Main goal of this Ph.D. thesis is to develop voltammetric methods for the electrochemical study of novel antimycobacterial compounds hydroxynaphthalene- carboxamides. Firstly, this study was focused on the miniaturization of voltammetric methods and construction of an electrochemical microcell due to usually small volume of samples that are associated with an analysis of biologically active compounds in biological matrices. Therefore, all aspects of the voltammetric procedure were studied in a relation to miniaturization. Microcells were based on commercially available electrodes: glassy carbon electrode as a reliable electrode material with well-described characteristics and a novel silver solid amalgam electrode. This study was carried out with analytes 4-nitrophenol, pesticide difenzoquat, and 1-hydroxy-N-(4-nitrophenyl)naphthalene-2-carboxamide. Attention was paid especially to the optimization of oxygen removal procedures in the drop of a solution. Developed miniaturized methods had the same parameters for the determination of studied compounds as in bigger volumes. The proposed electrochemical microcell can be generally used for voltammetric analysis of those samples of biological or environmental origin that are usually available in very limited volumes. Second part of the thesis was focused...

<p>Sukcinimidi su jedinjenja koja pokazuju vi&scaron;estruke farmakolo&scaron;ke efekte uključujući i antiproliferativnu aktivnost, zahvaljujući prisustvu farmakofore sa dva hidrofobna regiona i dva regiona bogata elektronima. Savremeni dizajn lekova ima za cilj da se modifikacijama u strukturi (promena vrste, položaja i orijentacije supstituenata) i in silico računarskim metodama predvide i optimizuju farmakokinetske osobine i bezbednosni profil kandidata za lek. U ranoj fazi razvoja lekova se koriste postojeće baze podataka o molekulskim, farmakokinetskim i toksikolo&scaron;kim parametrima već ispitanih jedinjenja i pomoću matematičkih modela i algoritama predviđaju se osobine novih molekula, elimini&scaron;u se neodgovarajući kandidati i postiže se u&scaron;teda u vremenu i materijalnim sredstvima. Da se ispitaju fizičko-hemijske karakteristike 11 novosintetisanih metil-etil-N-aril-sukcinimida na osnovu strukture, primenom različitih softverskih paketa; da se na osnovu strukture odrede farmakokinetski i toksikolo&scaron;ki parametri, primenom različitih softverskih paketa; da se ispita retenciono pona&scaron;anje, odnosno odrede retencione konstante za svako jedinjenje primenom visokoefikasne hromatografije na tankom sloju (HP-TLC) i ispita mogućnost primene retencionih konstanti kao mere lipofilnosti ispitivanih jedinjenja; da se ispita antiproliferativna aktivnost na odabranim kulturama ćelija karcinoma i na zdravim ćelijama fibroblasta pluća; da se analizom molekulskog dokinga ustanovi vezivanje za estrogene receptore. Ispitano je retenciono pona&scaron;anje 11 novosintetisanih derivata sukcinimida primenom visokoefikasne hromatografije na tankom sloju (HP-TLC) obrnute faze uz primenu dvokomponentne sme&scaron;e vode i organskog rastvarača (metanola, acetonitrila ili acetona), sa odgovarajućim zapreminskim udelom organskog rastvarača kao mobilne faze. Iz razvijenih hromatograma su izračunate retencione konstante RM0 i S. Logaritam podeonog koeficijenta (logP) određen je in silico, kori&scaron;ćenjem različitih računarskih programa. In silico su određene fizičko-hemijske karakteristike, farmakokinetski parametri, toksikolo&scaron;ki parametri, akvatična toksičnosti i afinitet vezivanja za estrogene receptore. Izračunate su vrednosti afiniteta za 4 vrste receptora (G-protein spregnuti receptori, jonski kanali, inhibitori kinaza, nuklearni receptori). Antiproliferativna aktivnost ispitivanih derivata sukcinimida određena je primenom kolorimetrijskog testa sa tetrazolijum solima (MTT testa) na komercijalnim kulturama ćelija (MRC-5, A549, HeLa, MDA-MB-231, MCF-7, HT-29) i izračunate su IC50 vrednosti. Urađena je i doking analiza sukcinimida prema ERA (estrogen receptor alfa) i ERB (estrogen receptor beta) i dobijene su vrednosti energije formiranja kompleksa sa posmatranim receptorima (MolDock Score). Statistički najznačajnije linearne korelacije dobijene su između eksperimentalno određenih hromatografskih parametara (RM0 i S) i in silico parametara lipofilnosti MlogP i ClogP. Ispitivanjem uticaja promene RM0 i S na farmakokinetske karakteristike dobijeni su rezultati koji pokazuju paraboličnu zavisnost konstante apsorpcije (Ka) i procenta vezivanja za proteine plazme (PPB) od posmatranih retencionih konstanti, dok je zavisnost sa volumenom distribucije (Vd) i sposobno&scaron;ću prolaska kroz krvno-moždanu barijeru (logBBB) bila linearnog tipa. Toksičnost ispitivanih jedinjenja, procenjena na osnovu in silico dobijenih LD50 vrednosti, nije bila vi&scaron;a od toksičnosti već registrovanih lekova sa strukturom sukcinimida, i dala je parabolične zavisnosti u odnosu na RM0 i S vrednosti. Eksperimentalno nijedno od ispitivanih jedinjenja nije pokazalo aktivnost u odnosu na zdrave fibroblaste pluća. Najznačajniju antiproliferativnu aktivnost (najniže IC50) su pokazala jedinjenja 6 i 7 u odnosu na ćelije linije MCF-7 i jedinjenje 11 u odnosu na A549 ćelijsku liniju. Doking analiza je pokazala niže energije formiranja kompleksa sa ERA, u odnosu na ERB. Eksperimentalno određeni parametri RM0 i S se mogu koristiti kao alternativne i pouzdane mere lipofilnosti analiziranih sukcinimida. Ispitivana jedinjenja pokazuju povoljne fizičko-hemijske karakteristike, predviđene in silico metodama i povoljne farmakokinetske karakteristike: male vrednosti konstante apsorpcije, umeren volumen distribucije, povoljan afinitet vezivanja za proteine plazme, favorizovan prolazak kroz krvno-moždanu barijeru za lipofilnija jedinjenja. Procenjuje se da sva ispitivana jedinjenja, izuzev derivata sa &ndash;CN supstituentom, imaju zahtevani nizak stepen toksičnosti. Po antiproliferativnoj aktivnosti u odnosu na ćelije ER-zavisnog karcinoma dojke (MCF-7) izdvajaju se jedinjenja sa metil i nitro supstituentom u para položaju. Na osnovu malih energija formiranja kompleksa sa ERA, koji su eksprimirani na ćelijama MCF-7 linije, pretpostavlja se da bi mehanizam njihovog delovanja delimično mogao biti obja&scaron;njen uticajem na ERA, ali su potrebna dodatna istraživanja na tom polju.</p> / <p>Succinimides have exhibited various pharmaceutical effects including antiproliferative activity due to an important structural fragment (a pharmacophore) presented in form of two hydrophobic regions and two electron-rich centers. Current development of new drugs involves modifications in structure (type, position and orientation of substituents) and usage of in silico computational programs to predict and optimize pharmacokinetic and safety profile of drug candidates. In early phase of drug development, databases regarding the molecular, pharmacokinetic and toxicological parameters of already tested compounds are used, mathematical models and algorithms are applied for predicting the properties of new molecules and inadequate candidates are eliminated saving time and resources. Determination of physico-chemical properties of the analyzed methyl-ethyl-N-phenilsuccinimide derivatives by software packages; virtual pharmacokinetic and toxicology screening; investigation of retention behavior of the compounds by the reversed-phase HPTLC analysis and calculation of retention constants and their correlation with lipophilicity; in vitro evaluation of antiproliferative activity toward five carcinoma cell lines and normal fetal lung cell line; molecular behavior study on target estrogen receptors by molecular docking and correlation of antiproliferative activity toward ER+ breast carcinoma cell lines and in silico estrogen receptor affinity binding. Retention behavior of 11 newly synthesized succinimide derivatives was determined by reversed phase high performance thin layer chromatography (RP HPTLC) with the application of two-component mixtures water - organic solvent (methanol, acetonitrile or acetone) with adequate volume fractions of the organic modifier. After chromatographic development RM0 and S parameters were calculated. The logarithm of partition coefficient, logP for the analyzed compounds were calculated by different softwares. Physico-chemical properties, pharmacokinetic and toxicological parameters, aquatic toxicity and relative affinity to estrogen receptors were predicted in silico. The affinity toward 4 types of receptors (G-proteine coupled receptors, ion channels, kinase inhibitors, nuclear receptors) were calculated as well. Standard MTT assay was applied to evaluate cytotoxic activities of the analyzed succinimides after cells were exposed. Antiproliferative activity were investigated toward commercial MRC-5, A549, HeLa, MDA-MB-231, MCF-7, HT-29 cell lines and IC50 values were calculated for each compound. MolDock Score that represents energy of binding to estrogen alfa and estrogen beta receptors was determined by molecular docking. Statistically significant linear correlations were determined between the chromatographic retention constants (RM0 and S) and calculated logP, and the best two were obtained in correlation of retention constants with MlogP and ClogP. The examination of RM0 and S influence on pharmacokinetics indicated parabolic dependence of the absorption constant (Ka) and plasma protein binding predictor (PPB) from the observed constants while the volume of distribution (Vd) and the ability to cross the brain blood barrier (logBBB) had linear association with the retention parameters. The toxicity of the analysed compounds evaluated in silico as LD50 on rodents was lower in comparison with the drugs with succinimide structure that are on the market and had parabolic correlation with the RM0 and S values. The experiments indicated that none of the compounds examined had cytotoxic activity toward the healthy lung fibroblast cells. The results of the in vitro assay shown that none of the investigated compounds demonstrated antiproliferative activity toward fetal lung cells. The most potent antiproliferative agents were compounds 6 and 7 toward MCF-7 cell line, and compound 11 toward A549 cell line. Molecular docking shown lower energy for binding to ERA in comparison to ERB.</p>

Indiana University-Purdue University Indianapolis (IUPUI) / Recent work has shown that specific ALDH isoenzymes can contribute to the underlying pathology of different diseases. Many ALDH isozymes are important in oxidizing reactive aldehydes resulting from lipid peroxidation, and, thus, help maintain cellular homeostasis. Increased expression and activity of ALDH isozymes are found in many human cancers and are often associated with poor prognosis. Therefore, the development of inhibitors of the different ALDH enzymes is of interest as means to treat some of these disease states. Here I describe the results of assays designed to characterize the site of interaction and the mode of inhibition for the unique compounds that function as inhibitors of aldehyde dehydrogenase 2 and determine their respective IC50 values with intent to develop structure-activity relationships for future development.

Indiana University-Purdue University Indianapolis (IUPUI) / Intrinsically disordered proteins (IDPs) are flexible proteins without defined 3D structures. Studies show that IDPs are abundant in nature and actively involved in numerous biological processes. Two crucial subjects in the study of IDPs lie in analyzing IDPs’ functions and identifying them. We thus carried out three projects to better understand IDPs. In the 1st project, we propose a method that separates IDPs into different function groups. We used the approach of CH-CDF plot, which is based the combined use of two predictors and subclassifies proteins into 4 groups: structured, mixed, disordered, and rare. Studies show different structural biases for each group. The mixed class has more order-promoting residues and more ordered regions than the disordered class. In addition, the disordered class is highly active in mitosis-related processes among others. Meanwhile, the mixed class is highly associated with signaling pathways, where having both ordered and disordered regions could possibly be important. The 2nd project is about identifying if an unknown protein is entirely disordered. One of the earliest predictors for this purpose, the charge-hydropathy plot (C-H plot), exploited the charge and hydropathy features of the protein. Not only is this algorithm simple yet powerful, its input parameters, charge and hydropathy, are informative and readily interpretable. We found that using different hydropathy scales significantly affects the prediction accuracy. Therefore, we sought to identify a new hydropathy scale that optimizes the prediction. This new scale achieves an accuracy of 91%, a significant improvement over the original 79%. In our 3rd project, we developed a per-residue C-H IDP predictor, in which three hydropathy scales are optimized individually. This is to account for the amino acid composition differences in three regions of a protein sequence (N, C terminus and internal). We then combined them into a single per-residue predictor that achieves an accuracy of 74% for per-residue predictions for proteins containing long IDP regions.

No description available.

Indiana University-Purdue University Indianapolis (IUPUI) / Murine double minute (Mdm2) is a highly modified and multi-faceted protein that is overexpressed in numerous human malignancies. It engages in many cellular activities and is essential for development since deletion of mdm2 is lethal in early stages of embryonic development. The most studied function of Mdm2 is as a negative regulator of the tumor suppressor protein p53. Mdm2 achieves this regulation by binding to p53 and inhibiting p53 transcriptional activity. Mdm2 also functions as an E3 ubiquitin ligase that signals p53 for destruction by the proteasome. Interestingly recent evidence has shown that Mdm2 can also function as an E3 neddylating enzyme that can conjugate the ubiquitin-like molecule, nedd8, to p53. This modification results in inhibition of p53 activity, while maintaining p53 protein levels. While the signaling events that regulate Mdm2 E3 ubiquitin ligase activity have been extensively studied, what activates the neddylating activity of Mdm2 has remained elusive. My investigations have centered on understanding whether tyrosine kinase signaling could activate the neddylating activity of Mdm2. I have shown that c-Src, a non-receptor protein tyrosine kinase that is involved in a variety of cellular processes, phosphorylates Mdm2 on tyrosines 281 and 302. This phosphorylation event increases the half-life and neddylating activity of Mdm2 resulting in a neddylation dependent reduction of p53 transcriptional activity. Mdm2 also has many p53-independent cellular functions that are beginning to be linked to its role as an oncogene. There is an emerging role for Mdm2 in tumor metastasis. Metastasis is a process involving tumor cells migrating from a primary site to a distal site and is a major cause of morbidity and mortality in cancer patients. To date, the involvement of Mdm2 in breast cancer metastasis has only been correlative, with no in vivo model to definitively define a role for Mdm2. Here I have shown in vivo that Mdm2 enhances breast to lung metastasis through the up regulation of multiple angiogenic factors, including HIF-1 alpha and VEGF. Taken together my data provide novel insights into important p53-dependent and independent functions of Mdm2 that represent potential new avenues for therapeutic intervention.

<p>G-protein coupled receptors (GPCRs) are membrane proteins that constitute ~30% of the FDA-approved drug targets. Opioid receptors are a subtype of GPCRs with four different receptor types: delta, kappa, mu, and nociception opioid receptors. Opioids such as morphine have been used for thousands of years and are deemed the most effective method for treating pain. However, opioids can have detrimental effects if used illicitly or over an extended period of time. Intriguingly, most of the clinically used opioids act on the mu opioid receptor (µOR). Hence, efforts in recent decades have focused on other opioid receptors to treat pain and other disorders. The delta opioid receptor (δOR) is one of four opioid receptors expressed in the central and peripheral nervous system. The δOR has attracted much attention as a potential target for a multitude of diseases and disorders including substance and alcohol use disorders, ischemia, migraine, and neurodegenerative diseases. However, to date, no δOR agonists, or drugs that act directly at the δOR, have been successful as clinical candidates. Nonetheless, the therapeutic potential of the δOR necessitates the targeting its pharmacologically. In this dissertation, I highlight peptide-based modulation as well as the identification of novel agonists at the δOR. I report research findings in the context of biased agonism at δOR, which is a hypothesized cellular signaling mechanism with potential therapeutic benefits. The focus on this work is the molecular determinants of biased agonism, which were investigated using a combination of cellular and computational approaches.  </p>

Die selektive Funktionalisierung nicht aktivierter C−H-Bindungen und die Disauerstoffreduktionsreaktion (ORR) sind extrem wichtig bei der Beschäftigung mit verschiedenen technologischen Problemstellungen wie der Energiekrise, der Synthese kommerziell relevanter organischer Verbindungen usw. Die Nutzung molekularen Sauerstoffs als reichlich vorhandenes und umweltverträgliches Oxidationsmittel ist von großem Interesse in der Entwicklung bioinspirierter synthetischer Oxidationskatalysatoren. Die katalytische Vier-Elektronen-Reduktion von Disauerstoff zu Wasser erlangte auch immer größere Aufmerksamkeit wegen ihrer Bedeutung in der Brennstoffzellentechnologie. Natürlich vorkommende Metalloenzyme aktivieren Disauerstoff durch die Nutzung günstiger Übergangsmetalle (z.B. Eisen, Nickel, Mangan und Kupfer) und weisen diverse oxidative Reaktivitäten auf. Des Weiteren werden solche Reaktionen unter Umgebungsbedingungen mit hoher Effizienz und Stereoselektivität durchgeführt. Deshalb kann die Isolierung und Charakterisierung hochvalenter Metall-Disauerstoff-Intermediate (wie Metall-Superoxo-, Metall-Peroxo-, Metall-Hydroperoxo- und Metall-Oxo-Verbindungen) eine Menge nützlicher Informationen über die Reaktionsmechanismen liefern und daher hilfreich für die zukünftige Entwicklung effizienterer Katalysatoren sein. Diese Arbeit hat die Chemie verschiedener Metall-Disauerstoff-Intermediate von end-on-1,2-Peroxo-dicobalt(III)-Spezies bis zu Superoxo-nickel(II)-Kernen erforscht. Detaillierte spektroskopische Untersuchungen sowie Reaktivitätsstudien der Intermediate wurden durchgeführt, um den Zusammenhang zwischen ihrer elektronischen Struktur und ihren Reaktivitätsmustern aufzuklären. In meiner Arbeit untersuchte ich den Effekt der ‚Struktur-Aktivität-Beziehung‘ verschiedener Metall-Disauerstoff-Intermediate gegenüber exogener Substrate. Diese Arbeit zeigte auch den Einfluss des Designs geeigneter Liganden auf das Verhalten eines gegebenen reaktiven Metall-Disauerstoff-Systems. / Selective functionalization of unactivated C−H bonds and dioxygen reduction reaction (ORR) are extremely important in the context of addressing various technological issues such as energy-crisis, synthesis of commercially important organic compounds, etc. The utilization of molecular oxygen as an abundant and environmentally benign oxidant is of great interest in the design of bioinspired synthetic oxidation catalysts. The catalytic four-electron reduction of dioxygen to water has also merited increasing attention because of its relevance to fuel cell technology. Naturally occurring metalloenzymes activate dioxygen by employing cheap transition metals (e.g. iron, nickel, manganese, and copper) and exhibit diverse oxidative reactivities. Moreover, such reactions are carried out under ambient conditions with high efficiency and stereospecificity. Therefore, the isolation and characterization of the high-valent metal-dioxygen intermediates (such as metal-superoxo, -peroxo, -hydroperoxo, and -oxo can provide a lot of useful information about the reaction mechanisms and is therefore helpful for the future design of more efficient catalysts. This thesis has explored the chemistry of different metal-dioxygen intermediates ranging from bridging end-on μ-1,2-peroxo-dicobalt(III) species to nickel(II)-superoxo cores. Detailed spectroscopic and reactivity studies of the intermediates have been performed to reveal the correlations between their electronic structures and reactivity patterns. In my present thesis, I investigated the effect of the ‘structure-activity relationship’ of different metal-dioxygen intermediates towards exogenous substrates. This thesis also demonstrated the impact of suitable ligand design on the behaviour of a given metal-dioxygen reactive system.

No description available.

No description available.