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Keywords: computer-assisted drug design, CADD, computer-assisted drug design, furin inhibitors, protease inhibitors, antivirals, protease inhibitors, furin assay, antiviral drug design
Published in DKUM: 20.03.2025; Views: 0; Downloads: 0
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Keywords: molecular dynamics simulations, personalized therapy, single nucleotide polymorphisms, SNPs, linear interaction energy, LIE, multiple sclerosis, MS
Published in DKUM: 03.02.2025; Views: 0; Downloads: 3
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Abstract: This study explores the antioxidative activities of xanthohumol (XN) and isoxanthohumol (IXN), prenylated flavonoids from Humulus lupulus (family Cannabaceae), utilizing the oxygen radical absorption capacity (ORAC) and ferric reducing antioxidant power (FRAP) assays along with computational Density Functional Theory methods. Experimentally, XN demonstrated significantly higher antioxidative capacities than IXN. Moreover, we determined IXN pKa values using the UV/Vis spectrophotometric method for the first time, facilitating its accurate computational modeling under physiological conditions. Through a thermodynamic approach, XN was found to efficiently scavenge HOO• and CH3O• radicals via Hydrogen Atom Transfer (HAT) and Radical Adduct Formation (RAF) mechanisms, while CH3OO• scavenging was feasible only through the HAT pathway. IXN exhibited its best antioxidative activity against CH3O• via both HAT and RAF mechanisms and could also scavenge HOO• through RAF. Both Single Electron Transfer (SET) and Sequential Proton Loss-Electron Transfer (SPLET) mechanisms were thermodynamically unfavorable for all radicals and both compounds.
Keywords: antioxidative activity, bio-active membranes, xanthohumol, isoxanthohumol, ORAC and FRAP assays, pKa determination, density functional theory, DFT
Published in DKUM: 31.01.2025; Views: 0; Downloads: 4
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Abstract: The aim of the Master’s thesis was to evaluate the current and potential applications of virtual reality technology in chemistry and chemical engineering, as well as to evaluate the use of virtual reality for educational purposes. First, we made an overview of the numerous applications of the virtual reality technology with a specific focus on its current use in the chemistry and chemical engineering fields, including research and educational environments as well as industrial applications. It was found that the use of virtual reality technology is growing in all areas, with training, remote collaboration, and interactive learning being the most prominent fields. To assess the effectiveness of virtual reality as an educational tool, we performed a study with second year students of Chemistry and Chemical Engineering programs at the Faculty of Chemistry and Chemical Engineering, University of Maribor. Students were divided into two groups, one undertaking a training on the proper use of fume hoods in virtual reality and the other group performing the same training in a real chemical laboratory. Students from both groups took a knowledge evaluation test and a personal experience survey after the training. The test results have shown that virtual reality can be just as effective or potentially even more effective than conventional training in the chemical laboratory. The average score of the virtual reality group was 2.5% higher than that of the group performing conventional training in a chemical laboratory, although we did not confirm a statistically significant difference between the scores. We also prepared a personal experience survey to evaluate the students’ personal experience and interest in using virtual reality as an educational tool. It was observed that there is a lot of enthusiasm from the students for the use of virtual reality technology and that the group performing the training in virtual reality reported a significantly better subjective experience scores, and due to fewer reported distractions remained more focused on the training content compared to the group that underwent the training in a real chemical laboratory. The results of the Master’s thesis suggest that virtual reality presents an effective alternative to traditional live training methods. Future research should be conducted with larger groups focusing especially on the long-term retention of the acquired knowledge and on the application in real-world scenarios, such as laboratory exercises, device training, and safety procedures training, to fully reveal the potential of virtual reality for educational purposes.
Keywords: virtual reality technology, Meta Quest, correct use of fume hoods in virtual reality, correct use of fume hoods in a chemical laboratory, R programming language
Published in DKUM: 20.11.2024; Views: 0; Downloads: 0

Abstract: V doktorski disertaciji smo s pomočjo najsodobnejših računalniških metod simulacij molekulske dinamike, nevronskih mrež in molekulskega sidranja preučevali in pojasnili sekundarno strukturo proteinov pod vplivom specifičnih mutacij, strukturo proteinov pod vplivom mikrovalovnega sevanja, napovedovali dihedralne kote fi in psi proteinskega ogrodja in analizirali vlogo nevropilinov pri različnih fizioloških in patoloških procesih. V prvem delu doktorske disertacije smo s pomočjo simulacij molekulske dinamike podrobno preučili vpliv polimorfizma rs4880 (mutacija Ala16Val) na sekundarno strukturo mitohondrijske tarčne sekvence človeškega encima mangan superoksidne dismutaze. Simulacije so pokazale, da alaninska varianta ohranja stabilno α-heliksno strukturo, kar je ugodno za pravilen transport v mitohondrije. Nasprotno pa se α-heliks valinske variante razgradi, kar vodi do tvorbe β-lista in s tem potencialno moti transport. Naši rezultati podpirajo predhodne eksperimentalne ugotovitve, da ima alaninska verzija višjo aktivnost tega encima v mitohondrijih. Ugotovitve pomembno prispevajo k razumevanju povezave med strukturo in funkcijo mitohondrijske tarčne sekvence ter vpliva polimorfizma Ala16Val na aktivnost manganove superoksidne dismutaze. V drugem delu doktorske disertacije smo razvili enostaven model globokega učenja za napovedovanje dihedralnih kotov fi (ϕ) in psi (ψ) proteinskega ogrodja zgolj na podlagi primarne strukture beljakovin. Model popolnoma povezanega nevronskega omrežja z drsečim oknom velikosti 21 aminokislinskih ostankov je dosegel zadovoljivo natančnost pri napovedovanju ϕ kotov in nekoliko nižjo, a še vedno sprejemljivo natančnost pri napovedovanju ψ kotov. Pokazali smo, da je mogoče tudi z enostavnim modelom nevronskih mrež doseči visoko natančnost pri napovedovanju dihedralnih kotov proteinskega ogrodja. V tretjem delu doktorske disertacije smo s pristopom molekularne dinamike preučevali vpliv mikrovalovnega sevanja na zvijanje beljakovin in možnost napačnega zvitja. Rezultati so pokazali, da mikrovalovno segrevanje povzroči pomik proti bolj kompaktnim konformacijam proteinov, kar se odraža v predvsem v manjših radijih sukanja. Mikrovalovno sevanje pa ni imelo večjega vpliva na sekundarne strukture beljakovin na skali 200 nanosekund. Naše delo predstavlja pomemben prispevek k razumevanju posledic izpostavljenosti beljakovin mikrovalovnemu sevanju. V četrtem delu doktorske disertacije smo temeljito raziskali vlogo nevropilinov v različnih fizioloških in patoloških procesih, kot so COVID-19, rak, nevropatska bolečina, srčno-žilne bolezni in diabetes. Pregledali smo terapevtske možnosti modulacije nevropilinov in predstavili serijo antagonistov, znanih kot zaviralcev signalizacije VEGF-A in rasti tumorjev. Ugotovitve predstavljajo trdne temelje za nadaljnji razvoj učinkovitih zdravil za klinično uporabo, s poudarkom na majhnih molekulskih antagonistih. Disertacija predstavlja izvirni znanstveni prispevek na področju molekularnega modeliranja, globokega učenja in strukturne biologije z neposredno uporabnostjo pri razumevanju in zdravljenju različnih bolezni ter razvoju terapevtskih strategij.
Keywords: molekulska dinamika, nevronske mreže, struktura proteinov, dihedralni koti, mikrovalovno sevanje, nevropilini
Published in DKUM: 09.10.2024; Views: 0; Downloads: 38
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