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1.
Application of Virtual Reality in Chemistry and Chemical Engineering : magistrsko delo
Maj Virant, 2024, magistrsko delo

Opis: 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.
Ključne besede: 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
Objavljeno v DKUM: 20.11.2024; Ogledov: 0; Prenosov: 0

2.
QM-CSA: a novel quantum mechanics-based protocol for evaluation of the carcinogen-scavenging activity of polyphenolic compounds
Veronika Furlan, Jelena Tošović, Urban Bren, 2024, izvirni znanstveni članek

Opis: In this study, a novel quantum mechanics-based protocol for the evaluation of carcinogenscavenging activity (QM-CSA) is developed. The QM-CSA protocol represents a universal and quantitative approach to evaluate and compare the activation-free energies for alkylation reactions between individual polyphenolic compounds and chemical carcinogens of the epoxy type at physiological conditions by applying two scales: the absolute scale allowing for the comparison with guanine and the relative scale allowing the comparison with glutathione as a reference compound. The devised quantum mechanical methodology was validated by comparing the activation-free energies calculated with 14 DFT functionals in conjunction with two implicit solvation models (SMD and CPCM) and the experimental activation-free energies for reactions between nine investigated chemical carcinogens and guanine. According to the obtained results, the best agreement with experimental data was achieved by applying DFT functionals M11-L and MN12-L in conjunction with the flexible 6-311++G(d,p) basis set and implicit solvation model SMD, and the obtained uncertainties were proven to be similar to the experimental ones. To demonstrate the applicability of the QM-CSA protocol, functionals M11-L, and MN12-L in conjunction with the SMD implicit solvation model were applied to calculate activation-free energies for the reactions of nine investigated chemical carcinogens of the epoxy type with three catechins, namely EGCG, EGC, and (+)-catechin. The order of CSA in this series of catechins in comparison to guanine and glutathione was determined as (+)-catechin > EGC > EGCG. The obtained results, for the first time, demonstrated the evaluation and comparison of CSA in a series of selected catechins with respect to glutathione and guanine. Moreover, the presented results provide valuable insights into the reaction mechanisms and configurations of the corresponding transition states. The novel QM-CSA protocol is also expected to expand the kinetic data for alkylation reactions between various polyphenolic compounds and chemical carcinogens of the epoxy type, which is currently lacking in the scientific literature
Ključne besede: activation-free energies, chemical carcinogens, polyphenols, guanine, glutathione, quantum mechanical calculations, M11-L and MN12-L DFT functionals
Objavljeno v DKUM: 04.09.2024; Ogledov: 39; Prenosov: 11
.pdf Celotno besedilo (10,13 MB)

3.
4.
Novel coumarin-6-sulfonamide-chalcone hybrids as glutathione transferase P1-1 inhibitors
Ahmed Sabt, Veronika Furlan, Urban Bren, 2024, izvirni znanstveni članek

Objavljeno v DKUM: 20.08.2024; Ogledov: 48; Prenosov: 14
.pdf Celotno besedilo (1,29 MB)

5.
Računalniško modeliranje antikarcinogenih učinkov naringenina : diplomsko delo univerzitetnega študijskega programa I. stopnje
Lamija Ahmetović, 2024, diplomsko delo

Opis: Naringenin je biološko aktiven polifenol iz citrusov z različnimi koristnimi učinki za človeško zdravje. Nedavna znanstvena literatura poroča, da naringenin lahko zavira razvoj in napredovanje tumorjev, kar kaže na njegov potencial za zdravljenje različnih vrst raka. To diplomsko delo je osredotočeno na naringenin v vlogi polifenolnega lovilca devetih končnih kemijskih karcinogenov, in sicer aflatoksin B1 ekso-8,9-epoksida, 2-cianoetilen oksida, etilen oksida, glicidamida, kloroetilen oksida, vinilkarbamat epoksida, stiren oksida, propilen oksida in β-propiolaktona. Cilj je izračunati aktivacijske proste energije in razjasniti molekularne mehanizme reakcij alkilacije naringenina z obravnavanimi genotoksičnimi kemijskimi karcinogeni z uporabo kvantno-mehanske metode Hartree-Fock v kombinaciji z dvema fleksibilnima baznima setoma 6-31G(d) in 6-311++G(d,p). Izračune aktivacijskih prostih energij smo izvedli na superračunalniški gruči VRANA s programom Gaussian 09 v vakuumu in z uporabo dveh implicitnih modelov topil: modela polarizabilnega kontinuuma in Langevinovih dipolov. Za oceno učinkovitosti naringenina kot polifenolnega lovilca smo izračunane aktivacijske proste energije v kombinaciji z modeli topil primerjali z eksperimentalnimi vrednostmi aktivacijskih prostih energij med istimi končnimi kemijskimi karcinogeni in najbolj reaktivno DNK bazo gvaninom. Rezultati kažejo na učinkovitost naringenina kot polifenolnega lovilca šestih končnih kemijskih karcinogenov, pri čemer najbolj izstopajo β-propiolakton, vinilkarbamat epoksid in propilen oksid. Znaten antikarcinogeni potencial je naringenin izkazal tudi kot lovilec kloroetilen oksida, aflatoksin B1-ekso-8,9-epoksida in etilen oksida, v primeru katerih so bile izračunane aktivacijske proste energije podobne z eksperimentalno določenimi vrednostmi. V primeru 2-cianoetilen oksida, glicidamida in stiren oksida zaščitne lastnosti naringenina niso tako izrazite, saj so bile izračunane aktivacijske proste energije višje v primerjavi z eksperimentalno določenimi vrednostmi za gvanin. Trdno verjamemo, da je diplomsko delo razjasnilo zapletene molekularne mehanizme naringenina in bo imelo velik vpliv na nadaljnje računalniške in eksperimentalne študije njegovih antikarcinogenih učinkov.
Ključne besede: naringenin, flavanoni, končni kemijski karcinogeni, aktivacijske proste energije, kvantno-mehanski izračuni, metoda Hartree-Fock, implicitni solvatacijski modeli
Objavljeno v DKUM: 15.07.2024; Ogledov: 145; Prenosov: 80
.pdf Celotno besedilo (4,21 MB)

6.
Helichrysum italicum : From Extraction, Distillation, and Encapsulation Techniques to Beneficial Health Effects
Veronika Furlan, Urban Bren, 2023, pregledni znanstveni članek

Opis: Helichrysum italicum (family Asteraceae), due to its various beneficial health effects, represents an important plant in the traditional medicine of Mediterranean countries. Currently, there is a renewed interest in this medicinal plant, especially in investigations involving the isolation and identification of its bioactive compounds from extracts and essential oils, as well as in experimental validation of their pharmacological activities. In this paper, we review the current knowledge on the beneficial health effects of Helichrysum italicum extracts, essential oils, and their major bioactive polyphenolic compounds, ranging from antioxidative, anti-inflammatory, and anticarcinogenic activities to their antiviral, antimicrobial, insecticidal, and antiparasitic effects. This review also provides an overview of the most promising extraction and distillation techniques for obtaining high-quality extracts and essential oils from Helichrysum italicum, as well as methods for determining their antioxidative, antimicrobial, anti-inflammatory, and anticarcinogenic activities. Finally, new ideas for in silico studies of molecular mechanisms of bioactive polyphenols from Helichrysum italicum, together with novel suggestions for their improved bioavailability through diverse encapsulation techniques, are introduced.
Ključne besede: Helichrysum italicum, polyphenolic compounds, biological effects, extraction methods, distillation methods, encapsulation methods
Objavljeno v DKUM: 15.03.2024; Ogledov: 327; Prenosov: 13
.pdf Celotno besedilo (2,78 MB)
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7.
Monocarbonyl Curcumin Analogues as Potent Inhibitors against Human Glutathione Transferase P1-1
Panagiota D. Pantiora, Veronika Furlan, Dimitris Matiadis, Barbara Mavroidi, Fereniki Perperopoulou, Anastassios C. Papageorgiou, Marina Sagnou, Urban Bren, Maria Pelecanou, Nikolaos E. Labrou, 2023, izvirni znanstveni članek

Opis: The isoenzyme of human glutathione transferase P1-1 (hGSTP1-1) is involved in multi-drug resistance (MDR) mechanisms in numerous cancer cell lines. In the present study, the inhibition potency of two curcuminoids and eleven monocarbonyl curcumin analogues against hGSTP1-1 was investigated. Demethoxycurcumin (Curcumin II) and three of the monocarbonyl curcumin analogues exhibited the highest inhibitory activity towards hGSTP1-1 with IC50 values ranging between 5.45 1.08 and 37.72 1.02 M. Kinetic inhibition studies of the most potent inhibitors demonstrated that they function as non-competitive/mixed-type inhibitors. These compounds were also evaluated for their toxicity against the prostate cancer cells DU-145. Interestingly, the strongest hGSTP1-1 inhibitor, (DM96), exhibited the highest cytotoxicity with an IC50 of 8.60 1.07 M, while the IC50 values of the rest of the compounds ranged between 44.59–48.52 M. Structural analysis employing molecular docking, molecular dynamics (MD) simulations, and binding-free-energy calculations was performed to study the four most potent curcumin analogues as hGSTP1-1 inhibitors. According to the obtained computational results, DM96 exhibited the lowest binding free energy, which is in agreement with the experimental data. All studied curcumin analogues were found to form hydrophobic interactions with the residue Gln52, as well as hydrogen bonds with the nearby residues Gln65 and Asn67. Additional hydrophobic interactions with the residues Phe9 and Val36 as well as – stacking interaction with Phe9 contributed to the superior inhibitory activity of DM96. The van derWaals component through shape complementarity was found to play the most important role in DM96-inhibitory activity. Overall, our results revealed that the monocarbonyl curcumin derivative DM96 acts as a strong hGSTP1-1 inhibitor, exerts high prostate cancer cell cytotoxicity, and may, therefore, be exploited for the suppression and chemosensitization of cancer cells. This study provides new insights into the development of safe and effective GST-targeted cancer chemosensitizers.
Ključne besede: curcuminoids, curcumin analogues, human glutathione transferase P1-1 (hGSTP1-1), glutathione transferase, enzyme inhibition, multi-drug resistance
Objavljeno v DKUM: 12.03.2024; Ogledov: 288; Prenosov: 13
.pdf Celotno besedilo (3,54 MB)
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8.
The effect of the Ala16Val mutation on the secondary structure of the manganese superoxide dismutase mitochondrial targeting sequence
Matic Broz, Veronika Furlan, Samo Lešnik, Marko Jukič, Urban Bren, 2022, izvirni znanstveni članek

Opis: Manganese Superoxide Dismutase (MnSOD) represents a mitochondrial protein that scavenges reactive oxygen species (ROS) responsible for oxidative stress. A known single nucleotide polymorphism (SNP) rs4880 on the SOD2 gene, causing a mutation from alanine to valine (Ala16Val) in the primary structure of immature MnSOD, has been associated with several types of cancer and other autoimmune diseases. However, no conclusive correlation has been established yet. This study aims to determine the effect of the alanine to valine mutation on the secondary structure of the MnSOD mitochondrial targeting sequence (MTS). A model for each variant of the MTS was prepared and extensively simulated with molecular dynamics simulations using the CHARMM36m force field. The results indicate that the alanine variant of the MTS preserves a uniform α-helical secondary structure favorable for the protein transport into mitochondria, whereas the valine variant quickly breaks down its α-helix. Thus, the alanine MTS represents the more active MnSOD variant, the benefits of which have yet to be determined experimentally.
Ključne besede: manganese superoxide dismutase, polymorphism rs4880, mutation Ala16Val, molecular dynamics simulations, oxidative stress
Objavljeno v DKUM: 21.08.2023; Ogledov: 370; Prenosov: 16
.pdf Celotno besedilo (5,14 MB)
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9.
Preučevanje mehanizmov antikarcinogenega in nevroprotektivnega delovanja naravnih polifenolnih spojin : doktorska disertacija
Veronika Furlan, 2022, doktorska disertacija

Opis: Namen doktorske disertacije je z uporabo inovativnih računalniških pristopov preučiti in pojasniti slabo raziskane molekularne mehanizme antikarcinogenega in nevroprotektivnega delovanja naravnih polifenolnih spojin v vlogi preprečevalcev nastanka raka ter v vlogi zaviralcev napredovanja karcinogeneze in Alzheimerjeve bolezni. V prvem delu doktorske disertacije smo z uporabo kvantomehanskih simulacij obravnavali polifenol [6]-gingerol in tripeptid glutation v vlogi lovilcev devetih genotoksičnih kemijskih karcinogenenov ter tako kot prvi omogočili dragocen vpogled v pripadajoče geometrije reaktantov in prehodnih stanj, ki potrjujejo veljavnost predpostavljenega SN2 reakcijskega mehanizma. Predstavljena kvantnomehanska metodologija ima velik potencial, da postane standardno orodje za napovedovanje kemozaščitnega potenciala številnih polifenolnih spojin v vlogi lovilcev kemijskih karcinogenov epoksidnega tipa. V drugem delu doktorske disertacije smo s kvantnomehansko obravnavo ksantohumola iz hmelja in njegovih derivatov izoksantohumola, 8-prenilnaringenina in 6-prenilnaringenina v vlogi lovilcev aflatoksin B1 ekso-8,9-epoksida razkrili povezavo med strukturo in antikarcinogeno aktivnostjo izbranih prenilflavonoidov ter potrdili veljavnost predpostavljenega SN2 reakcijskega mehanizma. Znižanje z aflatoksinom B1 inducirane citotoksičnosti in genotoksičnosti je bilo potrjeno tudi in vitro na celicah človeškega hepatoma HepG2 po dodatku ksantohumola. V tretjem delu doktorske disertacije smo razvili popolnoma nov protokol za inverzno molekulsko sidranje, s pomočjo katerega je mogoče identificirati zožen nabor najbolj verjetnih tarčnih človeških proteinov izbrane polifenolne spojine. Na podlagi afinitete izbranega polifenola kurkumina za vezavo na specifične človeške proteine, ki sodelujejo v onkogenih in nevrodegenerativnih signalnih kaskadah, smo kot prvi uspešno razkrili mehanizme njegovega antikarcinogenega in nevroprotektivnega delovanja. Predstavljeni protokol inverznega molekulskega sidranja ima velik potencial v farmacevtskih aplikacijah, saj gre za univerzalen pristop, s pomočjo katerega lahko predvidimo proteinske tarče in pojasnimo že opažene ter napovemo nove potencialne biološke učinke izbranih spojin vodnic. V četrtem delu doktorske disertacije smo z uporabo molekulskega sidranja, simulacij molekulske dinamike in prostoenergijskih izračunov preučevali štiri prehranske polifenole kot potencialne inhibitorje encima fosfodiesteraza 4D, ki predstavlja validirano terapevtsko tarčo za zdravljenje Alzheimerjeve bolezni. Izračunane vezavne proste energije potrjujejo, da kurkumin, [6]-gingerol, kapsaicin in resveratrol predstavljajo potencialne inhibitorje encima fosfodiesteraza 4D, pri čemer ima kurkumin največji inhibitorni potencial. S kombiniranim računalniškim pristopom smo tako prvič dobili mehanistični vpogled v povezavo med strukturo in nevroprotektivnim delovanjem štirih preučevanih polifenolov, ki je eksperimentu nedosegljiv. V petem delu doktorske disertacije smo predstavili ekstrakcijske, destilacijske in karakterizacijske metode za pridobivanje visoko kvalitetnih bioaktivnih ekstraktov, eteričnih olj in posameznih polifenolnih spojin iz rožmarina ter metode za določanje njihovega antioksidativnega, antimikrobnega, protivnetnega in antikarcinogenega potenciala. S temeljitim pregledom obstoječih raziskav in z usmeritvami za nadaljnje raziskave smo postavili temelje za uspešne aplikacije ekstraktov, eteričnih olj ter številnih polifenolnih spojin iz rožmarina v farmacevtski in prehranski industriji. Trdno verjamemo, da v doktorski disertaciji predstavljeni in silico pristopi in razkriti inhibitorni mehanizmi tvorijo izhodišče za hitrejši in cenejši razvoj novih funkcionalnih prehranskih dopolnil in zdravil za preprečevanje in zdravljenje raka ter Alzheimerjeve bolezni s potencialno širšim terapevtskim oknom in manjšimi stranskimi učinki.
Ključne besede: Polifenoli, antikarcinogeno delovanje, nevroprotektivno delovanje, molekularni mehanizmi, kvantna mehanika, inverzno molekulsko sidranje, molekulska dinamika, prostoenergijski izračuni
Objavljeno v DKUM: 04.07.2022; Ogledov: 871; Prenosov: 186
.pdf Celotno besedilo (29,80 MB)

10.
Pinocembrin iz medu kot potencialni lovilec kemijskih karcinogenov - računalniški pristop : diplomsko delo visokošolskega strokovnega študijskega programa I. stopnje
Urška Vtič, 2021, diplomsko delo

Opis: V diplomskem delu smo preučevali pinocembrin iz medu v vlogi lovilca končnih kemijskih karcinogenov s pomočjo kvantnomehanskih simulacij. Obravnavali smo devet končnih kemijskih karcinogenov: 2-cianoetilen oksid, aflatoksin B1-ekso-8,9-epoksid, β-propiolakton, etilen oksid, kloroetilen oksid, glicidamid, propilen oksid, stiren oksid in vinil karbamat epoksid. S pomočjo kvantnomehanskih simulacij z metodo Hartree-Fock, ki smo jih izvedli s programom Gaussian 09 na gruči računalnikov VRANA, smo izračunali aktivacijske proste energije pri treh različnih fleksibilnih baznih setih HF/6-31G(d), HF/6-31+G(d,p) in HF/6-311++G(d,p), ob uporabi dveh različnih modelov implicitnih topil. Grafični rezultati dokazujejo, da reakcije alkilacije med pinocembrinom in devetimi končnimi kemijskimi karcinogeni potekajo po mehanizmu nukleofilne substitucije SN2. Aktivacijske proste energije za reakcije alkilacije med kemijskimi karcinogeni in pinocembrinom, pridobljene po solvatacijskih metodah Samouglašenega reakcijskega polja in Langevinovih dipolov, pa smo primerjali z eksperimentalnimi vrednostmi aktivacijskih prostih energij med identičnimi karcinogeni in gvaninom - najreaktivnejšo bazo DNK. Na podlagi primerjave z gvaninom smo lahko določili, kako dober lovilec kemijskih karcinogenov je pinocembrin. Ugotovili smo, da pinocembrin predstavlja enakovredno učinkovit lovilec kemijskih karcinogenov v primeru etilen oksida, kloroetilen oksida in glicidamida kot gvanin, saj so izračunane aktivacijske energije podobne eksperimentalnim vrednostim za reakcije z gvaninom. V primeru 2-cianoetilen oksida, AFB1 ekso-8,9-epoksida, propilen oksida in stiren oksida pa pinocembrin ne more učinkovito zaščititi našega dednega materiala, saj je aktivacijska prosta energija pri omenjenih karcinogenih višja od eksperimentalno določene vrednosti za reakcije teh karcinogenov z gvaninom. Pinocembrin predstavlja bolj učinkovit lovilec le v primeru β-propiolaktona in vinil karbamat epoksida, kjer sta bili aktivacijski prosti energiji nižji kot v primeru reakcije z gvaninom.
Ključne besede: pinocembrin, med, flavonoidi, kemijski karcinogeni, aktivacijska prosta energija, kvantnomehanski izračuni
Objavljeno v DKUM: 22.09.2021; Ogledov: 787; Prenosov: 84
.pdf Celotno besedilo (2,38 MB)

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