
  • Han B, Isborn CM, Shi L. 2021. Determining partial atomic charges for liquid water: assessing electronic structure and charge models. J Chem Theory Comput. 17(2):889–901. doi:10.1021/acs.jctc.0c01102 Hız Çiçekliyurt MM, Dalyancı A. 2023. In silico interaction of Rhamnus’ flavonoids with fat mass and obesity associated protein. Eur J Sci Technol. 49:50–54. doi:10.31590/ejosat.1260495
  • Huzinaga S, Narita S, Sakai Y, Miyoshi E. 1990. Extended Mulliken electron population analysis. J Chem Phys. 93(5):3319–3325. doi:10.1063/1.458812
  • iLOGP: a simple, robust, and efficient description of n-octanol/water partition coefficient for drug design using the GB/SA approach. J. Chem. Inf. Model. (2014) 54(12):3284-3301.
  • İşcan Ö. 2023. An in silico study on structural aspects of caffeine by ArgusLab 4 software. J Phys Chem Funct Mater. 6(2):138–144. doi:10.54565/jphcfum.1402117
  • İşcan Ö. 2024. A hypothetical study on structural properties of limonene compounds using the semi-empirical (PM3) method with ArgusLab software. Eurasian J Biol Chem Sci. 7(2):157–164. doi:10.46239/ejbcs.1558302
  • Jug K. 1973. A new definition of atomic charges in molecules. Theor Chim Acta. 31(1):63–73. doi:10.1007/bf00527439
  • Kumar P, Bhardwaj VK, Purohit R. 2024. Molecular and quantum mechanical insights of conformational dynamics of Maltosyl-β-Cyclodextrin/Formononetin supramolecular complexes. J Mol Liq. 397:124196. doi:10.1016/j.molliq.2024.124196
  • Lipinski CA. 2004. Lead- and drug-like compounds: the rule-of-five revolution. Drug Discov Today Technol. 1(4):337–341.
  • Öztürk F, Aycan T. 2023. Investigation of spectroscopic properties of copper(II)–sulfamethazine-2,2'-bipyridine complex by computational chemistry method: a molecular modeling and ADME/T study. Sinop Univ J Nat Sci. 8:39–64.
  • Parr RG, Donnelly RA, Levy M, Palke WE. 1978. Electronegativity: the density functional viewpoint. J Chem Phys. 68:3801–3807.
  • Parr RG, Pearson RG. 1983. Absolute hardness: companion parameter to absolute electronegativity. J Am Chem Soc. 105:7512–7516.
  • Parr RG, Szentpály LV, Liu S. 1999. Electrophilicity index. J Am Chem Soc. 121:1922–1924.
  • PubChem. 2025. http://pubchem.ncbi.nlm.nih.gov. Accessed 06 May 2025.
  • Srivastava HK, Pasha FA, Singh PP. 2005. Atomic softness-based QSAR study of testosterone. Int J Quantum Chem. 103:237–245. Stewart JJP. 1989. Comp Chem. 10:209–220; 221–264.
  • SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci. Rep. (2017) 7:42717.
  • Thompson MA. 1996. J Phys Chem. 100:14492–14507.
  • Thompson MA. 2004. Molecular docking using ArgusLab, an efficient shape-based search algorithm and the AScoring function. ACS Meeting Philadelphia 172, CINF 42, PA.
  • Thompson MA, Glendening ED, Feller D. 1994. J Phys Chem. 98:10465–10476.
  • Thompson MA, Schenter GK. 1995. J Phys Chem. 99:6374–6386.
There are 26 citations in total.

Details

Primary Language English
Subjects Bioinformatic Methods Development, Theoretical and Computational Chemistry (Other)
Journal Section Research Article
Authors

Özlem İşcan 0000-0003-3282-1121

Submission Date October 20, 2025
Acceptance Date November 26, 2025
Publication Date December 29, 2025
Published in Issue Year 2025 Volume: 8 Issue: 2

Cite

APA İşcan, Ö. (2025). In Silico Evaluation of Formononetin as a Potential Anti-Obesity Agent: Quantum Chemical and Docking Insights. Eurasian Journal of Biological and Chemical Sciences, 8(2), 61-70. https://doi.org/10.46239/ejbcs.1807471
AMA İşcan Ö. In Silico Evaluation of Formononetin as a Potential Anti-Obesity Agent: Quantum Chemical and Docking Insights. Eurasian J. Bio. Chem. Sci. December 2025;8(2):61-70. doi:10.46239/ejbcs.1807471
Chicago İşcan, Özlem. “In Silico Evaluation of Formononetin As a Potential Anti-Obesity Agent: Quantum Chemical and Docking Insights”. Eurasian Journal of Biological and Chemical Sciences 8, no. 2 (December 2025): 61-70. https://doi.org/10.46239/ejbcs.1807471.
EndNote İşcan Ö (December 1, 2025) In Silico Evaluation of Formononetin as a Potential Anti-Obesity Agent: Quantum Chemical and Docking Insights. Eurasian Journal of Biological and Chemical Sciences 8 2 61–70.
IEEE Ö. İşcan, “In Silico Evaluation of Formononetin as a Potential Anti-Obesity Agent: Quantum Chemical and Docking Insights”, Eurasian J. Bio. Chem. Sci., vol. 8, no. 2, pp. 61–70, 2025, doi: 10.46239/ejbcs.1807471.
ISNAD İşcan, Özlem. “In Silico Evaluation of Formononetin As a Potential Anti-Obesity Agent: Quantum Chemical and Docking Insights”. Eurasian Journal of Biological and Chemical Sciences 8/2 (December2025), 61-70. https://doi.org/10.46239/ejbcs.1807471.
JAMA İşcan Ö. In Silico Evaluation of Formononetin as a Potential Anti-Obesity Agent: Quantum Chemical and Docking Insights. Eurasian J. Bio. Chem. Sci. 2025;8:61–70.
MLA İşcan, Özlem. “In Silico Evaluation of Formononetin As a Potential Anti-Obesity Agent: Quantum Chemical and Docking Insights”. Eurasian Journal of Biological and Chemical Sciences, vol. 8, no. 2, 2025, pp. 61-70, doi:10.46239/ejbcs.1807471.
Vancouver İşcan Ö. In Silico Evaluation of Formononetin as a Potential Anti-Obesity Agent: Quantum Chemical and Docking Insights. Eurasian J. Bio. Chem. Sci. 2025;8(2):61-70.