Chemicals and Drugs Commons^™

Attention-Based Multi-Omics Fusion For Drug Synergy Prediction, Kusal Debnath, Pratip Rana, Preetam Ghosh

Computer Science Faculty Publications

Drug combination therapy in disease management gained popularity in the last few decades. Computational modeling of such combinations is an active area of research in the drug discovery domain. While earlier approaches solely emphasized on the structural features of participating drugs for designing synergistic models, they lack other crucial factors directly linked with drug administration - omics expressions. As differential omics expression is a downstream consequence of the administered drug combinations, utilizing such expressions while designing synergistic models promises robust and dynamic modeling. In this work, we propose SynergyLM that fuses multi-omics features with drug embeddings to build an omics-aware …

Will They Be More Honest With An (External) Proctor? Evaluating Ufc Match Performance Before And After The Adoption Of The Usada Doping Program, Moonsup Hyun, Wonsok (Frank) Jee, Sehwon Kang, Yohan Lee

Human Movement Studies & Special Education Faculty Publications

Over the eight years from 2015 to 2023, the Ultimate Fighting Championship (UFC) partnered with the United States Anti-Doping Agency (USADA) to institute comprehensive external oversight of doping controls. This study investigates the effects of transitioning from internally administered anti-doping protocols to exclusive external governance by comparing UFC performance metrics before and during the USADA partnership. Using a Difference-in-Differences (DiD) approach with data from 2012 to 2018, we find that match duration significantly increased, while the likelihood of extreme outcomes, knockouts (KO), technical knockouts (TKO), and submissions, decreased during the USADA period. These results suggest that performance-enhancing drugs (PEDs) could …

Repurposing Of Fda-Approved Drugs Identifies Glipizide As A Potent Hmg-Coa Reductase Inhibitor: A High-Throughput Virtual Screening And Molecular Dynamics Approach For Targeting Hypercholesterolemia, Parvej Ahmad, Eswara N. Hanuma Kumar Ghali, Sahir S. Alvi

School of Medicine Publications

Purpose:

Atherosclerotic cardiovascular disease (ASCVD) is one of the leading causes of mortality worldwide. Several inhibitors of 3-hydroxy-3-methylglutaryl-CoA reductase (HMG-R), the key hepatic cholesterogenic enzyme, are prescribed to treat hypercholesterolemia and ASCVD. Statins, the established HMG-R inhibitors, exhibit promising cholesterol-lowering effects; however, their long-term use has prompted significant concerns, necessitating the search for additional therapeutic candidates with strong HMG-R inhibitory activity. Therefore, this study aims to find potential HMG-R inhibitor/s that may help reduce excess cholesterol levels via targeting HMG-R activity.

Methods: In this study, 1285 FDA-approved small molecules were assessed for their HMG-R inhibitory potential using …

Studies Towards Chemical Synthesis Of Homogeneous Prion Glycoprotein, Baotong Tian

Electronic Theses & Dissertations (2024 - present)

Prion diseases are fatal neurodegenerative disorders initiated by conformational misfolding of the prion protein (PrP), which generates pathogenic conformers that propagate via templated conversion and accumulate as aggregates. Glycosylation can modulate the PrP folding energy landscape, thereby biasing folding trajectories and the distribution of resulting conformational states. Bank vole PrP contains two N-linked glycosylation sites, and disentangling the contributions of site occupancy versus glycan structure requires homogeneous, site-defined glycoforms. In contrast, biosynthetic expression typically produces heterogeneous glycoform ensembles due to multistep Golgi processing, precluding independent control of glycan identity at each site. Here we report a chemical synthesis strategy of …

Photo And Spatial Control Of Rna Structures And Functions: Exploring Positional Effects And Photo-Responsiveness Of Azobenzene Modified Nucleotides, Jinxi Du

Electronic Theses & Dissertations (2024 - present)

RNA molecules perform many important biological functions by forming complex three-dimensional structures stabilized by base pairing, tertiary interactions, and metal ion coordination. Because RNA function depends strongly on its structure, methods that allow reversible control of RNA conformation and activity are important for understanding RNA behavior and for potential therapeutic applications. However, achieving reversible and site-specific control of RNA structure, especially at the single-nucleotide level, remains challenging. In this dissertation, I developed and applied azobenzene-modified nucleotides as a chemical tool to enable optical and spatial control of RNA structure and function.

The first part of this dissertation focuses on establishing …

A Unified Automated And Explainable Ai Framework For Drug Discovery, Clinical Diagnostics, And Public Health Data Prediction, Lord Coffie

College of Graduate Studies: Theses & Dissertations

This thesis investigates the development of automated, explainable artificial intelligence systems to improve automated scientific discovery, clinical diagnostic support, and public health decision-making. Three independent yet thematically aligned studies were conducted across cheminformatics, radiology, and population health. Study A introduces an automated and explainable machine learning pipeline for Quantitative Structure–Activity Relationship (QSAR) modeling using RDKit-derived molecular descriptors. The pipeline performs systematic preprocessing, consensus-based feature selection (mutual information, random forest importance, RFECV), and benchmarks six supervised models—Random Forest, XGBoost, Support Vector Machine, Balanced Random Forest, EasyEnsembleClassifier, and a blended meta-ensemble, achieving AUC = 0.90 and accuracy = 0.83, while ensuring interpretability …

Inflammatory Co-Regulation Of Voltage-Gated Sodium Channels And Na,K-Atpase In Metastatic Breast Cancer, Steven D. Scahill, Kelly Jean Sherman, Dennis Paul

School of Graduate Studies Faculty Publications

Sodium regulation is a potentially major driver of cancer metastasis. Voltage-gated sodium channels (VGSCs) and Na,K-ATPase are sodium transporters that are upregulated in many advanced carcinomas and are implicated as metastatic drivers. However, little is known about what drives this overexpression, how these proteins influence metastatic behavior, or whether these complementary sodium transporters are co-regulated in cancer. Using sodium transporter regulation in healthy neurons as a model, the present study demonstrated that the inflammatory mediator tumor necrosis factor alpha (TNFα) affects the expression of VGSCs and Na,K-ATPase in an in vitro model of metastatic breast cancer. Acute TNFα challenge increased …

The Evolving Therapeutic Landscape Of Nanoscale Cancer Drug Delivery Systems: Future Perspectives, Nafeesa Qudsia Hanif, Bushra Arshad, Anila Fariq, Syed Imam Hussain Abidi, Sohail Ameer Marwat, Aneela Fatima

Journal of Bioresource Management

Cancer is one of the main causes of deaths in the world. Conventional cancer therapeutic approaches such as chemo- and radiotherapy have burdened the cancer patients with arduous physical and psychological challenges. Moreover, in case of onset of this disease, huge amount is required against the medications (chemotherapy and radiotherapy). It is estimated that annually, the increasing cancer disease incidence rate is alarming. In developed countries, the health support is given by the nation. Therefore, the health managements in the developed nations are over-burdened due to heavy expanses against expansive cancer therapy treatments. Interestingly, tumor treatments have undergone a comprehensive …

Microglial Expression Of Serotonin Receptors Reveals Parallel Regulation Of 5-Ht2b And Bdnf In The Rat Hippocampus, Andrei Turkin, Maria Sidorova, Ekaterina Kurilova, Natalia Alenina, Oksana Tuchina, Friederike Klempin

School of Graduate Studies Faculty Publications

Growing evidence suggests that psychiatric disorders are characterized by a prolonged inflammatory state, which may influence the efficacy of compounds targeting serotonin. Serotonin is a key signaling molecule in neuroplasticity of the adult hippocampus and involved in antidepressant action. Recent in vitro studies indicate the neurotransmitter may also facilitate the response to inflammation and potentially modulate microglial function towards neuroprotection. Using Tph2−/− rats depleted of brain serotonin, we examined microglial expression of various serotonin receptors (5-HTRs) in vivo in both the hippocampus and prefrontal cortex and assessed mRNA levels of cytokines and brain-derived neurotrophic factor (BDNF). We observed age-dependent and …

Isg15 Dysregulates Endoplasmic Reticulum-Mitochondrial Contacts And Calcium Homeostasis In Ataxia Telangiectasia, Oygul Mirzalieva, Ryan E. Reed, Arthur L. Haas, Meredith A. Juncker, Patrick Logarbo, Jennifer M. Klein, David Worthylake, Shyamal D. Desai

School of Graduate Studies Faculty Publications

Dysregulation of endoplasmic reticulum and mitochondrial (ER:Mit) contacts and mitochondrial calcium (mitCa2+) homeostasis are found in several neurodegenerative disorders, including Ataxia Telangiectasia (A-T). However, the cellular basis of these defects remains unclear. Previously, we demonstrated that the aberrantly elevated Interferon-Stimulated Gene 15 (ISG15) pathway inhibits protein polyubiquitylation, its dependent protein turnover, and mitophagy pathways in A-T. Literature indicates that silencing of mitochondrial ubiquitin ligase 1 (MUL1) stabilizes mitofusin2 (MFN2) and attenuates mitCa2+ uptake from ER to Mit (mitCa2+influx) in primary neurons. We have replicated these findings in apparently healthy fibroblasts. We hypothesized that elevated ISG15 may inhibit ubiquitin-dependent MUL1-mediated degradation …

Hepatocyte-Specific Lrp1 Silencing Exacerbates Brain Amyloidosis Without Compensatory Ldl Receptor Family Involvement, Brian Carson, Josephine Chu, Devaraj V. Chandrashekar, Jerome Garcia, Rachita K. Sumbria, Derick Han

Pharmacy Faculty Articles and Research

Background

LDL receptor related protein 1 (LRP1) is a major hepatic receptor involved in lipoprotein metabolism, protease degradation, transmembrane receptor modulation, and clearance of excess protein, such as Aβ. Decreased expression of LRP1 due to liver injury can impair receptor-mediated clearance, increasing Aβ availability in the periphery. We investigated the effects of hepato-specific silencing of LRP1 on Aβ deposition in the brain. Additionally, other LDL family members (LRP5, LRP6, and LDLR) that may participate in Aβ clearance were monitored in the liver to ensure non-compensatory effects of LRP1 silencing.

Method

4-month-old male double transgenic (APP/PS1) AD mice were injected with …

The Mitochondria Is The Source Of Hepatic Amyloid Precursor Protein And Peripheral Amyloid Beta: Implications Of Alcohol-Induced Liver Steatosis In Alzheimer's Disease, Josephine Chu, Ross A. Steinberg, Brian Carson, Devaraj Venkatapura Chandrashekar, Rachita K. Sumbria, Derick Han

Pharmacy Faculty Articles and Research

Background

Alcohol-induced liver injury occurs in the pericentral region of the liver and can induce mitochondrial remodeling and exacerbate Alzheimer's Disease (AD) progression. Subpopulations of mitochondria: general mitochondria (GM), peridroplet mitochondria (PDM) and endoplasmic reticulum(ER)-bound mitochondria (ERM) maintain cellular homeostasis via energy synthesis, lipid homeostasis, and regulation of intracellular calcium. Hepatic amyloid precursor protein (APP) is a source of peripheral amyloid beta (aB) and affects AD pathology in the brain. Understanding the localization and expression of hepatic APP in mitochondrial subpopulations are critical to understanding aB metabolism and may play a role in identifying a potential mechanism for metabolic dysfunction. …

Quantitative Structure-Activity Relationship, Pharmacokinetics, Drug-Likeness, Toxicity, And Molecular Docking Studies Of 4-N-(Methyl)-4-Aminoquinoline Derivatives As Antimalarial Compounds, Muhamad Jalil Baari, Devi Hardiyanti

Makara Journal of Science

Antimalarial drug resistance has encouraged various innovations to develop novel drug compounds that are effective, feasible, and safe, adhering to health standards. One way to do that is by observing and predicting the biological activity of drug compounds using quantitative structure–activity relationship (QSAR) analysis. In this study, QSAR analysis was conducted on the 4-N-(methyl)-4-aminoquinoline derivatives, which effectively inhibit the growth of Plasmodium falciparum as a source of malaria. The research stages involved molecular structure modeling, molecular geometry optimization using the AM1 semi-empirical method, and QSAR descriptor calculations, including electronic (atomic charges (q), HOMO and LUMO energies, polarizability (α), …

Formulation And Characterisation Of Isoniazid By Spray Drying For Use By Dry Powder Inhalers To Treat Tuberculosis, Damiana Gabrielli, Seán Roche

SURE Journal: Science Undergraduate Research Experience Journal

The targeted delivery of antibiotics by dry powder inhalers (DPIs) is an increasingly important area of research, driven by the growing global burden of respiratory infections and the advantages of localized drug delivery to the lungs. Over the past five years, respiratory infections have risen significantly, with recent epidemiological data indicating a global increase in incidence by over 30%, largely due to factors such as air pollution, antimicrobial resistance, and emerging respiratory pathogens. One major challenge in developing DPI formulations for antibiotics is the need to optimize the particle physicochemical properties for deep lung deposition while accommodating the high doses …

Suitability Of Mobile Phase Recycling For Methylxanthine Quantification In Coffee Samples Using Hplc, Kaitlin O’Keeffe, Marcos Mariano, Brian Murphy

SURE Journal: Science Undergraduate Research Experience Journal

Caffeine, theobromine and theophylline fall under a drug class known as methylxanthines. These three compounds are of major interest in the food industry due to their presence in popular foods and beverages such as tea, coffee, and chocolate. As these compounds can cause physical and mental stress at high dosages, their quantification is essential to ensure product safety and quality. Here, we describe an eco-friendly HPLC method developed to quantify the amount of these analytes in coffee samples sourced across the SETU Waterford, Cork Road campus. Using an isocratic mixture of water and methanol, a mobile phase recycling approach was …

Developing A Tool To Measure Resistance To Sustainable Food Choices: A Pilot Study In Ireland And The Netherlands, Kate Flanagan, Bart Sinteur, Patricia J. Bulsing, John M. Kearney

SURE Journal: Science Undergraduate Research Experience Journal

Consumer uptake of a sustainable diet is critical for addressing environmental challenges and promoting public health. Understanding why consumers resist adopting sustainable eating habits can inform targeted interventions and policies. This pilot study examines whether a newly developed scale can effectively detect consumer resistance to a sustainable diet. Currently, there is a lack of research on a tool to measure consumer resistance to a sustainable diet, highlighting the need for a reliable instrument.

The aim of this study is to develop a scale, based on existing literature, to measure consumer resistance to a sustainable diet. Additionally, the study aims to …

Editorial-Sure Journal Volume 7, Issue 2, Geraldine M. Dowling, Eva Campion, Sinead Loughran, Ariane Perez-Gavilan, Josephine Treacy

SURE Journal: Science Undergraduate Research Experience Journal

No abstract provided.

Optimizing Solvent Composition For Enhanced Extraction Of Phenolic Content And Antioxidant Activity From Coleus Scutellarioides Through I-Optimal Mixture Design, Sinta Mutiara Dwi Lestari, Utami Dyah Syafitri, Waras Nurcholis

The Thai Journal of Pharmaceutical Sciences

Background: Reactive oxygen species are unstable molecules that contribute to oxidative stress and are associated with numerous degenerative diseases. The leaves of Coleus scutellarioides are rich in phenolic and flavonoid compounds, which possess strong antioxidant properties.
Objectives: This study aimed to optimize the composition of water, ethanol, and methanol as solvents using the I-optimal mixture design to enhance the extraction of total phenolic content (TPC), 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity, and ferric reducing antioxidant power (FRAP).
Methods: Each extraction was performed by macerating 1 g of powdered C. scutellarioides leaves in 20 mL of the designated …

P-E-S-T-O-G-O: This Third Circuit Ruling Has Got To Go, A Deep Dive Into The Circuit Split Issue Of Fifra Preemption, R. Dylan Smith

Journal of Food Law & Policy

The American public is becoming increasingly concerned about pesticides. From “forever chemicals” to environmental justice concerns, public awareness of pesticide issues is only becoming more prevalent. However, one pesticide has seized public attention in a significant way. Glyphosate, the active ingredient in Monsanto’s “Roundup” and other commercial pesticides has been the subject of heated debate in federal courtrooms across the nation. The rising controversy over glyphosate has even led some jurisdictions to attempt to ban or restrict the use of the product altogether.

While the scientific studies and legal definitions about glyphosate and its cancer link are inconsistent, a reasonable …

The Effect Of Glp-1 Receptor Agonists On Reoperation Following Anterior Cervical Discectomy And Fusion, Nicholas C. Bank, Daniel Whittingslow, Sam Duggan, Joshua L. Morningstar, Douglas S. Weinberg

Student Papers, Posters & Projects

BACKGROUND: Pseudarthrosis remains a significant complication of ACDF, contributing to patient morbidity and increased healthcare costs. Glucagon-like peptide-1 receptor agonists (GLP-1RA), widely prescribed for diabetes and obesity, have been shown to reduced odds of pseudoarthrosis after ACDF. However, it remains unclear whether these reductions meaningfully translate to reduced odds of subsequent cervical surgery.

METHODS: The TriNetX United States Collaborative Network was queried for patients who underwent single- or multi-level ACDF between 2013-2023. Patients with perioperative GLP-1RA use and propensity-score-matched controls without GLP-1RA use were compared for subsequent rates of pseudoarthrosis and cervical reoperation at 6-, 12-, and 24-month intervals. Odds …

Long Covid Incidence Across Sars-Cov-2 Lineages And Identification Of Conserved Spike Targets For Multivalent Vaccines, Grace J. Kim, Md Ashad Alam, Judy S. Crabtree, Rebecca Rose, Susanna L. Lamers, San Chu, Ronald Horswell, Daniel Fort, Lucio Miele

School of Graduate Studies Faculty Publications

Background: Long COVID remains poorly characterized at the genomic level. The primary aim of this study was to examine the relationship between viral sequences and the incidence of Long COVID at a tertiary care center in Louisiana between April 2020 and December 2022. A secondary aim was analysis of the Spike protein to identify conserved regions for multivalent vaccine targets. Method: To estimate Long COVID incidence across variants, we linked 4,789 SARS-CoV-2 sequences to 3,090 de-identified patient electronic health record information. The base population was defined as any patient with an International Classification of Diseases-10-Clinical Modification COVID-19 diagnosis code (U07.1) …

Early Intervention In Helminth Infections: Investigating Albendazole’S Effects On C. Elegans Egg Hatch Rate And Health, Giselle Domingo Diaz

Student Scholar Symposium

Over 1.5 billion of the poorest people are infected with soil-transmitted helminths (STH) such as whipworm, hookworm, and Ascaris which have devastating effects on human growth, nutrition, and cognition, perpetuating the cycle of poverty. The World Health Organization only approves four anthelmintic drugs to treat STH for mass drug administration (MDA), with Albendazole being the drug of choice. Due to these drugs only having two mechanisms of action, resistance to these drugs has been reported over the years. We aim to better understand STH susceptibility to drugs at multiple points in their life stage. Previously, the effects of Albendazole and …

Quantum Rings Simulations Of Cisplatin, Clinton Hutchins, Laci Walmer

Student Scholar Symposium

Cisplatin is a major chemotherapy drug that relies on a platinum-based core to deliver the properties necessary to combat cancer. This platinum-based core creates an undesired toxicity that poses challenges during treatment. The aim of this research is to employ quantum simulations to explore the stability of biochemicals such as cisplatin and predict their binding affinities for targets of interest. Variational Quantum Eigensolver (VQE) simulations are used to explore if the substitution of a core like Au or Pd are possible to retain anticancer efficacy but reduce its toxicity. With the use of these quantum simulations, we can run different …

Exploration Of Euclidean Distances In Five-Dimensional Color Space As Proof-Of-Concept For Identification Of Promising Alternatives To Platinum-Based Cancer Drug Candidates, Kiomi Tanakura, Elena G. Harvey

Student Scholar Symposium

Cisplatin, cis-Pt(NH₃)₂Cl₂, is one of the most successful anticancer drugs of all time. However, it has some negative aspects, including toxicity to healthy cells, side effects, and cost. Our goal in this project is to design metal-based anticancer drugs that would be less expensive, less toxic, and more efficient for cancer patients than cisplatin. To begin this research we calculated Euclidean distances - as used by computerized recognition systems - to compare the properties of colors within seasonal palettes that are proven and visible to the eye. These Euclidean distances were then used …

6ppd-Quinone In Middle Tennessee Waters: Assessing Ecological Impact, Andrew Davis Todd, Raphael Marquise Chandler, Kerolos Gerges Basalos, Denise Lori Loewinger

Student Scholar Symposium

This poster presents the dangers of a toxic chemical used on car tires that is entering aquatic ecosystems and harming fish populations.

Investigation Of Aldehyde Oxidase Inhibition By Clopidogrel And Its Thiol Metabolite, Rachel Crouch, Merna Kamal, Hilina Woldeamanuel

Student Scholar Symposium

Aldehyde oxidase (AO) is an enzyme that metabolizes drugs containing aromatic azaheterocycles. Small thiol-containing molecules have been reported to inactivate AO. Clopidogrel is an antiplatelet agent used to treat cardiovascular diseases. Clopidogrel is a prodrug that is bioactivated in vivo by cytochrome P450 enzymes CYP3A4 and CYP2C19 into a thiol metabolite. Our research aims to explore whether the clopidogrel thiol metabolite can inhibit AO, leading to potential drug-drug interactions when co-administered with other drugs that are metabolized by AO. In order to determine whether the prodrug clopidogrel and/or its thiol metabolite inhibit AO, O6-benzylguanine (AO substrate) was incubated with human …

Have You Had Your Vitamins Today? Development Of An Lc-Ms/Ms Method With A 100% Aqueous Gradient To Simultaneously Measure B Vitamins In Plasma From Study Participants In A “Greens” Nutritional Supplement Clinical Trial, Kennedy Brothers, Abigail Davis, Anna Losher, Yusra Ahmed, Sora Ghanem, Matthew J. Vergne

Student Scholar Symposium

This study assessed the absorption of key micronutrients from the multi-ingredient supplement using a novel developed LC-MS/MS method capable of analyzing B vitamins in a single run.

The study a randomized, double-blind, placebo-controlled crossover trial with 16 healthy participants (8 males, 8 females) to measure plasma nutrient appearance over 8 hours after supplement consumption. Serial blood samples were collected pre-consumption and at specified intervals post-ingestion. The novel LC-MS/MS method simultaneously quantified biotin, nicotinamide, pyridoxine, riboflavin, and thiamin in blood samples.

Results:The LC-MS/MS method had a range of 0.1 ng/mL to 1000 ng/mL and it proved to be robust and …

Investigating The Efficacy Of Mebendazole On C. Elegans: Implications For Anthelmintic Drug Development, Brooke Brewer, Saja Al-Saweily

Student Scholar Symposium

About 1.5 billion people in the world are infected with soil-transmitted helminths, especially those who live in high poverty areas. These infections affect communities with poor access to clean water, sanitation and hygiene in tropical and subtropical areas, keeping them in a state of poverty. Our research focuses on drugs that target the parasitic worms currently approved by the World Health Organization (WHO). The WHO currently only has 4 approved drugs for Mass Drug Administration, due to low profit margins, complex parasite life cycles, and rising drug resistance (World Health Organization 2023). While Mebendazole is effective against many common parasitic …

Isolation And Scale-Up Of Fimh, Audrey Cox, Kerolos Ghobrial, Caroline King

Student Scholar Symposium

No abstract provided.

The Equity Dead Zones: Legal Intersectionality Failure Points In Chapter 13 Bankruptcy, Tearria N. Simmons

The Guardianship Journal

Legal intersectionality failure points describe the systemic fractures that occur where overlapping legal, social, and economic inequalities converge, potentially producing compounded barriers to relief. Each failure point marks a site of marginalization. In what ways do individuals already recognized as vulnerable in Chapter 13 bankruptcy face a heightened risk when multiple forms of disadvantage intersect? When these intersections combine in mutually reinforcing ways—racial, economic, and relational disparities colliding with structural deficiencies in family, property, and bankruptcy law—does it result in pronounced negative outcomes, and, if so, what are those outcomes? Within this convergence, could there be a space where compounded …