Chemistry Commons^™

Incorporating Solvation Thermodynamic Mapping In Computer-Aided Drug Design, Yeonji Ji

Dissertations, Theses, and Capstone Projects

Advancements in computational techniques have revolutionized structure-based drug design, substantially improving the efficiency and effectiveness of the drug discovery process by reducing time, costs, and labor requirements. These advancements include various methods, such as investigating small molecule ligands binding to proteins, exploring alternative protein conformations, and solvation mapping on the protein surfaces. Among these methods, understanding the correlation between protein-ligand binding and the role of solvation is important.

A fundamental concept in protein-ligand binding is shape and electrostatic complementarity, which is complicated by the inherent flexibility of proteins. In the absence of small molecule ligands, proteins are complementary to surface …

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

Chemistry

No abstract provided.

Agnotology Of The E-Cigarette Industry: How The E-Cigarette Industry Continues The Tobacco Industry's Legacy Of Creating Controversy And Confusion Within The Scientific Community And The General Population, Calvin Lewis

University Honors Theses

The purpose of this paper is to determine the extent to which the e-cigarette industry follows in the footsteps of the tobacco industry's attempts to disrupt science and cause controversy. Four tactics are described that the tobacco industry uses to disrupt science: funding research that is designed to show results that support their position, criticizing and suppressing research that goes against their position, changing risk assessment and scientific research standards to fit their aims, and spreading data created by their interest groups to politicians and the nonacademic press. Evidence is found to show that both the tobacco industry and e-cigarette …

Chromium And Cobalt In Leather: A Danish Market Survey, Mikkel Bak Jensen, Farzad Seyed-Alinaghi, Ivan Chen, Jonas F. Hedberg, Yolanda S. Hedberg, Claus Zachariae, Jeanne Duus Johansen

Chemistry Publications

Introduction

Leather has been a significant source of chromium (Cr) allergy in Denmark since the 1990s. More recently, cobalt (Co) allergy has been identified in leather as a source of allergic contact dermatitis.

Objectives

To measure Cr and Co levels in Danish leather goods.

Methods

A total of 87 leather samples were collected, all tanned in Europe. Handheld X-ray fluorescence (XRF) device was used to screen for the presence of Cr and Co. The 20 leather samples with the highest concentrations of Co and Co were tested using International Organization for Standardization (ISO)-standards.

Results

XRF analysis showed Cr in 78/87 …

Iron Oxide Nanozymes Enhanced By Ascorbic Acid For Macrophage-Based Cancer Therapy, Zhongchao Yi, Xiaoyue Yang, Ying Liang, Sheng Tong

Markey Cancer Center Faculty Publications

In recent years, using pharmacological ascorbic acid has emerged as a promising therapeutic approach in cancer treatment, owing to its capacity to induce extracellular hydrogen peroxide (H2O 2) production in solid tumors. The H2 O 2 is then converted into cytotoxic hydroxyl free radicals (HO•) by redox-active Fe2+ inside cells. However, the high dosage of ascorbic acid required for efficacy is hampered by adverse effects such as kidney stone formation. In a recent study, we demonstrated the efficient catalytic conver- sion of H2 O2 to HO• by wüstite (Fe 1−xO) nanoparticles (WNPs) through a heterogenous Fenton reaction. Here, we explore …

Detection And Quantification Of Acetaminophen In Aquatic Samples From Cádiz, Spain, Hannah R. Desmarais, Michelle N. Mikos

DePaul Discoveries

Pharmaceutical contaminants in water are becoming increasingly prevalent. This could have potentially harmful effects on human health and aquatic environments, even at low concentrations. Acetaminophen, the active ingredient of Tylenol ®, was the target compound for this study, and the aim was to determine is presence and concentration in various aquatic samples in and around the city of Cádiz, Spain. It was predicted that acetaminophen would be detected in low concentrations in river water, drain outflow, University of Cádiz saltwater flow, and lagoon water, but undetectable in the University of Cádiz sink water and fountain water. The presence and concentration …

Use Of Cobalt(Iii) And Copper(Ii) Complexes With Thiosemicarbazone Ligands And Berberine Chloride As Anti-Cancer Agents Against Triple Negative Breast Cancer, Duaa Rashad Alajroush

Chemistry & Biochemistry Theses & Dissertations

It is a worrying fact that chemotherapeutic options for treating triple negative breast cancer are limited in nature, including the use of inorganic pharmaceuticals such as cisplatin and its analogues. It has been reported that cisplatin has undesirable side effects when used as a chemotherapeutic drug. As such, there is a need to use non-platinum-containing complexes as chemotherapeutic agents. Based on that issue, it has been reported by our research group and others that cobalt- and copper-containing complexes have shown great potential in anti-cancer properties when compared to cisplatin. In this research project, the cytotoxic effects of the following complexes: …

Response To Replication Stress And Maintenance Of Genome Stability By Wrn, The Werner Syndrome Protein, David K. Orren, Amrita Machwe

Markey Cancer Center Faculty Publications

Werner syndrome (WS) is an autosomal recessive disease caused by loss of function of WRN. WS is a segmental progeroid disease and shows early onset or increased frequency of many characteristics of normal aging. WRN possesses helicase, annealing, strand exchange, and exonuclease activities and acts on a variety of DNA substrates, even complex replication and re- combination intermediates. Here, we review the genetics, biochemistry, and probably physiological functions of the WRN protein. Although its precise role is unclear, evidence suggests WRN plays a role in pathways that respond to replication stress and maintain genome stability particularly in telomeric regions.

Discovering Potential In Non-Cancer Medications: A Promising Breakthrough For Multiple Myeloma Patients., Omar S Al-Odat, Emily Nelson, Tulin Budak-Alpdogan, Subash C. Jonnalagadda, Dhimant Desai, Manoj K Pandey

College of Science & Mathematics Departmental Research

Multiple myeloma (MM) is a common type of cancer that unfortunately leads to a significant number of deaths each year. The majority of the reported MM cases are detected in the advanced stages, posing significant challenges for treatment. Additionally, all MM patients eventually develop resistance or experience relapse; therefore, advances in treatment are needed. However, developing new anti-cancer drugs, especially for MM, requires significant financial investment and a lengthy development process. The study of drug repurposing involves exploring the potential of existing drugs for new therapeutic uses. This can significantly reduce both time and costs, which are typically a major …

Microencapsulation Of Cosmos Caudatus Kunth Extract Using Sodium Alginate And In Vitro Antioxidant Activity Test, Safina Samara Nur Fadlila, Oktavia Eka Puspita, Zubaidah Ningsih, Anna Safitri

Makara Journal of Science

This study aims to encapsulate Cosmos caudatus K. leaf extract in sodium alginate crosslinked with calcium chloride (CaCl₂) as coating materials through freeze-drying. Antioxidant assays were performed to evaluate the applicability of the microcapsules as antidiabetic medicines. Their characteristics, antioxidant activity, and encapsulation efficiency (EE) were also examined. Results indicated that the concentration of sodium alginate and pH influenced the manufacturing process of the microcapsules. The highest EE was obtained at pH 6 and alginate concentration of 2% (w/v). The IC₅₀ for the antioxidant activity of the microcapsules was 139.96 ± 1.094 μg/mL. Scanning electron microscopy confirmed …

Potent And Selective Small Molecule Mcl-1 Inhibitor Demonstrates Anti-Myeloma Activity And Overcomes Chemotherapy Resistance, Omar Sami Faleh Al-Odat

Theses and Dissertations

Despite a record number of clinical studies investigating various anti-myeloma treatments, the 5-year survival rate for multiple myeloma (MM) patients in the US is only 55%, and nearly all patients relapse. Poor patient outcomes demonstrate that myeloma cells are "born to survive” which means they can adapt and evolve following treatment. Thus, new therapeutic approaches to combat survival mechanisms and target treatment resistance are required. Importantly, Mcl-1, anti-apoptotic protein, is required for the development of MM and treatment resistance. This study looks at the possibility of KS18, a selective Mcl-1 inhibitor, to treat MM and overcome resistance. Our investigation demonstrates …

The Glucosylamine Oxidation Pathway Of Vitamin C Recycling, James M. Hempe, Daniel S. Hsia, Arthur Hagar, Larry Byers

School of Medicine Faculty Publications

The proposed glucosylamine oxidation pathway (GOP) is a two-step, intraerythrocyte, thermodynamically favorable nonenzymatic reaction that first binds glucose to the N-terminal valine of beta globin (βVal1) to form a closed-chain glucosylamine that can spontaneously reduce oxidized vitamin C to its antioxidant form. This review summarizes analytical, biochemical and clinical research supporting the existence of the GOP and the surprising hypothesis that βVal1 glucosylamine is a reducing agent that works cooperatively with reduced glutathione to dynamically regulate vitamin C recycling during naturally occurring periods of transiently or chronically elevated blood glucose and oxidant production. Rationale for the existence of the GOP …

Integrated Computational Approaches: Elucidating Molecular Mechanisms Of Pathogenic Proteins And Designing Novel Inhibitors Against Mycobacterium Tuberculosis And Sars-Cov-2, Justin David Carbone

Theses and Dissertations

Chapter 1 introduces computational strategies in computer aided drug design (CADD), focusing on physics-based methodologies to enhance drug discovery. This chapter also discusses the theoretical foundations and practical applications of molecular dynamics (MD) simulations including free energy and stochastic kinetic analysis. In Chapter 2, CADD methods lead to development of inhibitors targeting the RNA Dependent RNA Polymerase (RdRP) of SARS-CoV-2. Inspired by the nucleotide inhibitor Molnupiravir, we aim to design a combinatorial library of 72 novel inhibitors capable of impeding a dual threat inhibition mechanism inducing lethal mutations along with stalling viral replication with specific selectivity to RdRp over Human …

Clinically Proven Natural Products In Aid Of Treating Parkinson's Disease: A Comprehensive Review, Md Abul Hasan Roni, Md. Abu Bakar Siddique Jami, Sajidul Hoque, Md. Al Hasibuzzaman, Kazi Hamida Banu, Rozina, Farzana Ansari, Md Sohel, Md. Ashifuzzaman, Nazmul Huda

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Chemistry)

Parkinson's disease (PD) is a neurodegenerative disorder that is caused by degeneration of nerve cells in the part of the brain called the substantia nigra, which controls movement. Although there is some considerable evidence with conventional drugs for PD, treating patients becomes increasingly difficult due to their short- and long-term adverse effects and other restrictions. This dire circumstance emphasizes the need for an innovative, strong alternative treatment for PD. Plants and natural products are considered one of the most important sources of bioactive molecules against a wide range of health disorders. With mechanistic insights, this systematic review explains the efficacy …

Positron Emission Tomography In Oncology And Environmental Science, Samantha Delaney

Dissertations, Theses, and Capstone Projects

The last half century has played witness to the onset of molecular imaging for the clinical assessment of physiological targets. While several medical imaging modalities allow for the visualization of the functional and anatomical properties of humans and living systems, few offer accurate quantitation and the ability to detect biochemical processes with low-administered drug mass doses. This limits how physicians and scientists may diagnose and treat medical issues, such as cancer, disease, and foreign agents.

A promising alternative to extant invasive procedures and suboptimal imaging modalities to assess the nature of a biological environment is the use of positron emission …

A Potential Of Watercress Nasturtium Officinale Bioactive Compounds In Inhibiting Infectious Myonecrosis Virus (Imnv) By Targeting Rna-Dependent Rna Polymerase (Rdrp) Virus From Several Countries: In Silico Approach, Qurrota A’Yunin, Fatchiyah Fatchiyah, Maftuch Maftuch, Feri Eko Hermanto, Muhammad Hermawan Widyananda, Narendra Santika Hartana, Muhaimin Rifa’I, Yoga Dwi Jatmiko

Karbala International Journal of Modern Science

Infectious myonecrosis virus (IMNV) disease causes mass mortality and decreased shrimp production. The RdRp region projects to the interior, where it may function in transcription. The focus of this study was to determine the effect of amino acid polymorphisms from several countries on the structure of RdRp and identify the potential of watercress in inhibiting IMNV by targeting the RdRp protein of IMNV through an in silico approach. The results showed that the structure of the IMNV RdRp protein from Indonesia was similar to Mexico, and the protein structure from India_QDN was identical to India_QIL. Ligand binding affinity values showed …

Inchi Isotopologue And Isotopomer Specifications, Hunter N. B. Moseley, Philippe Rocca-Serra, Reza M. Salek, Masanori Arita, Emma L. Schymanski

Markey Cancer Center Faculty Publications

This work presents a proposed extension to the International Union of Pure and Applied Chemistry (IUPAC) International Chemical Identifier (InChI) standard that allows the representation of isotopically‑resolved chemi‑ cal entities at varying levels of ambiguity in isotope location. This extension includes an improved interpretation of the current isotopic layer within the InChI standard and a new isotopologue layer specification for representing chemical intensities with ambiguous isotope localization. Both improvements support the unique isotopically‑ resolved chemical identification of features detected and measured in analytical instrumentation, specifically nuclear magnetic resonance and mass spectrometry.

Scientific contribution

This new extension to the InChI standard …

Zeolitic Imidazolate Framework-8 Encapsulated With Mo-Based Polyoxometalates As Surfaces With Antibacterial Activity Against Escherichia Coli, Mariam M. Abdelkhalek, Aya M. Mohamed, Rehab Z. Abdallah, Ghada E. Khedr, Rania Siam, Nageh K. Allam

Faculty Journal Articles

Bacterial infections represent a major global health concern, causing millions of deaths and a significant economic burden. The development of antibacterial nanoporous surfaces with potential mechano-bactericidal effects can revolutionize infection control practices. In this study, a hybrid material of zeolitic imidazolate framework-8 (ZIF-8) doped with phosphomolybdic acid (PMA) was synthesized and characterized by field emission scanning electron microscopy (FESEM), energy-dispersive X-ray spectroscopy (EDS), X-ray diffraction (XRD), Fourier-transform infrared spectroscopy (FTIR), and N2 sorption isotherms. PMA@ZIF-8 performance as an antibacterial agent against E. coli was superior to that of its individual constituents, suggesting a synergistic effect of PMA and ZIF-8. The …

A Revised Synthesis Of The Cationic Lipids Dmri And Mlri, Benjamin A. Kostic

College of Arts & Sciences Senior Theses

Lipid nanoparticles (LNPs) are an increasingly utilized method of intracellular delivery for nucleic acids. The COVID-19 vaccines from Moderna and Pfizer-BioNTech have used LNP technology to combat the recent global SARS-CoV-2 pandemic, saving millions of lives.^1,2 These vaccines consist of a lipid formulation that binds to the anionic phosphate groups of mRNAs and serves as an effective way to transport the nucleic acid across membranes into cells.⁹The mRNA encodes a viral protein. When introduced to cells, the viral protein is produced so that the immune system then can generate an appropriate antibody response.³ However, this approach …

Synthesis Of Neoglycoproteins As Potential Biomarkers For Chagas Disease And Cutaneous Leishmaniasis Caused By Leishmania (Viannia) Braziliensis, Eileni Rodriguez Gil

Open Access Theses & Dissertations

Protozoan parasites are responsible for causing numerous diseases in humans and mammals worldwide. Among them are Chagas disease (CD), caused by the parasite Trypanosoma cruzi (T. cruzi), and tegumentary leishmaniasis (TL), caused by the parasite Leishmania (Viannia). Both diseases coexist in many regions of Latin America, and current hurdles to differentially diagnose them and determine chemotherapy success need to be overcome. CD can be diagnosed by traditional serological tests and polymerase chain reaction (PCR), but disadvantages of these methods are that they may produce false negatives because the antigens used in commercial CD kits are not conserved across all T.cruzi …

Table Of Contents

Journal of the South Carolina Academy of Science

No abstract provided.

Modeling Sex-Specific Changes In Myocardial Fibrosis, Grace Martin

Chemical Engineering Undergraduate Honors Theses

Heart disease the leading cause of death for both men and women in the United States. Cardiac fibrosis, or accumulation of extracellular matrix proteins in the heart, can occur after a heart attack and increase the risk for further complications. Current treatments for heart disease do not include extracellular matrix regulators, partly due to the complicated signaling network responsible for the production of these proteins. By using a computational model of the signaling network in cardia fibroblasts, the relationship between particular molecules and downstream extracellular matrix production can be examined.

Biological sex is an important factor for cardiac health and …

Synthesis Of Thermoresponsive Poly(N-Isopropyl Acrylamide) Based Core-Shell And Hollow Shell Nanogel With Tunable Core And Shell Thickness, Mohamad Hijazi, Molla R. Islam

Student Scholar Symposium Abstracts and Posters

Nanogels have emerged as a notably safer and more effective means for drug delivery, primarily due to their adjustable drug-loading capabilities. Hollow-core nanoparticles offer some unique properties that are desirable for drug delivery applications. Initially, silica core nanoparticles were synthesized using the Stöber process at different temperatures where Tetraethoxysilane (TEOS) undergoes hydrolysis in the presence of ethanol and then a condensation reaction to form silica nanoparticles. Scanning Electron Microscopy (SEM) and Optical Microscopy (OM) analysis revealed that the size of silica core particles varied with the synthesis temperature (300 nm at 30°C to 150 at 60°C). The core silica particles …

Selective Transfection Of A Transferrin Receptor-Expressing Cell Line With Dna-Lipid Nanoparticles And Synthesis Of Parasite-Derived Glycans As Biomarkers For Leishmaniasis, Irodiel Vinales Lozano

Open Access Theses & Dissertations

Despite notable progress in lipid nanoparticle (LNP)-mediated gene delivery, achieving selective transfection of specific cell types, such as cancer cells, remains a significant hurdle, hindering the advancement of innovative gene therapies. In this study, we engineered an LNP formulation encapsulating plasmid DNA (pDNA) encoding the monomeric Green Lantern (mGL) fluorescent reporter protein. The DT7 peptide ligand targeting human transferrin receptor 1 (hTfR1) was also conjugated to the LNP surface for targeted delivery to hTfR1-expressing cells. Optimization of LNP composition yielded favorable particle diameter, ζ-potential, yield, and pDNA encapsulation efficiency. Evaluation of transfection selectivity using a panel of two engineered cell …

3d-Printed Microfluidic Devices For Electrochemiluminescence Detection Of Mirna, Oscar Clement

Honors Scholar Theses

This thesis outlines the research conducted over the past two years on the production and application of microfluidic devices (MFDs) in electrochemiluminescent-based bioanalytical assays. The work is categorized into two main projects: designing and manufacturing MFDs and developing electrochemiluminescent (ECL) assays for detecting Alzheimer's disease (AD) associated microRNAs (miRNAs) using CRISPR technology. The process of learning to design MFDs involved acquiring proficiency in computer-aided design (CAD) software, stereolithography (SLA) 3D printing, and iterative design techniques. The development of the ECL-based assay for AD miRNA was a multidisciplinary endeavor, combining elements of inorganic and biological chemistry. Although the research on the …

Electrochemical Modulation Of Surface Plasmon Wave To Investigate Dna-Based Sensing Platforms And Detection Of Sars-Cov2., Anil Sharma

Electronic Theses and Dissertations

This study offers a thorough comparative analysis of optical and electrical signaling strategies for assessing the electrochemical properties of different redox-labeled DNA-based biosensing platforms. In addition, it illustrates the development of an optical interrogation technique with electrochemical modulation of surface plasmon waves (ECM-SPW) as a route for analyzing and implementing DNA-based hybridization sensors. For those quantitative analyses, we chose a model sensing platform composed of a methylene blue (MB)-modified single-stranded DNA (ssDNA) signaling probe and an unlabeled capture ssDNA probe that complements the signaling probe. Two types of signaling probes were employed in this work: one with MB attached to …

The Purification And Thermal Stability Of The Peroxidase Enzyme In Cucurbita Moschata, Garen Hamner

Senior Honors Theses

Peroxidases are enzymes that catalyze the reduction of hydrogen peroxide to water while oxidizing organic substrates and are valuable in spheres like industrial and medical applications and histochemistry. Limitations still exist in the use of the well-studied horseradish peroxidase for certain activities due to limitations like poor thermal stability, thus the search for novel peroxidases that can overcome these limitations is an active area of research. Butternut squash peroxidase (Cucurbita moschata) (BSP) shows promise due to significant activity being found in the skin and apparent enhanced thermal stability, but an efficient purification scheme for it is lacking, as well as …

Modern Approaches To Treating Hospital Acquired Infections: An Overview Of Current Treatments Using Antibiotics And New Therapies Centered Around Photo-Activated Porphyrins, Meghan Johns

Senior Honors Theses

Annually, hospital-acquired infections (HAIs) affect hundreds of thousands of people in the U.S. and impose a great economic burden. The current problem is further exacerbated due to the failure of traditional treatment strategies considering the rise in antimicrobial resistance rates. Besides the fact that antimicrobial resistances complicates clinical treatment strategies, patients are also more vulnerable to secondary infections and complications from prolonged antibiotic use. As a result, research investigating novel treatment strategies for bacterial infections has recently increased. A strategy using porphyrin-based compounds is showing promise. Porphyrins and their derivatives have exhibited bactericidal effects against Gram-positive bacteria by the destruction …

Hgs-3 The Influence Of A Tandem Cycling Program In The Community On Physical And Functional Health, Therapeutic Bonds, And Quality Of Life For Individuals And Care Partners Coping With Parkinson’S Disease, Leila Djerdjour, Jennifer L. Trilk

SC Upstate Research Symposium

Purpose Statement: Several studies have shown that aerobic exercise can have a positive impact on alleviating symptoms experienced by individuals with Parkinson's disease (PD). Despite this evidence, the potential benefits of exercise for both PD patients and their care partners (PD dyad) remain unexplored. This research project investigates the effectiveness, therapeutic collaborations, and physical outcomes of a virtual reality (VR) tandem cycling program specifically designed for PD dyads.

Methods: Following approval from the Prisma Health Institutional Review Board, individuals with PD were identified and screened by clinical neurologists. The pre-testing measures for PD dyads (N=9) included emotional and cognitive status …

Shared Genomic Segments Analysis Identifies Mhc Class I And Class Iii Molecules As Genetic Risk Factors For Juvenile Idiopathic Arthritis, Cecile N. Avery, Nicole D. Russell, Cody J. Steely, Aimee O. Hersh, John F. Bohnsack, Sampath Prahalad, Lynn B. Jorde

Markey Cancer Center Faculty Publications

Juvenile idiopathic arthritis (JIA) is a complex rheumatic disease encompassing several clinically defined subtypes of varying severity. The etiology of JIA remains largely unknown, but genome-wide association studies (GWASs) have identified up to 22 genes associated with JIA susceptibility, including a well-established association with HLA-DRB1. Continued investigation of heritable risk factors has been hindered by disease heterogeneity and low disease prevalence. In this study, we utilized shared genomic segments (SGS) analysis on whole-genome sequencing of 40 cases from 12 multi-generational pedigrees significantly enriched for JIA. Subsets of cases are connected by a common ancestor in large extended pedigrees, increasing the …