Preučevanje polifenolov iz timijana kot modulatorjev receptorja PPARγ s pomočjo molekulskega sidranja in simulacij molekulske dinamike

Pantner, Ana Lee

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Title:	Preučevanje polifenolov iz timijana kot modulatorjev receptorja PPARγ s pomočjo molekulskega sidranja in simulacij molekulske dinamike
Authors:	ID Pantner, Ana Lee (Author) ID Bren, Urban (Mentor) More about this mentor... ID Furlan, Veronika (Comentor)
Files:	VS_Pantner_Ana_Lee_2026.pdf (2,07 MB) MD5: 93DC335A69E3429D1E125FB60DCC502A
Language:	Slovenian
Work type:	Bachelor thesis/paper
Typology:	2.11 - Undergraduate Thesis
Organization:	FKKT - Faculty of Chemistry and Chemical Engineering
Abstract:	Diplomsko delo obravnava luteolin, polifenol iz timijana (Thymus vulgaris), kot potencialni modulator jedrnega receptorja PPARγ . Receptor PPARγ ima ključno vlogo pri uravnavanju presnove glukoze in lipidov, zato predstavlja pomembno tarčo pri zdravljenju sladkorne bolezni tipa 2. Sintetični agonisti PPARγ sicer učinkovito povečajo občutljivost na inzulin, vendar so povezani z resnimi stranskimi učinki, med katerimi so povečanje telesne mase, edemi in srčno-žilni zapleti. Naravni polifenoli kot selektivni modulatorji PPARγ tako predstavljajo bolj varno alternativo. V diplomskem delu smo za preučevanje vezave luteolina na ligand-vezavno domeno PPARγ uporabili sodobne računalniške metode, ki vključujejo molekulsko sidranje, simulacije molekulske dinamike in metodo linearne interakcijske energije (LIE). Molekulsko sidranje smo izvedli s programom CmDock, simulacije molekulske dinamike dolžine 200 ns pa z programom NAMD na superračunalniku HPC Vega. Trajektorije smo analizirali s programoma VMD in PyMol, vezavno prosto energijo pa smo izračunali z metodo LIE z empiričnima parametroma α = 0,18 in β = 0,33. Rezultati kažejo, da se luteolin verjetno veže na receptor PPARγ. Ugotovili smo, da je kompleks luteolin-PPARγ med simulacijo molekulske dinamike stabilen ter da luteolin tvori ključne medmolekulske interakcije z aminokislinskimi preostanki na vezavnem mestu receptorja. Na podlagi negativne vrednosti vezavne proste energije sklepamo, da bi luteolin lahko deloval kot selektivni modulator PPARγ.
Keywords:	PPARγ, polifenoli, luteolin, timijan, molekulsko sidranje, molekulska dinamika
Place of publishing:	Maribor
Year of publishing:	2026
PID:	20.500.12556/DKUM-99645
Publication date in DKUM:	14.09.2026
Views:	249
Downloads:	7
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Categories:	KTFMB - FKKT
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Licences

License:	CC BY-NC-ND 4.0, Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International

Link:	http://creativecommons.org/licenses/by-nc-nd/4.0/
Description:	The most restrictive Creative Commons license. This only allows people to download and share the work for no commercial gain and for no other purposes.
Licensing start date:	21.08.2026

Secondary language

Language:	English
Title:	Investigation of thyme polyphenols as modulators of the receptor PPARγ using molecular docking and molecular dynamics simulations
Abstract:	This diploma thesis investigates luteolin, a polyphenol from thyme (Thymus vulgaris), as a potential modulator of the receptor PPARγ. PPARγ plays a key role in regulating glucose and lipid metabolism and, therefore, represents an important therapeutic target in the treatment of type 2 diabetes. Synthetic PPARγ agonists effectively enhance insulin sensitivity, however, they are associated with serious side effects, including weight gain, oedema, and cardiovascular complications. Naturally occurring polyphenols s thus represent a safer alternative as selective PPARγ modulators. To investigate the binding of luteolin to the PPARγ ligand-binding domain, we employed modern computational techniques, including molecular docking, molecular dynamics simulations, and the Linear Interaction Energy (LIE) method. Molecular docking was performed using CmDock, while 200 ns molecular dynamics simulations were conducted using NAMD on the HPC Vega supercomputer. Trajectories were analysed in VMD and PyMOL, and the binding free energy was calculated using the LIE method with empirical parameters α = 0.18 and β = 0.33. The results indicate that luteolin likely binds to PPARγ. We found that the luteolin–PPARγ complex remains stable throughout the molecular dynamics simulation and that luteolin forms specific intermolecular interactions within the receptor binding site amino-acid residues. Based on the negative binding free energy value, we conclude that luteolin may act as a selective PPARγ modulator.
Keywords:	PPARγ, polyphenols, lutheolin, thyme, molecular docking, molecular dynamics

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