Search

Metil salicilat ali metil 2-hidroksibenzoat je ester, rastlinskega izvora. Po videzu je pri sobni temperaturi bistra brezbarvna tekočina. Zaradi svojega močnega vonja se uporablja v dekorativni kozmetiki, šamponih, toaletnih milih, čistilih ali kot aroma za živila. Dokazano je tudi njegovo protibakterijsko, analgetično in protivnetno delovanje, zato se pogosto uporablja kot lokalna protivnetna ali analgetična učinkovina. Predstavlja glavno sestavino aromatične rastline zelenke (Gaultheria procumbens), iz listov katere pridobivamo eterično olje. Gre za eno bolj nevarnih eteričnih olj, saj se hitro absorbira iz prebavnega trakta in skozi kožo. Draži lahko oči, sluznice, zgornje dihalne poti in kožo, ob zaužitju pa je lahko celo smrtonosno. Vedno bolj priljubljeno postaja sintezno pridobivanje metil salicilata iz salicilne kisline. Namen diplomskega dela je bil sintetizirati derivate metil salicilata in končne produkte olfaktorno vrednotiti s pomočjo prostovoljcev. Želeli smo dobiti čim več hlapnih nizkomolekularnih derivatov s prijetnim vonjem, ki bi jih lahko uporabljali v kozmetični industriji. Reakcije estrenja in etrenja so potekale na prosti fenolni -OH skupini metil salicilata. Uspelo nam je sintetizirati štiri estre in tri etre, njihovo identiteto pa smo potrdili z instrumentalnima metodama: jedrsko magnetno resonanco in infrardečo spektroskopijo. Nastalim derivatom so nato prostovoljci določali prijetnost in jakost vonjev ter navedli tudi asociacije na druge vonje. Večini vzorcev so pripisali prijeten vonj in šibko ali srednje močno jakost. Za najprijetnejše so se izkazali 2-acetoksibenzoat, metil 2-(propioniloksi)benzoat in metil 2-izopropoksibenzoat. S pomočjo rezultatov te analize smo ugotovili, da ima sprememba kemijske strukture močan vpliv na prijetnost in jakost vonja. Methyl salicylate or methyl 2-hydroxybenzoate is an ester of plant origin. It looks like a clear, colorless liquid at room temperature. Due to its strong smell, it is used in decorative cosmetics, shampoos, toilet soaps, cleaning products or as a food flavoring. Its antibacterial, analgesic and anti-inflammatory effects have also been proven, so it is often used as a local anti-inflammatory or analgesic agent. It is the main component of the aromatic wintergreen plant. Essential oil is obtained from its leaves. It is one of the more dangerous essential oils, as it is quickly absorbed by the digestive system and through the skin. It may irritate the eyes, mucous membranes, upper respiratory tract and skin and can even be fatal if swallowed. Synthetic production of methyl salicylate from salicylic acid is becoming increasingly popular. The aim of the thesis was to synthesize methyl salicylate derivatives and evaluate the final products in an olfactory test with the help of volunteers. We strived to obtain as many volatile low-molecular derivatives with a pleasant smell as possible, which could be used in the cosmetics industry. Esterification and etherification reactions occurred on the free phenolic -OH group of methyl salicylate. We managed to synthesize four esters and three ethers and confirmed their identity by instrumental methods: nuclear magnetic resonance and infrared spectroscopy. The volunteers then determined how pleasant and strong each odor of the resulting derivates was. They also indicated associations with other odors. Most samples were attributed to a pleasant smell and a weak or medium strength. 2-acetoxybenzoate, methyl 2-(propionyloxy)benzoate and methyl 2-isopropoxybenzoate proved the most pleasant. The results of this analysis led us to discover that the change in chemical structure strongly influences the pleasantness and strength of the smell.

Salicilaldehid (SA) ali 2-hidroksibenzaldehid je organska aldehidna spojina, ki ima na orto mestu prosto fenolno skupino (-OH). Je brezbarvna do svetlo rumena oljnata tekočina, ki ima pri višjih koncentracijah grenak okus in vonj po mandljih. Ta aromatična spojina je poznana zaradi svoje prijetne dišave in hlapljivosti, zaradi česar jo uporabljajo v proizvodnji parfumov. Poleg tega je zaradi svojih aromatičnih lastnosti primerna za izboljšanje okusa različnih prehrambnih izdelkov in pijač. Deluje tudi fungicidno in larvicidno, kar prispeva k vsestranski uporabi. Pomembno vlogo ima kot reagent pri sintezi kumarina. SA je v naravi prisoten v rastlinah in v izločku ličink listnatega hrošča. Namen diplomske naloge je bila sinteza in olfaktorno vrednotenje 2-alkoksibenzaldehidov in 2-aciloksibenzaldehidov. To so različni lipofilni derivati salicilaldehida s prijetnim vonjem, ki bi jih lahko uporabili kot dišave v kozmetiki. Reakcije estrenja in etrenja smo izvajali na prosti hidroksilni skupini z nukleofilno substitucijo. Potek in uspešnost reakcij smo preverjali s tankoplastno kromatografijo. Surove produkte smo očistili s kolonsko kromatografijo. Nato smo čiste produkte analizirali z uporabo dveh spektroskopskih metod, jedrsko magnetno resonanco in infrardečo spektroskopijo, ki sta potrdili ustreznost spojin. Sledilo je olfaktorno vrednotenje spojin z vonjalnim testom, s katerim so prostovoljci ocenjevali prijetnost vonja, jakost vonja in na kaj jih vonj spominja. Etri, pridobljeni iz salicilaldehida, imajo bolj prijeten vonj v primerjavi z estri. Med vsemi vzorci je najbolj izrazit vonj imel 2-formilfenil acetat, ki je bil izbran tudi kot najbolj neprijeten vonj. Etil 4-(2-formilfenoksi)butanoat je izstopal z najbolj prijetnim vonjem, ki je bil opisan kot sladek, cvetličen in je močno spominjal na vonj parfuma. Salicylaldehyde (SA) or 2-hydroxybenzaldehyde is an organic aldehyde compound with a free phenolic group (-OH) at the ortho position. It is a colorless to light yellow, oily liquid that exhibits an almond-like odor at higher concentrations. This aromatic compound is renowned for its pleasant fragrance and volatility, making it a popular ingredient in perfume production. Additionally, it is suitable for enhancing the taste of various food and beverage products due to its aromatic properties. It also exhibits fungicidal and larvicidal activities contributing to its versatile applications. It plays a significant role as a reagent in the synthesis of coumarin. Salicylaldehyde is naturally present in plants and in the secretion of leaf beetle larvae. The objective of the thesis was the synthesis and olfactory evaluation of 2-alkoxybenzaldehydes and 2-acyloxybenzaldehydes. These are various lipophilic derivatives of salicylaldehyde with pleasant smells which could be utilized as fragrances in cosmetics. Esterification and etherification reactions were performed on the free hydroxyl group through nucleophilic substitution. The progress and success of the reactions were monitored using thin-layer chromatography. The raw products were purified through column chromatography. Subsequently, the pure products were analyzed using two spectroscopic techniques, nuclear magnetic resonance, and infrared spectroscopy, which confirmed the structure of the products. This was followed by an olfactory evaluation of the compounds with an olfactory test, with which the volunteers evaluated the pleasantness of the smell, the strength of the smell, and what the smell reminded them of. Ethers derived from salicylaldehyde have a more pleasant smell compared to esters. Among all the samples, 2-formylphenyl acetate had the most prominent smell, which was also described as the most unpleasant. Ethyl 4-(2-formylphenoxy) butanoate stood out with the most pleasant odor, which was described as sweet, floral, and strongly perfume-like.

U okviru ovog diplomskog rada pripravljene su halogenidne soli alifatskih triamina dietilentriamina ((H3DETA)Cl3), N-(2-aminoetil)-1,3-propandiamina ((H3N-1,3-PDA)Cl3 i (H3N-1,3-PDA)Br3) kao i kloridna sol trietilentetraaamina ((H4TETA)Cl4). Klasičnom otopinskom sintezom pripravljena je serija hibridno organsko-anorganskih halogenokuprata(II): (H3DETA)[CuCl5], (H3DETA)[CuBr5], (H3N-1,3-PDA)[CuCl5], (H3N1,3-PDA)[CuBr5], (H4TETA)[CuCl6] i (H4PEEA)[CuBr6]·H2O. Anorganske graĎevne jedinke kod svih prireĎenih halogenometalata su stehiometrije CuX4, te se većinom udružuju u slojevite okosnice. Kod hibridnih halogenometalata sa slojevitom strukturom dolazi do ugraĎivanja organskih kationa izmeĎu anorganskih slojeva. Organski kationi povezuju se putem protoniranih terminalnih amino skupina za halogenokupratne(II) jedinke, a meĎusobno se udružuju putem N‒H···X···H‒N vodikovih veza. Pripravljenim hibridnim halogenometalatima odreĎene su kristalne strukture pomoću difrakcije rendgenskog zračenja na jediničnom kristalu, a spojevi su dodatno okarakterizirani pomoću infracrvene spektroskopije, difrakcije rendgenskog zračenja na polikristalnom uzorku te metodama termičke analize. In this work, halide salts of aliphatic triamines diethylenetriamine, ((H3DETA)Cl3), N-(2- aminoethyl)-1,3-propanediamine, (H3N-1,3-PDA)Cl3 and (H3N-1,3 -PDA)Br3, and the chloride salt of triethylenetetraamine, (H4TETA)Cl4, were prepared. A series of hybrid organic-inorganic halocuprates(II) were prepared by solution crystallization: (H3DETA)[CuCl5], (H3DETA)[CuBr5], (H3N-1,3-PDA)[CuCl5], (H3N-1,3-PDA)[CuBr5], (H4TETA)[CuCl6] and (H4PEEA)[CuBr6]·H2O. The inorganic building blocks of all prepared halogenometalates have stoichiometry CuX4, and they are mostly combined into layered frameworks. In the case of hybrid halometallates with a layered structure, organic cations are incorporated between the inorganic layers. Organic cations are connected via protonated terminal amino groups to halocuprate(II) units, and interlinked to each other via N‒ H···X···H‒N hydrogen bonds. The crystal structures of the prepared hybrid halogenometalates were determined using single-crystal X-ray diffraction, and the compounds were additionally characterized using infrared spectroscopy, powder X-ray diffraction and thermal analyses.

Z litijem bogati oksidi prehodnih kovin (LMR-TMO) so skupina katodnih materialov, ki se jih lahko uporablja v litij ionskih akumulatorjih. Zaradi večjega deleža litija in odsotnosti kobalta v strukturi materiala, predstavljajo LMR-TMO cenejšo in bolj zmogljivo alternativo katodnim materialom na trgu. Z magistrskim delom smo želeli uspešno uporabiti sintezni postopek, ki se ga uporablja za pridobivanje NMC katodnih materialov, za sintezo LMR-TMO materiala. Po uspešni sintezi NMC materialov, smo sintezno tehniko uporabili za pridobitev ciljnega materiala. Vzorce smo nato analizirali s pomočjo vrstične elektronske mikroskopije in rentgenske praškovne difrakcije. Sintetizirane materiale smo uporabili kot aktivni material v katodah. Sestavili smo laboratorijske akumulatorje ter jih podvrgli ciklom polnjenja in praznjenja. Z analizami smo ugotovili, da smo uspešno pridobili želene materiale, hkrati pa smo preučili kako se je material odrezal, ko smo ga uporabili v celicah. Lithium rich transition metal oxides (LMR-TMO) are a group of cathode materials, which can be used in Lithium-ion batteries. Higher lithium percentage and the lack of cobalt in the structure of the material, makes LMR-TMO cheaper and more capable alternative for cathode materials in use. In this master’s thesis, we used a modified synthesis method, which is used to attain NMC cathode materials, to produce LMR-TMO materials. After the successful acquisition of NMC dust, we used the method for the synthesis of the desired material. Samples were analysed by scanning electron microscopy and x-ray powder diffraction. Synthesised materials were used as active material in cathodes, put in battery cells, and subjected to charging cycles. By doing before mentioned analyses, we concluded, that we successfully acquired LMR-TMOs and proved they can be used in battery cells.

U ovom radu pripravljene su jodidne soli gvanidina u svrhu ispitivanja njihove kokatalitičke aktivnosti u reakciji aldolne kondenzacije cikloheksanona i 4-klorbenzaldehida uz katalizator L-prolin. Odabrani aciklički i ciklički gvanidinski derivati razlikuju se prema usmjerenosti NH veza, steričkim utjecajima i supstituentima. Dobivenim su spojevima ispitana kiselobazna svojstva u acetonitrilu uz referentni spoj poznate bazičnosti UV titracijom i NMR spektroskopijom. Spektrometrijom masa provedeno je kinetičko mjerenje relativnih afiniteta vezanja jodida fragmentacijom jodidom premoštenog dimera ispitivanog i referentnog gvanidina. Omjer dijastereomera produkata aldolne kondenzacije nastalog kao rezultat kokatalitičke aktivnosti gvanidina praćen je HPLC i NMR tehnikom. Pokazano je da dijastereomerni omjer produkata ovisi o kiselo-baznim svojstvima gvanidina, usmjerenosti NH veza i stvaranju međumolekulske i unutarmolekulske vodikove veze. Navedeni čimbenici utječu na stabilnost katalitičkog kompleksa među gvanidinom, supstratom i L-prolinom te time imaju izravan utjecaj na konačan ishod reakcije. In this master thesis, iodide salts of guanidine were prepared for the purpose of testing their cocatalytic activity in the aldol condensation of cyclohexanone and 4-chlorobenzaldehyde with L-proline as catalyst. Acyclic and cyclic guanidine derivatives differ by the orientation of NH bonds, steric effect and substituents. Acid-base properties of the obtained compounds were determined in acetonitrile with a reference compound of known basicity using UV titration and NMR spectroscopy. Mass spectrometry was used to measure the relative affinity of iodide binding by fragmentation of the iodide-bound dimer of the tested and reference guanidine. Diastereomeric ratio of the aldol condensation products, as a result of cocatalytic activity of guanidines, was monitored by HPLC and NMR techniques. It was shown that the diastereomeric ratio of the products depends on the acid-base properties, orientation of NH bonds in guanidine and formation of intramolecular and intermolecular hydrogen bonds. The mentioned factors influence the stability of the catalytic complex between guanidine, substrate and L-proline and thus have a direct effect on the final outcome of the reaction.

Antibacterial resistance has become a huge problem lately. The big euphoria from the middle of the previous century with the discovery of the antibiotics did not last for long. Soon after the discovery of the first antibiotics, researchers realized that the fight with the microbes would not be so easy. The fast evolution of microorganisms and their ability to adapt to different external influences led to the development of resistance against most known and clinically used antibacterial drugs. Despite the increased need of new antibacterial compounds, not many new antibacterials reached the market in the last 20 years. DNA gyrase is a well-established and an attractive target in the search for new antibacterial compounds, with an important role in the process of DNA replication. DNA gyrase is an ATPase and the ATP binding site of the enzyme offers an opportunity for designing new antibacterial compounds with a mechanism of action that until now has not been enough exploited. Well-known structure of fragments of DNA gyrase offers great opportunity for structure-based design of new antibacterials, while many discovered inhibitors of DNA gyrase with different scaffolds and good inhibitory potential offer opportunity for ligand-based design of antibacterial compounds with an inhibitory activity on DNA gyrase. Dual targeting is an attractive approach in the design of new biologically active compounds, especially in the design of new antibacterial compounds, since the possibility for developing bacterial resistance is lower if two bacterial targets are inhibited simultaneously. Topoisomerase IV is a “twin” enzyme of DNA gyrase with a similar structure and function. Structural similarity between these two enzymes give an exceptional opportunity for designing dual targeting antibacterial compounds. Clinically used quinolones are a good example of successful dual inhibitors of DNA gyrase and topoisomerase IV, targeting their GyrA and ParC subunits. Lately, more attention has been paid to the less used part as antibacterial target of these enzymes, GyrB and ParE subunits, where the ATP-binding site is situated. Within the framework of the doctoral dissertation we designed, synthesized and biologically evaluated compounds with benzothiazole scaffold as potential inhibitors of DNA gyrase. Design of our compounds was based on modification of recently discovered inhibitors of DNA gyrase based on 4,5,6,7-tetrahydrobenzo-[d]thiazole scaffold in our research group. In this context we replaced the 4,5,6,7-tetrahydrobenzo-[d]thiazole scaffold with benzo[d]thiazole scaffold, performed similar structural modification as were done in the case of 4,5,6,7-tetrahydrobenzo-[d]thiazole compounds and studied the influence of the structural modification on the inhibitory activity. Our benzothiazole compounds were evaluated for inhibitory activities against DNA gyrase, isolated from Staphylococcus aureus and from Escherichia coli. Since topoisomerase IV is an enzyme that has similar structure, novel benzothiazole compounds were also evaluated for inhibitory activities against topoisomerase IV isolated also from S. aureus and E. coli. Most of our compounds exhibited potent in vitro inhibitory activities against E. coli DNA gyrase and some of the compounds also showed inhibitory activities against S. aureus DNA gyrase. The best inhibitor of E. coli gyrase was exhibited by compound 2-((6-(4,5-dibromo-1H-pyrrole-2-carboxamido)benzo[d]thiazol-2-yl)amino)-2-oxoacetic acid (13) with an IC50 of 33 nM. Certain compounds showed dual inhibition against gyrase and topoisomerase IV isolated from both bacterial types. The best dual inhibition was observed by compound 2-((2-(4,5-dichloro-1H-pyrrole-2-carboxamido)benzo[d]thiazol-6-yl)amino)-2-oxoacetic acid (27) (IC50 values for E. coli DNA gyrase, S. aureus DNA gyrase, E. coli topoisomerase IV and S. aureus topoisomerase IV are 0.087, 0.51, 1.8 and 1.7 μM, respectively). Molecular docking studies showed that benzothiazole compounds bind to the ATP-binding site of the gyrase, which was further confirmed with a crystal structure of compound 2-((2-(4,5-dibromo-1H-pyrrole-2-carboxamido)benzothiazol-6-yl)amino)-2-oxoacetic acid (24) bound to the ATP binding site of the gyrase. Our benzothiazole-based inhibitors of DNA gyrase and topoisomerase IV were biologically evaluated for antibacterial activity against Gram-positive (S. aureus ATCC 25923, Enterococcus faecalis ATCC 29212) and Gram-negative (Escherichia coli ATCC 25922, Pseudomonas aeruginosa ATCC 27853). In general, most of the compounds did not show significant antibacterial activity against all tested bacterial strains. Notable activities showed only compounds ethyl 2-((6-(4,5-dichloro-1H-pyrrole-2-carboxamido)benzo[d]thiazol-2-yl)amino)-2-oxoacetate (11) and 3-((2-(4,5-dibromo-1H-pyrrole-2-carboxamido) benzo[d]thiazol-6-yl)amino)-3-oxopropanoic acid (25) against Gram-positive E. faecalis with 47 % and 59 % inhibition of the bacterial growth of E. faecalis at a 50 μM concentration after 24 h incubation, respectively. Compound 25 was found as potential ligand of AcrAB-tolC efflux pump, which could explain its weak antibacterial activity against Gram-negative bacterial strains (12 % inhibition of the growth of E. coli after a 24 h incubation and 11 % inhibition of the growth of P. aeruginosa after 24 h incubation). Furthermore, in a larger screening project, benzothiazole inhibitors of DNA gyrase, synthesized within the framework of this doctoral dissertation, were found to possess potent antiviral activity against influenza viruses (Influenza A/H1N1, Influenza A/H3N2 and Influenza B). Considering the importance of Hsp90 chaperon in the replication of virus influenza and also the similarities in the structure of the ATP binding sites of Hsp90 and Gyrase B (members of the GHKL group of enzymes with resembles in the ATP binding sites) we hypothesized that the antiviral activity of benzothiazole compounds is probably due to the inhibition of Hsp90. In a microscale thermophoresis assay, eleven of our compounds showed good binding to Hsp90 with Kd in the range of 0.26-51 μM. Compound 27 has the best Kd value (0.26 μM) which is highly comparable with the already known Hsp90 inhibitor, 17-desmethoxy-17-N,N-dimethylaminoethylamino geldanamycin (17-DMAG) (Kd = 0.27 μM). This study provided an excellent series of compounds with dual inhibition of both DNA gyrase and topoisomerase IV from E. coli and S. aureus. The crystal structure of compound 24 in the ATP-binding place of DNA gyrase B gives also opportunities for further optimization of these compounds in order to improve their inhibitory activities. The finding that compounds have antiviral activity against virus influenza with inhibition of Hsp90 host chaperone, gives a good starting point for designing and developing compounds with dual action that will combine both antibacterial and antiviral activity in the same molecule. Bakterijska odpornost proti večini protibakterijskih učinkovin postaja vse večji problem. Odkritje antibiotikov v sredini prejšnjega stoletja je vzbudilo velika pričakovanja, ki pa so se žal kmalu izkazala kot nerealna. Kmalu po tem, ko so znanstveniki odkrili prvi antibiotik, so ugotovili, da borba z mikroogranizmi ne bo tako lahka. Sposobnost mikroogranizmov, da se prilagodijo različnim zunanjim vplivom je bila vzrok za pojav odpornosti proti protibakterijskim učinkovinam. Zaradi tega se potreba po novih protibakterijskih učinkovinah vedno bolj povečuje, med tem ko je vse bolj zaskrbljujoče dejstvo, da je na trg v zadnjih dvajsetih letih prišlo zelo malo novih protibakterijskih učinkovin. DNA giraza je encim, ki ima pomembno vlogo pri replikaciji DNA molekule v bakterijski celici in predstavlja dobro uveljavljeno in privlačno tarčo v iskanju novih protibakterijskih učinkovin. DNA giraza je ATPaza in njeno ATP vezavno mesto ponuja dobro priložnost za načrtovanje novih protibakterijskih učinkovin z mehanizmom delovanja, ki do sedaj ni dovolj izkoriščen v boju proti bakterijam. Pri načrtovanju novih inhibitorjev DNA giraze se lahko izkoristijo znane strukturne informacije o posameznih delih giraze (kot je struktura ATP vezavnega mesta), ki ponujajo priložnost za strukturno podprto načrtovanje novih inhibitorjev ter že znane inhibitorje DNA giraze (tudi inhibitorji, ki se vežejo v ATP vezavno mesto), ki ponujajo priložnost za načrtovanje novih inhibitorjev na osnovi ligandov. Načrtovanje inhibitorjev, ki bi delovali na dve ali več tarč je zelo privlačen pristop pri iskanju novih učinkovin in posebej pri iskanju novih protibakterijskih učinkovin, zaradi tega ker se z modulacijo dveh ali več tarč v bakterijski celici zmanjšuje možnost za razvoj bakterijske rezistence. Topoizomeraza IV je encim, ki je po svoji strukturi in funkciji zelo podoben DNA girazi. Podobnost v strukturi med tema dvema encimoma ponuja dobro priložnost za načrtovanje protibakterijskih učinkovin, ki bi imeli dve tarči v bakterijski celici. Dober primer za protibakterijske učinkovine, ki inhibirajo tako DNA girazo kot topoizomerazo IV so dobro znani in v klinični praksi veliko uporabljani kinoloni. Kinoloni so inhibitorji gyrA in parC podenot DNA giraze in topoizomeraze IV. V zadnjem času je vedno večja pozornost namenjena gyrB podenoti giraze in parE podenoti topoizomeraze IV, ki sta bili doslej manj izkoriščeni. V okviru doktorskega dela smo načrtovali, sintetizirali in biološko ovrednotili potencijalne inhibitorje DNA giraze, ki vsebujejo benzotiazolski skelet. Načrtovanje je izhajalo iz že znanih inhibitorjev DNA giraze s 4,5,6,7-tetrahidrobenzo[d]tiazolnim ogrodjem, ki so bili pred kratkim odkriti v naši raziskovalni skupini. Pri tem smo 4,5,6,7-tetrahidrobenzo-[d]tiazolni obroč zamenjali z benzo[d]tiazolnim obročem ter naredili podobne strukturne modifikacije kot v 2,6- diamino-4,5,6,7-tetrahidrobenzo-[d]tiazolski seriji in študirali vpliv strukturnih sprememb na inhibitorno aktivnost. Benzotiazolne spojine, ki so bile sintetizirane v sklopu doktorskega dela so bile najprej testirane na inhibitorno aktivnost na DNA girazo iz Escherichia coli in Staphylococcus aures. Glede na zgoraj omenjeno podobnost v strukturi med DNA girazo in topoizomerazo IV, so bile pripravljene spojine testirane tudi na topoizomerazo IV, prav tako iz E. coli in S. aureus. Benzotiazolne spojine so pokazale močno in vitro inhibitorno aktivnost na E. coli DNA girazo, in nekatere spojine pa so izkazale tudi zaviralno aktivnost na S. aureus DNA girazo. Najboljši inhibitor na E. coli DNA girazo je bila spojina 2-((6-(4,5-dibromo-1H-pirol-2-karboksamido)benzo[d]tiazol-6-il)amino)-2-oksoacetna kislina (13), z nanomolarno IC50 vrednostjo 33 nM. Določene spojine so pokazale dvojno inhibicijo, tako na DNA girazo iz E. coli in S. aureus kot tudi na topoizomerazo IV iz E. coli in S. aureus. Najboljši inhibitor obeh encimov je bila spojina 2-((2-(4,5-dikloro-1H-pirol-2-karboksamido)benzo[d]tiazol-6-il)amino)-2-oksoocetna kislina (27) s 87 nM in 510 nM IC50 vrednostmi za inhibicijo DNA giraze iz E. coli in S. aureus ter 1.8 in 1.7 μM IC50 vrednostmi za inhibicijo topoizomeraze IV in iz E. coli in S. aureus. Študije sidranja so pokazale, da se benzotiazolni inhibitorji vežejo v ATP vezavno mesto DNA giraze, kar smo potrdili tudi s kristalno strukturo kompleksa giraze B iz E. coli in 2-((2-(4,5-dibromo-1H-pirol-2-karboksamido)benzotiazol-6-il)amino)-2-oksoocetne kisline (24) vezane v ATP vezavnem mestu. Benzotiazolni inhibitorji DNA giraze in topoizomeraze IV so bili testirani tudi za protibakterijsko aktivnost na Gram-pozitivne (S. aureus ATCC 25923, Enterococcus faecalis ATCC 29212) in Gram-negativne bakterijske seve (Escherichia coli ATCC 25922 in Pseudomonas aeruginosa ATCC 27853). Na splošno spojine niso pokazale znatne protibakterijske aktivnosti na vse testirane bakterijske seve. Edine opazne aktivnosti sta pokazali spojini etil 2-((6-(4,5-dikloro-1H-pirol-2-karboksamido)benzo[d]tiazol-2-il)amino)-2-oksoacetat (11) in 3-((2-(4,5-dibromo-1H-pirol-2-karboksamido)benzo[d]tiazol-6-il)amino)-3-oksopropanojska kislina (25) (47 % in 59 % inhibicija rasti bakterije E. faecalis pri 50 μM koncentraciji po 24 h inkubaciji). Za spojino 25 je bilo ugotovljeno, da je potencialni ligand AcrAB-tolC efluksne črpalke in s tem tudi lahko razložimo njeno slabo protibakterijsko aktivnost na testirane Gram-negativne bakterijske seve (12 % inhibicija rasti E. coli po 24 h inkubacije in 11 % inhibicija P. aeruginosa po 24 h inkubacije). Nadalje smo naše spojine vključili v projekt rešetanja spojin, ki je bil namenjen odkrivanje novih spojin s protivirusnim delovanjem. Pri tem so nekateri benzotiazolni inhibitorji giraze izkazali protivirusno aktivnost na viruse influence A/H1N1, A/H3N2 in influence B. Hsp90 šaperon je pomemben pri replikaciji virusa influence in pri tem, ker je struktura ATP vezavnega mesta DNA giraze zelo podobna strukturi ATP vezavnega mesta šaperona Hsp90 (oba sta člana GHKL grupe encimov, ki imajo podobnosti v strukturi ATP vezavnega mesta), ki je udeležen pri procesiranju virusnih proteinov, smo domnevali, da je protivirusna aktivnost benzotiazolnih inhibitorjev giraze B morda posledica inhibicije Hsp90. Pri mikroforeznem testu, s katerim smo ovrednotili vezavo benzotiazolnih inhibitorjev giraze na Hsp90, je enajst benzotiazolnih spojin izkazalo vrednosti za konstanto disocijacije Kd v območju od 0.26 do 51 μM. Najboljšo aktivnost je pokazala spojina 27, s Kd vrednostjo 0.26 μM, ki je primerljiva Kd vrednosti znanega inhibitorja Hsp90 17-desmetoksi-17-N,N-dimetilaminoetilaminogeldanamicina (17-DMAG) (Kd = 0.27 μM). Z raziskavami v okviru doktorskega dela smo uspeli pripraviti spojine, ki imajo tako inhibitorno delovanje na DNA girazo kot tudi na topoizomerazo IV iz E. coli in S. aureus. Kristalna struktura spojine 24 v kompleksu z DNA girazo B iz E. coli daje priložnost za nadaljnjo optimizacijo teh spojin za izboljšanje njihovih inhibitornih aktivnosti. Ugotovitev, da imajo naši benzotiazolni inhibitorji giraze tudi delovanje proti virusu influence in se vežejo na Hsp90 šaperon, daje dobro izhodišče za nadaljnje načrtovanje in razvoj učinkovin, ki bi imele protibakterijsko in protivirusno delovanje.

Napetostno odvisni natrijevi kanalčki so veliki transmembranski proteinski kompleksi odgovorni za prevajanje električnih tokov v živčnih, mišičnih in endokrinih celicah in tkivih. Napake v njihovi ekspresiji in funkcijske spremembe so povezane z mnogimi patološkimi stanji. Tako se pri zdravljenju epilepsije, bolezni centralnega živčevja, bolezni srca in bolečinskih stanj uporabljajo učinkovine z modulatornim delovanjem na natrijevih kanalčkih. Le-te delujejo neselektivno na tip natrijevega kanalčka in izkazujejo širok nabor neželenih stranskih učinkov. Spojine, ki bi selektivno delovale na posameznih tipih napetostno odvisnih natrijevih kanalčkov, bi omogočile razvoj indikacijsko specifičnih učinkovin in olajšale študij vloge posamezenih tipov natrijevih kanalčkov v patofiziologiji. Ker so organizmi morskega izvora razmeroma neraziskan vir spojin vodnic, smo v okviru doktorskega študija uporabili alkaloida oroidin in klatrodin iz morskih spužev rodu Agelas kot izhodišče za načrtovanje in sintezo novih modulatorjev ionskih kanalčkov. Spojini vsebujeta terminalni 2-aminoimidazol povezan preko 3-aminopropenskega distančnika s halogeniranim ali nesubstituiranim pirolom na drugem koncu molekule. Pri načrtovanju spojin smo ohranili v oroidinu in klatrodinu prisotni aminoimidazolni strukturni element, saj predvidevamo da gre za ključni farmakoforni element. S pomočjo načrtovanja na osnovi liganda smo pripravili osredotočeno knjižnico analogov oroidina in klatrodina, kjer smo 3-aminopropenski distančnik zamenjali z delno rigidiziranim centralnim piperazinskim fragmentom. V okviru načrtovanja potencialnih modulatorjev napetostno odvisnih natrijevih kanalčkov smo preučili tudi vpliv zamenjave terminalnega pirola z različnimi aromatskimi ali heteroaromatskimi obroči na delovanje spojin. Sintetizirane spojine smo biološko ovrednotili na več tipih napetostno odvisnih natrijevih kanalčkov z metodo vpete krpice membrane. Ugotovili smo, da pripravljene spojine izkazujejo šibko jakost delovanja na tip 1.3 natrijevih kanalčkov, pri čemer je pomembna razdalja med terminalnima heteroaromatskima dušikoma. Potrdili smo domnevo, da je za delovanje ključen aminoimidazolni fragment, katerega bioizosterne zamenjave niso bile tolerirane v kontekstu delovanja na kanalčke. Opazili smo tudi ključno prisotnost karbonilne skupine ob terminalnem pirol-2-karboksilnem strukturnem fragmentu. Le-tega smo zamenjali z večjim heteroaromatskim indol-2-karbonilom in pripravili piperazinski analog klatrodina z IC50 vrednostjo 19 μM in selektivnim delovanjem na 1.3 tipu napetostno odvisnih natrijevih kanalčkov. Spojina ni izkazovala delovanja na 1.4, 1.5 ter 1.7 tipih napetostno odvisnih natrijevih kanalčkov in predstavlja dobro izhodišče za nadaljnji razvoj piperazinskih analogov klatrodina in oroidina kot selektivnih modulatorjev 1.3 tipa napetostno odvisnih natrijevih kanalčkov. Sekundarni metaboliti morskih spužev in njihovih simbiotskih organizmov nastopajo v razmnoževalnih, signalnih, regulacijskih in obrambnih vlogah ter imajo posledično polifarmakološke učinke. Raziskovana alkaloida klatrodin in oroidin iz morskih spužev Agelas sta tako poleg modulacije napetostno odvisnih natrijevih kanalčkov v literaturi opisana kot zaviralca nastanka bakterijskih biofilmov in kot protibakterijski učinkovini. Ker opažamo naraščajoči pojav bakterijske rezistence in upad učinkovitosti že uporabljanih farmakoloških pristopov, smo se v drugem delu doktorskega dela osredotočili na razvoj protibakterijskih učinkovin. Odkrili smo strukturne podobnosti med oroidinom oz. klatrodinom, njunimi piperazinskimi analogi in v literaturi prisotnimi piroloamidnimi zaviralci DNA giraze B. Bakterijska DNA giraza je esencialen encim, ki katalizira uvajanje negativnih zavojev na molekuli DNA oziroma katalizira topološko sproščanje ob podvajanju bakterijske DNA. Podenota B skrbi za hidrolizo molekule ATP in dovaja energijo za funkcionalno delovanje encima. Kjub substratu ATP, encim predstavlja ustrezno in validirano tarčo za razvoj novih protibakterijskih učinkovin. V nasprotju s ključnim aminoimidazolnim fragmentom, ki je bil potreben za modulatorno delovanje piperazinskih analogov oroidina ter klatrodina na napetostno odvisnih natrijevih kanalčkih, smo se pri načrtovanju spojin s potencialnim zaviralnim delovanjem na DNA girazi B osredotočili na piroloamidni oziroma amidni strukturni fragment, katerega smo pri načrtovanih spojinah ohranili. Po naših ugotovitvah ta predstavlja ključni strukturni element, ki omogoča zaviralcem DNA giraze B vzpostavitev vodikovih vezi z aminokislinskimi ostanki v adeninskem žepku ATP vezavnega mesta. Piroloamidna oziroma amidna struktura je pri zaviralcih DNA giraze B podobno povezana preko cikličnih, aromatskih, heteroaromatskih, bicikličnih in kondenziranih cikličnih distančnikov do drugega ključnega strukturnega elementa, ki pa poseduje polarno oziroma kislo funkcionalno skupino. Slednja omogoča drugi ključni kontakt zaviralcev DNA giraze B z bazičnimi argininskimi aminokislinskimi ostanki na vhodu v ATP vezavno mesto. Raziskovana naravna alkaloida in serijo njunih piperazinskih analogov smo uporabili pri in silico metodologiji virtualnega rešetanja in identificirali še aminopiperidinski in cikloheksanski distančnik kot primerna za pripravo knjižnice potencialnih zaviralcev DNA giraze B. Sintetizirali smo več kot 60 spojin treh strukturnih tipov in raziskovali vpliv strukture in konfiguracije uporabljenih distančnikov na zaviralno delovanje izoliranega encima DNA giraze B iz bakterijskega seva E. coli. Poleg centralnega skeleta smo poskušali preučiti tudi optimalno dolžino in velikost terminalnega strukturnega fragmenta z estrsko oziroma karboksilno funkcionalno skupino ter vpliv zamenjave ključnega piroloamidnega fragmenta z večjim indoloamidom. Identificirali in validirali smo pirolo-amino-piperidinski skelet s pripravljenimi spojinami, ki so izkazovale IC50 vrednosti na DNA girazi B v nizkem mikromolarnem območju. Spojina z alifatskim glutaratnim terminalnim fragmentom in pirolo-amino-piperidinskim skeletom pa je izkazovala zaviranje DNA giraze B z IC50 vrednostjo 480 nM. Prav tako smo identificirali primerno konfiguracijo cikloheksanskega distančnika in pripravili spojino s pirolo-1,4-trans-substituiranim cikloheksanskim skeletom in terminalnim glicinskim fragmentom ter IC50 vrednostjo 15.1 μM na DNA girazi B. Na podlagi podatkov vrednotenja encimske inhibicije smo pripravljene piperazinske, piperidinske in cikloheksanske zaviralce DNA giraze B uporabili za študij samega ATP vezavnega mesta. Z in silico metodami molekulskega sidranja in molekulske dinamike smo ocenili sposobnost vezave pripravljenih spojin v ATP vezavno mesto DNA giraze B in preučevali nastanek ključnih interakcij z Asp73 (E. coli številčenje) in bazičnimi argininskimi aminokislinski ostanki na vhodu v vezavno mesto. Preučili smo konformacijo uporabljenih distančnikov in dolžino terminalega fragmenta s karboksilno funkcionalno skupino. Prav tako smo razvili in silico pristop za identifikacijo ključnih ohranjenih molekul vode v ATP vezavnem mestu DNA giraze B ter dodatno potrdili vlogo ohranjene molekule vode pri vzpostavitvi vodikovih vezi med ligandom in adeninskim žepkom v aktivnem mestu DNA giraze B. Spojine s pirolo-amino-piperidinskim skeletom in zaviralnim delovanjem in vitro smo ovrednotili še z metodo površinske plazmonske resonance, kjer smo merili Kd vrednosti zaviralcev pri vezavi na fragment G24, ki je poznan kot najmanjši ATP-vezajoči proteinski fragment giraze B. Za spojine smo izmerili Kd vrednosti od 11 do 12 μM ter potrdili predhodne izmerjene IC50 vrednosti v nizkem mikromolarnem območju. Raziskovalno delo potrjuje obstoječe rezultate in strukturne študije potencialnih zaviralcev DNA giraze B ter omogoča trdne temelje za nadaljnji razvoj ključno potrebnih protibakterijskih učinkovin na terapevtski tarči DNA girazi B. Nadalje smo na podlagi farmakoinformatike identificirali knjižnico 1,3-tiazolidin-4-onov kot potencialnih protibakterijskih učinkovin in s pomočjo in silico podpore molekulskega modeliranja predlagali njihov mehanizem delovanja na encimski tarči undekaprenilpirofosfat sintazi. Spojine smo mikrobiološko ovrednotili ter določili minimalne zaviralne koncentracije na rast petih bakterijskih sevov in glivnega seva C. albicans. Knjižnica je izkazovala protibakterijsko delovanje pri čemer smo spojini (Z)-4-((2-(4-metil-piperidin-1-il)-4-oksotiazol-5(4H)-iliden)metil)benzonitril izmerili MIC vrednost 10 μg/mL na bakterijskem sevu P. aeruginosa. Voltage-gated sodium channels are large transmembrane protein complexes responsible for ion current transmission in nerve, muscle and endocrine cells and cell systems. Defects in their expression and function are linked to multiple pathological conditions. Treatment of these conditions such as epilepsy, central nervous system diseases, heart complications and various pain states is still challenging due to nonselective action of used drugs on multiple voltage-gated sodium channels and subsequent adverse side effects. Development of selective modulators of specific voltage-gated sodium channel isoforms would thus be beneficial and would enable profound studies on the role of individual voltage-gated sodium channel isoform in patophysiology. Due to under-explored chemical space of marine natural products we selected alkaloids oroidin and clathrodin as starting point for the discovery of novel modulators of voltage-gated sodium channels. Compounds are composed of two terminal fragments, namely 2-aminoimidazole and pyrrole-2-carboxamide, interconnected by a central 3-aminopropene linker moiety. In the scope of our research hypothesis we postulated that terminal aminoimidazole represents key pharmacophoric element, hence we primarily exchanged the central linker moiety with a sterically rigidified piperazine structure by using ligand based drug design methodology. Our next goal was a systematic study of the influence of terminal fragment exchange on potency of synthesized compounds and involvement of postulated pharmacophoric element. All compounds were biologically evaluated on multiple voltage-gated sodium channel isoforms using patch clamp technique. On some of prepared compounds we measured modest potency on voltage-gated sodium channel 1.3 isoform and determined that distance between terminal heterocyclic nitrogens is a crucial parameter. We confirmed our pharmacophoric element assumption as replacement of terminal aminoimidazole led to loss of potency. The role of heterocyclic moiety opposite of aminoimidazole was also elaborated and presence of carbony group at the heterocyclic amide identified as necessary for potency. Replacement of pyrrolo-2-carboxyl fragment with larger indolo-2-carbonyl led to piperazine clathrodin analogue with an IC50 value of 19 μM, selective on 1.3 voltage-gated sodium channel isoform. Prepared library of piperazine oroidin (clathrodin) analogues is a suitable starting point for further research on 1.3 voltage-gated sodium channel selective modulators, especially in the light of emerging new channel structural data. Secondary metabolites of sea sponges and their symbiotic organisms are involved in reproduction, signalling, regulation and defence roles in wholesome biological systems and they accordingly often display polypharmacological effects. Studied alkaloids oroidin and clathrodin from see sponges of the genus Agelas are reported in literature also as inhibitors of bacterial biofilm formation and antibacterial compounds. The latter observation is especially interesting in the light of emerging incidence of bacterial resistence and downfall of antibacterial therapy effectiveness. In the second part of research thesis we focused on antibacterial targets and identified structural similarity between oroidin lead compounds, prepared oroidin piperazine analogues and small molecule inhibitors of DNA gyrase B reported in literature. DNA Gyrase B is an essential bacterial enzyme responsible for the introduction of negativive supercoils or topological relaxation of DNA molecule during replication. It is composed of two subunits where subunit A performs operations on DNA molecule and subunit B hydrolises ATP supplying the required free energy. In spite of ATP as the substrate of DNA gyrase B, this enzyme subunit is a validated target for discovery of antibacterial compounds. In contrast with key aminoimidazole fragment, that was essential for potency of piperazine oroidin (clathrodin) analogues on voltage-gated sodium channels, we focused on second pyrrole-2-carboxamide terminal fragment in the design of potential inhibitors of DNA gyrase B. The latter fragment was reported as a structure element that enables crucial interactions with amino acid residues in adenine pocket of ATP binding site on DNA gyrase B. Pyrrole-2-carboxamide or amide moiety is similarly connected to the second pharmacophoric element via a cyclic, aromatic, heteroaromatic, bicyclic, condensed bicyclic or other similar linker in small molecule DNA gyrase B inhibitors reported in literature. Aforementioned second pharmacophoric element is where our initially observed similarities end. Here a structural fragment incorporating a polar or preferably acidic group is imperative as it enables key interactions towards arginine residues at the ATP binding site entrance of DNA gyrase B. We employed our leads and their piperazine analogues in the in silico virtual screening campaign only to identify additional aminopiperidine and cyclohexane central linkers for the development of focused library of potential DNA gyrase B inhibitors. We synthesized more than 60 compounds of three structural types in order to evaluate the influence of central linker and suitability of various simple aliphatic and aromatic terminal fragments incorporating a carboxyl or ester group on the inhibitory potency of compounds on isolated DNA gyrase B from E. coli. We also investigated the effects of pyrrole-2-carboxamide / indole-2-carboxamide pharmacophore exchange. We identified and validated pyrrolo-aminopiperidine scaffold in combination with prepared compounds that displayed IC50 values in low micromolar range. Compound with pyrrolo-aminopiperidine scaffold and glutaryl terminal acidic fragment possessed an IC50 value of 480 nM. Secondly, we recognised a suitable 1,4-substituted cyclohexane central linker. Representative pyrrolo-1,4-trans-cyclohexane scaffold compound incorporating a terminal glycine fragment displayed an IC50 value of 15.1 μM on DNA gyrase B. With the biological evaluation data in hand, we used prepared compounds to study the possible binding modes. With in silico methodology of molecular docking and molecular dynamics the possible binding into ATP active site was confirmed. Furthermore, previously published binding mode of small molecule DNA gyrase B inhibitors was corroborated and our compounds were found capable of interacting with Asp73 (E. coli numbering) at the adenine binding pocket and arginine residues near the ATP binding site entrance. We also developed an in silico approach towards identification of key conserved water molecules in ATP binding site and substantiated previous reports on water-mediated hydrogen bonds between ligand and amino acid residues in adenine pocket of DNA gyrase B ATP binding site. Compounds of the pyrrolo-aminopiperidine structural class were also evaluated using surface plasmon resonance where binding to the G24 protein known as the smallest ATP binding fragment of DNA gyrase B. Most potent compounds displayed affinity to the G24 protein with the Kd values of 11–12 μM, a result in agreement with our IC50 experiments. Our research confirms preceding results and strucutral studies on DNA gyrase B inhibitors and enables a solid foundation for futere design and development of DNA gyrase B as potential antibacterial compounds. In the additional investigation, we selected a library of 1,3-tiazolidin-4-one compounds and with the help of pharmacoinformatics and in silico molecluar modelling proposed their mechanism of action on the bacterial enzyme undecaprenylpyrophosphate synthase. Compounds were biologically evaluated and minimal inhibitory concentrations were measured on 5 bacterial strains and C albicans yeast. The library displayed modest antibacterial activity where (Z)-4-((2-(4-methyl-piperidin-1-yl)-4-oxothiazol-5(4H)-ylidene)methyl)benzonitrile was the most potent with a MIC value of 10 μg/mL on P. aeruginosa bacterial strain.

Alzheimerjeva bolezen je kronična progresivna nevrodegenerativna bolezen možganov. Vzroki za nastanek te bolezni še niso znani, je pa znano, da kopičenje amiloidni proteina β, proteina tau in oksidativni stres v možganih povzročijo odmiranje nevronov in propadanje sinaps. Ta nevrodegeneracija je najizrazitejša v holinergičnem živčno-prenašalnem sistemu. Posledica tega je zmanjšana koncentracija živčnega prenašalca acetilholina v možganih, kar povzroči motnje spomina, ki so značilne za bolnike z Alzheimerjevo boleznijo. Trenutno zdravljenje ali preprečevanje te bolezni ni mogoče in bolnikom so na voljo le štiri učinkovine za lajšanje simptomov. Holin-esterazi acetilholin-esteraza in butirilholin-esteraza prekineta holinergični živčni prenos v možganih tako, da katalizirata hidrolizo acetilholina. V možganih zdravih odraslih je acetilholin-esteraza odgovorna za 80%, butirilholin-esteraza pa za 20% holin-esterazne encimske aktivnosti. Z napredovanjem bolezni se encimska aktivnost acetilholin-esteraze zmanjšuje, butirilholin-esteraze pa povečuje. Tri od štirih učinkovin za lajšanje simptomov Alzheimerjeve bolezni so zaviralci holin-esteraz: selektivna zaviralca acetilholin-esteraze donepezil in galantamin ter zaviralec acetilholin-esteraze in butirilholin-esteraze rivastigmin. Te učinkovine imajo, zaradi zaviranja acetilholin-esteraze, številne slabosti (neželeni učinki zaradi zaviranja acetilholin-esteraze v perifernem živčnem sistemu in s tem povezan omejen odmerek ter neučinkovitost v poznih stadijih bolezni), katerim se da izogniti s selektivnim zaviranjem butirilholin-esteraze. Načrtovali, sintetizirali in ovrednotili smo obsežno serijo novih selektivnih reverzibilnih zaviralcev butirilholin-esteraze: sulfonamidne in N-propargilpiperidinske derivate spojine zadetka 1 (IC50 = 21,3 nM) in določili odnos med njihovo strukturo in delovanjem. Za sintezo ključih intermediatov v sintezni poti do načrtovanih zaviralcev smo razvili splošni in enostavni sintezni postopek. Sulfonamidni derivat 2 (IC50 = 4,9 nM) je obetavna spojini za nadaljnji predklinični razvoj. Spojina ni citotoksična in ščiti živčne celice pred strupenimi amiloidnega proteina β. Zavira butirilholin-esterazo v rezinah podganjih možganov in prehaja v možgane podgan po intraperitonealni aplikaciji. Dokazali smo, da spojina 2 izboljša spomin, kognitivne funkcije in učne sposobnosti miši v bolezenskem modelu zmanjšane holinergične aktivnosti pri Alzheimerjevi bolezni. V možganih bolnikov je povišana encimska aktivnost monoaminske oksidaze B. Produkti, ki nastanejo pri reakciji, ki jo katalizira ta encim, prispevajo k oksidativnemu stresu in nevrodegeneraciji pri Alzheimerjevi bolezni. Trije N-propargilpiperidnski derivati spojine zadetka 1 poleg butirilholin-esteraze zavirajo tudi monoaminsko oksidazo B. Zaviralec obeh encimov z nevroprotektivnim delovanjem (N-propargilpiperidin 6) je spojina vodnica za načrtovanje novih spojin z delovanjem na več tarč. V doktorski disertaciji predstavljamo, da smo s sistematičnimi spremembami strukture spojine zadetka 1 prišli do (i) obetavne spojine za nadaljni predklinični razvoj, (ii) štirih kristalnih struktur kompleksov butirilholin-esteraz z zaviralci, (iii) ortogonalno zaščitenih intermediatov za sintezo novih zaviralcev in (iv) spojine vodnice kot izhodišča za načrtovanje novih spojin z delovanjem na več tarč. Alzheimer's disease is a chronic progressive neurodegenerative brain disorder. The etiology of this disease is not entirely understood, although it is known that accumulation of amyloid β peptide, protein tau and oxidative stress in the brain cause neuronal death and synaptic loss. This neurodegeneration is most severe in the cholinergic neurotransmitter system and results in a decrease in the levels of the neurotransmitter acetylcholine, which in turn produces memory deficits, characteristic for patients with Alzheimer's disease. Currently, there are no means to cure or prevent Alzheimer's disease, and only four drugs are available to patients for alleviating its symptoms. Cholinesterases acetylcholinesterase and butyrycholinesterase terminate cholinergic neurotransmission in the brain by catalyzing the hydrolysis of acetylcholine. In the healthy brain, acetylcholinesterase accounts for 80% and butyrycholinesterase accounts for 20% of the cholinesterase enzymatic activity. As the disease progresses, enzymatic activity of acetylcholinesterase is reduced, while that of butyrycholinesterase increases. Three out of the four approved drugs for alleviating symptoms of patients with AD are cholinesterase inhibitors: the selective acetycholinesterase inhibitors donepezil and galantamine, and the pseudo-irreversible acetylcholinesterase and butyrycholinesterase inhibitor rivastigmine. These drugs have numerous limitations due to inhibition of acetycholinesterase (adverse side effects due to acetylcholinesterase inhibition in the peripheral nervous system, limited dosing and limited clinical efficacy in advanced stages of the disease) which can be overcome by selectively inhibiting butyrylcholinesterase. We have designed, synthesized and evaluated a comprehensive series of new selective reversible butyrycholinesterase inhibitors: sulfonamide and N-propargypiperidine derivatives of hit compound 1 (IC50 = 21.3 nM) and determined their structure–activity relationships. For preparing key intermediates in the synthesis of designed compounds, we developed a general and simple synthetic procedure. Sulfonamide derivative 2 (IC50 = 4.9 nM) is promising candidate for further preclinical development. This compound is noncytotoxic and protects neuronal cells from toxic amyloid β peptide species. Its inhibits butyrycholinesterase in rat brain slices and partitions into the brains of rats after intraperitoneal injection. Compound 2 and improves memory, cognitive functions, and learning abilities of mice in a disease model of the cholinergic hypofunction in Alzheimer's disease. In the brains of patients with Alzheimer's disease the enzymatic activity of monoamine oxidase B is increased and products formed in the reaction catalyzed by this enzyme contribute to the neurodegeneration. We developed three N-propargypiperidines derivatives of hit compound 1 that inhibit both butyrycholinesterase and monoamine oxidase B. N-propargylpiperidine 6 also has neuroprotective activity and therefore represents a lead compound for design of multitarget-directed ligands against Alzheimer’s disease. In this thesis, we describe the use of structural modifications of hit compound 1 to obtain (i) a promising candidate for further preclinical development, (ii) four crystal structures of complexes of butyrycholinesterase with its inhibitors, (iii) orthogonally protected intermediates for synthesis of new cholinesterase inhibitors, and (iv) lead compounds for design of new multitarget-directed ligands.

Medicinska koordinaciona hemija predstavlja važnu oblast interdisciplinarnog istraživanja čiji je osnovni cilj dizajniranje efikasnih antikancerskih agenasa koji sadrže metal. Na početku, istraživanja o koordinacionim jedinjenjima sa antikancerogenim aktivnostima bila su usmerena na veoma uspešne hemioterapeutike na bazi platine. Međutim, sinteza novih jedinjenja sa poboljšanim svojstvima je od velike važnosti zbog pojave rezistencije, slabe aktivnosti na neke vrste raka i pojave nuspojava, tako da je cilj sinteza novih kompleksnih jedinjenja, ne samo platinskih, nego i kompleksa na bazi drugih prelaznih metala. Koordinaciona jedinjenja su veoma važna ne samo zbog njihove primene u medicini za lečenje različitih oboljenja, nego i u dijagnostici kao i u njihovoj primeni kao katalizatora u organskoj hemiji. Cilj ovog završnog rada je sinteza i karakterizacija novih kompleksnih jedinjenja na bazi rutenijuma sa 6-brompikolinskom kiselinom kao ligandom.

The reaction of the HL ligand, (E)-2-(1-(thiazol-2-ypethylidene)hydrazine-1 carbothioamide, with the metal salt MnCl2.4H20 in a molar ratio 1:1 in methanol/water mixture results in the formation of bis Mn(II) complex with composition [MnL2]. Complex crystallizes in the triclinic crystal system with space group P-1. The asymmetric unit consists of two crystallographically independent [Mn(L)2] complex molecules. The Mn(II) ion is hexacoordinated with two tridentate ligands L through NNS sets of donor atoms. The geometry around the Mn is described as a distorted trigonal prism. У реакцији лиганда HL, (Е)-2-(1-(тиазол-2-ил)етилиден)хидразин-1 карботиоамид, са MnCl2•4Н2= у молском односу 1: 1 у смеши метанол/вода добијен је комплекс, опште формуле [MnL2]. Комплекс кристалише у триклиничном кристалном систему просторне групе Р-1. Асиметрична јединица комплекса састоји се од два кристалографски независна молекула комплекса [MnL2]. Jон Мn(II) је хексакоординован преко два тридентатно депротонована лиганда која садрже NNS донорски сет атома. Геометрија око централног металног јона је искривљена тригонална-призма. Poster presented at 28th Conference of the Serbian Crystallographic Society, June 14–15th, 2023 Čačak, Serbia Poster prezentovan na XXVIII Konferenciji Srpskog kristalografskog društva Abstract: [https://cer.ihtm.bg.ac.rs/handle/123456789/6307]

In the reaction of HLC1 with Zn(BF4)2.6H20 and NaN3 in molar ratio 1 : 1 : 4 in acetonitrile/water/methanol mixture of solvents, an mononuclear Zn(II) complex (1) was obtained, with composition [ZnL(N3)2]. In complex 1, the ligand is coordinated in deprotonated, formally neutral, zwitterionic form to Zn(II) ion through the pyridine nitrogen, the imine nitrogen, and the carbonyl oxygen atoms, forming a pentacoordinated complex. Мононуклеарни азидо комплекс Zn(II), [ZnL(N3)2] (1), добијен је у реакцији Zn(BF4)2•6Н20, NaN3 и кондензационог производа 2-ацетилпиридина и Жираровог П реагенса (HLCl) у молском односу 1: 4: 1 у смеши растварача ацетонитрил/метанол/вода. У комплексу 1 јон Zn(II) је пентакоординован NNO донорским сетом атома лиганда (L) и са два азидо лиганда (Слика 1). Лиганд (L) је координован у депротонованом, формалио неутрапном, цвитерјонском облику, преко пиридинског азота, азометинског азота и карбонилног кисеоника. Poster presented at 28th Conference of the Serbian Crystallographic Society, June 14–15th, 2023 Čačak, Serbia Poster prezentovan na XXVIII Konferenciji Srpskog kristalografskog društva Abstract: [https://cer.ihtm.bg.ac.rs/handle/123456789/6306]

The ligand (E)-2-(1-(thiazol-2-yl)ethylidene)hydrazine-1-carbothioamide (HL) was obtained from the condensation of 2-acetylthiazole and thiosemicarbazide. Upon reacting HL with Zn(BF4)2.6H20 and NaN3 in a solvent mixture of water/methanol, mononuclear Zn(II) complex 1 with the composition [ZnL(N3)2] was obtained. Complex 1 crystallises in the monoclinic crystal system with space group No.14 (P21/c cell setting). The unit cell of 1 contains four [ZnL(N3)2] asymmetric units. The Zn(II) site shows a distorted pentacoordinated geometry, almost midway between the square pyramid and trigonal bipyramid. Кондензационом реакцијом 2-адетилтиазола и тиосемикарбазида добијен је лиганд (Е)-2(1-(тиазол-2-ил)етилендиен)хидразин-1-карботиоамид (HL). Комплекс 1 опште формуле [ZnL(N3)2] добијен је у реакцији лиrанда са Zn(BF4)2.6H20 и NaN3, у смеши меrанол/вода. Из података рендreнтске сlруктурне анализе утврђено је да комплекс кристалише у моноклиничном кристапном систему просторне трупе Р21lс. Јединична ћелија комплекса 1 састоји се од четири асиметричне [ZnL(N3)] јединице. Геометрија око пентакоординованог Zп(II) је искривљена, између квадратнo-пирамидaлне и тригонanно-бипирамидaлне геометрије. Oral presentation

The reaction of the HL ligand, (E)-2-(1-(thiazol-2-ypethylidene)hydrazine-1 carbothioamide, with the metal salt MnCl2.4H20 in a molar ratio 1:1 in methanol/water mixture results in the formation of bis Mn(II) complex with composition [MnL2]. Complex crystallizes in the triclinic crystal system with space group P-1. The asymmetric unit consists of two crystallographically independent [Mn(L)2] complex molecules. The Mn(II) ion is hexacoordinated with two tridentate ligands L through NNS sets of donor atoms. The geometry around the Mn is described as a distorted trigonal prism. У реакцији лиганда HL, (Е)-2-(1-(тиазол-2-ил)етилиден)хидразин-1 карботиоамид, са MnCl2•4Н2= у молском односу 1: 1 у смеши метанол/вода добијен је комплекс, опште формуле [MnL2]. Комплекс кристалише у триклиничном кристалном систему просторне групе Р-1. Асиметрична јединица комплекса састоји се од два кристалографски независна молекула комплекса [MnL2]. Jон Мn(II) је хексакоординован преко два тридентатно депротонована лиганда која садрже NNS донорски сет атома. Геометрија око централног металног јона је искривљена тригонална-призма. Poster: [https://cer.ihtm.bg.ac.rs/handle/123456789/6310]

The HL ligand, (E)-2-(1-(thiazol-2-ypethylidene)hydrazine-1-carbothioamide, was obtained from the condensation reaction of thiosemicarbazide and 2-acetylthiazole in water. The reaction of the ligand HL with Fe(BF4)2.6H20 in a molar ratio 1:1 in methanol results in the formation of bis-ligand Fe(III) complex with composition [Fe(L)2]BF4.H2O. The Fe(III) ion with L form six-coordinate complexes [Fe(L)2]3F4.H20 (1) in which two deprotonated ligand molecules coordinate in a mer arrangement, forming a distorted octahedral complex by chelation through NNS sets of donor atoms. Complex crystallizes in the orthorhombic crystal system with space group Pbca. The asymmetric unit consists of a complex cation [Fe(L)2]+, BF4- counter anion, and one water molecule. Лиганд (HL), (Е)-2-(1-(тиазол-2-ил)етилиден)хидразин-1-карботиоамид, добијен је у кондензационој реакцији тиосемикарбазида и 2-ацетилтиазола у води. Реакција лиганда и Fe(BF4)2•бН20 у молском односу 1: 1 у метанолу резултовалаје добијањем бис-лиганд комплекса Fe(III), формуле [Fe(L)2]BF4•Н20. Координовањем два молекула депротонованог лиганда (L), преко NNS донорског сета атома формира се mer окружење око Fe(III) јона искривљене октаедарске геометрије. Комплекс кристалише у орторомбичном кристалном систему, у просторној групи Pbca. Асиметричнајединица комплекса састоји се од комплексног катјона [Fe(L)2]+, анјона BF4- и једног молекула воде. Poster presented at 28th Conference of the Serbian Crystallographic Society, June 14–15th, 2023 Čačak, Serbia Poster prezentovan na XXVIII Konferenciji Srpskog kristalografskog društva Abstract: [https://cer.ihtm.bg.ac.rs/handle/123456789/6308]

The HL ligand, (E)-2-(1-(thiazol-2-ypethylidene)hydrazine-1-carbothioamide, was obtained from the condensation reaction of thiosemicarbazide and 2-acetylthiazole in water. The reaction of the ligand HL with Fe(BF4)2.6H20 in a molar ratio 1:1 in methanol results in the formation of bis-ligand Fe(III) complex with composition [Fe(L)2]BF4.H2O. The Fe(III) ion with L form six-coordinate complexes [Fe(L)2]3F4.H20 (1) in which two deprotonated ligand molecules coordinate in a mer arrangement, forming a distorted octahedral complex by chelation through NNS sets of donor atoms. Complex crystallizes in the orthorhombic crystal system with space group Pbca. The asymmetric unit consists of a complex cation [Fe(L)2]+, BF4- counter anion, and one water molecule. Лиганд (HL), (Е)-2-(1-(тиазол-2-ил)етилиден)хидразин-1-карботиоамид, добијен је у кондензационој реакцији тиосемикарбазида и 2-ацетилтиазола у води. Реакција лиганда и Fe(BF4)2•бН20 у молском односу 1: 1 у метанолу резултовалаје добијањем бис-лиганд комплекса Fe(III), формуле [Fe(L)2]BF4•Н20. Координовањем два молекула депротонованог лиганда (L), преко NNS донорског сета атома формира се mer окружење око Fe(III) јона искривљене октаедарске геометрије. Комплекс кристалише у орторомбичном кристалном систему, у просторној групи Pbca. Асиметричнајединица комплекса састоји се од комплексног катјона [Fe(L)2]+, анјона BF4- и једног молекула воде. Poster: [https://cer.ihtm.bg.ac.rs/handle/123456789/6311]

Iako su prvi plemeniti metali u medicinske svrhe korišćeni još pre 3500 godina, način na koji oni tačno deluju još uvek je u fazi ispitivanja. Mehanizmi delovanja kao i biološke mete otkrivaju se jedna po jedna, a sve dobijene informacije se koriste za dizajn novih lekova. Medicinska neorganska hemija je relativno mlada istraživačka oblast koja veliku pažnju posvećuje dizajnu i ispitivanju kompleksa sa potencijalnim antitumorskim efektom. Nakon otkrića cisplatine i njenog uspeha u kliničkoj primeni, ova interdisciplinarna istraživačka oblast razvija se velikom brzinom. Za medicinsku neorgansku hemiju su od velikog značaja kompleksi platine i rutenijuma, koji su se pokazali kao potencijalno dobri antitumorski lekovi. Primarni cilj sinteze neplatinskih lekova koji će imati potencijalno antitumorsko dejstvo jeste da se pronađu kompleksi koji će imati aktivnost prema tumorima koji su otporni na dejstvo cisplatine. U ovoj oblasti istraživanja rutenijum(II)-polipiridil kompleksi su se pokazali kao potencijalno dobri citostatici. Cilj ovog rada je sinteza i karakterizacija novih kompleksa ovog tipa. Kao ligandi su korišćeni nesteroidni antinflamatorni lekovi (NSAIL) indoprofen i nifluminska kiselina koji mogu da imaju sinergističko delovanje u lečenju tumora sa ostatkom kompleksa. Prednost ovih kompleksa predstavlja i njihova potencijalna mogućnost korišćenja kao fotosenzibilitatora u fotodinamičkoj terapiji, zasnovana na pogodnim strukturnim karakteristikama ovih supstanci.

In the reaction of HLC1 with Zn(BF4)2.6H20 and NaN3 in molar ratio 1 : 1 : 4 in acetonitrile/water/methanol mixture of solvents, an mononuclear Zn(II) complex (1) was obtained, with composition [ZnL(N3)2]. In complex 1, the ligand is coordinated in deprotonated, formally neutral, zwitterionic form to Zn(II) ion through the pyridine nitrogen, the imine nitrogen, and the carbonyl oxygen atoms, forming a pentacoordinated complex. Мононуклеарни азидо комплекс Zn(II), [ZnL(N3)2] (1), добијен је у реакцији Zn(BF4)2•6Н20, NaN3 и кондензационог производа 2-ацетилпиридина и Жираровог П реагенса (HLCl) у молском односу 1: 4: 1 у смеши растварача ацетонитрил/метанол/вода. У комплексу 1 јон Zn(II) је пентакоординован NNO донорским сетом атома лиганда (L) и са два азидо лиганда (Слика 1). Лиганд (L) је координован у депротонованом, формалио неутрапном, цвитерјонском облику, преко пиридинског азота, азометинског азота и карбонилног кисеоника. Poster: [https://cer.ihtm.bg.ac.rs/handle/123456789/6309]

Ova doktorska disertacija temelji se na istraživanju (i) diskretnih i metalocikličkih spojeva, koordinacijskih polimera MoVI s nikotinhidrazonskim ligandima, (ii) soli, solvata i kokristala koordinacijskih spojeva MoVI s izonikotinhidrazonskim ligandima, (iii) organsko-anorganskih polioksomolibdatnih hibrida, i konačno (iv) metalosupramolekulskih spojeva temeljenih na različitim supstituentima i hidrazidnim komponentama liganda. Opisani su čimbenici koji utječu na njihovo nastajanje, specifični uvjeti pri kojima dolazi do nastajanja različitih izomera ili polimorfa kao i strukturne transformacije u čvrstom stanju i u otopini. Naglasak je dan na strukturnu raznolikost navedenih spojeva s obzirom na (i) protonaciju i deprotonaciju liganda, (ii) kristalizaciju različitih polimorfa; (iii) zamjenu liganada; (iv) procese samoudruživanja i kristalni rast; (v) reakcije transmetalacije i (vi) zamjene aniona. Dobiveno je 64 novih spojeva te su karakterizirani na temelju kemijske analize, difrakcijom rendgenskog zračenja na polikristalnom uzorku te spektroskopskim i termičkim metodama, a 55 spojeva identificirano je na temelju difrakcije rendgenskog zračenja na jediničnom kristalu. This doctoral thesis is based on the research of (i) MoVI discrete, metallocyclic compounds and coordination polymers with nicotinic hydrazone ligands, (ii) salts, solvates, and co-crystals of MoVI coordination compounds with isonicotinhydrazone ligands, (iii) organic-inorganic polyoxomolybdate hybrids, and finally (iv) metallosupramolecular architectures based on different ligand substituents and hydrazide components. The factors that influence their formation, specific conditions that lead to the formation of different isomers or polymorphs, as well as structural transformations in the solid state and solution, are described. Emphasis is given on the structural diversity concerning (i) the ligand protonation and deprotonation, (ii) crystallization of different polymorphs, (iii) substitutions of ligands, (iv) processes of selfassociation and crystal growth, (v) transmetalation reactions and (vi) anion exchange. 64 new compounds were obtained and characterized by chemical analysis, powder X-ray diffraction, spectroscopic and thermal methods, and 55 monocrystalline samples were identified by the single crystal X-ray diffraction method.

V magistrskem delu sem po modificiranih postopkih sintetiziral enoatomske elektrokatalizatorje kovin prehoda (SAC) na osnovi niklja, kobalta, mangana in železa na reduciranem grafen oksidu (rGO), ki naj bi izkazovali selektivnost za elektrosintezo vodikovega perksida. Vse sintetizirane SAC materiale na rGO sem ustrezno okarakteriziral s sledečimi metodami: vrstični elektronski mikroskop (SEM), energijsko disperzijska rentgenska spektroskopija (EDS), rentgenska fotoelektronska spektroskopija (XPS), ramanska spektroskopija in BET analiza specifične površine. Prav tako sem pri karakterizaciji elektrokatalizatorjev uporabil elektrokemijske metode, kot so: ciklična voltametrija (CV) v kombinaciji z rotirajočo disk elektrodo (RDE) in rotirajočo disk elektrodo z obročem (RRDE). Proučil in primerjal sem njihovo morfologijo, kemijsko strukturo in elektrokemijske lastnosti. Rezultati so pokazali, da je najustreznejši elektrokatalizator za elektrosintezo vodikovega peroksida, Ni na rGO v alkalnem elektrolitu. Rezultati raziskave so uporabni za nadaljnje raziskave, razvoj in optimizacijo elektrokatalizatorjev za selektivno in učinkovito elektrosintezo vodikovega peroksida. In the master's thesis, I synthesized transition metal single atom electrocatalysts (SAC) based on nickel, cobalt, manganese and iron on reduced graphene oxide (rGO) using modified procedures, which should show selectivity for the electrosynthesis of hydrogen peroxide. All synthesized SAC materials on rGO were properly characterized by the following methods: scanning electron microscope (SEM), energy dispersive X-ray spectroscopy (EDS), X-ray photoelectron spectroscopy (XPS), raman spectroscopy and BET specific surface area analysis. To investigate their electrochemical performance additional characterization methods such as cyclic voltammetry (CV), chronoamperometry (CA) with rotating disk electrode (RDE) and rotating ring-disk electrode (RRDE) were used. The morphology, chemical structure and electrochemical properties were compared. The results showed that the most suitable electrocatalyst for the electrosynthesis of hydrogen peroxide is Ni on rGO in an alkaline electrolyte. The research results are useful for further research, development and optimization of electrocatalysts for the selective and efficient electrosynthesis of hydrogen peroxide.

Walking mechanisms are a solution for cases in which wheels are not applicable, such as uneven or stepped surfaces and surfaces withobstacles. Furthermore, it is possible to tailor mechanism footpaths to expected working conditions through optimization. Thus, in this paper, a mechanism optimization process was proposed, focusing on single-leg performance. Numerical Simulink calculations were used to determine objective function values, which were then input to a non-dominated sorting genetic algorithm (NSGA-II) for optimization. In each following generation, NSGA-II provided a new set of units for evaluation. The procedure was applied to the single leg of the Chebyshev lambda mechanism to better illustrate it, enabling a comprehensive analysis of candidates. Four objective functions (i.e., length in the x-direction, trajectory height variation, maximum foot acceleration, and foot speed fluctuation) were used to carry out a multi-objective optimization. The calculation time was approximately 2 s/unit.

Poraba električne energije od začetka industrijske revolucije vztrajno narašča. Ker so zaloge fosilnih goriv omejene, se raziskovalci usmerjajo v iskanje novih, alternativnih virov, predvsem obnovljivih. Glede na podatek, da lahko Sonce v enem dnevu proizvede več energije, kot jo človeštvo porabi v enem letu, je presenetljivo da ta vir energije ni pogosteje uporabljen. Razlog za to so previsoki stroški proizvodnje glede na nizke izkoristke pretvorbe električne energije, ki jo dosegajo silicijeve sončne celice. Zato strokovnjaki na fotovoltaičnem področju raziskujejo nadomestke silicijevih sončnih celic. Eden od bolj obetavnih alternativ so perovskitni materiali. Prvič so bili predlagani v fotovoltaične namene šele leta 2006, od takrat pa je njihova učinkovitost narasla od 2,2 % do 25,5 % v letu 2020. Absorpcijsko plast v perovskitni sončni celici sestavljajo 3D mešani organsko-anorganski perovskiti s splošno formulo ABX3. Najbolj raziskan in uporabljen je trenutno metilamonijev svinčev jodid, CH3NH3PbI3, vendar se zaradi strupene narave svinca raziskuje uporaba drugih kovin. Poleg kovine se lahko menja organski kation na A mestu ter halogenidni anion X. S spreminjanjem ionov se spreminja kristalna struktura, kar vpliva na električne in optične lastnosti materiala. Niso pa vsi perovskiti primerni za sončne celice. Parametra, ki določata ali bo nek perovskit uporaben v fotovoltaiki ali ne, sta tolerančni in oktaedrični faktor. V magistrski nalogi smo se osredotočili na sintezo in karakterizacijo mešanih organsko-anorganskih perovskitov, ki imajo na anionskem mestu jodidni ion. Po pregledu ustrezne literature ter izračunu tolerančnih in oktaedričnih faktorjev, s katerimi smo preverili, da pride do tvorbe idealne kubične strukture, je sledila sinteza petih različnih perovskitov. Sinteza je potekala v dveh delih, in sicer smo najprej pripravili organski del, v drugem delu pa smo tega raztopili skupaj z anorganskim jodidom v izbranem topilu. Štirje od pripravljenih perovskitov so imeli na A mestu metilamonijev jodid, za raztapljanje pa smo uporabili topilo GBL. Zadnji sintetiziran perovskit je imel na mestu A mešan kation, sestavljen iz formamidinijevega in cezijevega jodida, kot topilo pa smo uporabili mešanico DMF in DMSO. Pripravljene perovskite smo okarakterizirali s pomočjo rentgenske praškovne difrakcije, difrakcije monokristala ter optične mikroskopije. Tistim perovskitom, ki so bili uspešno sintetizirani, pa smo preverili še UV ter termično obstojnost. XRD analiza je pokazala, da smo uspešno sintetizirali oba organska prekurzorja, MAI ter FAI. Od perovskitov pa smo dobili željen produkt le pri sintezi MAPbI3. Pri kositrovem analogu se je v strukturo vrinil Br, pri Ca in Cd perovskitu pa smo imeli precej težav že s samo sintezo, zato smo jo morali nekako prilagoditi. Nov način sušenja je rezultiral v perovskitni strukturi MACdI3, medtem ko je pri Ca analogu nastala nova, še neraziskana spojina. Tej spojini smo s pomočjo difrakcije monokristala uspešno določili kristalno strukturo. Pri sintezi FA0,83Cs0,17PbI3 pa nismo dobili homogenega perovskita, temveč je produkt vseboval dve fazi. Electricity consumption has been steadily increasing since the beginning of the industrial revolution. Since fossil fuel reserves are limited, researchers are focusing on the search for new, alternative sources, especially renewable ones. Considering that the Sun can produce more energy in one day than humanity consumes in a year, it is surprising that this source of energy is not used more often. The reason for this is the cost of production, given the low efficiencies of electricity conversion achieved by silicon solar cells. Therefore, experts in the photovoltaic field are researching substitutes for silicon solar cells. One of the more promising alternatives are perovskite materials. They were first proposed for photovoltaic purposes only in 2006, and since then their efficiency has increased from 2.2 % to 25.5 % in 2020. The absorption layer in a perovskite solar cell consists of 3D mixed organic-inorganic perovskites with the general formula ABX3. The most studied and used currently is methylammonium lead iodide, CH3NH3PbI3, but due to the toxic nature of lead, the use of other metals is being explored. In addition to the metal, the organic cation in the A site and the halide anion X can be changed. By changing the ions, the crystal structure changes, which affects the electrical and optical properties of the material. However, not all perovskites are suitable for solar cells. The parameters that determine whether a perovskite will be suitable in photovoltaics or not are the tolerance factor and the octahedral factor. In the master thesis, we focused on the synthesis and characterization of mixed organic-inorganic perovskites, which have an iodide ion at the anionic site. After reviewing the relavant literature and calculating the tolerance and octahedral factors, which were used to verify that an ideal cubic structure would be formed, the synthesis of five different perovskites was done. The synthesis took place in two parts: first, we prepared the organic part, and in the second part, we dissolved it together with the inorganic iodide in the selected solvent. Four of the prepared perovskites had methylammonium iodide at the A site, and GBL solvent was used for dissolution. The last synthesized perovskite had a mixed cation consisting of formamidinium and cesium iodide at the A site, while DMF and DMSO were used as a solvent mixture. The prepared perovskites were characterized using X-ray powder diffraction, single crystal diffraction and optical microscopy. Those perovskites that were successfully synthesized were also tested for UV and thermal stability. XRD analysis showed that we successfully synthesized both organic precursors, MAI and FAI. From perovskites, the desired product was obtained only in the synthesis of MAPbI3. With the tin analogue, Br crept into the structure, and with the Ca and Cd perovskite, we had a lot of troubles with the synthesis itself, so we had to somehow adapt it. A new drying method resulted in the MACdI3 perovskite structure, while the Ca analogue resulted in a new, yet unexplored compound. The crystal structure of this compound was successfully determined using single crystal diffraction. In the synthesis of FA0.83Cs0.17PbI3, we did not obtain a homogeneous perovskite, but the product contained two phases.

V okviru diplomske naloge sem pregledala znanstveno literaturo za postopke sintez kovinskih kompleksov 6-metoksikinolina z zlatom(I/III) oziroma platino(II). Enake sintezne postopke sem po preizkušenih reakcijah s 6-metoksikinolinom preizkusila še z molekulo dihidrokinidina. Pri tem sem v reakcijah spreminjala reakcijske pogoje in sinteze preizkušala z uporabo različnih topil. Večino reakcij sem opravljala v temi zaradi občutljivosti na svetlobo zlatovih in platinskih soli. Cilj diplomske naloge je bil pripraviti kompleks 6-metoksikinolina ali dihidrokinidina z zlatom oziroma platino brez nečistoč. Sintetizirane produkte sem okarakterizirala z NMR, masno spektrometrijo in rentgensko strukturno analizo. As part of my diploma thesis, I reviewed the scientific literature for the synthesis procedures of metal complexes of 6-methoxyquinoline with gold(I/III) and platinum(II). After the tested reactions with 6-methoxyquinoline, I tried the same synthesis procedures with the dihydroquinidine molecule. While doing that, I changed the reaction conditions in the reactions and tested the syntheses using different solvents. Most of the reactions were preformed in the dark, due to the light sensitivity of gold and platinum salts. The goal of my thesis was to prepare a complex of 6-methoxyquinoline or dihydroquinidine with gold or platinum without impurities. I characterized the synthesized products by NMR, mass spectrometry and X-ray structural analysis.

Cilj rada je prikazati sintezu i evaluaciju konjugata fenilboronične i cimetne kiseline. Fenilboronična kiselina pripada derivatima borne kiseline. Poznata je po svojim mogućim medicinskim svojstvima te je istraživana kao sredstvo u liječenje raka. Cimetna kiselina je široko zastupljena u biljnom svijetu, a izvor je većine derivata hidroksicimetne kiseline poput kumarinske, kafeinske, ferulinske i sinapinske kiseline. U ovom radu opisane su fenilboronična i cimetna kiselina općenito, njihova kemijska svojstva i strukture, upotreba njihovih derivata, te konačno sinteza fenilboronične i cimetne kiseline. Za potrebe rada korištena je relevantna literatura koja se odnosi na stručne članke i knjige koji su u skladu sa temom rada. The aim of this work is to present the synthesis and evaluation of the conjugate of phenylboronic acid and cinnamic acid. Phenylboronic acid belongs to the derivatives of boric acid. It is known for its potential medicinal properties and has been explored as a treatment for cancer. Cinnamic acid is widely distributed in the plant world and is the source of most hydroxycinnamic acid derivatives such as coumarin, caffeic acid, ferulic acid, and sinapic acid. In this paper, phenylboronic and cinnamic acids in general, their chemical properties and structures, the use of their derivatives and finally the synthesis of phenylboronic and cinnamic acids are described. Relevant literature was consulted for the paper, referring to technical articles and books corresponding to the subject of the paper.

Gvajakol ali 2-metoksifenol je naravni produkt, ki se nahaja v gvajakovi smoli in nastaja pri oksidaciji lignina. Je brezbarvna do rumenkasta viskozna tekočina z značilnim vonjem po dimu. Prav zaradi tega ga uporabljamo kot aromatično sredstvo pri pripravi kave, viskija, pomemben je kot izhodna snov pri sintezi vanilina. V medicini ga uporabljamo kot antiseptik, ekspektorant in lokalni anestetik. Kot vsa eterična olja (EO), oziroma pravilneje kot oleorezin, je tudi gvajakova smola zmes med 10 in 200 hlapnih lipofilnih sestavin, med katerimi prevladujejo monoterpenski in seskviterpenski ogljikovodiki. EO so zelo hlapna, kar omogoča, da jih zavohamo tudi v zelo razredčenih oblikah. Namen diplomske naloge je bila sinteza lipofilnih derivatov gvajakola in njihovo olfaktorno ovrednotenje. Iskali smo tiste derivate, ki imajo prijeten vonj za uporabo v parfumih. Spremembe smo izvajali na prosti -OH skupini gvajakola, da smo dobili hlapne estre in etre. Pri reakcijah smo dobili zmesi produktov, ki smo jih nato očistili s kolonsko kromatografijo. Produkte smo analizirali z 1H NMR in IR spektroskopijo ter potrdili, da je 9 od 10 reakcij uspešno poteklo. Nastale produkte smo nato ovrednotili z vonjalnim testom, kjer so prostovoljci ocenjevali prijetnost in jakost vonjev ter ovrednotili svoje asociacije na vzorce. Večina vzorcev jim ni bila prijetna, saj so le tri od devetih označili za prijetne. Pri štirih vzorcih pa so navedli asociacijo na dim, kar pomeni, da so nastali sintezni produkti obdržali značilen (in željen) aromatični vonj gvajakola. Guaiacol or 2-methoxyphenol is a natural product found in guaiac resin and is formed by the oxidation of lignin. is the compound is colourless or yellow and it has a distinctive smell of smoke. Because of this it is commonly used as an aromatic agent in making coffee, whisky and is an important starting material in the synthesis of vanillin. It is used in medicine because of its antiseptic, expectorant and local anaesthetic properties. As most essential oils or correctly oleoresins, guaiac resin is a mixture of 10 to 200 volatile and lipophilic components, most of which are monoterpene and sesquiterpene hydrocarbons. EO are highly volatile, which allows them to be smelled in dilute forms. The purpose of this thesis was the synthesis of lipophilic guaiacol derivatives and their olfactory evaluation. Our aim was to find derivatives that have a pleasant smell, which might be used in perfumes. Modifications were made on the free -OH group of guaiacol to synthesise esters and ethers. The reaction yielded mixtures of products, which we then cleaned by column chromatography to get the isolated synthesis products. We then analysed those with 1H NMR and IR spectroscopy to confirm 9 out of 10 reactions were successful. Afterwards we made an olfactory evaluation of the synthesised products. Volunteers evaluated the pleasantness and intensity of the derivatives and listed their associations to the smells. They rated most of the smells as not pleasant, with only 3 derivatives out of 9 rated as pleasant. They associated 4 out of 9 samples with smoke and smoky smell, which means the derivatives retained the distinctive smell of guaiacol.

Cinamil alkohol in cimetova kislina sta naravni spojini, ki se uporabljata v parfumski in kozmetični industriji ter farmaciji. Najbolj znana je njuna prisotnost v cimetovcu, ki spada v družino lovorovk (Lauraceae). Cinamil alkohol in cimetova kislina sta sestavini eteričnega olja cimeta, ki ga pridobivajo iz listov, lubja in korenin. Pri standardnih pogojih je cinamil alkohol bela do rumenkasta kristalna trdna snov, s prijetnim, cvetličnim in sladkim vonjem ter okusom po cimetu. Cimetova kislina pa je bela kristalna organska spojina, katere vonj spominja na med. V naravi so cimetova kislina in njeni derivati zelo razširjeni, a jih večinoma najdemo v zelo nizkih koncentracijah. Sintezno pridobljena cimetova kislina pa nastaja s Perkinovo reakcijo. Namen diplomske naloge je bil sintetizirati derivate cinamil alkohola in cimetove kisline ter nastale produkte olfaktorno ovrednotiti. Uspešno smo sintetizirali deset njunih derivatov, po strukturi estrov in etrov. Ena reakcija ni potekla. Vse produkte smo očistili s kolonsko adsorpcijsko kromatografijo, kjer smo za razvijanje kromatogramov uporabili mobilno fazo, sestavljeno iz zmesi etilacetata in heksana v volumskem razmerju 1 : 4 ter 1 : 6. Uspešnost reakcij in identiteto produktov smo preverili z instrumentalnimi analiznimi metodami, in sicer z uporabo jedrske magnetne resonance ter infrardeče spektroskopije. Nato smo končne spojine olfaktorno vrednotili z vonjalnim testom, s katerim smo preverjali prijetnost in jakost vonjav ter asociacije na druge vonje. Večina derivatov cinamil alkohola in cimetove kisline ima prijeten vonj. Povprečna ocena jakosti vonjev testiranih vzorcev ima šibek do zmerno močan vonj. Vonji niso bili konstantni in so se tekom vonjalne analize spreminjali. Pri vrednotenju vzorcev so anketiranci označili cinamil butirat, cinamil fenilacetat in cinamil heksileter kot najprijetnejše vonjave. Pri opisovanju vonjav nismo ugotovili nobenih razlik med osebami, ki parfume uporabljajo in tistimi, ki jih ne. Cinnamyl alcohol and cinnamic acid are natural compounds used in the perfume, cosmetics and pharmaceutical industries. They are best known to be found in cinnamon tree, which belongs to the family of laurels (Lauraceae). Cinnamyl alcohol and cinnamic acid are components of cinnamon essential oil, which is extracted from the leaves, bark and roots of cinnamon. Under standard conditions, cinnamyl alcohol is a white to yellowish crystalline solid, with a pleasant, floral and sweet aroma and cinnamon taste. Cinnamic acid is a white crystalline organic compound with an odour reminiscent of honey. Cinnamic acid and its derivatives are widespread in nature, but are mostly found in very low concentrations. Synthetically produced cinnamic acid is produced by the Perkin reaction. The aim of the thesis was to synthesize derivatives of cinnamyl alcohol and cinnamic acid derivatives and and evaluate these products in an olfactory analysis. Ten of their derivatives were successfully synthesised, according to the structure of esters and ethers. One reaction did not proceed. All the products were cleaned by column adsorption chromatography, where chromatograms were developed using a mobile phase consisting of a mixture of ethyl acetate and hexane in volume ratios of 1 : 4 and 1 : 6. The success of the reactions and the identity of the products were verified by instrumental analytical methods, nuclear magnetic resonance and infrared spectroscopy. The final products were then evaluated olfactorially by an odour test, which was used to check the pleasantness and strength of aromas and their associations with other odours. Most derivatives of cinnamyl alcohol and cinnamic acid have a pleasant smell. The average odour strength rating of the tasted samples has a weak to moderately strong odour. The odours were not constant and varied during the odour analysis. When evaluating the samples, respondents indicated cinnamyl butyrate, cinnamyl phenylacetate and cinnamyl hexyl ether as the most pleasant odours. No differences were found between respondents who use perfumes and those who do not.

Halicin je spojina, ki je sestavljena iz dveh heterocikličnih obročev, ki ju povezuje žveplov atom. V okviru diplomskega dela sem pripravila različne spojine podobne halicinu, v katerih sem spreminjala heterociklične substituente. Cilj raziskovalnega dela je bil optimizirati izkoristek reakcij in odstraniti prisotne nečistoče. Spojine sem karakterizirala z jedrsko magnetno resonanco, elementno analizo in masno spektrometrijo visoke ločljivosti. Kristali so bili karakterizirani z rentgensko strukturno analizo. Rezultati karakterizacij so pri nekaterih sintezah pokazali uspešno sintetiziran produkt. Halicin is a compound in which two heterocycles are connected by a sulfur atom. In the framework of the diploma thesis, I prepared different compounds similar to halicin in which I varied heterocyclic substituents. The goal of the research was to optimise the yield of reactions and to remove any impurities present. The compounds were characterized with nuclear magnetic resonance, elemental analysis and mass spectrometry of high resolution. The crystals were characterized by X-ray structural analysis. The results of characterizations have shown a successfully synthetised product in some syntheses.

Liginin je makromolekula sestavljena iz fenilpropanskih enot zamreženih preko etrskih vezi, med katerimi prevladujejo beta-O-4 vezi. Molekula lignina je zelo kompleksna, zato se za študij njegove reaktivnosti in tudi strukture pogosto uporabljajo modelne molekule. V diplomskem delu se bom tako posvetil sintezi modela, ki vsebuje beta-O-4 vez, kar lahko na primer poenostavi študij depolimerizacije lignina, analizo produktov, ki nastanejo pri depolimerizaciji lignina in razumevanje njenega mehanizma. V sedanjem času je depolimerizacija lignina eden izmed bolj perspektivnih postopkov pridobivanja aromatskih molekul iz trajnostnih virov, zato je zanimanje za raziskave veliko. S samo sintezo modelne molekule želim tudi prispevati k boljšemu razumevanju kompleksnosti lignina. Lignin is a macromolecule composed of phenylpropyl units cross-linked by ether bonds, with beta-O-4 bonds predominating. Lignin molecule is very complex, so model compounds are usually used to study its reactivity and structure. In my diploma thesis I will focus on the synthesis of a model containing a beta-O-4 bond – this model can simplify the study of depolymerization, the analysis of products of depolymerization and the mechanism itself. Currently, the depolymerization of lignin is one of the most promising processes for the production of aromatic molecules from sustainable sources – thus, the interest in lignin model compounds is high. With the synthesis of lignin model compound, I would also like to contribute to a better understanding of the complexity of lignin itself.

Glavni je zadatak ovog rada analiza i sinteza sustava upravljanja korištenjem MATLAB programa. Najprije je proveden opis procesa koji uključuje određivanje matematičkog modela za zadani proces. Nakon što je bila utvrđena nelinearnost procesa izvršena je linearizacije istog. Potom je slijedila analiza procesa grafoanalitičkom metodom, odnosno krivuljom mjesta korijena. Analizom je utvrđena nestabilnost procesa, stoga je bilo potrebno projektirati takav regulator koji će ga stabilizirati. Za regulator odabran je regulator s faznim prethođenjem. Sinteza regulatora se provodi na temelju zahtjeva korisnika unešenih u korisničko sučelje izgrađenog u App Designeru. U konačnici, izvršena je simulacija kojom se pokazalo primjer korištenja sučelja te je kroz dva primjera pokazano kako su zadovoljena tražena dinamička vladanja. The main task of this paper is the analysis and synthesis of a control system using MATLAB program. Firstly, a description of the process was made, which included determining a mathematical model for the given process. After nonlinearity of the process was determined, its linearization was performed. Then followed the analysis of the process using graphoanalytical method, ie the root locus diagram. The analysis confirmed the instability of the process, so it was necessary to design such a controller to stabilize it. A phase lead controller was selected. The design of the controller is performed based on the user requirements entered in the user interface built in the App Designer. Finally, a simulation was performed which showed an example of using the interface and showed through two examples how the dynamic requirements of the control system were met.

U ovom završnom radu provedena je sinteza i spektroskopska karakterizacija novih supstituiranih derivata amino-heterostilbena kao potencijalno biološki aktivnih molekula. Sinteza novih amino-heterostilbena provedena je u nekoliko koraka. Wittigovom reakcijom dobiveni su cis- i trans-heterostilbeni iz tiofen-2-karbaldehida i 1-brom-2-(4-klorbenzil)fosfonijeve soli, koji su u sljedećem koraku reakcijom Buchwald-Hartwigovog aminiranja prevedeni u spojeve 2-6. Novonastali spojevi pročišćeni su uzastopnom kolonskom i tankoslojnom kromatografijom pomoću preparativnih ploča obloženih silikagelom. Dobiveni produkti uspješno su izolirani i okarakterizirani spektroskopskim metodama. Prilikom izrade ovog završnog rada ukupno je dobiveno deset amino-heterostilbena, te pet elektrociklizacijskih produkata. In this final work, the synthesis and spectroscopic characterization of new substituted derivatives of amino-heterostilbene were performed as potential biologically active molecules. The Wittig reaction gave cis- and trans-heterostilbenes from thiophene-2-carbaldehyde and 1-bromo-2-(4-chlorobenzyl)phosphonium salt, which were converted into compounds 2-6 by the Buchwald-Hartwig amination reaction in the second step. The newly formed compounds were purified by repeated column and thin-layer chromatography using preparative plates coated with silica gel. The obtained products were successfully isolated and characterized by spectroscopic methods. During the preparation of this work, a total of ten amino-heterostilbenes and five electrocyclization products were obtained.

In this study, we present the synthesis, kinetic studies of inhibitory activity toward aldo-keto reductase 1C (AKR1C) enzymes, and anticancer potential toward chemoresistant ovarian cancer of 10 organoruthenium compounds bearing diketonate (1–6) and hydroxyquinolinate (7–10) chelating ligands with the general formula [(η6-p-cymene)Ru(chel)(X)]n+ where chel represents the chelating ligand and X the chlorido or pta ligand. Our studies show that these compounds are potent inhibitors of the AKR enzymes with an uncommon inhibitory mechanism, where two inhibitor molecules bind to the enzyme in a first fast and reversible step and a second slower and irreversible step. The binding potency of each step is dependent on the chemical structure of the monodentate ligands in the metalloinhibitors with the chlorido complexes generally acting as reversible inhibitors and pta complexes as irreversible inhibitors. Our study also shows that compounds 1–9 have a moderate yet better anti-proliferative and anti-migration action on the chemoresistant ovarian cancer cell line COV362 compared to carboplatin and similar effects to cisplatin.

Cilj ove doktorske disertacije je razumevanje i proučavanje organizacijemolekula vode i njihovog uticaja na fizičko-hemijska svojstva odabranih biološki aktivnih jedinjenja, kao i dobijanje novih biološki aktivnihjedinjenja u obliku jonskih tečnosti sa poboljšanom rastvroljivošću i bioraspoloživošću. Iz fizičko-hemijskih parametara vodenihrastvora biološki aktivnih jedinjenja, dobijenih upotrebom različitih eksperimentalnih tehnika, računarskih simulacija, kao i toksikoloških ispitivanja, uspostavljena je korelacija njihove strukture sa organizacijom vode oko njih, kao i metaboličkih procesa u kojima učestvuju, The aim of this doctoral dissertation is to understand and study the organization of water molecules and their impact on the physicochemical properties of selected biologically active compounds, as well as obtaining new biologically active compounds in the form of ionic liquids with improved solubility and bioavailability. From the physicochemical parameters of aqueous solutions of biologically active compounds, obtained by various experimental techniques, computer simulations, as well as toxicological tests, the correlation of their structure with the organization of water around them, as well as metabolic processes in which they participate.

U radu se objašnjavaju pojmovi vezani za zvučne signale, posebice glasovne te njihove značajke poput amplitude, spektralne ovojnice i formanta. Predstavlja se anatomski model vokalnog trakta i objašnjava kako se odvija cijeli proces proizvodnje glasa, od pluća koja u suradnji s glasnicama služe kao generator zvučnog signala, do vokalnog trakta koji modulira zvučne valove i daje im specifične značajke. Potom, preko nekoliko iteracija mehaničkih modela za proizvodnju glasa, dolazimo do računalnih modela koji sintetiziraju glas te prepreka koje postoje u tom pristupu. Konačno, prikazana je usporedna analiza sintetiziranog i prirodnog glasa. This paper explains the basics of audio signals, especially voice signals and their features such as amplitude, spectral envelope and formants. An anatomical model of the vocal tract is present, and the complete voice production process is explained, from the lungs which alongside the vocal cords serve as the sound wave generator, to the vocal tract which modulates the sound waves and gives them their specific features. Then, after a few iterations of mechanical models for voice production, we arrive at the modern voice synthesis computer models and the obstacles that follow. Finally, a comparative analysis of the synthesised and natural voice is shown.

Človeška katepsina K in S sta člana družine papainu podobnih peptidaz z zelo podobnima terciarnima strukturama. V človeškem telesu imata številne fiziološke vloge, pri čemer je najpomembnejša biološka vloga katepsina K razgradnja kolagenskih vlaken kostnega tkiva, medtem ko ima katepsin S zelo pomembno fiziološko vlogo pri regulaciji predstavitve antigenov. Katepsina K in S morata biti ustrezno regulirana, saj njuni povečani encimski aktivnosti lahko prispevata k napredovanju številnih bolezni. Glede na to, da so nekateri inhibitorji katepsinov K in S dosegli klinične faze razvoja, ta dva encima predstavljata pomembni potencialni terapevtski tarči za razvoj zdravilnih učinkovin. Ciljanje evolucijsko manj ohranjenih alosteričnih mest bi lahko omogočilo bolj selektivno inhibicijo, ki bi povzročala manj stranskih učinkov, kar bi tako predstavljalo alternativni način za terapevtske namene. Hiperbolični inhibitor katepsina K, metil [(3RS)-2,5-dioksopirolidin-3-il]glicinat (3a), smo podrobneje okarakterizirali in pokazali, da je selektiven na katepsin K glede na človeške katepsine B, L, S in V. Glede na to, da je 3a imel šibek inhibitorni učinek tudi na katepsin S, smo na njegovi osnovi zasnovali in pripravili potencialne inhibitorje katepsinov K in S, ki bi se z večjo afiniteto in bolj selektivno vezali na posamezen encim. Tistim z največjo potentnostjo smo določili njihove točnejše vrednosti afinitet ter mehanizme delovanja. Namen raziskovalnega dela je bil tudi, da bi na osnovi superpozicije terciarnih struktur človeških katepsinov K in S in na osnovi potencialnih alosteričnih poti človeškega katepsina K, predvidenih s simulacijami molekularne dinamike, načrtali in pripravili mutantne oblike teh dveh encimov ter identificirali aminokislinske ostanke, ki so pomembni za njuno alosterično regulacijo. Načrtali in pripravili smo spojine s substituenti na dveh mestih za diverzifikacijo sukcinimidnega ogrodja spojine 3a. Med njimi smo spojino metil [(3R)-2,5-dioksopirolidin-3-il]-L-treoninat (R-3c) okarakterizirali kot hiperbolični inhibitor katepsina S ter ji z rentgensko strukturno analizo določili absolutno (2S,3R,3'R)-konfiguracijo. Nato smo načrtali in pripravili ciklične derivate spojine R-3c ter med štirimi derivati spojino (3’RS)-3-{[(1S,2R)-2- hidroksicikloheksil]amino}pirolidin-2,5-dion ((1S,2R)-7) identificirali in okarakterizirali kot hiperbolični in selektivni inhibitor katepsina S z največjo potentnostjo. Z meritvami encimske kinetke smo pokazali, da hiperbolični inhibitorji katepsina K oz. S, in sicer spojine 3a, R-3c in (1S,2R)-7, delujejo po podobnih mehanizmih kot alosterična efektorja katepsina K. Na ta način smo identificirali in okarakterizirali prva malomolekulska hiperbolična inhibitorja katepsina S (R-3c in (1S,2R-7). Poleg tega smo potrdili del hipoteze raziskovalnega dela, saj smo dokazali, da spojina (1S,2R)-7 selektivno inhibira katepsin S glede na katepsin K. Mehanizmi delovanja, ki smo jih določili tem spojinam, so v skladu z rezultati testiranj spojin na razgradnjo makromolekulskih substratov s katepsinoma K in S. Hiperbolični inhibitorji 3a, R-3c in (1S,2R)- 7 imajo potencial za nadaljnji razvoj do spojin vodnic, uporabnih v raziskovalne namene. Načrtali in pripravili smo mutantne oblike katepsinov K in S z ostanki zamenjanimi z ostankom alanina v predvideni alosterični poti in v alosteričnem mestu katepsina K ter v homolognem mestu katepsina S. Pokazali smo, da sta ostanka v alosterični poti N202 in N208 pomembna za alosterično komunikacijo katepsina K med alosteričnim mestom in mestom S2. Human cathepsins K and S are members of the protein family of cysteine cathepsins with very similar tertiary structures. They have numerous physiological roles in human body, particularly the most important biological role of cathepsin K is degradation of collagen fibre in bone tissue, whereas cathepsin S plays a very important physiological role in regulating antigen presentation. Cathepsins K and S have to be sufficiently regulated since their increased enzyme activities could contribute to the progression of numerous diseases. Considering certain inhibitors of individual cathepsins K and S have reached clinical trials, these two enzymes represent important potential therapeutic targets for drug design. Targeting evolutionary less conserved allosteric sites could enable more selective inhibition, which could cause less side effects and could therefore represent an alternative approach for therapeutic purposes. After detailed characterization of hyperbolic inhibitor of cathepsin K, methyl [(3RS)-2,5- dioxopyrrolidin-3-yl]glycinate (3a), it was shown that it is selective against cathepsin K over human cathepsins B, L, S in V. Since 3a displayed weak inhibitory effect for cathepsin S, as well, we designed and prepared potential inhibitors of cathepsins K and S based on 3a, which would bind with higher affinities and more selectively to individual enzyme. For the most potent inhibitors, more accurate values of affinities and mechanisms of action were determined. The aim of the research work was also to design and prepare mutant forms of enzymes based on superposition of tertiary structures of human cathepsins K and S and based on potential allosteric pathways of human cathepsin K, predicted by molecular dynamic simulations, as well, and to identify residues important for their allosteric regulation. We designed and prepared compounds with substituents at two sites for diversification of the succinimide scaffold of compound 3a. Among them, methyl [(3R)-2,5-dioxopyrrolidin-3-yl]-L-threoninate (R-3c) was characterized as a hyperbolic inhibitor of cathepsin S and its absolute (2S,3R,3'R)-configuration was determined by X-ray structural analysis. Then, we designed and prepared cyclic derivatives of the compound R-3c and among four derivatives, (3’RS)-3- {[(1S,2R)-2- hydroxycyclohexyl]amino}pyrrolidine-2,5-dione ((1S,2R)-7) was identified and characterized as the most potent hyperbolic selective inhibitor of cathepsin S. It was shown by enzyme kinetics that allosteric modifiers of cathepsin K or S, compounds 3a, R-3c and (1S,2R)- 7, act via similar mechanisms as allosteric effectors of cathepsin K NSC13345 in NSC94914. Therefore, the first small-molecule allosteric effectors of cathepsin S (R-3c and (1S,2R)-7) were identified and characterized. Apart from that, one part of the hypotheses of our research work was confirmed since it was shown that the compound (1S,2R)-7 selectively inhibits cathepsin S over cathepsin K. The mechanisms of action, which were determined for the compounds, are consistent with the results of compound screening on degradation of macromolecular substrates via cathepsins K and S. Hyperbolic inhibitors 3a, R-3c in (1S,2R)-7 have the potential to be used for further development to lead compounds, which could be used for research purposes. Mutant forms of cathepsins K and S with residues substituted by alanine residue in predicted allosteric pathway and allosteric site of cathepsin K as well as its homologous site of cathepsin S were designed and prepared. We have shown that residues in predicted allosteric pathway N202 and N208 are important for allosteric communication in cathepsin K between allosteric site and site S.

Zdravljenje bakterijskih okužb zaradi porasta števila odpornih bakterijskih sevov postaja vse večji klinični problem. Številni neuspeli poskusi razvoja protibakterijskih učinkovin so terjali svoj davek v farmacevtski industriji, kjer so z leti začeli postopoma ukinjati ali pa vsaj omejevati finančni vložek v ta namen, kar pa je le še poslabšalo stanje v zdravstvenih ustanovah. Velik delež razvoja protibakterijskih učinkovin se je tako prenesel v akademske in druge raziskovalne ustanove. Za eno najpomembnejših tarč pri razvoju protibakterijskih učinkovin velja bakterijska celična stena. Ta je nujna za preživetje bakterij, saj ščiti organizem pred okoljskimi dejavniki, ohranja značilno obliko celice, vzdržuje osmotski pritisk znotraj celice in opravlja vlogo polprepustne membrane. Celična stena bakterij je v večji meri zgrajena iz peptidoglikana, sestavljenega iz ponavljajočih se amino sladkornih enot, ki so med sabo prečno povezane s peptidnim mostom. Biosinteza peptidoglikana poteka tako znotraj kot zunaj celične membrane. V tem procesu so udeleženi številni encimi, ki so potencialne tarče za razvoj protibakterijskih učinkovin. Protibakterijske učinkovine, ki delujejo na biosintezo peptidoglikana, tako onemogočijo nastanek celične stene bakterije in njeno smrt. Njihova glavna prednost je selektivna toksičnost in specifičnost. Posebnost mikobakterijske celične stene je debela plast mikolil-arabinogalaktana v kompleksu s peptidoglikanom, ki je prepredena s prostimi lipidi in številnimi proteini. Kompleksnost take celične stene predstavlja največjo oviro in hkrati izziv v razvoju novih učinkovin za zdravljenje tuberkuloze. V doktorskem delu predstavljamo načrtovanje zaviralcev encimov Mur, UppS in PPB2a, ki sodelujejo pri biosintezi peptidoglikana bodisi v citoplazemskih ali končnih modifikacijskih stopnjah. Prav tako smo se posvetili razvoju zaviralcev encima InhA, vpletenega v sintezo mikolnih kislin, ki predstavljajo pomemben del celične stene mikobakterij. Osredotočili smo se na moderne metode načrtovanja učinkovin, kot sta strukturno podprto načrtovanje in rešetanje visoke zmogljivosti. Razvoj računalniških metod je v zadnjih letih doživel velik vzpon in je trenutno vodilni pristop odkrivanja novih spojin zadetkov na številnih terapevtskih tarčah. V okviru doktorskega dela smo uporabili različne starejše metode in validirali nekatere novejše računalinške programe, ki so jih Kaja Rožman: Strukturno-podprto načrtovanje, sinteza in vrednotenje novih zaviralcev biosinteze peptidoglikana razvili naši partnerji iz Kemijskega inštituta v Ljubljani. Pridobljene spojine zadetke smo v nadaljevanju biološko ovrednotili in uporabili kot izhodišče za nadaljnjo optimizacijo. Encimi Mur v citoplazmi bakterijske celice katalizirajo nastanek UDP-N-acetilmuramoil pentapeptida, prekurzorja peptidoglikanske verige. Z uporabo spletnega strežnika ProBiS-CHARMMing smo simulirali proces induciranega prileganja encima MurA iz Escherichia coli ob vezavi liganda TAV iz kristalne strukture encima MurA iz Enterobacter cloacae. Tako smo povzročili odprtje in povečanje aktivnega mesta encima, ki smo ga uspešno uporabili kot osnovo virtualnega rešetanja filtrirane knjižnice spojin `ZINC Drugs Now´. Pridobili smo tri spojine zadetke, in sicer derivate dikarboksilne kisline, kinazolinona ter pirolopiridina, ki so in vitro zavirali encim MurA iz E. coli v mikromolarnem območju (v istem zaporedju, IC50 = 1 μM, 82 μM in 109 μM). Sintetizirali smo večjo serijo derivatov kinazolinonskega tipa, pri čemer smo sistematično spreminjali posamezne fragmente kinazolinona in vpeljali različne substituente. Velika večina sprememb je povzročila znižanje jakosti delovanja zaviralcev. Z odstranitvijo metilenskega distančnika na mestu 2 med obema dušikoma kinazolinona ter sočasno vpeljavo 5-nitrofuranilne skupine na to mesto pa smo poleg zaviralnega delovanja na MurA pridobili še dobro protibakterijsko delovanje na seva E. coli in Staphylococcus aureus. Spojini 2-(5-nitro-furan-2-il)-3H-kinazolin-4-on (IC50 = 47 μM, MIC = 1-8 μg/mL) in njegov 3-izopropilni derivat (IC50 = 87 μM, MIC = 2-8 μg/mL) predstavljata dobro izhodišče za nadaljnjo optimizacijo zaviralcev MurA pri razvoju protibakterijskih učinkovin. Z rešetanjem knjižnice kinaznih zaviralcev podjetja GlaxoSmithKline na ligazah Mur smo prišli do 5 različnih strukturnih razredov zaviralcev. Vse zadetke smo najprej ponovno sintetizirali in tako potrdili njihovo strukturo. Z biokemijskimi testi smo potrdili zaviralno delovanje stilbenskega derivata MH-96 in mu določili mikromolarno območje delovanja na encimih MurC, MurD in MuF (IC50 = 39-104 μM) ter z metodo STD-NMR potrdili tudi vezavo na encim MurD. Domnevamo, da bi se ta spojina lahko vezala v ATP vezavno mesto in delovala kot ATP kompetitiven zaviralec, kar bomo v prihodnosti poskušali tudi dokazati. Spojina tako predstavlja obetavno izhodiščno točko za nadaljnjo optimizacijo in razvoj protibakterijskih učinkovin. Sintaza UppS sodeluje pri nastanku lipida II v citoplazmi bakterijske celice, tako da katalizira nastanek undekaprenil pirofosfata. Mehanizem delovanja in zaviranje samega encima je še precej neraziskano, kljub temu, da je za bakterijo esencialen encim. Na osnovi trenutno najbolj odmevnih bisfosfonatnih zaviralcev UppS, natančneje bisfosfonata BPH-629, smo zasnovali in silico farmakoforni model, ki nam je služil kot filter za presejanje več milijonske knjižnice spojin. Vzporedno s pripravo knjižnice pa smo upoštevajoč pomembnost dveh vezavnih mest, med katerim mesto 1 sovpada z vezavnim mestom substrata farnezil pirofosfata, protein oblikovali tako, da je postal primeren za sidranje spojin. Z biokemijskim vrednotenjem smo nato dokazali zaviralno delovanje trem derivatov benzojske kisline v mikromolarnem območju (IC50 = 24-45 μM). Spojine s kislinskim delom oponašajo pirofosfatni del substratov, zato predpostavljamo kompetitiven mehanizem zaviranja encima UppS. Kljub temu, da spojine nimajo protibakterijskega delovanja, pa predstavljajo dobro izhodišče za nadaljnjo optimizacijo spojin s ciljem izboljšanja prehajanja celične membrane bakterij. Transpeptidaza PBP2a je odgovorna za prečno premreženje peptidoglikanskih verig v zaključnih stopnjah sinteze celične stene bakterij. Specifično zaviranje PBP2a je v literaturi omenjeno kot ključno v razvoju ozkospektralnega antibiotika, saj je encim značilno izražen v na meticilin odpornem bakterijskem sevu (MRSA) kot mehanizem obrambe pred učinki penicilinov. Kot izhodišče iskanja novih zaviralcev smo vzeli kinazolinonski derivat, ki po kristalografskih podatkih za svoje zaviralno delovanje, podobno kot učinkovina ceftarolin, izkorišča vezavo v alosterično mesto PBP2a. Pripravili smo knjižnico spojin na osnovi podobnosti z omenjenim kinazolinonskim zaviralcem in spojine sidrali v alosterično mesto encima. Z biokemijskimi testi smo dokazali vezavo in zaviralno delovanje trem spojinam. Med temi je najboljši kinazolinski derivat Z729094432 zaviral encim pri koncentraciji 100 μM, hkrati pa deloval zaviralno na rast MRSA (MIC = 16 μg/mL), ne pa tudi na neodporni sev S. aureus (MIC > 128 μg/mL), kar priča o vzročni povezavi med zaviranjem encima in protibakterijskim delovanjem. Odkriti strukturno različni zaviralci PBP2a s protibakterijskim delovanjem po naši oceni predstavljajo izjemno obetajočo osnovo za nadaljnjo optimizacijo oziroma razvoj protibakterijskih učinkovin. Reduktaza enoil acil prenašalnega proteina InhA je pomembna tarča pri razvoju učinkovin za zdravljenje tuberkuloze. Nove zaviralce encima smo načrtovali po dveh poteh. V prvem primeru smo s programom LiSiCa na osnovi podobnosti z znanima nanomolarnima zaviralcema, tiadiazolom 8 in tetrahidropiranom 9, poiskali nove, strukturno različne spojine, v drugem primeru pa smo z vtičnikom ProBiS iskali ligande iz proteinske baze PDB, ki se vežejo v aktivna mesta encimov s podobno strukturo kot jo ima InhA. Najbolje ocenjenih 17 spojin na osnovi podobnosti in 8 ligandov iz baze PDB smo naročili ter biokemijsko ovrednotili. Najboljši spojini, ligandu 09T, smo določili mešani tip zaviranja z določeno Ki vrednostjo 4 ± 1 μM. Čeprav je spojina šibkejši zaviralec od izhodiščnih molekul, pa zaradi precej majhne molekulske mase lahko služi kot dober fragment za nadaljnjo optimizacijo. Treatment of bacterial infections is becoming a substantial clinical problem due to the increasing number of resistant bacterial strains. Many failed experiments in the development of antibacterial agents over the years have forced the pharmaceutical industry to gradually began to phase out or at least limit the financial contribution for this purpose, which only worsened the situation in healthcare institutions. A large part of the development of antibacterial agents was therefore transferred to the academia and other research institutions. Bacterial cell wall is one of the most important targets in the development of antibacterial agents. It is essential for the survival of bacteria, because it maintains the osmotic pressure inside the cell, protects the organism from environmental factors, preserves the characteristic cell shape and acts as a semi-permeable membrane. The cell wall of the bacteria is largely constructed of peptidoglycan, consisting of repeated amino sugar units that are cross-linked to another peptidoglycan chain through a peptide bridge. The biosynthesis of peptidoglycan is performed both on the inside and outside of the cell membrane. Many enzymes are involved in this process and they represent potential targets for the development of antibacterial agents. Antibacterial agents that act on the peptidoglycan biosynthesis lead to cell lysis and death of bacteria. Their main advantage is a selective toxicity and specificity. The specificity of the mycobacterial cell wall is a thick layer of mycolyl-arabinogalactan-peptidoglycan complex, which is interspersed with free lipids and numerous proteins. The complexity of such cell wall thus represents the biggest obstacle and concurrently also a challenge in the development of new agents for the treatment of tuberculosis. In this doctoral thesis, we present the design of novel inhibitors of Mur enzymes, UppS and PPB2a, which participate in either the cytoplasmic or the final modification stages of the peptidoglycan biosynthesis. We also devoted our effords to develop inhibitors of the InhA enzyme, which involved in the synthesis of mycolic acids that represent a significant proportion of the cell wall of mycobacteria. We focused on the modern methods for drug design, such as structure-based design and screening of focused libraries. The development of computational methods has undergone a major upswing in the recent years and is currently the leading approach of new compounds design for many therapeutic targets. Within the doctoral thesis we used various well established computational methods and at the same time we also validated some recent programs developed by our partners from the National Institute of Chemistry in Ljubljana. The obtained compounds were subsequently biologically evaluated and used as a starting point for further optimization. The cytoplasmic Mur enzymes catalyze the formation of UDP-N-acetylmuramoyl-pentapeptide, the soluble precursor of the peptidoglycan chain. The inhibition of these enzymes thus prevents the formation of the cell wall of the bacterium and consequently causes its death. The ProBiS-CHARMMing web server was used to simulate the induced-fit effect of MurA from E. coli upon binding of the TAV ligand from the crystal structure of the MurA from E. cloacae. This led to the opening and enlarging of the active site of the enzyme, which was successfully used for docking of filtered `ZINC Drugs Now´ compound library. Three hit compounds were obtained, namely the dicarboxylic acid, quinazolinone and pyrrolopyridine, which in vitro inhibited MurA from E. coli in the micromolar concentrations (IC50 = 1 μM, 82 μM and 109 μM, respectively). A large series of quinazolinone type derivatives were synthesized by systematically modifying individual quinazolinone fragments and introducing different substituents. The vast majority of changes led to a decreased inhibitory potency. The removal of the methylene bridge at the site 2 between the two nitrogen of quinazolinone and the simultaneous introduction of the 5-nitrofuranyl group to this site, not only improved the inhibitory potency against MurA, but also gained antibacterial activity against E. coli and S. aureus. The 2-(5-nitro-furan-2-yl)-3H-quinazolin-4-one (IC50 = 47 μM, MIC = 1-8 μg/mL) and its 3-isopropyl derivative (IC50 = 87 μM, MIC = 2-8 μg mL) are considered a good starting point for further optimization of MurA inhibitors in the development of antibacterials. During the screening of GlaxoSmithKline focused library of kinase inhibitors on Mur ligases, 5 different structural classes of inhibitors were discovered and then re-synthesized. The inhibitory potency of styrene derivative MH-96 against MurC, MurD and MuF enzymes (IC50 = 39-104 μM) was confirmed using biochemical assays. In addition, the binding of this compound to MurD was confirmed using the STD-NMR. We postulate that this inhibitor could bind to the ATP binding site and act as an ATP competitive inhibitor however additional experiments are needed to confirm this hypothesis. This compound thus represents a promising starting point for further optimization and development of antibacterial agents. UppS synthase is involved in the formation of lipid II in the cytoplasm of the bacteria via catalyzing the formation of UPP. Although the enzyme is a validated antibacterial drug discovery target, the mechanism of action and inhibition of the enzyme is still fairly unexplored. Based on the currently most promising bisphosphonate inhibitors of UppS, more specifically BPH-629, an in silico pharmacophore model was designed and used to filter a library of several million compounds. Simultaneously with the library preparation, the protein construction was carried out by taking into account the importance of the two binding sites, among which site 1 coincide with the binding sites of the farnesyl pyrophosphate substrate. The biochemical evaluation further demonstrated the inhibitory potency of three benzoic acid derivatives in the micromolar range (IC50 = 24-45 μM). Carboxylic groups of the compounds mimic the pyrophosphate parts of the substrates, therefore a competitive mechanism of UppS inhibition was assumed. Despite the fact that the compounds do not posses antibacterial activity, they provide a good starting point for further optimization. Transpeptidase PBP2a is responsible for peptidoglycan cross-linking in the final stages of bacterial cell wall synthesis. Specific inhibition of PBP2a is crucial in the development of narrow-spectrum antibiotics, since the enzyme is typically expressed in methicillin resistant bacterial strain (MRSA) as a mechanism of defense against the effects of penicillins. Similarity search was performed based on previously mentioned query quinazolinone, which according to crystallographic data utilizes the binding to the allosteric site of PBP2a as mechanism of inhibition, similarly to a known drug ceftarolin. Further on, the pre-filtered compound library was docked in the allosteric site of the enzyme. Biochemical assays demonstrated the binding and inhibitory potencies of three hit compounds. Among these, quinazoline derivative Z729094432 inhibited PBP2a at 100 μM, while showing antibacterial activity against MRSA (MIC = 16 μg/mL), but not against S. aureus (MIC > 128 μg/mL), indicating a possible link between enzymatic inhibition and antibacterial activity. The discovery of PBP2a inhibitors with distinctive chemical structures supported by antibacterial activities, in our opinion, present a promising basis for further development of antibacterials. The enoyl acyl carrier protein reductase InhA is an important target in the development of drugs for the treatment of tuberculosis. The new inhibitors were designed using two methods. First, a similarity search based on the known nanomolar inhibitors, thiadiazole 8 and tetrahydropyrane 9, was performed using program LiSiCa. In the second case, the search for known ligands from the PDB bank was implemented using the ProBiS plugin, which collects ligands from active sites of all enzymes whose structure resembles the structure of InhA. 17 top-scoring compounds based on similarity and 8 ligands from the PDB database were purchased and biochemically evaluated. For the most potent compound, the ligand 09T, a mixed type of inhibition with a given Ki value of 4 ± 1 μM was determined. Although the compound is a less potent inhibitor than query compounds, it can serve as a good fragment for further optimization due to its relatively small molecular weight.

Kalijevi kanali se vpletajo v raznolike celične procese s primarno vlogo pri vzdrževanju ionske homeostaze. Ključno vlogo imajo tudi pri patofiziologiji napredovanja rakavih obolenj. Napetostno odvisni kalijev kanal hEAG1 je primer kanala, ki se vpleta v različne procese razvoja raka, saj se njegovo povečano izražanje pojavlja pri večini vrst raka pri človeku. Fiziološko se hEAG1 pojavlja skoraj izključno v centralnem živčnem sistemu in tako predstavlja skoraj popolno novo tarčo za razvoj novih protirakavih učinkovin. Težavo pri razvoju zaviralcev hEAG1 predstavlja kanal hERG, ki spada v isto družino ionskih kanalov kot hEAG1. Posledica zaviranja hERG je lahko podaljšanje srčnega intervala QT. Možnost pojava potencialno smrtno nevarnih aritmij zaradi zaviranja kanala hERG predstavlja velik izziv pri načrtovanju novih zaviralcev hEAG1. V sklopu doktorske disertacije smo začeli z iskanjem novega strukturnega tipa zaviralcev hEAG1. S pristopom na podlagi strukture znanih ligandov smo pripravili farmakoforni model, ki opisuje vezavo analogov naravne spojine purpurealidina I. Ti se vežejo na zunanjo stran napetostnega senzorja hEAG1, ki je odgovoren za prenos spremembe membranske napetosti v spremembo konformacije kanala. Poenostavljen farmakoforni model smo uporabili za virtualno rešetanje, pri katerem smo dobili 18 spojin zadetkov. Izbrane virtualne zadetke smo testirali z metodo vpete krpice membrane ter odkrili spojino z nizkim mikromolarnim zaviralnim delovanjem na hEAG1. Spojina zadetek virtualnega rešetanja, ki je izkazala dobro zaviralno delovanje hEAG1 in vitro, je služila kot osnova za sintezo novih analogov, s katerimi smo želeli izboljšati zaviralno delovanje na hEAG1 in selektivnost napram kanalu hERG. Selektivnost je bila dosežena na številne natrijeve in kalijeve ionske kanale z izjemo kanala hERG. Kljub temu, da nismo uspeli izboljšati selektivnosti na kanal hERG, pa nam je uspelo značilno povečati zaviranje hEAG1. Tako smo ugotovili, da je za zaviralno delovanje najpomembnejša pozitivno nabita aminska skupina, poleg tega pa je potrebno ohraniti tudi nitro in trifluorometilno skupino na aromatskem obroču. Z odstranitvijo hidroksilne skupine smo spojino zadetek pretvorili v nanomolarni zaviralec hEAG1 in tako petkrat povečali zaviralno delovanje v primerjavi z aktivno spojino iz virtualnega rešetanja. Glede na kinetiko vezave spojine zadetka, ki je značilno za spojine, ki se vežejo v osrednjo votlino kanala, smo natančneje preverili potencialno mesto, kamor se novoodkrite spojine vežejo. Pri tem smo uporabili pristope in silico in in vitro, s katerimi smo prišli do skupnega zaključka, da se nove spojine vežejo v še neovrednoteno mesto kanala hEAG1. Metoda in vitro je temeljila na izpodrivanju spojin, ki se vežejo na isto vezavno mesto. Preverili smo, ali spojina zadetek tekmuje s spojinama, katerih vezavno mesto je v osrednji votlini kanala oziroma na zunanji strani napetostnega senzorja (VSD). Nismo zaznali kompeticije niti z astemizolom, ki se veže v poro kanala, niti z mibefradilom, ki se veže v VSD. Na podlagi tega smo se odločili, da z metodo in silico še dodatno preverimo najpogosteje in najbolje raziskano mesto vezave v osrednji votlini. Za ta pristop smo pripravili homologni model hEAG1 v odprti konformaciji in vanj sidrali znane zaviralce hEAG1. Najboljše poze sidranja smo uporabili za simulacije molekulske dinamike. Na podlagi simulacij molekulske dinamike smo pripravili skupen farmakoforni model, ki opisuje vezavo zaviralcev v osrednjo votlino kanala. Ta model ni prepoznal novih zaviralcev hEAG1, kar je v skladu z rezultati in vitro potrdilo, da se kljub značilnemu pozitivno nabitemu centru v zaviralcih le-ti ne vežejo v osrednjo votlino. Velika podobnost tega skupnega farmakofornega modela s farmakofornim modelom za hERG pojasnjuje neselektivnost zaviralcev hEAG1, ki se vežejo v osrednjo votlino. Skupni farmakoforni model predstavlja nove možnosti za odkritje novih strukturnih razredov zaviralcev, ki se ne bodo vezali v osrednjo votlino in bodo izkazovali večjo selektivno delovanje na hEAG1 napram hERG. Antiproliferativno delovanje novih zaviralcev na različnih rakavih celičnih linijah smo preverili z 2D in 3D celičnimi modeli. Celično linijo MCF-7, z visokim izražanjem hEAG1, zavirajo novi zaviralci v mikromolarnem območju. Podobno jakost apoptotičnega delovanja smo opazili tudi na sferoidih celične linije Colo357. Zaradi prisotnosti skupine nitro, ki je nismo uspeli zamenjati z bioizosternimi zamenjavami, smo vrednotili mutagenost spojine zadetka z AMES-ovim testom. Ta ni izkazovala mutagenega delovanja pri necitotoksičnih koncentracijah, a je vseeno potrebna nadaljnja previdnost pri razvoju zaviralcev hEAG1 tega strukturnega razreda. Odkritje novega strukturnega tipa zaviralcev hEAG1 v sklopu doktorske disertacije predstavlja izvirni prispevek k znanosti na področju odkrivanja novih protirakavih učinkovin s tem novim mehanizmom delovanja. V delu smo uporabili inovativne pristope farmakofornega modeliranja v kombinaciji z molekulsko dinamiko za pripravo 3D farmakofornih modelov za odkrivanje in vrednotenje zaviralcev hEAG1. Rezultati doktorske disertacije predstavljajo novo izhodišče za nadaljnji razvoj zaviralcev hEAG1 s protirakavim delovanjem. Potassium channels are involved in a variety of cellular processes and play a primary role in maintaining ion homeostasis. They also play a critical role in the pathophysiology of cancer progression. The voltage-gated potassium channel hEAG1 is one such example involved in development of various cancers, as its increased expression occurs in most human cancers. Physiologically, it is found almost exclusively in the central nervous system and would therefore be an almost perfect target for cancer therapy. The problem is the hERG channel, which belongs to the same family of ion channels as hEAG1 and as an off-target can cause prolongation of the cardiac QT interval. The potential for potentially life-threatening arrhythmias presents a major challenge in the development of hEAG1 inhibitors. The primary goal of doctoral dissertation was to discover a new structural type of hEAG1 inhibitors. Using a computer-aided drug design approach, we created a pharmacophore model describing the binding of analogs of the natural compound purpurealidin I. These bind to the outside of the hEAG1 voltage sensor, which is responsible for transferring the change in membrane potential to the structural conformational change of the channel. A simplified pharmacophore model was used for virtual screening where 18 hit compounds were identified. Selected virtual hits were tested using the patch-clamp method and a compound with low micromolar inhibitory activity on hEAG1 was discovered. Hit compound from virtual screening with in vitro activity served as the basis for the synthesis of new analogs with which we aimed to improve inhibitory activity and selectivity. Selectivity was achieved for several sodium and potassium ion channels with the exception of the hERG channel. Although we were unable to improve selectivity at hERG, we were able to significantly increase activity at hEAG1. Thus, we found that the positively charged amino group is most important for the inhibitory effect, and in addition, it is necessary to retain the nitro and trifluoromethyl groups on the phenyl ring. Removal of the hydroxyl group transformed the hit compound into a nanomolar inhibitor, which increased the inhibitory activity fivefold compared to the virtual screening hit.Given the binding kinetics of the hit compound, which is characteristic of compounds that bind to the central cavity of the channel, we further investigated the potential binding site of the newly discovered compounds. We used both the in silico and in vitro approaches, with which we reached the common conclusion that the new compounds bind to the previously unevaluated site of the hEAG1 channel. The in vitro method was used to evaluate the potential displacement of compounds that bind to the same binding site. Thus, we checked whether the hit compound competes with compounds whose binding site is located in the central cavity or on the outside of the voltage sensor (VSD). We could not find any competition between astemizole that binds in central cavity or mibefradil that binds in VSD with the hit compound. Therefore, we decided to further verify the most common and best studied binding site in the central cavity using the in silico method. For this approach, we prepared a homology model of hEAG1 in the open conformation and docking of the known hEAG1 inhibitors into the binding site in the central cavity. The best-scored docking poses per ligand were used in molecular dynamics simulations. Based on the molecular dynamics simulations, we created a merged pharmacophore model describing the binding of the inhibitors to the central cavity. This model did not recognize our new hEAG1 inhibitors, confirming that they do not bind to the central cavity, as also observed in the in vitro asays, despite the characteristic positively charged center in the structure of the inhibitors. High similarity of the merged pharmacophore model with hERG pharmacophore model explains the non-selectivity of the hEAG1 inhibitors binding to the central cavity. The use of merged pharmacophore model will increase the chance of discovering new inhibitors that do not bind to the central cavity and thus have a higher probability of selective hEAG1 inhibition. The antiproliferative activity of the new hEAG1 inhibitors on various cancer cell lines was tested using 2D and 3D cell models. The MCF-7 cell line with high hEAG1 expression was inhibited by the addition of micromolar concentrations of the new inhibitors and similar apoptotic activity was also observed on the spheroids of the Colo357 cell line. Due to the presence of the nitro group, which we could not replace with bioisosteric substitutions, the mutagenicity of the hit compound was also evaluated using AMES assay. It showed no mutagenic effects at non-cytotoxic concentrations, but further caution is advised in development of hEAG1 inhibitors of this structural class. The discovery of a new structural type of hEAG1 inhibitors in this doctoral dissertation represents an original contribution to the science in the field of anticancer drug discovery. In this work, we used an innovative ligand-based pharmacophore modeling approach to create 3D pharmacophore models in combination with molecular dynamics to discover and evaluate hEAG1 inhibitors. The obtained results represent a good foundation for further development of hEAG1 inhibitors with antiproliferative activity.

Ovaj rad predlaže sveobuhvatnu i računalno efikasnu metodu temeljenu na Markovljevim lancima za sintezu realističnih voznih ciklusa s visokom frekvencijom uzorkovanja temeljem statističkih značajki segmenata izvučenih iz snimanih telemetrijskih podataka niske frekvencije uzorkovanja. U slučaju gradskog autobusnog prijevoza, segmenti rute označavaju dijelove između dvije uzastopne autobusne stanice. Segmenti rute su karakterizirani duljinom, srednjom brzinom te učestalosti zaustavljanja i vremenom mirovanja na završnoj stanici. U procesu sinteze voznih ciklusa, matrica prijelaznih vjerojatnosti generirana je temeljem voznih ciklusa visoke frekvencije uzorkovanja snimljenih u zasebnom, referentnom gradu. Pritom je poseban naglasak stavljen na zadovoljavanje početnog i konačnog uvjeta brzine segmenta, koji mogu biti nula ili različiti od nule, ovisno o uvjetu zaustavljanja autobusa na završnoj stanici segmenta. Ovakav pristup omogućava spajanje uzastopnih sintetiziranih voznih ciklusa segmenata u cjelokupni sintetički vozni ciklus rute. Predložena metoda sinteze validirana je temeljem proširene statističke analize generiranih voznih ciklusa u smislu zadovoljenja postavljenih zahtjeva na navedene uvjete i statističke značajke te računalne učinkovitosti cjelokupnog postupka. This thesis proposes a comprehensive and computationally efficient Markov chain‐based method for the synthesis of realistic high-sampling-rate driving cycles, where statistical features on each bus route segment are explicitly defined based on extracted low-sampling-rate recorded data. The bus route segments correspond to road sections between two consecutive bus stations. Route segments are characterized by length, mean velocity, frequency of stopping at the final station and final station dwell time. In the driving cycle synthesis process, the transition probability matrix is established by a rich set of high-sampling-rate driving cycles recorded in a separate, reference city. The special emphasis of the synthesis process is on satisfying the route segment's initial and final conditions, which may be zero or not depending on whether the bus stops at a segment's final station or not. By ensuring proper boundary conditions, consecutive synthetic driving cycles can be concatenated into full route driving cycles. The synthesis method is validated based on an extensive statistical analysis of generated synthetic driving cycles in terms of satisfying predefined conditions and statistical features, as well as the overall computational efficiency aspect.

U ovom radu optimizovana je sinteza pektina, prirodnog heteropolisaharida, modifikovanog furfurilaminom. Uspešnost modifikacije pektina je ispitivana pomoću ultraljubiĉasto-vidljive spektroskopije, Furijeove transformisane infracrvene spektroskopije i protonske nuklearne magnetne rezonancije. Nakon uspešne ekspresije lignin peroksidaze na površini ćelija kvasca i uspešnog liziranja ćelija, dobijeni ćelijski zidovi sa lignin peroksidazom su imobilizovani u kalcijum-furfurilamin-pektin kuglicama u cilju dobijanja biokatalizatora sa poboljšanim karakteristikama i sposobnošću višekratne primene OdreĊena je pH i temperaturna stabilnost imobilizovanog i slobodnog enzima, kao i efikasnost biokatalizatora u ponovljenim ciklusima dekolorizacije otpadnih boja. TakoĊe su ispitane sposobnosti fotopolimerizacije furfurilamin-pektinskih kuglica ćelijskim zidovima sa lignin u prisustvu fotoinicijatora Rose Bengal-a i Riboflavina, pod dejstvom vidljive svetlosti. Ispitan je uticaj fotopolimerizacije imobilizacionog matriksa na pH i temperaturnu stabilnost imobilizovanog biokatalizatora, kao i oĉuvanje aktivnosti lignin peroksidaze tokom vremena, odreĊivanjem procenta zadrţane aktivnosti tokom procesa dekolorizacije boja raĊene u ponovljenim ciklusima.

Prelazni metali su elementi d bloka Periodnog sistema elemenata koji mogu imati različita oksidaciona stanja i mogu se koordinovati sa različitim anjonima ili neutralnim molekulima. U zavisnosti od prirode metalnog jona i/ili upotrebljenog/ih liganada, ova jedinjenja ispoljavaju različita svojstva. Poslednjih godina kompleksi prelaznih metala nalaze primenu u različitim naučnim oblastima od katalizatora i biološki aktivnih jedinjenja do najsavremnijih nanomaterijala i (polu)provodnika. Jedna od najznačajnijih primena je svakako primena kompleksa prelaznih metala kao biološki aktivnih agenasa s obzirom da je decenijama unazad sintetisan značajan broj ovih jedinjenja koja su se pokazala kao dobra antitumorska, antibakterijska, antifungalna, antiinfektivna, antiupalna i antidijabetska sredstva. U ovoj grupi kompleksnih jedinjenja posebno se izdvajaju kompleksi rutenijuma, platine, osmijuma i iridijuma. Heterociklični ligandi, posebno piridinskog ili polipiridinskog tipa i njihovi derivati, često su upotrebljavani u svrhe sinteze biološki aktivnih kompleksa pomenutih metala. Cilj ovog rada jeste optimizacija uslova sinteze i potpuna karakterizacija kompleksa rutenijuma(II) sa ligandima tipa piridindikarboksilnih kiselina.

Grupi prelaznih metala pripadaju svi elementi koji se nalaze od 3. do 11. grupe u periodnom sistemu elemenata. Ovi elementi su karakteristični zbog svojih delimično popunjenih d orbitala. Elementi koji se još nazivaju „platinski metali“, a u koje se ubrajaju rutenijum, osmijum, rodijum, iridijum, paladijum i platina, vrlo često grade kompleksna jedinjenja koja su jako značajna zbog svoje široke upotrebe u raznim sferama nauke i industrije. U današnje vreme jedna od najznačajnijih primena kompleksa prelaznih metala jeste upotreba u medicinske svrhe, bilo da je u pitanju dijagnostika ili terapija. Pojedini kompleksi platine su već u kliničkoj upotrebi, dok su određeni kompleksi rutenijuma u fazi kliničkih ispitivanja. Upravo zbog toga je i značajna sinteza ovih kompleksa, analiza njihove aktivnosti, kao i potencijalni mehanizmi delovanja.1 Kao ligandi u ovim kompleksnim jedinjenjima uglavnom se koriste neutralni organski molekuli ili njihovi anjoni. Neretko se dešava da već poznati lekovi, po hemijskom sastavu organski molekuli, koordinacijom za jone prelaznih metala menjaju svoje farmakološko dejstvo ili ga poboljšavaju. Primer takvih lekova su i nesteroidni antiinflamatorni lekovi (NSAIL), koji su do sada najviše opisani kao ligandi u kompleksima Cu, Ag, Mn, Ni, kao potencijalni antitumorski i DNK vezujući agensi. Razvoj metoda sinteze i ispitivanje potencijalne antitumorske aktivnosti Ru(II) kompleksa sa ovim ligandima je tek u razvoju. U ovom master završnom radu biće opisana sinteza i karakterizacija Ru(II) kompleksa sa diflunisalom i indometacinom kao predstavnicima NSAIL.

Stalnim oslobađanjem toksičnih hemikalija, značajno se pogoršava stanje voda, atmosfere i zemljišta na globalnom nivou. Imajući u vidu neophodnost zaštite zdravlja ljudi i ekosistema planete u celini, od ogromnog su značaja sve inovacije savremenih tehnologija koje omogućavaju uklanjanje toksičnih supstanci iz ovih izvora. Ovo postavlja brojna pitanja relevantna za ekosistem i zdravlje ljudi koji intenziviraju izazove primene konvencionalnih tehnologija tretmana. Najčešći zagađivači životne sredine su teški metali i organska jedinjenja koja potiču iz različitih industrija poput tekstilne i hemijske, kao i iz poljoprivrede. Pesticidi su supstance koje su posebno razvijene i proizvedene za upotrebu u kontroli štetočina u poljoprivredi, za povećanje proizvodnje hrane i za olakšavanje savremenih poljoprivrednih metoda. Usled njihove slabe biorazgradivosti i toksičnosti u većim dozama, predstavljaju opasnost kako za zdravlje ljudi, tako i za životnu sredinu. Toksični efekti pesticida podrazumevaju njihovo dejstvo kao inhibitora različitih enzima, ometača ćelijske signalizacije i narušivača osmotske i pH ravnoteže u organizmu čoveka. Lindan, organohlorni pesticid, i dalje je u upotrebi u određenim državama i usled njegove toksičnosti i velike raspršivosti predmet je brojnih istraživanja vezanih za zaštitu životne sredine. Usled sve veće svesti o toksičnim efektima zagađivača, razvijen je veliki broj metoda koje omogućavaju uklanjanje istih iz zemljišta i voda. Sorpcija se može primeti za različite supstance, i prema potrebi mogu se razviti različiti specifični sorbenti. Polimerni materijali su najpopularniji usled njihove lake modifikacije i raznovrsnosti. Predmet i cilj ovog rada je sinteza i karakterizacija makroporoznog kopolimera na bazi glicidil-metakrilata i ispitivanje adsorptivnih svojstava i optimizacije istih prilikom sorpcije lindana u vodenim rastvorima.

U reakciji Zn(II) jona sa (E)-N,N,N-trimetil-2-okso-2-(2-(1-(tiazol-2-[ZnL1(NCS)2]·2H2O -il)etiliden)hidrazinil)etan-1-aminijum hlorida (HL1Cl), u prisustvu NH4SCN, dobijen je kompleks [ZnL1(NCS)2]‧2H2O. Kompleks Zn(II) okarakterisan je elementalnom analizom, spektroskopskim metodama (IC i NMR) i rendgentskom strukturnom analizom. Jon Zn(II) je pentakoordinovan sa tridentatnim ligandom L1 i dva tiocijanatna anjona koja formiraju distorgovanu kvadratno-piramidalnu geometriju.

Šifove baze ili imini su analozi aldehida i ketona kod kojih je karbonilna grupa zamenjena iminskom grupom. Nastaju reakcijama kondenzacije primarnih amina i karbonilnih jedinjenja (aldehida ili ketona) u umereno kiselim uslovima. Šifove baze su bidentatni, tridentatni ili polidentatni ligandi koji mogu da formiraju vrlo stabilne komplekse sa metalima. Šifove baze i njihovi kompleksi imaju veliku primenu u organskoj i analitičkoj hemiji, industriji hrane i boja, biološkim procesima kao i u farmaciji. U ovom radu je dat prikaz postupka sinteze liganda tipa Šifovih baza bis-trifluoroacetilaceton-propilendiimina H2(tfacac2 pn), acetilaceton-trifluoroacetilaceton-propilendiimina H2(acactfacac pn), fenilacetilaceton-trifluoroacetilaceton-propilendiimina H2(phacactfacac pn) i njihovih Rh(III) kompleksa. Navedena je karakterizacija sintetisanih liganda IR, 1H NMR, 13C NMR spektroskopijom. Opšti deo završnog rada opisuje mehanizam sinteze Šifovih baza, njihovu primenu u sintezi kompleksa metala i načine identifikacije dobijenih proizvoda sinteze, dok eksperimentalni deo opisuje tehničke aspekte rada. U rezultatima i diskusiji, prikazani su i objašnjeni dobijeni rezultati istraživanja.

Prelazni metali su elementi koji se nalaze od treće do dvanaeste grupe i od četvrte do sedme periode, odosno elementi poznati pod imenom d-elementi. Svojstva ovih elemenata su između s i p-bloka elemenata, tj. d-blok koji predstavlja prelaz između ovih blokova. Njihove d orbitale se progresvino popunjavaju. Pošto su ove orbitale djelimično popunjene ovi metali mogu imati širok spektar oksidacionih stanja. Na primjer, gvožđe se može naći u oksidacionim stanjima +2 i +3, bakar može imati oksidaciono stanje +1 i +2. Pozitivno oksidaciono stanje prelaznih metala znači da formiraju jonska ili djelimično jonska jedinjenja. Formiranje kompleksa uzrokuje podjelu d orbitala na dva energetska podnivoa, što omogućava kompleksima da apsorbuju svjetlost određene talasne dužine. Dakle prelazni metali formiraju obojene komplekse i rastvore. Najupečatiljivije sličnosti sva 24 prelazna metala su to da su većina njih čvrsti, tvrdi, sjajni, visoke tačke ključanja i topljenja, dobri provodnici toplote i elektriciteta i imaju mogućnost građenja kompleksnih jedinjenja. Zbog ovih svojstava zastupljeni su u metalurgiji, građevinarstvu, medicini, farmaciji i mnogim granama industrije. Jako važna upotreba prelaznih metala i njihovih jedinjenja je u svojstvu katalizatora u mnogim hemijskim reakcijama. Kuplovane reakcije u kojima su kao katalizaori korišćeni paladijum, platina, bakar, nikl, rodijum, rutenijum često su upotrebljivane za organske transformacije koje je bilo teško izvesti klasičnim sintetičkim putem bez upotrebe metalnih katalizatora. Najvažniji razlog zašto su prelazni metali dobri katalizatori je to što mogu preuzeti elektrone iz rastvarača u zavisnosti od prirode reackije. Sposobnost prelaznih metala da imaju različita oksidaciona stanja, sposobnost prelaska iz jednog oksidacionog stanja u drugo, sposobnost da formiraju komplekse sa rastvaračima čine prelazne metale dobrim katalizatorima. Kompleksi metala sa Šifovim bazama su poznati od sredine 19. vijeka. Šifove baze su našle veliku primjenu u koordinacionoj hemiji jer grade stablina jedinjenja sa prelaznim metalima. Ovi kompleski prelaznih metala zbog svoje biološke aktivnosti, redoks svojstava i potencijalne primjene u katalizi su korišćeni u industriji boja, polimera, modelima enzima i kao katalizatori u biološkim sistemima.

U ovom radu opisana je totalna sinteza izabranih derivata diarilheptanoida. Osnovni skelet diarilheptanoida dobijen je aldolnom adicijom derivata benzalacetona i derivata cinamaldehida, a zatim je vršena Steglich-ova esterifikacija u cilju dobijanja konačnog proizvoda. Za sinezu diarilheptanoida smo se odlučili zbog širokog sprektra biloških aktivnosti koje poseduje ova klasa jedinjenja, a izabrali smo derivate koji nisu poznati u literaturi.

Cilj ovog diplomskog rada je bio sinteza supstituisanih 2-piridona 5 polazeći od jednostavnih, komercijalno dostupnih reagenasa, primarnih amina 1, etil-propiolata 2 ili dietil-acetilendikarboksilata 6 preko diena 4 kao intermedijera. Sinteza je planirana da se izvede na čvrstoj fazi, bez prisustva rastvarača, korišćenjem različitih baza.

Kada molekuli apsorbuju svetlost prelaze u pobuđeno stanje i postaju reaktivniji nego kada se nalaze u osnovnom stanju. Energija svetlosti se na taj način koristi za aktivaciju malih organskih molekula i generisanje reaktivnih vrsta koji potom podležu hemijskim transformacijama. Hemijske reakcije pomoću vidljive svetlosti su važne za organsku sintezu jer su efikasnije ili omogućavaju reaktivnost koju je nemoguće postići upotrebom tradicionalnih metoda. Ove reakcije se odigravaju na sličan način kao i biološki procesi potpomognuti svetlošću (poput fotosinteze) – uz pomoć katalizatora koji apsorbuje svetlost. U fotoredoks katalizi,1 molekul fotokatalizatora u pobuđenom stanju razmenjuje jedan elektron sa molekulom supstrata. Tokom ovog procesa, koji je u hemijskoj literaturi poznat kao PET (eng. photoinduced electron transfer) supstrat se transformiše u reaktivni slobodni radikal i potom podleže daljim transformacijama dajući jedan ili više krajnjih proizvoda. Ove reakcije se obično dešavaju na sobnoj temperaturi, jer se energetska barijera neophodna da bi se odigrala hemijska reakcija prevazilazi pomoću energije svetlosti. U proteklih deset godina, polje fotoredoks katalize je doživelo izuzetno veliku ekspanziju, ali ipak neka ograničenja i dalje postoje. Jedno od njih je da pobuđeni fotokatalizator bude izuzetno jako redukciono sredstvo, po jačini uporedivo sa alkalnim metalima (poput elementarnog litijuma ili natrijuma). Razlog ovog ograničenja je taj što foton vidljive svetlosti ne poseduje dovoljno energije. Međutim, u literaturi je opisano nekoliko fotokatalitičkih sistema i strategija kojima se ovaj problem može prevazići i čijom se upotrebom mogu postići jako redukcioni uslovi i dostići izuzetno niski redoks potencijali. Zajedničko za sve ove strategije je to da se u reakciji generiše radikal-anjon fotokatalizatora koji (takođe) apsorbuje vidljivu svetlost, prelazi u pobuđeno stanje i postaje izuzetno jako redukciono sredstvo (super-reducens) po jačini uporedivo sa alkalnim metalima.

Utična hibridna električna vozila (engl. Plug-in Hybrid Electric Vehicle, PHEV) predstavljaju jednu od ključnih tranzicijskih tehnologija prema energetski učinkovitom, čistom, tihom i održivom transportu u budućnosti. Budući da su vozni ciklusi vezani uz uvjete vožnje i ponašanje vozača, oni su od ključnog značaja za procjenu potrošnje energije i emisija štetnih plinova, te se naširoko koriste kod projektiranja i parametriranja strukture PHEV pogona i njegove upravljačke strategije. Većina studija vezanih uz PHEV kao i druge tipove vozila temelje se na certifikacijskim voznim ciklusima, koji ne uzimaju u obzir realne uvjete vožnje uključujući nagib ceste, već se temelje na "umjetno" generiranom profilu brzine vozila u ovisnosti o vremenu. Međutim, za potrebe projektiranja i ispitivanja sustava upravljanja vozilom trebali bi se koristiti realistični vozni ciklusi, koji odražavaju stvarno ponašanje u vožnji i uvjete na cesti. U tom smislu, glavni cilj ovog rada usmjeren je na sintezu i validaciju realističnih voznih ciklusa predstavljenih vremenskim profilima brzine i ubrzanja vozila te nagiba ceste, koji su izvedeni iz snimljenih GPS podataka praćenja vozila. U radu se prvo uspostavlja stohastički model voznih ciklusa temeljen na Markovljevim lancima, koji uključuje kombinacije diskretnih vrijednosti brzine vozila, akceleracije vozila, nagiba ceste i vremenske promjene nagiba ceste kao Markovljeva stanja. U tu svrhu prikupljen je bogat skup voznih ciklusa gradskih autobusa u gradu Dubrovniku. Zatim se slučajnim uzorkovanjem višedimenzionalne matrice prijelaznih vjerojatnosti (engl. Transition Probability Matrix, TPM) generira veliki skup sintetičkih voznih ciklusa. Kako bi se smanjio zahtjev za memorijom, a istovremeno poboljšala računalna učinkovitost, predlaže se programska implementacija TPM u obliku rijetke matrice temeljene na rječniku ključeva. K tome, razmatra se postupak uključivanja mase putnika u sintezu voznih ciklusa temeljen na događajima zaustavljanja vozila. Zagušenje prometa uzima se u obzir kroz tvorbu zasebnih TPM za svaku kategoriju zagušenosti prometa, koja se provodi klasteriranjem snimljenih voznih ciklusa s obzirom na uspostavljene kriterije zagušenja prometa. Za potrebe validacije sintetičkih voznih ciklusa predlaže se neuronska mreža koja za dani vozni ciklus predviđa potrošnju goriva. Kao podrška validaciji sintetičkih voznih ciklusa, uzimaju se u obzir brojne statističke značajke iz vremenske i frekvencijske domene, uključujući jedinstvene pokazatelje unakrsne korelacije brzine i ubrzanja vozila te nagiba ceste. Značaj svake nominirane statističke značajke i njezin utjecaj na potrošnju goriva raščlanjuje se pomoću linearne regresijske analize i LASSO (engl. Least Absolute Shrinkage and Selection Operator) metode odabira značajki. Za jednoznačnu, jednokriterijsku validaciju sintetičkih voznih ciklusa u odnosu na skup snimljenih voznih ciklusa predlaže se regresijski model koji uključuje samo nekoliko najrelevantnijih statističkih značajki kao ulaze i potrošnju goriva kao izlaz. Također se kao potencijalno daljnje unaprjeđenje ispituje metoda validacije voznih ciklusa temeljem višestrukih kriterija. Predloženi pristupi validacije temelje se na minimiziranju odstupanja statističkih značajki sintetičkih voznih ciklusa u odnosu na očekivane vrijednosti snimljenih voznih ciklusa. Konačno, u radu se predlažu deterministički i stohastički modeli za predviđanje brzine vozila na horizontu u budućnosti, a s tim povezanim i značajki voznih ciklusa relevantnih za potrebe modelskog prediktivnog upravljanja PHEV pogonom. Prediktivni modeli temelje se na višeslojnoj unaprijednoj neuronskoj mreži, koja se parametrira korištenjem podatka o trenutnoj poziciji vozila, trenutnoj brzini ili povijesti brzina vozila, dobu dana i dana u tjednu, a kao izlaz daje sekvencu brzina vozila na pomičnom vremenskom horizontu. Točnost predviđanja brzine vozila demonstrira se na izdvojenom skupu snimljenih voznih ciklusa. Plug-in Hybrid Electric Vehicles (PHEV) represent a key enabling technology to make the transport system more efficient, cleaner, quieter, and less dependent on oil reserves. Since driving cycles are related to driving conditions and driver behaviour, they are crucial for estimating energy consumption and pollutant emissions, and they are widely used in designing and parameterising the structure of PHEV powertrain and its control strategy. Nowadays, various studies related to PHEVs, as well as other vehicle types, are usually based on certification driving cycles, which do not take into account realistic driving conditions including road slope, but are rather based on “artificially” generated vehicle velocity-time profiles. However, for the purposes of designing and testing a vehicle control system, realistic driving cycles should be used, which reflect the actual driving behavior and road conditions. In this sense, the main aim of this thesis is focused on the synthesis and validation of realistic driving cycles represented by vehicle velocity, acceleration and road slope time profiles, which are derived from recorded GPS vehicle tracking data. The thesis first establishes a stochastic model of driving cycles based on Markov chains, which includes combinations of discrete values of vehicle velocity, vehicle acceleration, road slope and road slope time derivative as Markov states. For this purpose, a rich set of driving cycles of city buses operating in the city of Dubrovnik has been collected. By random sampling of a multidimensional transition probability matrix (TPM), a large set of synthetic driving cycles is generated. To reduce the memory requirement while improving computational efficiency, the implementation of TPM in the form of a sparse matrix based on a dictionary of keys (DOK) is proposed. In addition, including of passengers' mass into driving cycle synthesis process is considered based on vehicle stopping events. Traffic congestion is taken into account through the formation of separate TPMs for each traffic congestion category, which is carried out through clustering of recorded driving cycles based on established traffic congestion criteria. For the purpose of synthetic driving cycles validation, a dedicated neural network (NN) is proposed, which predicts the vehicle fuel consumption for a given driving cycle. The NN approach is based on driving cycle time series input data arranged in a form of fixed‐dimension histogram of counted discrete values of vehicle velocity, acceleration, and road slope. In support of validation of synthetic driving cycles, a rich set of statistical features from the time and frequency domains are considered, including unique indicators of cross-correlation of vehicle velocity, vehicle acceleration, and road slope. The significance of each nominated statistical feature and its impact on fuel consumption is analyzed by using a linear regression analysis and Least Absolute Shrinkage and Selection Operator (LASSO) feature selection method. For unambiguous, single-criteria validation of synthetic driving cycles with respect to recorded driving cycles, a reduced-order LASSO regression model is proposed that takes only a few most significant statistical features as inputs and gives fuel consumption as output. The driving cycle validation method based on multiple criteria is also examined as a potential further improvement. The proposed validation approaches are based on minimizing the deviation of statistical features of synthetic driving cycles from the mean/expected values of recorded driving cycles. Finally, the thesis proposes deterministic and stochastic models for predicting vehicle velocity on receding time horizon, and accordingly driving cycle features relevant for model predictive control of PHEV. Predictive models are based on a feedforward multilayer neural networks, which are trained by using the data on current vehicle position, current vehicle velocity or velocity history, time of day, and weekday, and as an output give sequence of vehicle velocities on the receding time horizon. The accuracy of vehicle velocity prediction is demonstrated on a separate set of recorded driving cycles. The main aim of the thesis is to propose a systematic procedure of multi-dimensional driving cycle synthesis, which utilizes driving data recorded using a vehicle telemetry tracking system and at the end results in a minimum number of representative synthetic driving cycles for a wide range of driving conditions. The thesis is organized in eight chapters, whose content is summarized in what follows. Chapter 1, „Introduction“ outlines the motivation for the conducted research, presents the literature overview, and provides the main hypothesis and an overview of the thesis. Chapter 2, „Recording, pre-processing and analysis of driving cycles“ describes the procedure of driving data recording by utilizing GPS/GPRS vehicle tracking devices for the case of a city bus fleet. Pre-processing of recorded driving data is carried out in terms of extracting driving cycles defined by recorded data between end stations of a certain route, filtering of driving cycles with respect to various criteria, reconstruction of precise road slope profiles using regression method based on Gaussian processes, and categorization of driving cycles in accordance to a traffic congestion index. A comprehensive analysis of interdependence of vehicle velocity, acceleration, road slope, and passengers mass is performed to determine whether the synthesis of driving cycles should be carried out jointly with respect to velocity, acceleration, road slope and passengers mass' states or the road slope and passengers' mass can be modeled independently of velocity and acceleration. Chapter 3, „Synthesis of multidimensional driving cycles“ proposes a method for synthesis of multidimensional driving cycles based on Markov chains. Different ways of realizing the transition probability matrix (TPM) are considered along with related implementation aspects, including computational efficiency analysis. It is proposed to adopt a stochastic driving cycle model represented by an 8D TPM using vehicle velocity, acceleration, road slope, and road slope time derivative states, and based on this model a rich set of synthetic driving cycles is generated. An independent, vehicle stopping event-based synthesis method of passengers’ mass profiles is also proposed. Traffic congestion is considered through the formation of separate TPMs for three levels of congestion (light, medium, and heavy). The chapter concludes with a preliminary analysis of validity of the generated synthetic driving cycles, based on a comparison of distributions of characteristic statistical features between synthetic and recorded driving cycles. Chapter 4, „Regression model for predicting fuel consumption“ establishes a regression model for predicting fuel consumption based on appropriately formed input features of synthetic driving cycles and corresponding neural network (NN). The emphasis is on including a road slope feature when designing the model inputs to improve prediction accuracy. The proposed regression models are trained, validated, and tested on an augmented dataset of combined driving cycles, which are derived through random addition of recorded microcycles whose length corresponds to resolution of fuel consumption measurement. A comparative analysis of fuel consumption prediction accuracy is performed between NN and simpler, linear-in-parameter polynomial regression models, for the case with included and excluded road slope information. In addition, several methods for fine-tuning of NN models are conducted and described in detail, which are related to dimensionality reduction, finding the most appropriate architecture, determining the optimal learning rate, and regularizing the NN. Although the proposed regression model for predicting fuel consumption can be applied to various transport-related studies, in this thesis it is used for determining the fuel consumption related to a set of synthetic driving cycles generated in third chapter for the purpose of their validation. Chapter 5, „Multi-criteria validation of driving cycles“ deals with validation of multidimensional synthetic driving cycles generated in the third chapter. A rich set of driving cycle-related statistical features are nominated to describe different driving patterns, which in addition to general statistical indices includes frequency domain ones and cross-correlation of vehicle speed, vehicle acceleration and road slope features. A comparative analysis of the characteristic statistical features calculated for each recorded and synthetic driving cycle is performed to verify that the distributions of the statistical features for the synthetic driving cycles resembles well those obtained for the recorded driving cycles. For the needs of unambiguous validation of driving cycles, several lumped indicators of driving cycle representativeness are derived, which are based on consolidation of individual statistical features or similarity index between two vectors/matrices used to model driving cycles. The selection of the most appropriate representativeness indicator for the final validation of driving cycles is carried out based on correlation analysis in relation to fuel consumption deviation from the mean value of concatenated recorded driving cycles. Finally, a multi-criteria validation procedure is proposed, which highlights and analyzes several most representative driving cycles from the Pareto frontier of lumped representativeness indicators. Chapter 6, „Feature selection-supported validation of driving cycles“ deals with feature selection techniques based on linear regression analysis and least absolute shrinkage and selection operator (LASSO), which serves to determine the relevance of each nominated statistical feature. The competitiveness of the fuel consumption prediction accuracy of linear and LASSO regression models of reduced order is examined in relation to baseline neural network model established in the fourth chapter. The procedure of extracting representative synthetic driving cycles based on LASSO-predicted fuel consumption is presented and compared with the Euclidean distance lumped indicator-based approach. To further improve the process of unambiguous validation of synthetic driving cycles, a dual-criterion validation method based on both Euclidean distance and LASSO-predicted fuel consumption is examined, as well. Chapter 7, „Prediction of driving cycle features“ first describes the process of data preparation for learning, validation, and testing of a vehicle velocity prediction models. Next, static stochastic and deterministic deep feedforward neural network prediction models are proposed, where the former predicts the vehicle velocity distribution along the route, while the latter predicts the vehicle velocity profile on receding time horizon. A comprehensive analysis of the prediction accuracy of the developed predictive models is performed based on test dataset and considering different forecast quality indicators. Deterministic model is additionally examined in terms of influence of each input variable candidates (current vehicle position, current velocity or history of vehicle velocities, time of day, and weekday), velocity history length, and prediction horizon length on the accuracy of vehicle velocity profile prediction. Finally, a dynamic stochastic model is proposed, which combines the properties of both previously developed predictive models, in terms of predicting expectations and standard deviations of velocity patterns on the receding time horizon. Chapter 8, „Conclusion“ outlines the main results, guidelines for future research, and the following major contributions of the doctoral thesis: 1) Driving cycle model based on Markov chains, which in addition to vehicle velocity and acceleration as the Markov states accounts for the road slope, vehicle mass, and traffic congestion features; 2) Validation of driving cycle model based on recorded fuel consumption data and fuel consumption predictions obtained by using a neural network parameterized based on the driving cycle model features; 3) Stochastic model for predicting driving cycle statistical features meant to be applied in stochastic model predictive control of PHEV.

U ovom master radu sintetisano je tri heterogena katalizatora, na bazi magnetita. Uspešnost izvođenih reakcija potvrđivana je infracrvenom spektroskopijom. U narednom koraku istraživanja, cilj je ispitati katalitičku aktivnost sintetisanih jedinjena.

Polimeri mlečne kiseline (PLA) ispunjavaju dva važna kriterijuma koja ih čine veoma poželjnim materijalom sa širokom primenom. Mogućnost njihove biorazgradnje je ključni faktor za biomedicinsku primenu, dok činjenica da se dobijaju iz obnovljivih resursa im omogućava da budu poželjni u pogledu očuvanja životne sredine. Pored ovih važnih osobina, kojima se teži da svaki novi materijal u današnje vreme poseduje, polimeri mlečne kiseline su u potpunosti netoksični i mogu se reciklirati. Neki od primera u medicini za čiju se izgradnju koriste PLA su šavovi, stentovi, medijumi za dijalizu i uređaji za isporuku lekova. Rad sa mlečnom kiselinom je izuzetno zahtevan. Polimeri mlečne kiseline nemaju reaktivne bočne grupe, te se često radi daljih reakcija moraju funkcionalizovati pomoću različitih jedinjenja. Modifikacije PLA sa ciljem poboljšanja osobina ovog materijala, takođe, može biti zahtevna zbog prethodno pomenute osobine. Polimerizacija mlečne kiseline obično počinje hidrolizom laktida. Trud se ulaže u razvoj metoda koje bi omogućile drugačije, kontrolisane načine polimerizacije. Prilikom građenja oligomera slobodna hidroksilna grupe monomera mlečne kiseline se mora zaštititi da ne bi došlo do sporednih, neželjenjih reakcija. Cilj ovog rada je sinteza oligomera (dimera, trimera i tetramera) i obeleženih oligomera mlečne kiseline kao i njihova analiza pomoću UV spektroskopije. Poseban značaj je posvećen izboru odgovarajućih zaštitnih grupa koje bi omogućile ovu sintezu. Obeležavanje oligomera je izvođeno sa UV aktivnom p-nitrofenil-grupom što ima za cilj proizvodnju takvih molekula koji bi mogli poslužiti kao modeli na osnovu kojih bi se razvile metode brzog praćenja hemijske ili enzimske hidrolize polimera UV spektroskopijom.