A sol-gel process has been utilized to develop novel hybrid materials incorporating organic and inorganic species. The objectives of this project were to study the feasibility of this new bridging route and, if successful, study the structure-property relationships of these new materials. In this thesis, tetraorthosilicate was used to combine with one of three types of oligomers, which included silanol terminated polydimethylsiloxane (PDMS), triethoxysilane endcapped polytetramethyleneoxide (PTMO), and PTMO with multiple triethoxysilane functional groups. The general reaction scheme was to first generate silanols from both components through the hydrolysis reaction, and then form the network structure by a co-condensation reaction with the silanol groups. The preparation of these hybrid materials was successful. Most of these hybrid materials were obtained without significant cracking problems with an initial TEOS loading up to 80 wt%, and the final products were always transparent. For the PDMS containing systems, the tensile strength was always lower than 8 MPa. and the elongation at break was in the range of 5-25%. Dynamic mechanical results showed a bimodal tan<i>δ</i> behavior, which was attributed to two different physico-chemical environments of the oligomers: one was PDMS rich phase and one represented more dispersed PDMS oligomers. The dispersion of the oligomers increased with acid and silicate content of the system, and this postulation of better PDMS dispersion was strongly supported by the SAXS results which showed a systematic decrease in the mean square electron density fluctuation. The mechanical properties of PTMO containing materials were considerably enhanced compared to the PDMS hybrid systems. Depending on the composition and oligomeric molecular weight, the tensile strength could reach 33 MPa. Also, the range of the elongation at break increased up to ca. 100%. The tan<i>δ</i> spectra showed a single, broad maximum at temperatures much higher than the T_g of pure PTMO oligomers, which indicated the absence of a pure oligomer phase. A broad maximum in the SAXS profile was observed in most cases, implying the existence of a correlation distance in these PTMO containing materials. To rationalize all the experimental observations, a schematic model was suggested which contains highly condensed TEOS clusters and mixed regions of partially condensed TEOS and PTMO. This model was further supported by swelling data and by agreement between the SAXS correlation length and the estimated PTMO end-to-end distance. The systems prepared with PTMO possessing multiple triethoxysilane groups showed the most promising results in terms of mechanical properties. The tensile strength ranged from ca. 30 to 55 MPa., and the ambient modulus was nearly 10⁸ Pa. Also, a yield point was observed in some cases and was postulated to be an indication of partial continuity of the silicate phase. / Ph. D.

A flavoenzima diidroorotato desidrogenase (DHODH) catalisa a quarta reação da via de novo de biossíntese de pirimidinas, se destacando como alvo molecular chave para parasitos causadores de Doenças Negligenciadas (DNs). Tendo em vista a demanda por novas alternativas terapêuticas para estas doenças, o objetivo deste trabalho foi a triagem in vitro de inibidores da enzima DHODH de Leishmania major (LmDHODH) em Asteraceae. Esta triagem foi acompanhada por abordagem metabolômica em UHPLC-ESI-HRFTMS para os extratos vegetais e estudos de QSAR (Quantitative Structure-Activity Relationships) para as substâncias isoladas. As etapas experimentais realizadas e os resultados obtidos foram: 1) Ensaios enzimáticos: os valores de IC50 foram determinados para 59 extratos (?IC50: 148,0 ?g.mL-1 a 9,4 mg.mL-1) e 57 substâncias isoladas (?IC50: 27,0 ?M a 2,6 mM). As substâncias mais ativas frente à LmDHODH apresentaram seletividade, ao exercer inibição irrelevante sobre DHODH humana. Adicionalmente, estudos de termoestabilidade confirmaram que as lactonas sesquiterpênicas (STLs) são, de fato, capazes de se ligar a esta enzima; 2) Estudos metabolômicos: as impressões digitais metabólicas por LC-MS foram obtidas com sucesso para os 59 extratos e o processamento dos dados forneceu 3.694 substâncias. A desreplicação por meio de uma biblioteca de padrões identificou com segurança 49 metabólitos secundários. Por meio da correlação in silico com os dados de inibição enzimática, foram determinados com êxito os principais biomarcadores dos extratos e obteve-se um modelo de regressão confiável para predição do potencial de inibição de novos extratos provindos de espécies ainda não testadas frente à LmDHODH, classificando-os como ativos ou inativos com base exclusivamente na sua impressão digital por UHPLC-ESI-HRFTMS; 3) Estudos de QSAR com 21 STLs: o modelo de QSAR baseado em descritores moleculares apresentou robustez e confiabilidade (R2 / Q2 / P2 > 0,6 e RMSE < 0,3), revelando que uma maior inibição desta enzima requer a distribuição balanceada das regiões hidrofóbicas através da superfície molecular, maior largura das moléculas e menor hidrofobicidade. O modelo 3D baseado em descritores farmacofóricos também foi útil (R2: 0,79; Q2: 0,55) e confirmou a importância da orientação adequada dos ligantes, propriedades superficiais e formato das moléculas, refletindo propriedades de um possível sítio de ligação para as STLs na enzima. Portanto, alguns dos produtos naturais testados nesta triagem in vitro são, de fato, capazes de inibir seletivamente a enzima LmDHODH, tratando-se de uma descoberta relevante, visto que uma infinidade de metabólitos secundários leishmanicidas já foram descritos, porém, para a maioria deles, o mecanismo de ação segue desconhecido. Os resultados evidenciaram (1) as espécies de Asteraceae como importante fonte na busca por novos inibidores desta enzima e (2) as substâncias mais ativas como ponto de partida para novas estruturas guias (lead compounds) visando novos fármacos antiparasitários para o tratamento de DNs, especialmente a leishmaniose. / The flavoenzyme dihydroorotate dehydrogenase (DHODH) catalyzes the fourth reaction of the de novo pyrimidine biosynthetic pathway, standing out as a key molecular target for trypanosomatid parasites causing Neglected Diseases (NDs). In view of the global demand for new therapies for such diseases, this study aimed for the in vitro screening of inhibitors of Leishmania major DHODH (LmDHODH) in Asteraceae, accompanied by metabolomic approach with UHPLC-ESI-HRFTMS for plant extracts and QSAR studies (Quantitative Structure-Activity Relationships) for isolated compounds. The experimental steps performed and the results obtained were: 1) Enzymatic assays: the IC50 values were determined for 59 plant extracts (?IC50: 148.0 ?g.mL-1 a 9.4 mg.mL-1) and 57 natural compounds (?IC50: 27.0 ?M a 2.6 mM). The most active compounds showed selectivity against LmDHODH by exercising irrelevant inhibition of human DHODH. In addition, thermostability studies have confirmed that sesquiterpene lactones (STLs) are indeed capable of binding to this enzyme; 2) Metabolomic studies: the metabolic fingerprints by LC-MS were successfully obtained for the 59 extracts and 3,694 peaks/compounds were provided after data processing. The dereplication using a library of natural compounds has safely identified 49 secondary metabolites. By means of in silico correlation with the enzymatic inhibition data, the main biomarkers of the extracts were successfully determined and a reliable regression model was obtained to predict the inhibition potential of new extracts from species not yet tested against LmDHODH, classifying it as active or inactive based solely on their fingerprint by UHPLC-ESI-HRFTMS; 3) QSAR studies with 21 STLs: a reliable QSAR model based on molecular descriptors was obtained (R2 / Q2 / P2 > 0.6 and RMSE < 0.3), which indicated that stronger inhibition requires a balanced distribution of the hydrophobic regions across the molecular surface, as well as higher width and lower hydrophobicity of the molecules. A pharmacophore-based 3D-QSAR approach also afforded a useful model (R2: 0.79; Q2: 0.55), which confirmed the importance of proper orientation of the ligands, molecular surface features and shape for stronger inhibition, reflecting properties of a putative common binding site. Thus, some of the natural products tested in this in vitro screening are actually capable of selectively inhibiting LmDHODH. This constitutes a relevant finding, since an infinity of leishmanicidal compounds have been described, however, for most of them, the mechanism of action remains unknown. The results highlighted (1) Asteraceae species as important sources of new LmDHODH inhibitors and (2) the most active metabolites as promising starting points for new led compounds aiming new antiparasitc drugs for treatment of NDs caused by trypanosomatids, especially leishmaniasis.

There is a dogma in molecular biology that biological functions of peptides are determined by their structure ("function" code), coded in their primary structure ("structure" code). This work describes a new approach that attempts to elucidate these relationships by peptide topology design based on intriguing conformational properties of pipecolic acid based amino acids--like 1,2,3,4 tetrahydroisoquinoline (Tic). Opioid peptides, owing to the heterogeneity of opioid receptors, display a wide variety of physiological actions. The mu opioid receptor selective octapeptide I (D-Tic-Cys-Tyr-D-Trp-Orn-Thr-Pen-Thr-NH₂) is a model compound for topographical modifications induced by sequential substitutions by Tic residue. Thus, the closely related peptides I and II (Gly-D-Tic-Cys-Tyr-D-Trp-Orn-Thr-Pen-Thr-NH₂, obtained by coupling Gly residue to I) have contrasting affinities for the mu opioid receptor (IC₅₀ = 1.2 and 278 nM, respectively). Conformational analysis of I and II by means of 1D and 2D ¹H NMR spectroscopy allowed to determine dramatic differences in the side chain orientation of D-Tic in both peptides and to propose features of the bioactive conformation. The extended conformation of I (due to g(-) side chain conformation of D-Tic) is well recognized by the mu receptor in contrast to the folded conformation of II (due to a g(+) side chain conformation of D-Tic¹, that places the aromatic ring on the opposite side of the molecule), which is not. Peptide III (D-Phe-Cys-Tic-D-Trp-Orn-Thr-Pen-Thr-NH₂), featuring replacement of Tyr³ by Tic³, binds very weakly to the mu opioid receptor, due to rotation of the Tic aromatic side chain to the opposite side of the molecule (Tic side chain is in a g(+) conformation again). As these substitutions conserve the conformation of the backbone, constrained cyclic amino acids (picolic acid derivatives) can modify the topography of the peptide in a predictable manner, and (in conjunction with biological data) disclose structural elements of bioactive conformations. The mechanisms of pipecolic acid side chain rotamer selection, will be discussed in the context of design principles.

The metabolism of ADP-ribose polymers (PAR) is involved in several cellular processes with a primary focus on maintaining genomic integrity. PAR metabolism following genotoxic stress is transient due to a close coordination between poly(ADP-ribose) polymerases (PARPs) which synthesize PAR and poly(ADP-ribose) glycohydrolase (PARG) which degrades PAR. PARP-1 inhibitors have emerged as promising anticancer therapeutics by increasing chemotherapy sensitivity and selectively target tumors harboring DNA repair defects. Several pharmaceutical companies have PARP-1 inhibitors in clinical trials for treatment of cancer. PARP-1 inhibitors are generally well tolerated, although they typically have poor selectivity among PARPs, and potentially other NAD binding enzymes. The promise of PARP-1 inhibitors as cancer therapeutics has led this dissertation research towards developing alternative tools and approaches to target PAR metabolism.One approach described is an evaluation of high-throughput PARP-1 screening assays as potential tools to discover new classes of PARP-1 inhibitors. These assays were compared to a widely used radiolabeling PARP-1 assay. They were found to offer several advantages that include simplicity, sensitivity, reproducibility, accuracy and eliminating the need for radioactive materials.The primary focus of this dissertation research was to develop PARG inhibitors as an alternative way of targeting PAR metabolism. Lack of viable genetically engineered animals, effective siRNA, and useful pharmacological 20 inhibitors has prevented PARG from being evaluated as a therapeutic target. This dissertation describes the first systematic approach, using Target related Affinity Profiling (TRAP) technology, for the discovery of PARG inhibitors. Identification of several hits led to the first detailed structural activity relationship (SAR) studies defining a pharmacophore for PARG inhibition. Interestingly, these molecules show varying degrees of PARP-1 inhibition, providing the first direct evidence for homology in the active sites of PARP-1 and PARG. Evaluation of a lead inhibitor has provided the first evidence for PARG inhibition in intact cells. Further optimization resulted in a cell permeable inhibitor with reduced toxicity and poor selectivity, providing evidence for a new class of inhibitors that disrupt PAR metabolism by inhibiting both enzymes. The use of dual PARG/PARP-1 inhibitors represents a new approach for therapeutic development of anticancer agents. Finally, directions aimed to overcome remaining challenges are discussed.

Millions of people in the US currently suffer from chronic pain but available therapeutics do not provide effective chronic pain treatment. Opiate therapy is still the gold standard for chronic pain management with detrimental side effects, such as tolerance, addiction, constipation, and respiratory depression that limit their therapeutic potential. Opiates exert their positive and negative effects by activating the μ opioid receptor (MOR). Conversely, the κ opioid receptor (KOR) has been shown to modulate the tolerance and addiction produced by MOR agonists and is also involved in mood modulation (anxiety and depression). Therefore, blocking KOR activation results in positive effects against opiate side effects and stress-related depression. Dynorphin A (Dyn A) is the endogenous opioid peptide for the KOR. Structure-activity relationship (SAR) studies were carried out to develop a KOR selective antagonist based on the Dyn A structure. A minimum Dyn A pharmacophore with improved stability, no cell toxicity, and antagonist activity was discovered. Peptidomimetic enkephalin analogues previously developed in our group as MOR and δ opioid receptor (DOR) agonists have shown multifunctional activity, with MOR/DOR agonist and KOR antagonist activities. To our knowledge, this finding is first of its class for the opioid receptors. Novel design and synthesis of KOR selective ligands based on our multifunctional enkephalin analogues was done. Successful peptide synthesis resulted in analogues with high stability in rat plasma and no cell toxicity.

by Paula A. Livingston. / Thesis (M.S.)--Florida Atlantic University, 2009. / Includes bibliography. / Electronic reproduction. Boca Raton, Fla., 2009. Mode of access: World Wide Web. / Two protein tyrosine phosphatases, dual specificity phosphatase PVP and low molecular weight phosphatase WZB were purified and characterized. PVP was expressed as inclusion bodies and a suitable purification and refolding method was devised. Enzyme kinetics revealed that p-nitrophenylphosphate and (Sb(B-naphthyl phosphate were substrates with KM of 4.0mM and 8.1mM respectively. PVP showed no reactivity towards phosphoserine. Kinetic characterization of WZB showed that only pnitrophenylphosphate was a substrate with no affinity for Ç-naphthyl phosphate and phosphoserine. Optimal conditions for activity with PNPP were found at a pH of 5 with a KM of 1.1mM, kcat of 35.4s-1 and kcat/KM of 32.2s-1mM-1. Inhibition studies showed that phosphate, fluoride, and molybdate were competitive inhibitors with Ki of 3.2mM, 71.7mM, and 50.4(So(BM respectively and hydrogen peroxide abolished activity. Active site mutants of WZB Cys9Ser and Asp115Asn showed no activity.

Previous research showed that the C-terminal tail of TCS can be deleted to generate a mini-TCS (C7-TCS) with antigenicity. The second topic of my study is to resolve the role of the C-terminal of TCS. Structure of C7-TCS showed that deletion of the C-terminal tail destabilizes the protein structure and makes Trp192 more solvent exposed. The relationship between the C-terminal tail and Trp192 was determined by mutating Trp192 to Phe in wild-type TCS and C7-TCS, generating W192F-TCS and W192F-C7-TCS. The crystal structure of C7-TCS, [W192F]-TCS and [W192F]-C7-TCS were determined and compared. Trp192 was identified as an important residue in stabilizing the conformation of TCS. Besides, the accumulative effect of Trp192 and the C-terminal tail is significant on the ribosome-inactivating activity. By comparing the structures, it was found that, the hydrogen bond formed by amino acids 240 and 35 seems to be essential for the structure and amino acid 240 should be a critical residue for the connection of the N-terminal and C-terminal domains in trichosanthin. / Ribosome-inactivating activity is the most important activity of TCS and RIPs. Therefore, the third topic of my study is to find the important of interaction between TCS and ribosomal proteins. Two ribosomal proteins, P0 and P1, have been identified previously to interact with TCS. By yeast two-hybrid screening, three cut of ten charge residues in TCS were identified to be the interaction sites between TCS and ribosomal protein P0. The interaction region was located on the surface of TCS near the entrance to the active pocket. The interaction with P0 was shown to be carried out by electrostatic interaction between the positively charge residues of TCS. However, the mutation of all the concerned residues in TCS gave only a mild reduction in inhibiting the protein synthesis of an in vitro reticulocyte translation system, showing that the interaction between TCS and P0 only plays a minor role in the ribosomal inactivating activity of TCS. / The first topic of my research is to find the role of Glu-85. The structure of [E85Q]-TCS and AMP complex was obtained. It is deduced that there are two sites for substrate binding in TCS, one is for recognition and another ion hydrolysis. The structure also indicated that protonation of substrate adenine is carried out by a water molecule in the active pocket of TCS during its N-glycosidase action. / Trichosanthin (TCS) is a Chinese medicinal protein isolated froth the root tuber of Trichosanthes kirilowi Maximowicz. It is a 27kDa protein with multiple pharmacological properties, including abortifacient, anti-tumor and anti-human immunodeficiency virus (HIV). It is believed that the pharmacological properties of TCS are related to ribosome-inactivation, by breaking, the specific glycosidic bond of adenine 4324 from the 28S rRNA. / Too Hiu Mei. / "February 2006." / Advisers: Pang-Chui Shaw; Kam-Bo Wong. / Source: Dissertation Abstracts International, Volume: 67-11, Section: B, page: 6213. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2006. / Includes bibliographical references (p. 164-175). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Electronic reproduction. [Ann Arbor, MI] : ProQuest Information and Learning, [200-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstracts in English and Chinese. / School code: 1307.

Transient receptor potential (TRP) channels comprise a superfamily of cation-selective ion channels that are largely calcium (Ca2+) permeable and that play diverse physiological roles ranging from nociception in primary afferent neurons to the absorption of dietary Ca2+. The 28 mammalian TRP channels are categorized into 6 subfamilies. The vanilloid subfamily is named for its founding member, TRPV1, the capsaicin receptor, and has 6 members. TRPV1-4 are all heat sensitive ion channels whereas TRPV5 and TRPV6 are involved in renal Ca2+ reabsorption and Ca2+ absorption in the intestine, respectively. In our structural studies, we have focused on TRPV3 and TRPV6. TRPV6 is a highly Ca2+ selective TRP channel (PCa/PNa ~ 130) that functions in active Ca2+ absorption in the intestine. Its expression is upregulated by vitamin D and is, on the molecular level, regulated by PIP2 and calmodulin (CaM). Previously, the structure of TRPV6 was solved using X-ray crystallography. Using the crystal structure, a negatively charged extracellular vestibule was identified and anomalous diffraction was used to identify ion binding sites in the pore. Also, at the top of the selectivity filter, four aspartates were identified that coordinate Ca2+ entering the pore and confer to TRPV6 its selectivity for Ca2+. However, only the structure of the rat orthologue was solved and only in the closed, apo state. We used cryo-electron microscopy (cryo-EM) to solve structures of the human orthologue of TRPV6 in the open and closed (we used the mutation R470E to close the channel) states. The closed-to-open TRPV6 transition is accompanied by the formation of short π-helices in the middle of the pore-lining S6 helices, which in turn results in their turning and a different set of residues facing the pore. Additionally, the formation of the π-helices results in kinking of the S6 helices, which further widens the pore. TRPV6 is constitutively active when expressed heterologously. In other words, the addition of external stimuli is not necessary for the activation of the channel. Therefore, its activity needs to be regulated to prevent toxic Ca2+ overload. One mechanism by which this occurs is through its regulation by CaM. CaM has been shown to bind TRPV6 and regulate its function, however, the way it binds to and regulates TRPV6 remained unknown. To uncover this mechanism, we solved the structure of TRPV6 bound to CaM. We found that CaM binds TRPV6 in a 1:1 stoichiometric ratio and that CaM directly blocks the TRPV6 pore by inserting a positively charged lysine into a tera-tryptophan cage at the bottom of the pore. As a result, the channel adopts an inactivated conformation; although the pore-lining S6 helices still contain local π-helices, they are pulled closer together, narrowing the pore and further blocking it with hydrophobic side chains. We have also conducted studies of TRPV3. Unlike TRPV6, TRPV3 is a heat-activated vanilloid TRP channel. TRPV3 is expressed highly in keratinocytes where it has been implicated in wound healing and maintenance of the skin barrier, and in the regulation of hair growth. We solved the structure of apo TRPV3 in a closed state, and the structure of a TRPV3 mutant bound to 2-APB in an open state. Like TRPV6, the opening of TRPV3 is accompanied by the formation of local π-helices in the middle of the pore-lining S6 helices. The formation of the π-helices results in the lining of the ion permeation pathway with a different set of residues, resulting in a largely negatively charged pathway. Unlike TRPV6, TRPV3 is only slightly selective for Ca2+ and correspondingly, during gating state transitions, rearrangements were not only observed only in its pore-lining helices, but also in the cytosolic domain and the selectivity filter. Based on a comparison of our structures, we proposed a model of TRPV3 regulation by 2-APB. Together, our studies provide insight into the regulatory and gating mechanisms of the vanilloid subtype TRP channels and can provide the foundation for future studies.

Fluoroquinolones, broad-spectrum bactericidal antibiotics, exert their effects by inhibiting type II topoisomerases through the formation of a fluoroquinolone-DNA-topoisomerase ternary complex. Recently, newer, structurally unique fluoroquinolones have been shown to kill bacteria by promoting chromosomal fragmentation in the presence and absence of protein synthesis, thus allowing fluoroquinolones to potentially be used in the treatment of microorganisms that go into a dormant state. There is a need to further understand the structure activity relationships (SAR) of fluoroquinolones to develop new antibiotics that can kill dormant bacteria and are active against current resistant strains. The hypothesis that structurally unique fluoroquinolones interact with the DNA- fluoroquinolone-topoisomerase ternary complex in a unique way that leads to different killing pathways is the basis of this work. The first approach to understand SAR for fluoroquinolones to kill non-growing bacteria was to evaluate the effect of modifications at the C-8 and C-5 positions on lethality. Novel, synthetically-derived and commercially-available fluoroquinolones were evaluated for ability to kill Escherichia coli in the presence and absence of chloramphenicol, a known protein synthesis inhibitor used to simulate non-growing bacteria. The second study was to understand SAR of fluoroquinolone-class agents necessary to maintain antibacterial activity against common fluoroquinolone resistance-causing bacterial mutations on topoisomerase IV. A panel of novel fluoroquinolones, 2,4-quinazoline diones, and fluoroquinolone-like analogues with unique substitution combinations at C-8 and C-7 was synthesized and evaluated for ability to poison wild-type and mutant Bacillus anthracis topoisomerase IV. The third study to understand the contribution of SAR of fluoroquinolone-class agents to novel killing mechanisms was to evaluate the binding interaction of fluoroquinolones to double-stranded and nicked DNA. Binding affinities of fluoroquinolones to DNA were determined; fluoroquinolones were found to bind different DNA types with varied affinities. The ability of a series of C-8 and C-7 modified fluoroquinolones to stabilize or destabilize DNA was assessed. The results of these studies also add broadly to the understanding of SAR associated with fluoroquinolone-class antibiotics for killing in the presence and absence of protein synthesis, maintaining activity in the presence of resistance-causing mutations in the target enzymes, and increasing binding interactions with different types of DNA.

Abstract not available