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Protein And Water Modeling In Computer-Aided Drug Discovery, Mossa Ghattas

Dissertations, Theses, and Capstone Projects

The field of Computer-Aided Drug Design (CADD) is continuously evolving to improve protein modeling, a crucial step in the drug discovery process. However, limitations exist in how CADD accounts for the various configurations a protein can adopt due to different rotamer and protonation states of its residues. This thesis explores advancements in CADD to address this challenge, focusing on protein modeling and water interactions.

In Chapter 1, I introduce the drug discovery process with a brief overview of its history, the purpose of FDA clinical trials, and the cost and time duration for bringing a drug to the market. I …

Deciphering The Interdomain Coupling In A Gram-Negative Bacterial Membrane Insertase, Adithya Polasa, Shadi A. Badiee, Mahmoud Moradi

Chemistry & Biochemistry Faculty Publications and Presentations

YidC is a membrane protein that plays an important role in inserting newly generated proteins into lipid membranes. The Sec-dependent complex is responsible for inserting proteins into the lipid bilayer in bacteria. YidC facilitates the insertion and folding of membrane proteins, both in conjunction with the Sec complex and independently. Additionally, YidC acts as a chaperone during the folding of proteins. Multiple investigations have conclusively shown that Gram-positive bacterial YidC has Sec-independent insertion mechanisms. Through the use of microsecond-level all-atom molecular dynamics (MD) simulations, we have carried out an in-depth investigation of the YidC protein originating from Gram-negative bacteria. This …

Highly Toxic Aβ Begets More Aβ, Merc M. Kemeh, Noel Lazo

Chemistry

No abstract provided.

Synthesis Of C-Di- And C-Tri- Saccharides From Glycosyl Crotylating Agents, Steven Truong

Dissertations, Theses, and Capstone Projects

The involvement of carbohydrates in a plethora of fundamental biological pathways, including disease related processes, has created a demand for molecular probes for elucidating these mechanisms. Accordingly, synthesis of tailored and diverse carbohydrate-like molecules, commonly referred to as glycomimetics, is a very active area of research. Among the more popular classes of glycomimetics are C-glycosides, analogues in which the anomeric carbon of a parent sugar is attached to a carbon substituent. C-glycosides have attracted attention in the medicinal chemistry community as there are several naturally occurring examples with interesting pharmacologically activity. C-glycosides are also of interest because in …

Drying Techniques For Precooked Hybrid Rice To Ensure Quality Of Instantized Rice, Anne Adhiambo Okeyo, Kaushik Luthra, Justin Siebenmorgen, Alan R. Vazquez, Griffiths Atungulu

Food Science Faculty Publications and Presentations

Background and Objectives

Due to the emergence of new hybrid rice cultivars, rice processors must refine their processing protocols to maintain the production of high-quality products. This is crucial for the instant rice processing industry. Therefore, this study aims to refine current convective heated air-drying processing methods to suit the new hybrid rice cultivars intended for instant rice production. New strategies to dry cooked rice were investigated. These included drying in a stepwise manner with high (230–200°C) and medium (190–160°C) air temperatures and drying at constant high (200°C) and medium (160°C) air temperatures. Changes in quality attributes of two new …

Michael Mcgraw: Profile Of The Newest Chbc Faculty Member, Danna Jaimes-Fajardo, Jeremy J. Smith, Lutishoor Salisbury

University Libraries Faculty Publications and Presentations

Presents the research profile of Michael McGraw, Assistant Professor, Chemistry and Biochemistry department. It highlights his research interests, education, and impact of his research.

Antioxidant, Photoprotective, And Cytotoxic Activities Of Tristaniopsis Merguensis Leaf Fractions With Molecular Docking Study Of Potential Fraction, Boima Situmeang, Respati Tri Swasono, Tri Joko Raharjo

Karbala International Journal of Modern Science

Through experimental along with molecular docking techniques of potential fraction, this study intended to evaluate the essential phytochemical elements of Tristaniopsis merguensis leaflets as well as potential antioxidant, photoprotective, along with cytotoxic activities. The DPPH and ABTS tests were used to evaluate the antioxidant efficacy of the n-hexane (HPF), ethyl acetate (EPF), and methanol (MPF) fractions. Using an in-vitro solar protection factor (SPF) assessment, the photoprotective ability of T. merguensis components against UV damage was examined. Subsequently, invitro cytotoxic research were carried out against MCF-7 cell line (breast cancer line) assay. This was followed by molecular docking stimulation testing against …

A Dft Comparison Of C–C Reductive Coupling From Terminal Cyanido And Cyaphido Complexes Of Nickel, Roberto Escobar, Jessica Meza, Javier Pena, Abdurrahman Atesin, William D. Jones, Christian Müller, Tülay A. Ateşin

School of Integrative Biological & Chemical Sciences Faculty Publications

The density functional theory study of the thermal C–C reductive coupling from terminal cyanido and hypothetical cyaphido complexes of [Ni(dmpe)] (dmpe = 1,2-bis(dimethylphosphino)ethane) revealed the key reaction intermediate in the reductive C–CP coupling being a σ-CC complex unlike an η2-aryl complex in the Ni C–CN system, as already observed in our previous studies. The reaction in THF is endothermic by 4.9 kcal/mol for cyanido with a 32.0 kcal/mol activation barrier and exothermic by 28.5 kcal/mol for cyaphido with an 11.3 kcal/mol activation barrier. To compare our results with the existing experimental data, we chose mesityl as the aryl group and …

Improvement Of Single-Crystal Structures Of Very Heavy Element Compounds By Refining Anomalous Dispersion Parameters, Florian Meurer, Gregory Morrison, Birgit Hischa, Hans Conrad Zur Loye, Christoph Hennig, Michael Bodensteiner

Faculty Publications

Refining the anomalous dispersion parameters of the four uranium compounds NaUF5, NaU2F9, Cs2(UO2)TiO4, and Cs2(UO2)Ti2O6 gave insights into the crystallographic model improvement of very heavy atoms. We found that the values for the dispersive and absorptive parts, f′ and f″, closely followed the X-ray absorption spectra on their L3, L2, and L1 edges. The obtained values are sensitive to the chemical environment at each crystallographically independent position. An incorrect treatment of the anomalous dispersion correction can lead to a wrong crystallographic model. The above-mentioned, already published structures were improved by this process. General guidelines were given for the crystal structure …

Sequence Specificity Of Non-Structural Protein 15 From Sars-Cov-2, John Vincent Mcguire

Electronic Theses and Dissertations

The SARS-CoV-2 virus was recently able to cause a global pandemic, largely due to the asymptomatic period that occurs during initial infection. During this period, patients are infectious but do not exhibit symptoms, resulting in the unintentional spread of the virus. This occurs because the virus effectively avoids detection by the immune system during the early stages of infection, and as symptoms are the result of immune system activation, they never manifest. Non-structural Protein 15 (Nsp15) is one of the tools the virus uses to remain undetected, via its degradation of Pathogen-Associated Molecular Patterns (PAMPs) that would otherwise be recognized …

On The Formation And Detectability Of H2Cncn And Its Progenitors, Ryan C. Fortenberry, Vincent J. Esposito

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

New highly exothermic formation pathways incorporating both thermodynamic and kinetic control for the newly astronomically detected H₂CNCN molecule are paired with extremely accurate quantum chemical rovibrational spectroscopic computations. The reactions between astronomically known CH₂CN/CH₂CCH + HNCN follow effectively identical pathways and proceed through stable intermediates and over deeply submerged transition states to form H₂CNCN and HCN/HCCH coproducts. Similarly, the reaction between CHM₂CN and NCN⁻ can also form H₂CNCN, although this pathway first requires the initial formation of NCN⁻, which is currently undetected in space, via …

Investigating The Cellular Localization, Trafficking, And Biological Function Of Ghrelin O-Acyltransferase, Sadie Xiao Hua Novak

Dissertations - ALL

Ghrelin O-acyltransferase (GOAT) catalyzes the acylation and activation of ghrelin, a peptide hormone involved in a range of physiological pathways and therapeutic target for metabolism-linked diseases such as obesity and diabetes. GOAT was determined to be localized in the membrane of the endoplasmic reticulum (ER) in early cell-based studies, but recent patient studies detected this integral membrane enzyme in blood plasma and urine. These findings challenge the current understanding of GOAT’s cellular localization, and it may provide a potential mechanism for ghrelin re-acylation by plasma membrane-resident GOAT. The work described in this dissertation aimed to define the intracellular trafficking mechanism …

An Online Nanoinformatics Platform Empowering Computational Modeling Of Nanomaterials By Nanostructure Annotations And Machine Learning Toolkits., Tong Wang, Daniel P Russo, Philip Demokritou, Xuelian Jia, Heng Huang, Xinyu Yang, Hao Zhu

College of Science & Mathematics Departmental Research

Modern nanotechnology has generated numerous datasets from in vitro and in vivo studies on nanomaterials, with some available on nanoinformatics portals. However, these existing databases lack the digital data and tools suitable for machine learning studies. Here, we report a nanoinformatics platform that accurately annotates nanostructures into machine-readable data files and provides modeling toolkits. This platform, accessible to the public at https://vinas-toolbox.com/, has annotated nanostructures of 14 material types. The associated nanodescriptor data and assay test results are appropriate for modeling purposes. The modeling toolkits enable data standardization, data visualization, and machine learning model development to predict properties and bioactivities …

Molecular Docking, Pharmacological Profiling, And Molecular Dynamics Simulation Of Potential Antihyperuricemic Agent From Secondary Metabolites Of Dillenia Philippinensis Rolfe (Dilleniaceae), Louie Rince C. Suyo, John P. Paulin, Nicole Clarence Louise L. Gapaz, Markus Brent S. Arevalo, Vince Tyrell P. Yongco, Librado A. Santiago

Karbala International Journal of Modern Science

Crystal accumulation in the joints due to increased serum uric acid (sUA) may lead to an inflammatory condition called gout. Increased sUA is caused by the excessive reabsorption of the urate anion transporter-1 (URAT-1). Therefore, URAT-1 inhibition will promote uric acid excretion and reduce the risk of having gout. Dillenia philippinensis Rolfe, often known as katmon, is an endemic plant in the Philippines with bioactive compounds associated with several therapeutic benefits. The present study represents the first scientific inquiry into the antihyperuricemic potential of compounds isolated from D. philippinensis. This study aimed to assess the interaction of URAT-1 with …

Synthesis And Characterization Of New Hexahydroquinoline Derivatives, Evaluation Of Their Cytotoxicity, Intracellular Ros Production And Inhibitory Effects On Inflammatory Mediators, Ezgi̇ Pehli̇vanlar, Deni̇z Arca Çakir, Sonia Sanajou, Hülya Tezel Yalçin, Terken Baydar, Pinar Erkekoğlu, Hani̇fe Avci, Rahi̇me Şi̇mşek

Turkish Journal of Chemistry

Inflammation is a response to injury and infection in the organism. It can be categorized as acute and chronic inflammation. Chronic inflammation is the underlying cause of many diseases such as Alzheimer's, diabetes, rheumatoid arthritis, atherosclerosis and cardiovascular diseases. Recent studies have proven the anti-inflammatory properties of 1,4-dihydropyridines (1,4-DHPs) and its derivatives, which have many biological properties including calcium channel blockers. The structures of the synthesized compounds were elucidated by IR, 1H-NMR, 13C-NMR and HRMS methods. The cytotoxic properties of the compounds were determined by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) method in 3T3 cell line. Among the 15 compounds, the three compounds …

A Coarse-Grained Molecular Dynamics Study Of Gas Hydrate Formation And Dissociation, Meisam Adibifard

LSU Doctoral Dissertations

The study of gas hydrates has increased significantly over the last two decades because of their potential application in energy storage, production and transportation, water desalination, refrigeration, gas separation, etc. There is a significant interest in commercially developing natural gas hydrates because the energy content of methane hydrate reservoirs (MHRs) is at least twice that of all conventional fossil fuels combined. Additionally, due to the higher storage capacity of hydrates, it is proposed to sequester CO₂ in the form of CO₂ hydrate, thereby reducing the amount of greenhouse gases. Hence, hydrates offer a dual solution to two of …

Synthesis And Photooxygenation Of 3-(P-Substituted Phenyl)-3a,8a-Dihydro-4h-Cyclohepta[D]Isoxazoles: Facial Selectivity, Mahi̇re Emel Olgun, Abdullah Menzek, Ertan Şahi̇n, Yasi̇n Çeti̇nkaya

Turkish Journal of Chemistry

Two 3-(p-substituted phenyl)-3a,8a-dihydro-4H-cyclohepta[d]isoxazoles were synthesized by 1,3-dipolar cycloaddition of the corresponding nitrile oxides with cycloheptatriene. Two endoperoxides were synthesized as facially selective and single products in high yields (93-95%) from the reactions of isoxazole derivatives with singlet oxygen. The exact configurations of the endoperoxide with a methyl group in the phenyl ring and the diol synthesized from it were confirmed by X-ray analysis. To elucidate the mechanism, the formation energy of the endoperoxide was investigated by simulations using the software package Gaussian 09 and density functional theory calculations via the M06-2X/6-311+G(d,p) level method in dichloromethane. The results were consistent with …

New Imidazolidindionedioximes And Their Pt(Ii) Complexes: Synthesis And Investigation Of Their Antitumoral Activities On Breast Cancer Cells, Emrah Karahan, Tuğba Gençoğlu Katmerli̇kaya, Emel Önal, Aydan Dağ, Ayşe Gül Gürek, Vefa Ahsen

Turkish Journal of Chemistry

Breast cancer is one of the most common types of cancer worldwide and has the most lethality ratio for females among all cancers. Although current cancer therapeutics have made considerable advancements, there is still room for improvement in terms of efficacy. Many anticancer drugs have a risk of causing serious adverse effects due to their non-specific cytotoxic effects on both tumor and healthy cells. New therapeutics might have a greater ability to kill cancer cells, reduce the volume of tumors, and improve overall therapy response rates. Herein, we report the efficient synthesis and characterization of three amphi vic-dioximes and their …

Synthesis And Characterization Of Nial-Hydride Heterometallics: Perturbing Electron Density Within Al–H–Ni Subunits, Aleida G. Gonzalez, Fernando Gonzalez, Edgar De Leon, Kaitlyn M. Birkhoff, Sam Yruegas, Haoyuan Chen, Manar Shoshani

School of Integrative Biological & Chemical Sciences Faculty Publications

Heterometallic hydride complexes are of growing interest due to their potential to contribute to highly active insertion-based catalysis; however, methods to modulate electron density within this class of molecules are underexplored. Addition of ancillary ligands to heterotrimetallic NiAl2H2 species (1) results in the formation of heterobimetallic NiAl-hydride complexes with varying phosphine donors (2-(L)2). Incorporation of sigma donating ancillary ligands of increasing strength led to contractions of the Ni–Al distances correlated to a strengthening of a back donation interaction to the Al–H sigma antibonding orbital, most prominently present in 2-(PMe3)2. Demethylation of the aryl ether from 2-(PMe3)2 provides access to a …

Synergetic And Orthogonal Switching In Dual Photochromic Metal-Organic Frameworks, Gina Rene Wilson

Theses and Dissertations

Cooperative behavior and orthogonal responses of two classes of coordinatively integrated photochromic molecules towards distinct external stimuli were demonstrated on the first example of a photo-thermo-responsive hierarchical platform. Synergetic and orthogonal responses to temperature and excitation wavelength are achieved by confining the stimuli-responsive moieties within a metal-organic framework (MOF), leading to the preparation of a novel photo-thermo-responsive spiropyran-diarylethene based material. Synergistic behavior of two photoswitches enables the study of stimuli-responsive resonance energy transfer as well as control of the photoinduced charge transfer processes, milestones required to advance optoelectronics development. Spectroscopic studies in combination with theoretical modeling revealed a nonlinear effect …

Preparation Of A Chiral Hyperbranched Polymer Based On Cinchona Alkaloids And Investigation Of Its Catalytic Activity In Asymmetric Reactions, Rafiqul Islam, Mohammad Shahid Ullah, Abdus Salam, Shinichi Itsuno

Turkish Journal of Chemistry

Cinchona alkaloid-derived sulfonamides and ester dimers containing chiral hyperbranched polymers have been successfully synthesized and applied as catalysts in asymmetric reactions. Several hyperbranched polymers derived from cinchona alkaloids, incorporating sulfonamides and esters, were synthesized through Mizoroki–Heck coupling polymerization. These polymers were subsequently applied in enantioselective Michael addition reactions. As the prepared polymers are not soluble in frequently used organic solvents, they act as efficient catalysts in the enantioselective reaction of β-ketoesters to nitroolefins, achieving up to 99% enantioselectivity with good yields. The insoluble property allows them to better satisfy “green chemistry” requirements and be used several times without losing the …

Magnetic Solid-Phase Extraction Technique Based On Fe3o4@Coppy-Pth Nanocomposite For Extraction Of Cobalt, Chromium, And Nickel Prior To Determination By Micro-Sample Injection System-Flame Atomic Absorption Spectrometry In Alcoholic And Nonalcoholic Beverages, Meli̇ke Küçüksakalli, Qamar Salamat, Buket Ti̇reli̇, Şükrü Gökhan Elçi̇

Turkish Journal of Chemistry

A novel Fe3O4@coPPy-PTH nanocomposite-based sorbent was prepared via in-situ oxidative polymerization using Fe3O4 nanoparticles with spherical and flower-like morphologies of thiophene and pyrrole as the feedstocks. The synthesized nanocomposite utilized sensitive extraction and determination of the metal ions Co(II), Cr(III), and Ni(II) without a chelating agent, followed by a micro-sample injection system-flame atomic absorption spectrometer (MIS-FAAS). The composition and morphology of Fe3O4@coPPy-PTH nanocomposite were characterized by advanced spectroscopic and imaging techniques like SEM and FT-IR. SEM observations showed the size of Fe3O4 nanoparticles changed from 30 nm to 120 nm in diameter after the copolymer (PPy-PTH) coating. The Fe3O4@coPPy-PTH nanocomposite …

Identification Of Blood At Simulated Crime Scenes Using Silver Nanoparticles With Sers, Uğur Köroğlu, Necdet Sağlam, Uğur Tamer, Ramazan Akcan, İsmai̇l Hakki Boyaci, Eylül Evran

Turkish Journal of Chemistry

Analysis of substances and samples obtained from the crime scene are very important in solving forensic cases. In order to determine the variables involved in a crime and to expedite the investigation process, especially the rapid analysis of body fluids in a small quantity and within an environment containing diverse components is necessary. For this reason, it is of great importance to analyse biological fluids with rapid, non-chemical contamination, non-destructive, low-cost and accurate techniques. In recent years, with advancements in laser technology, spectroscopic methods have been introduced as an analytical technique in forensic medicine and chemical studies. This study focuses …

Experimental Determination Of The Unusual Ch Stretch Frequency Of Protonated Fullerenes, Laura Finazzi, Vincent J. Esposito, Julianna Palotás, Jonathan Martens, Els Peeters, Jan Cami, Giel Berden, Jos Oomens

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

We report experimental values for the CH stretch frequencies of the protonated fullerenes C₆₀H⁺ and C₇₀H⁺. Anharmonic frequency calculations at the B3LYP/6-31G level of theory, which are independent of empirical scaling factors, reproduce the experimental values to within approximately 5 cm⁻¹. Scaling theoretical harmonic frequencies by applying factors derived for polycyclic aromatic hydrocarbons deviate significantly from the experimentally measured frequency. We attribute this deviation to the unusual hydrocarbon structure that affects the degree of anharmonicity of the CH stretch. This result allows us to propose an original, specific scaling factor of …

Impaired Waters: New Treatments And Improved Methods For Pfas And Algae Toxins, Alexandria Forster

Theses and Dissertations

Per- and polyfluoroalkyl substances (PFAS) are high-profile environmental contaminants, many having long persistence in the environment and widespread presence in humans and wildlife. Following phase-out of perfluorooctane sulfonate (PFOS) and perfluorooctanoic acid (PFOA) in North America and restrictions in Europe, PFAS replacements are now widely found in the environment. While liquid chromatography (LC)-mass spectrometry (MS) is typically used for measurement, much of the PFAS is missed. To more comprehensively capture organic fluorine, we developed sensitive and robust methods using activated carbon adsorption, solid phase extraction, and combustion ion chromatography (CIC) to measure total organic fluorine (TOF) in industrial wastewaters, river …

Synthesis Of Addressable Libraries: New Lessons And The Need For Proper Characterization For Microelectrode Array-Based Reactions, Albert Huang

Arts & Sciences Graduate Student Theses and Dissertations

The Moeller group has been developing synthetic tools for building molecular libraries on microelectrode arrays since 2004. Such a library is intriguing because one can take advantage of the library for biological signaling studies. Microelectrode arrays can serve as a powerful platform for those experiments since every electrode in the array can be addressed individually. Unique members of the library targeting biological receptors that one is interested in can be restricted only above unique electrodes in an array. Thus, high-affinity ligands for those receptors can be identified with this strategy. To make this method work, one has to make sure …

Assimilating Satellite-Derived Snow Cover And Albedo Data To Improve 3-D Weather And Photochemical Models, Colleen Jones, Huy Tran, Trang Tran, Seth Lyman

Chemistry and Biochemistry Faculty Publications

During wintertime temperature inversion episodes, ozone in the Uinta Basin sometimes exceeds the standard of 70 ppb set by the US Environmental Protection Agency. Since ozone formation depends on sunlight, and less sunlight is available during winter, wintertime ozone can only form if snow cover and albedo are high. Researchers have encountered difficulties replicating high albedo values in 3-D weather and photochemical transport model simulations for winter episodes. In this study, a process to assimilate MODIS satellite data into WRF and CAMx models was developed, streamlined, and tested to demonstrate the impacts of data assimilation on the models’ performance. Improvements …

Making And Breaking Bonds: Studying Intrinsic Chemistry In The Gas-Phase, Luke Metzler

Electronic Theses and Dissertations

The nature of chemical interactions can be difficult to ascertain in the condensed phase; chemistry can be observed, but with the plethora of variables such as solvation, mixes of counter-ions, and complex equilibria, the true intrinsic chemical properties of a given chemical species may be obfuscated. By conducting research in the gas-phase, many of these variables can be reduced, if not eliminated entirely, which can allow for the careful observation of the true physical phenomena driving chemical reactivity.

The research presented herein focuses on the use of ion-trapping (specifically in a linear ion trap) as a method for unveiling the …

Rna Secondary Structures: Structure-Function Studies In Viral And Neurodegenerative Diseases, Caylee Cunningham

Electronic Theses and Dissertations

The studies within this dissertation highlight the importance of RNA structure and function, highlighting potential mechanisms in the pathogenesis of the SARS-CoV-2 virus and hallmarks of ALS. Specifically, the s2m, a 41-nt structure found within the hyper variable region of the 3’ UTR of the SARS-CoV-2 virus, was investigated as this element has no definitive role in viruses but its high conservation in several viral families warrants investigation. We used various biophysical techniques to determine if a palindromic sequence in the terminal loop could participate in dimerization activities, which may have implications in recombination and the longevity of the virus. …

Flora And Fauna Lexical Indicators Of Prehistoric Movement Of Yuman Peoples, Adam Ingwerson

Master's Theses

Amyloid fibrils are locally ordered protein aggregates characterized by a filamentous morphology held together by a hydrogen bonding motif known as cross-β structure whereby hydrogen bonds form between backbone amide bond moieties across separate protein segments. The most notable medical significance of amyloid fibrils is their central role in the etiology of Alzheimer’s disease, type 2 diabetes, and other human diseases. Although amyloid fibrils have been studied extensively, the mechanism of their formation is still not fully understood. X-ray crystallography is a leading experimental technique for resolving amyloid fibril structures from crystallized proteins; however, inherent limitations leave open the possibility …