Chemicals and Drugs Commons^™

Predicting Flavonoid Ugt Regioselectivity With Graphical Residue Models And Machine Learning., Arthur Rhydon Jackson

Electronic Theses and Dissertations

Machine learning is applied to a challenging and biologically significant protein classification problem: the prediction of flavonoid UGT acceptor regioselectivity from primary protein sequence. Novel indices characterizing graphical models of protein residues are introduced. The indices are compared with existing amino acid indices and found to cluster residues appropriately. A variety of models employing the indices are then investigated by examining their performance when analyzed using nearest neighbor, support vector machine, and Bayesian neural network classifiers. Improvements over nearest neighbor classifications relying on standard alignment similarity scores are reported.

Vitamin B6 Metabolism And Regulation Of Pyridoxal Kinase, Amit Gandhi

Theses and Dissertations

Pyridoxal 5'-phosphate (PLP) is the cofactor for over 140 vitamin B6 (PLP)-dependent enzymes that are involved in various metabolic and biosynthetic pathways. Pyridoxal kinase (PL kinase) and pyridoxine 5’-phosphate oxidase (PNP oxidase) are the two key enzymes that metabolize nutritional forms of vitamin B6, including pyridoxal (PL), pyridoxine (PN), and pyridoxamine (PM) to the active cofactor form, PLP. Disruption of the PLP metabolic pathway due to mutations in PNP oxidase or PL kinase result in PLP deficiency, which is implicated in several neurological pathologies. Several ingested compounds are also known to result in PLP deficiency with concomitant neurotoxic effects. How …

Computational Prediction Of The Agregated Structure Of Denatured Lysozyme, Pongsathorn Chotikasemsri

Masters Theses & Specialist Projects

Mis-folded proteins and their associated aggregates are a contributing factor in some human diseases. In this study we used the protein lysozyme as a model to define aggregation structures under denaturing conditions. Sasahara et al. (2007), Frare et al. (2009, 2006), and Rubin et al. (2008) observed conditions where heat denatured lysozyme formed fibril structures that were observed to be 8-17 nanometers in diameter under the electron microscope. Even though the crystal structure of lysozyme is known, the denatured form of this protein is still unknown. Therefore, we used Rosetta++ protein folding and blind docking software to create in silico …

Stromal Caveolin-1 Levels Predict Early Ductal Carcinoma In Situ Progression To Invasive Breast Carcinoma, A. K. Witkiewicz, A. Dasgupta, G. F. Schwartz, Kh H. Nguyen, H. R. Rui, M. P. Lisanti

Department of Cancer Biology Faculty Papers

With the increased use of screening mammography, the incidence of ductal carcinoma in situ (DCIS) has increased substantially and it currently accounts for 20-30% of newly diagnosed breast carcinomas in United States. Breast conserving therapy with or without radiotherapy is the accepted treatment for most cases of DCIS. However, the local recurrence rate with such therapy rages from 10 to 40% with half of these patients developing invasive carcinoma. Tamoxifen, used as an adjuvant systemic therapy for DCIS, does not increase overall survival and data on reduction of local recurrence rates are conflicting.

The current classification for DCIS based on …

Synthesis And Evaluation Of Anibamine And Its Analogs As Novel Anti-Prostate Cancer Agents, Kendra Haney

Theses and Dissertations

The chemokine receptor CCR5 has been implicated in the pathogenesis of prostate cancer. A novel natural product, anibamine, was isolated and found to be a micromolar inhibitor of the receptor. Anibamine was used as a new anti-prostate cancer lead compound. To discover the pharmacophore, analogs of anibamine were designed using the “deconstruction-reconstruction-elaboration” approach and synthesized. The establishment of a stereoselective route to only one isomer was explored, to increase yield and eliminate elaborate purification procedures. Analogs were found to have anti-prostate cancer activity at levels higher than the parent compound. The molecular modeling studies of the deconstructed analogs indicate that …

Trnas: Cellular Barcodes For Amino Acids, Ranat Banerjee, Shawn Chen, Kiley Dare, Marla Gilreath, Mette Praetorius-Ibba, Medha Raina, Noah M. Reynolds, Theresa E. Rogers, Hervé Roy, Srujana S. Yadavalli, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

The role of tRNA in translating the genetic code has received considerable attention over the last 50 years, and we now know in great detail how particular amino acids are specifically selected and brought to the ribosome in response to the corresponding mRNA codon. Over the same period, it has also become increasingly clear that the ribosome is not the only destination to which tRNAs deliver amino acids, with processes ranging from lipid modification to antibiotic biosynthesis all using aminoacyl‐tRNAs as substrates. Here we review examples of alternative functions for tRNA beyond translation, which together suggest that the role of …

The Production Of Antibody By Invading B Cells Is Required For The Clearance Of Rabies Virus From The Central Nervous System., D Craig Hooper, Timothy W Phares, Marzena J Fabis, Anirban Roy

Department of Cancer Biology Faculty Papers

BACKGROUND: The pathogenesis of rabies is associated with the inability to deliver immune effectors across the blood-brain barrier and to clear virulent rabies virus from CNS tissues. However, the mechanisms that facilitate immune effector entry into CNS tissues are induced by infection with attenuated rabies virus.

METHODOLOGY/PRINCIPAL FINDINGS: Infection of normal mice with attenuated rabies virus but not immunization with killed virus can promote the clearance of pathogenic rabies virus from the CNS. T cell activity in B cell-deficient mice can control the replication of attenuated virus in the CNS, but viral mRNA persists. Low levels of passively administered rabies …

The Effect Of All-Trans Retinoic Acid And Fatty Acids On Mcf-7 Breast Cancer Cell Progression, David A. Brown

Master's Theses

Vitamin A metabolites and retinoids may slow the progression of breast cancer and elicit anti-neoplastic properties similar to those of omega-3 fatty acids. Studies using animal models show a decrease in the incidence, growth and metastisis of mammary tumors in the presence of specific fatty acids. This effect is also seen with use of retinoids, specifically all-trans retinoic acid (AtRA). Thus, fatty acids may also alter retinoid homeostasis in mammary carcinoma cells (MCF-7s). The potential for inter/co dependency among fatty acids and retinoids is considerable, and here it has been hypothesized that a decrease in cancer progression will occur in …

Proteomic And Phospho-Proteomic Profile Of Human Platelets In Basal, Resting State: Insights Into Integrin Signaling, Amir H. Qureshi, Vineet Chaoji, Dony Maiguel, Mohd Hafeez Faridi, Constantinos J. Barth, Saeed M. Salem, Mudita Singhal, Darren Stoub, Bryan Krastins, Mitsunori Ogihara, Mohammed J. Zaki, Vineet Gupta

Faculty Work Comprehensive List

During atherogenesis and vascular inflammation quiescent platelets are activated to increase the surface expression and ligand affinity of the integrin αIIbβ3 via inside-out signaling. Diverse signals such as thrombin, ADP and epinephrine transduce signals through their respective GPCRs to activate protein kinases that ultimately lead to the phosphorylation of the cytoplasmic tail of the integrin αIIbβ3 and augment its function. The signaling pathways that transmit signals from the GPCR to the cytosolic domain of the integrin are not well defined. In an effort to better understand these pathways, we employed a combination of proteomic profiling and computational analyses of isolated …

Baseline Predictors Of Virological Response For Chronic Hepatitis B Patients, Xue-Jie Wu, Yan Wang, Ji Chen, Gui-Qiang Wang

Pharmacology and Toxicology Faculty Publications

AIM: To determine which baseline factors of chronic hepatitis B patients are predictive of virological response to Peginterferon α-2b therapy. METHODS: A total of 21 HBeAg-positive chronic hepatitis B (CHB) patients treated with Peginterferon α-2b were recruited. They were treated with Peginterferon α-2b (0.5-1.0 µg/kg per week) for 24 wk and followed up for 24 wk. Clinical and laboratory data of the patients were determined at pretreatment and at week 12, at 24 during treatment, and at week 48 during follow up. RESULTS: Ten patients achieved a virological response at the end of treatment. Their baseline serum alanine aminotransferase (ALT), …

Broad Range Amino Acid Specificity Of Rna-Dependent Lipid Remodelling By Multiple Peptide Resistance Factors, Hervé Roy, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Aminoacylphosphatidylglycerol synthases (aaPGSs) are multiple peptide resistance factors that transfer amino acids from aminoacyl-tRNAs to phosphatidylglycerol (PG) in the cytoplasmic membrane. Aminoacylation of PG is used by bacteria to decrease the net negative charge of the cell envelope, diminishing affinity for charged molecules and allowing for adaptation to environmental changes. Lys-PGS, which transfers lysine to PG, is essential for the virulence of certain pathogens, providing resistance to both host cationic antimicrobial peptides and therapeutic antibiotics. Ala-PGS was also recently described, but little is known about the possible activities of other members of the highly diverse aaPGS family of proteins. Systematic …

The Cca Anticodon Specifies Separate Functions Inside And Outside Translation In Bacillus Cereus, Sandro F. Ataide, Theresa E. Rogers, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Bacillus cereus 14579 encodes two tRNAs with the CCA anticodon, tRNA^Trp and tRNA^Other. tRNA^Trp was separately aminoacylated by two enzymes, TrpRS1 and TrpRS2, which share only 34% similarity and display different catalytic capacities and specificities. TrpRS1 was 18-fold more proficient at aminoacylating tRNA^Trp with Trp, while TrpRS2 more efficiently utilizes the Trp analog 5-hydroxy Trp. tRNA^Other was not aminoacylated by either TrpRS but instead by the combined activity of LysRS1 and LysRS2, which recognized sequence elements absent from tRNA^Trp. Polysomes were found to contain tRNA^Trp, consistent with its role in …

Adenosine Dimethyltransferase Ksga: Biochemical Characterization Of The Protein And Its Interaction With The 30s Subunit, Pooja Desai

Theses and Dissertations

Ribosomes form the core of the protein biosynthesis machinery and are essential to life. Ribosome biogenesis is a complex cellular process involving transcription of rRNA, pre-rRNA processing, rRNA modification and simultaneous assembly of ribosomal proteins. RNA nucleotide modification is observed in all domains of life. While there is enormous conservation of ribosome structure, very few post-transcriptional rRNA modifications have been conserved throughout evolution. A notable example of such rare conservation is the dimethylation of two adjacent adenosines in the 3’-terminal helix, a highly conserved region of the small subunit rRNA. Enzymes that carry out these dimethylations are equally conserved and …

Mutagenesis And Spectroscopic Studies Of Mycobacterium Tuberculosis Sterol 14alpha Demethylase., Anuja R. Modi

Theses and Dissertations

P450s are heme containing enzymes which affect oxidation of substrates via catalytic intermediates having transient lifetimes. These oxidative catalytic intermediates are formed by a sequential interplay of electrons and protons at the active site of the enzyme bearing molecular dioxygen. The proton transfer to the active site from bulk solvent is coordinated by an “acid-alcohol” pair of active site residues which are conserved in all P450s. Sterol 14α-demethylases (CYP51) are P450 enzymes which catalyze oxidative deformylation of lanosterol in the cholesterol/ergosterol biosynthetic pathway. Both cholesterol and ergosterol are important regulators of membrane fluidity. CYP51 differs from other P450s in that …

Attitudes Toward Psychotropic Medications Among Psychotropic Medications Among Psychiatric Outpatients And The General Population, Stephanie A. Fife

Graduate Theses

Attitudes and beliefs towards psychotropic medication were evaluated among psychiatric outpatients, patients seeking buprenorphine for substance abuse, and nonusers in a general population. The Drug Attitude Inventory scale (DAI-10) and the Beliefs about Medicines Questionnaire General (BMQ-G) were used to assess attitudes and beliefs of 49 participants. The general population had a negative attitude toward psychotropic medication and the psychiatric groups showed positive attitudes. Compliance and noncompliance were not associated with attitudes or beliefs toward psychotropic medication. Other findings include that females had less positive attitudes and beliefs towards psychotropic medication than males. The current findings expand and support research …

Spiroadamantyl 1,2,4-Trioxolane, 1,2,4-Trioxane, And 1,2,4-Trioxepane Pairs: Relationship Between Peroxide Bond Iron(Ii) Reactivity, Heme Alkylation Efficiency, And Antimalarial Activity, Xiaofang Wang, Darren J. Creek, Yuxiang Dong, Jacques Chollet, Christian Scheurer, Sergio Wittlin, Susan A. Charman, Patrick H. Dussault, James K. Wood, Jonathan L. Vennerstrom

Chemistry Faculty Publications

These data suggest that iron(II) reactivity for a set of homologous spiroadamantyl 1,2,4-trioxolane, 1,2,4-trioxane, and 1,2,4-trioxepane peroxide heterocycles is a necessary, but insufficient, property of animalarial peroxides. Heme alkylation efficiency appears to give a more accurate prediction of antimalarial activity than FeSO4-mediated reaction rates, suggesting that antimalarial activity is not merely dependent on peroxide bond cleavage, but also on the ability of reactive intermediates to alkylate heme or other proximal targets.

Novel Allosteric Inhibitors Of Thrombin, Bijoy Desai

Theses and Dissertations

Thrombin is a critical enzyme involved in blood coagulation and haemostasis. For this reason the study of its interactions with substrates, inhibitors and modulator is essential. It is also a unique enzyme in the serine protease family because unlike enzymes like trypsin and chymotrypsin its activity is modulated by various endogenous and exogenous ligands. This is due to the presence of “exosites” on the thrombin surface. Exosite II, unlike exosite-I, has not been characterized for its allosteric effect. In order to understand the structural basis of interaction and inhibition of inhibitor 4AS, which possibly interacts with exosite-II, native bovine thrombin …

Synthesis And Biochemical Studies On Sulfated Monomers Of Low Molecular Weight Lignins, Jenson Verghese

Theses and Dissertations

Anticoagulants are used as the first line therapy for management and prevention of thrombotic disorders. Thrombin and factor Xa have been the prime targets for regulation of the coagulation cascade. In this work, a small library of 17 benzofuran derivatives were synthesized and screened against thrombin and factor Xa. The derivatives that displayed inhibitory potential were docked on the exosite-II of factor Xa using a docking protocol that was developed in our research group. These compounds were based on the β-5 structural unit found in the oligomer -'CDSO3‘, which was prepared in our lab and was found to inhibit both …

Development Of Hint Based Computational Tools For Drug Design: Applications In The Design And Development Of Novel Anti-Cancer Agents, Ashutosh Tripathi

Theses and Dissertations

The overall aim of the research is to develop a computational platform based on HINT paradigm for manipulating, predicting and analyzing biomacromolecular-ligand structure. A second synergistic goal is to apply the above methodology to design novel and potent anti-cancer agents. The crucial role of the microtubule in cell division has identified tubulin as an interesting target for the development of therapeutics for cancer. Pyrrole-containing molecules derived from nature have proven to be particularly useful as lead compounds for drug development. We have designed and developed a series of substituted pyrroles that inhibit growth and promote death of breast tumor cells …

Coupling Between The Voltage-Sensing And Phosphatase Domains Of Ci-Vsp, Carlos A. Villalba-Galea, Francesco Miceli, Maurizio Taglialatela, Francisco Bezanilla

School of Pharmacy Faculty Articles

The Ciona intestinalis voltage sensor-containing phosphatase (Ci-VSP) shares high homology with the phosphatidylinositol phosphatase enzyme known as PTEN (phosphatase and tensin homologue deleted on chromosome 10). We have taken advantage of the similarity between these proteins to inquire about the coupling between the voltage sensing and the phosphatase domains in Ci-VSP. Recently, it was shown that four basic residues (R11, K13, R14, and R15) in PTEN are critical for its binding onto the membrane, required for its catalytic activity. Ci-VSP has three of the basic residues of PTEN. Here, we show that when R253 and R254 (which are the homologues …

Postprandial Effects Of Pecans Ingestion On Plasma Level Of Nutrients, Polyphenolic Compounds And Biomarkers Of Antioxidant Status In Human Volunteers, Chatrapa Hudthagosol

Loma Linda University Electronic Theses, Dissertations & Projects

Pecans (Carya illinoinensis) are rich sources of polyphenolic compounds and nutrients, which have antioxidant capacity results in favorable reductions in plasma lipids and lipoproteins. However, the health benefits of pecans may not be limited to blood lipid changes. There has been very little investigation into the contribution of bioactive components found in nuts to antioxidant protection. The purposes of the study were 1) to determine the impact of pecan consumption on concentration of total plasma polyphenols and their peak concentration over time. 2) to measure the effect of a pecan diet on postprandial levels of plasma lipid peroxidation …

Fetal Cocaine Exposure Causes Epigenetic Changes In The Rat Heart, Kurt D. Meyer

Loma Linda University Electronic Theses, Dissertations & Projects

Cocaine abuse continues to be prevalent in the United States and other industrialized nations, in addition to the negative health effects that cocaine abuse has on the user, a mother who uses cocaine while pregnant also exposes the developing fetus to cocaine. Although there have been many studies of the effects of cocaine on the adult heart, studies of cocaine on the fetal heart and its potential delayed pathophysiological effects on cardiac function in adult offspring are extremely limited. The studies of the present project sought to enhance the understanding of the effect of cocaine exposure on the fetal heart …

Localization And Expression Of The Aer Receptor In Escherichia Coli, Daniel Salcedo

Loma Linda University Electronic Theses, Dissertations & Projects

In Escherichia coli, chemotactic movement towards an energetically-favorable environment is mediated by five transmembrane chemoreceptors. These sensory proteins respond to numerous environmental signals, including amino acids, sugars, and pH. The aerotaxis receptor, Aer, is an intracellular sensor that responds to oxygen concentration and other parameters affecting cellular energy levels. Bacterial chemotaxis receptors form dimeric signaling units that organize into tetramers and hexamers and form large clusters at the cell poles. A cluster arrangement could increase receptor sensitivity by lateral communication between dimers, thus amplifying the signal from one dimer. We have shown that Aer forms dimers, trimer of dimers, …

“Design And Synthesis Of Molecular Probes For The Study Of 5-Ht2a And H1 Receptors”, Jitesh Shah

Theses and Dissertations

The serotonin (5-HT) receptors, with seven subtypes and at least fifteen distinct members, mediate a wide range of physiological functions both in the central nervous system and in the periphery. All members of the 5-HT family except the 5-HT3 subtype belong to the family of aminergic G protein-coupled receptors (GPCRs). Over the years, various molecules have been reported which act selectively at 5-HT2 receptors. However, there are no ligands that exhibit complete selectivity for one subpopulation of 5-HT2 receptors. Insight into how drugs bind to 5-HT2 receptors could contribute significantly to the development of subtype-selective agents with enhanced therapeutic effects. …

Development Of Ppar-Γ Receptor Agonists As Therapeutic Agents For Diabetes, Ashwini Goswami

Theses and Dissertations

The peroxisome proliferator-activated receptors (PPARs) are the transcriptional regulators of glucose, lipids and cholesterol metabolisms. It has been established that PPAR-γ is the receptor for thiazolidinediones (TZDs) class of type II anti-diabetic drugs. These compounds act as agonists of PPAR-γ. They may delay the development of type II diabetes in individuals at high risk of developing the condition, and have been shown to have potentially beneficial effects on cardiovascular risk factors. PPAR-γ receptor activation by TZDs improves insulin sensitivity by promoting fatty acid uptake into adipose tissue, increasing production of adiponectin (responsible for glucose regulation and fatty acid metabolism) and …

The Role Of Interferon Gamma In The Regulation Of Il-18 Binding Protein And The Development Of Autoimmune Arthritis In A Genetically Non-Susceptible Mouse Strain, Timothy Daniel Kayes

Theses and Dissertations (ETD)

The etiology of the autoimmune disease rheumatoid arthritis (RA) is unknown, but the role of cytokines, including IFN-g, as effectors of immune cell function has been established by the examination of cytokine production in RA patients and through the use of animal models. C57BL/6 (B6) mice that express MHC class II molecules of the b haplotype (I-A^b) are not typically susceptible to collagen-induced arthritis (CIA), the most widely studied animal model of RA. When the gene encoding IFN-g is removed by genetic deletion, however, susceptibility to CIA is conferred. In addition, T cell responses against the immunogen that …

Photochemical Delivery Of Bleomycin In Malignant Glioma Cells, Joseph William Blickenstaff Iii

UNLV Theses, Dissertations, Professional Papers, and Capstones

Despite continued efforts, glioblastoma multiforme (GBM) remains an incurable form of primary brain cancer. Surgical resection followed by radiation treatment and chemotherapy have been the most effective modalities in prolonging median survival time to 14 months. This research aims to study the response of two different cell culture models to a novel drug delivery method termed photochemical internalization (PCI). PCI is a technique to improve the utilization of macromolecules (e.g. the chemotherapeutic drug bleomycin) in site-specific cancer therapy. This concept is based on the use of specially designed photosensitizers (e.g. aluminum phthalocyanine disulfonate; AlPcS _2a ) which preferentially localize in …

Identifying Biomarkers For Resistance To Novel Cisplatin Analogues In Human Lung, Breast And Prostate Cancers, Becky Michelle Hess

UNLV Theses, Dissertations, Professional Papers, and Capstones

Cisplatin is a common therapeutic agent used in cancer treatment. Unfortunately, resistance to cisplatin in addition to severe side effects limits its use in cancer treatment. Two novel cisplatin analogues, 4DB and 4TB were shown to have varying cytotoxicity in lung, breast and prostate cancer cells. The hypothesis for this study states that the differences in 4DB and 4TB cytotoxicity among different tissue types is due to the type and efficiency of DNA repair mechanisms involved in response to these drugs.

To test the hypothesis, proteins involved in the rate limiting step of nucleotide excision repair (NER) and mismatch repair …

Contribution Of Organic Cation Transporter 2 (Oct2) To Cisplatin-Induced Nephrotoxicity, Kelly K. Filipski

Theses and Dissertations (ETD)

Cisplatin is the most widely used anticancer agent; however, the cellular pharmacokinetics are poorly understood. Cisplatin is predominantly eliminated through the urine via active secretion and is associated with nephrotoxicity. Currently, prehydration therapy is employed to prevent toxic renal side effects; however it has not been completely ameliorated. The studies described herein aim to determine the mechanism in which cisplatin enters the kidney cell from the blood and how it is subsequently secreted into the urine. Organic cation transporter 2 (OCT2) and ABCC2 are highly expressed in the kidney on the basolateral and apical membrane, respectively. We determined the contribution …

Insights Into Btb-Cul3 Ubiquitin Ligases From The Structures Of Spop-Substrate Complexes, Min Zhuang

Theses and Dissertations (ETD)

Cullin-Ring ubiquitin ligases (CRLs) are E3 complexes that specifically recognize substrates through substrate adaptors. In the largest CRL subfamily, Cul3 binds a BTB domain, and a protein-interaction domain such as MATH recruits substrates for ubiquitination. Here we present biochemical and structural analyses of the MATH and BTB domain containing protein, SPOP, which regulates diverse signaling pathways. First, we identified a conserved SPOP Binding Consensus (SBC) motif in the transcriptional regulator Ci, the protein phosphatase Puc, and the chromatin component MacroH2A. The SBC motif specifically binds the MATH domain of SPOP, and is required for Puc ubiquitination in vitro and in …