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Full-Text Articles in Chemicals and Drugs

Enantioselectivity Of The Photochemical Continuous-Flow Isomerization Of Humulones, Gregory M. Giovine, Trevor Smith, Bruce Hamper Sep 2026

Enantioselectivity Of The Photochemical Continuous-Flow Isomerization Of Humulones, Gregory M. Giovine, Trevor Smith, Bruce Hamper

Undergraduate Research Symposium

Humulones, the primary natural product present in the historically significant hop flower, represent a largely unexplored candidate for structure-based pharmaceutical design.  Showing promising biological activity as an anti-bacterial and anti-inflammatory agent, humulones are of interest both for their bioactive properties and for their long-established tolerability and natural abundance.  Humulones undergo a characteristic isomerization reaction, where the six-membered substituted phloroglucinol ring contracts to a five-membered ring isohumulone, under a variety of conditions, including those enabled by brewing conditions (thermal, metal-catalyzed) and by exposure to UV light.  Optimization of the photocatalyzed isomerization of n-humulone to n-isohumulone in flow conditions resulted in a …


Development Of Ultrafast Protein Digestion And Standards Free Quantitation Methods For Mass Spectrometric Analysis, Praneeth Ivan Joel Fnu Aug 2026

Development Of Ultrafast Protein Digestion And Standards Free Quantitation Methods For Mass Spectrometric Analysis, Praneeth Ivan Joel Fnu

Dissertations

A wide variety of biologically important molecules, such as enzymes, antibodies, hormones, transporters and receptors are proteins by composition and they play key roles in biological functions such as cellular regulation, communication, metabolism and physiological function. Protein dysfunctions and abnormalities are associated with numerous diseases, making proteins critical targets for understanding disease mechanisms and developing therapeutic interventions. Protein-based therapeutics such as monoclonal antibodies, hormones and vaccines gained popularity due to their high specificity, efficacy, and ability to treat complex diseases that are often difficult to address with small-molecule drugs.

Given the important role of proteins in a variety of biological …


Norman H. Cromwell, Unl Chemistry; Nu System Dean; Eppley Cancer Center Director, Norman H. Cromwell, Pete Boughn, Mark A. Griep Aug 2026

Norman H. Cromwell, Unl Chemistry; Nu System Dean; Eppley Cancer Center Director, Norman H. Cromwell, Pete Boughn, Mark A. Griep

UNL ORCA Interview Series

This 1980 interview of Normal Cromwell was done by Pete Boughn at the University of Nebraska Medical Center in Omaha. He asked about Cromwell’s history but mostly about his time as director of the Eppley Cancer Center. The interview is reproduced with permission from the UNMC McGoogan Library.

Cromwell was born in 1913 in Terre Haute, Indiana. In 1935, he earned a bachelor’s degree in chemical engineering from the Rose-Hulman Institute of Technology in his hometown. In 1939, three things happened: he earned a doctorate in organic chemistry from the University of Minnesota, he got married, and he was hired …


Exploring Red Palm Oil As A Sustainable Plasticizer For Carbon Black-Filled Ssbr/Br Tire Tread Compounds: A Comparative Evaluation Of Commercial Alternatives, Norma Arisanti Kinasih, Mohamad Irfan Fathurrohman, Santi Puspitasari, Dewi Kusuma Arti, Abdulhakim Masa Aug 2026

Exploring Red Palm Oil As A Sustainable Plasticizer For Carbon Black-Filled Ssbr/Br Tire Tread Compounds: A Comparative Evaluation Of Commercial Alternatives, Norma Arisanti Kinasih, Mohamad Irfan Fathurrohman, Santi Puspitasari, Dewi Kusuma Arti, Abdulhakim Masa

Journal of Materials Exploration and Findings

This study investigates the application of red palm oil (RPO) as an alternative vegetable oil resource to substitute petroleum-based plasticizers, which have environmental and health concerns, in carbon black (CB)-filled SSBR/BR tire tread compounds. The plasticizing effects of RPO were thoroughly evaluated by comparing them with a commercial bio-based plasticizer, Epoxidized Soybean Oil (ESBO), and two safer petroleum-based oils, Naphthenic Oil (NYNAS) and Treated Distillate Aromatic Extract (TDAE). The initial investigation shows that fatty acid composition is imposing regarding the plasticizing effect. The higher unsaturated fatty acid content in RPO than in ESBO improved tensile strength and degraded rolling resistance …


Metallurgical Investigation Of A Modified Eye Bolt Failure Caused By Improper Weld Extension, Specification Deviation, And Crevice Corrosion, Dimas Muhammad Fawwaz, Reza Miftahul Ulum, Johny Wahyuadi Soedarsono, Yudha Pratesa Aug 2026

Metallurgical Investigation Of A Modified Eye Bolt Failure Caused By Improper Weld Extension, Specification Deviation, And Crevice Corrosion, Dimas Muhammad Fawwaz, Reza Miftahul Ulum, Johny Wahyuadi Soedarsono, Yudha Pratesa

Journal of Materials Exploration and Findings

A modified eye bolt from the David Arm Manhole Storage Tank underwent thorough metallurgical study due to the consequences of the bolt's malfunction during operation. Safety issues arose when the manhole door detached during operation. The mechanical testing and chemical composition analysis of the bolts indicated they were manufactured from an ASTM A193 Grade B7 material used for high-temperature bolting. This material did not conform to the engineering drawing, which mentioned SA 563A, which is about nuts, not bolts. This contradiction clearly shows that the eye bolt which was installed does not conform to the intended design. Welded connections of …


Rejection Of Fe (Iron) And Kmno4 (Organic Substance) Parameters In Peat Water Using Organic Membranes, Muhamad Rafli Sakti Mulia Gonera, Siti Umi Kalsum, Sarah Fiebrina Heraningsih Aug 2026

Rejection Of Fe (Iron) And Kmno4 (Organic Substance) Parameters In Peat Water Using Organic Membranes, Muhamad Rafli Sakti Mulia Gonera, Siti Umi Kalsum, Sarah Fiebrina Heraningsih

Journal of Materials Exploration and Findings

Peat water is a surface water source widely used by people in swampy and lowland areas, but it has poor quality characteristics such as high organic matter content, low pH, and dissolved metal levels such as iron that exceed the threshold. These conditions can cause health problems and reduce the quality of clean water so that effective treatment technology is needed. This study aims to analyze the effectiveness of ultrafiltration membranes made from chitosan from shrimp shell waste in rejecting iron (Fe) and organic substances in peat water, and to determine the effect of pressure on separation performance. This study …


Analysis Of Terpenes In Cannabis Flowers Using Gas Chromatography Via Headspace-Solid Phase Microextraction (Hs-Spme), Hannah I. Bergner Aug 2026

Analysis Of Terpenes In Cannabis Flowers Using Gas Chromatography Via Headspace-Solid Phase Microextraction (Hs-Spme), Hannah I. Bergner

Forensic Science Master's Projects

As cannabis commercialization grows, rigorous profiling of cannabinoids, terpenes, and chemical contaminants is legally required for industry standardization and consumer safety. Terpenes are highly volatile components that dictate the unique aromatic profiles and therapeutic properties of cannabis via receptor pathways. This project focused on a gas chromatography-flame ionization detector/mass selective detector (GC-FID/MSD) combined with headspace-solid phase microextraction (HS-SPME) sampling to analyze terpenes present in four cannabis samples. Cannabis samples were tightly sealed in vials (10 mL) and heated to vaporize terpenes in the headspace above the samples, followed by the extraction of the vaporized terpenes using a polydimethylsiloxane (PDMS)-coated SPME …


Computational Insights Into Nucleosome Dynamics In Epigenetics Using Molecular Dynamics Simulations, Rutika Patel Jun 2026

Computational Insights Into Nucleosome Dynamics In Epigenetics Using Molecular Dynamics Simulations, Rutika Patel

Dissertations, Theses, and Capstone Projects

Nucleosome core particles (NCP) are the building blocks that form a highly organized and compact chromatin structure. Nucleosomes package DNA in the nucleus of eukaryotic cells. The NCP consists of about 147 base pairs of DNA wrapped around the histone octamer, with 1.65 superhelical turns in a left-handed manner. The histone octamer is composed of two copies of H3, H4, H2A, and H2B. Together with histone H1 and linker DNA, they further assemble into a higher-order chromatin structure. The nucleosome complex is stabilized by electrostatic interactions between positively charged histone residues and the negatively charged DNA backbone. To effectively access …


The Influence Of Fermentation Duration And Secondary Fermentation Conditions On The Bioactive Compound Profile Of Kombucha, Jordan Vereen May 2026

The Influence Of Fermentation Duration And Secondary Fermentation Conditions On The Bioactive Compound Profile Of Kombucha, Jordan Vereen

Honors Theses

Kombucha is a fermented sweet tea produced using a symbiotic culture of bacteria and yeast (SCOBY) and has gained widespread popularity due to its proposed health benefits. Kombucha has been studied to understand these advantages in cardiovascular support, improved metabolism, increased antioxidant effects, enhanced antimicrobial properties, and even potentially slowing the progression of certain diseases. Despite its increasing popularity, the way in which the specific bioactive compounds responsible for these effects and the fermentation conditions that influence their production remain unclear. The present study, conducted in collaboration with Dr. Budner, focuses on quantifying bioactive compounds in kombucha to better understand …


Predicting And Decoding Allosteric Binding Sites Using Protein Language Models And Structure-Based Machine Learning: An Energy Landscape-Guided Explainable Ai Framework, Kamila Riedlová, Vít Skrhák, William G. Gatlin, Max Ludwick, Lucas Turano, Marian Novotný, David Hoksza, Gennady M. Verkhivker May 2026

Predicting And Decoding Allosteric Binding Sites Using Protein Language Models And Structure-Based Machine Learning: An Energy Landscape-Guided Explainable Ai Framework, Kamila Riedlová, Vít Skrhák, William G. Gatlin, Max Ludwick, Lucas Turano, Marian Novotný, David Hoksza, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

Computational prediction of allosteric binding sites in protein structures remains a persistent challenge, as these regulatory pockets evade detection by both sequence-based and structure-based algorithms. Both computational and physical origins of this predictive asymmetry remain insufficiently understood. In this study, we systematically examine the determinants of binding site predictability using a dual framework that integrates a fine-tuned protein language model and the structure-based method P2Rank as complementary tools probing a diverse data set of 453 human kinases, together with a physics-based interpretability layer derived from energy landscape frustration analysis. Both predictors exhibit a sharp and reproducible dichotomy on protein kinases, …


Herbularyo (Folk Healer): An Herbal Medicine Card Game, Maryjane T. Magsino, Inah Marie Q. Rivera, Armando M. Guidote, Genejane M. Adarlo May 2026

Herbularyo (Folk Healer): An Herbal Medicine Card Game, Maryjane T. Magsino, Inah Marie Q. Rivera, Armando M. Guidote, Genejane M. Adarlo

Chemistry Faculty Publications

Herbularyo, a card game teaching about herbal plants (HPs), was created and evaluated as a viable educational card game based on Tuomisto and Aksela’s criteria. A quasi-experiment was performed on 81 Grade 8 students from a private high school and 50 Grade 11 from a public high school. Independent t-test revealed that the control group (CG) and experimental group (EG) (p=0.386), and EG1 (played ≤5) and EG2 (played >5) (p=0.681) are not comparable with each other. Paired t-test showed EG performed better (p=0.001) than CG (p=0.901) whereas ANCOVA showed that playing Herbularyo improved students’ information retention (p=0.006). EG1 and EG2 …


Investigating The Synthesis And Antibacterial Activity Of A Main-Chain Cationic Polymer, Emily Smith Apr 2026

Investigating The Synthesis And Antibacterial Activity Of A Main-Chain Cationic Polymer, Emily Smith

Honors Theses

Antibiotic resistance is a growing threat to public health. Due to the overuse of antibiotics in agriculture, the overprescription of antibiotics, and the misuse of antibiotics by patients, antibiotic resistance is spreading at an alarming rate. As antibiotic resistance spreads, the antibiotics we depend on to treat common infections become ineffective. Therefore, it is imperative to develop novel treatments for infections that do not increase the prevalence of antibiotic resistance. One treatment being explored is the use of synthetic polymers with antibacterial properties. Synthetic polymers are advantageous because they can be synthesized from widely available precursors and their structure is …


Synthesizing Fluorescent 3,4-Dihydropyrimidin-2(1h)-Ones Using A One-Pot Synthesis Reaction, John R. Griggs Apr 2026

Synthesizing Fluorescent 3,4-Dihydropyrimidin-2(1h)-Ones Using A One-Pot Synthesis Reaction, John R. Griggs

Create@State

In medical and pharmaceutical practices, Biginelli (3,4-dihydropyrimidin-2(1H)-ones) products have a number of potential uses due to their anticancer and anti-inflammatory properties.  In addition, they are a possible treatment for acquired immunodeficiency syndrome (AIDS). These compounds can be further modified to exhibit fluorescent properties. However, before using them in medicinal studies, it is useful to establish a procedure that can easily be modified and is synthetically accessible to allow for further optimization. The experiment was performed using the Biginelli compounds as a substrate, along with a variety of aromatic aldehydes and acids. After obtaining the products and purifying them with vacuum …


Feasibility Analysis Of Thermal Oxidizer To Determine Remaining Life Using Fitness- For-Service Level 3 Method, Yudhi Yudistirawan, Donanta Dhaneswara, Wahyuaji Narottama Putra, Gama Widyaputra, Dewi Kurnia Suci, Agung Putra Mahardhika Apr 2026

Feasibility Analysis Of Thermal Oxidizer To Determine Remaining Life Using Fitness- For-Service Level 3 Method, Yudhi Yudistirawan, Donanta Dhaneswara, Wahyuaji Narottama Putra, Gama Widyaputra, Dewi Kurnia Suci, Agung Putra Mahardhika

Journal of Materials Exploration and Findings

An aged thermal oxidizer (TOX) in the oil and gas industry necessitates a comprehensive evaluation to ensure its continued safe operation. This study presents a Remaining Life Assessment (RLA) and a Fitness for Service (FFS) evaluation for the four main components of the TOX, in accordance with API 510, API 579/ASME FFS-1, and ASME BPVC Section VIII Div-1 standards. The investigation includes the determination of maximum stress and maximum temperature required to assess the operational viability of the reactor. The four components are radiant, convection, transition, and stack sections—were modeled using the finite element method (FEM). Following the geometric modeling, …


Folic Acid–Carbon Dot–Gemcitabine Nanoparticles For Targeted Cancer Drug Delivery, Irfan Huda, Hua Mei Apr 2026

Folic Acid–Carbon Dot–Gemcitabine Nanoparticles For Targeted Cancer Drug Delivery, Irfan Huda, Hua Mei

SPARK Symposium Presentations

This project aims to develop a folic acid-attached carbon dot nanoparticle system (FA-CDs-GEM) for the targeted delivery of gemcitabine to cancer cells. While gemcitabine is widely used, its effectiveness is limited because a short in vivo half life and lack of selectivity, which lead to severe side effects. Carbon dots offer a simple and modifiable platform as the drug delivery and bioimaging agent. Conjugation of folic acid to the carbon dots enables selective targeting of cancer cells that overexpress folate receptors. In this study, we synthesized and characterized FA-CD-GEM nanoparticles and developed an HPLC calibration curve of GEM to accurately …


Increased Backbone Rigidity Of Artificial Transcription Factors, Jasmine Glover, Emma Otey, Joanna K. Kwao, Nicholas Truex Apr 2026

Increased Backbone Rigidity Of Artificial Transcription Factors, Jasmine Glover, Emma Otey, Joanna K. Kwao, Nicholas Truex

Senior Theses

Programming DNA-binding proteins is an effective strategy for developing therapeutics that regulate gene expression. These proteins can directly bind to DNA to activate or repress transcription of specific genes. Zinc finger proteins are a class of DNA-binding proteins commonly found in eukaryotic organisms. Their DNA-binding function is derived from unique amino acid sequences within each domain that recognizes specific nucleotides, allowing each finger to selectively recognize three DNA base pairs. Adjoining of multiple domains in tandem allows recognition of a specific DNA sequence. Artificial transcription factors can be made of multiple zinc finger domains arranged in tandem and engineered to …


Design And In Silico Modeling Of Heterocyclic-Based Xanthone Derivatives As Potential Anticancer Agents Through Tyrosine Kinase Inhibition, Yehezkiel Steven Kurniawan, Ervan Yudha, Nela Fatmasari, Radite Yogaswara, Harno Dwi Pranowo, Eti Nurwening Sholikhah, Jumina Jumina Mar 2026

Design And In Silico Modeling Of Heterocyclic-Based Xanthone Derivatives As Potential Anticancer Agents Through Tyrosine Kinase Inhibition, Yehezkiel Steven Kurniawan, Ervan Yudha, Nela Fatmasari, Radite Yogaswara, Harno Dwi Pranowo, Eti Nurwening Sholikhah, Jumina Jumina

Makara Journal of Science

Cancer is one of the deadliest diseases nowadays, and tyrosine kinase receptors play crucial roles in cancer cell survival, differentiation, proliferation, and migration. This study designed and developed a new inhibitor from heterocyclic-based xanthone derivatives to target two tyrosine kinase receptors, epidermal growth factor receptor (EGFR) and platelet-derived growth factor receptor (PDGFR), through in silico screening. Eighteen heterocyclic-based xanthones were evaluated through molecular docking for both receptors. All heterocyclic-based xanthones gave the root mean square deviation (RMSD) value lower than 2.00 Å. Xanthone with isobenzothiazole substituent (iBzThio) was found as the most potent inhibitor with binding energies of -10.60 and …


From Latent Manifolds To Targeted Molecular Probes: An Interpretable, Kinome-Scale Generative Machine Learning Framework For Family-Based Kinase Ligand Design, Gennady M. Verkhivker, Ryan Kassab, Keerthi Krishnan Jan 2026

From Latent Manifolds To Targeted Molecular Probes: An Interpretable, Kinome-Scale Generative Machine Learning Framework For Family-Based Kinase Ligand Design, Gennady M. Verkhivker, Ryan Kassab, Keerthi Krishnan

Mathematics, Physics, and Computer Science Faculty Articles and Research

Scaffold-aware artificial intelligence (AI) models enable systematic exploration of chemical space conditioned on protein-interacting ligands, yet the representational principles governing their behavior remain poorly understood. The computational representation of structurally complex kinase small molecules remains a formidable challenge due to the high conservation of ATP active site architecture across the kinome and the topological complexity of structural scaffolds in current generative AI frameworks. In this study, we present a diagnostic, modular and chemistry-first generative framework for design of targeted SRC kinase ligands by integrating ChemVAE-based latent space modeling, a chemically interpretable structural similarity metric (Kinase Likelihood Score), Bayesian optimization, and …


Investigating The Role Of Humic Acid In The Adsorption Mechanics Of Acetaminophen On Potassium Persulfate-Aged Polyethylene Terephthalate (Pet), Andrew Littleton, Maria Danielle Garrett, Phd Jan 2026

Investigating The Role Of Humic Acid In The Adsorption Mechanics Of Acetaminophen On Potassium Persulfate-Aged Polyethylene Terephthalate (Pet), Andrew Littleton, Maria Danielle Garrett, Phd

SPARK Symposium Presentations

Pharmaceutical contaminants such as acetaminophen (APAP) are showing a rising presence in aquatic environments, where their interactions with microplastics (MPs) can potentially modulate natural degradation mechanisms. Concurrent presence of the two substances has been shown to potentiate increase their individual harmful effects. This study investigates whether oxidative aging and humic-acid surface modification of PET microplastics influence APAP adsorption.

In this study, UV-aging was reproduced using an iron (II)-activated potassium persulfate (Fe(II)-KPS) oxidation system. Aqueous dissolved organic matter (DOM) is simulated using multi-hour exposure to humic acid. The MPs are then removed from the solution to examine adsorption mechanisms. While most …


Expanded Scorpionate And Siderophore-Inspired Ligands: From Foundational Designs To Modern Applications, Austin Winfield Medley, Trandon Allen Bender Jan 2026

Expanded Scorpionate And Siderophore-Inspired Ligands: From Foundational Designs To Modern Applications, Austin Winfield Medley, Trandon Allen Bender

Chemistry & Biochemistry Faculty Publications

Scorpionate ligands have been advanced significantly through systematic modifications of their apical atoms and heterocyclic arms, expanding their structural diversity and chemical reactivity. Recent biologically inspired variants now enable accurate modeling of complex bioinorganic motifs, such as the Fe₄S₄ clusters of nitrogenase, and support enzyme‐like reactivity under mild aqueous conditions. These developments have broadened the impact of scorpionate chemistry across bioinorganic modeling, homogeneous catalysis, and biorthogonal transformations. In particular, expanded tripodal scaffolds provide modular, tunable platforms for mimicking enzyme active sites and probing biological nitrogen fixation pathways. Beyond fundamental insight, these ligands present practical opportunities for sustainable catalysis by enabling …


Investigating The In Vitro Antimicrobial Potential And Comprehensive Computational Studies Of New Schiff Base Derivatives, Abrar Hussain, Shahzaib Akhter, Hammad Nasir, Khurram Shahzad, Muhammad Arfan, Sand Hyun Park Jan 2026

Investigating The In Vitro Antimicrobial Potential And Comprehensive Computational Studies Of New Schiff Base Derivatives, Abrar Hussain, Shahzaib Akhter, Hammad Nasir, Khurram Shahzad, Muhammad Arfan, Sand Hyun Park

Chemistry & Biochemistry Faculty Publications

Antimicrobial resistance (AMR) is a growing global health threat driven by multidrug-resistant bacteria (Staphylococcus aureus, Pseudomonas aeruginosa), and fungi (Candida albicans, and C. parapsilosis). This study evaluated six novel Schiff base derivatives (HSB-1 to HSB-6) through integrated in vitro antimicrobial activity and comprehensive computational studies. In vitro disk diffusion assay demonstrated the largest zones of inhibition against S. aureus for HSB-6 and HSB-1 (15–17 mm), activity against P. aeruginosa for HSB-5 and HSB-6 (12 mm), and moderate antifungal activity for HSB-4 (8–11 mm). Molecular docking results correlated with the in vitro findings with the binding energy ΔG = −12.3 kcal/mol …


Green Modification Of A Coupling Reaction Between N-Acetylated Amino Acids And P-Nitrothiophenol, Kaitlyn S. Marley, Hannah M. Werle, John P. Morgan Jan 2026

Green Modification Of A Coupling Reaction Between N-Acetylated Amino Acids And P-Nitrothiophenol, Kaitlyn S. Marley, Hannah M. Werle, John P. Morgan

SURF Posters 2026

Native Chemical Ligation (NCL) is a process by which smaller peptides can be linked together to form larger peptides and proteins, but the preparation of necessary thioester starting materials often relies on hazardous reagents. We report a greener synthesis of S-(4- nitrophenyl) N-acetylphenylalaninethioate, building upon the methodology reported by Raines et al.1 This literature synthesis uses N,N-dimethylformamide (DMF) as solvent in the final thioester coupling step to accommodate the limited solubility of N-acetylphenylalanine in less polar solvents. However, DMF is a known reproductive toxin and environmental hazard. Our research demonstrates that acidic water serves as a highly effective, benign alternative …


Absolute Quantification And Identification Of Rna From Rna-Lipid Nanoparticles Using High Resolution Mass Spectrometry, Jason C. Funderburk Jan 2026

Absolute Quantification And Identification Of Rna From Rna-Lipid Nanoparticles Using High Resolution Mass Spectrometry, Jason C. Funderburk

Theses and Dissertations

RNA therapeutics are a rising drug category with potential use for a range of conditions encompassing infectious diseases to therapies for cancer, diseases, and genetic disorders. RNA-lipid nanoparticles (RNA-LNPs) are the prominent delivery method for these therapeutics approved products include mRNA vaccines and polyneuropathy treatments. The emergency use authorizations and orphan drug status of current RNA-LNP drugs has allowed approval without finalization of the regulatory analytical procedures for quality monitoring. The objective of the study was to develop an LC-MS assay to simultaneously measure identity and concentration of two therapeutically relevant intact RNA constructs extracted from RNA-LNPs to enhance quality …


Synthesis And Characterization Of Succinate Dehydrogenase Inhibitors H2/Z14 And C6/Z96 In Order To Combat Small Cell Lung Cancer, Lauren M. Graves Jan 2026

Synthesis And Characterization Of Succinate Dehydrogenase Inhibitors H2/Z14 And C6/Z96 In Order To Combat Small Cell Lung Cancer, Lauren M. Graves

Honors Undergraduate Theses

The use of ubiquinone inhibitors to combat cancer is a recent development in medicinal science and procedures to efficiently synthesize these drugs remain limited. C6/Z96 and H2/Z14, two succinate dehydrogenase inhibitors, have been previously tested in vitro against NSCLC with positive results. Their similarity to ubiquinone is what makes them a strong candidate for a succinate dehydrogenase inhibitor at the ubiquinone binding site. The heterocyclic scaffolds and substituents are proposed to bind strongly through a combination of electronics, hydrogen-bonding, and fit, allowing them to bind well and prove to be more favorable than ubiquinone when competing for the Q-site. By …


Photo And Spatial Control Of Rna Structures And Functions: Exploring Positional Effects And Photo-Responsiveness Of Azobenzene Modified Nucleotides, Jinxi Du Jan 2026

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 …


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 Dec 2025

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), …


Suitability Of Mobile Phase Recycling For Methylxanthine Quantification In Coffee Samples Using Hplc, Kaitlin O’Keeffe, Marcos Mariano, Brian Murphy Dec 2025

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 …


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 Dec 2025

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 …


Assessment Of The Melt Quality Of A 30% Scrap Adc12 Aluminium Alloy Using The Inclusion And Fluidity Measurement Instrument (Ifmi) With Mullite Ceramic Filters, Gusti Ruri Ruri Lestari, Sandya Ananda Riswan, Muhammad Anis, Ahmad Ashari, Paramita Vidya Ayuningtyas, Bambang Suharno Prof, Donanta Dhaneswara Dec 2025

Assessment Of The Melt Quality Of A 30% Scrap Adc12 Aluminium Alloy Using The Inclusion And Fluidity Measurement Instrument (Ifmi) With Mullite Ceramic Filters, Gusti Ruri Ruri Lestari, Sandya Ananda Riswan, Muhammad Anis, Ahmad Ashari, Paramita Vidya Ayuningtyas, Bambang Suharno Prof, Donanta Dhaneswara

Journal of Materials Exploration and Findings

The increasing demand for sustainable practices in the metal casting industry has driven the use of recycled aluminum alloys such as ADC12. However, the addition of aluminum scrap tends to increase oxide inclusions, which reduce melt fluidity and compromise casting quality. This study utilizes the Inclusion and Fluidity Measurement Instrument (IFMI), equipped with mullite ceramic filters, to assess the melt quality of ADC12 aluminum alloy containing 30% scrap. Fluidity and inclusion characteristics were evaluated at five pouring temperatures (660°C, 680°C, 700°C, 720°C, and 740°C). The results show that fluidity increased with temperature, reaching a peak of 84.6 g·s⁻¹ at 740°C, …


Equipment Criticality Analysis To Determine Asset Integrity Management System Scheme In Supporting Production Optimization Scenarios In The Aeging Field, Donny Andryanto, Donanta Dhaneswara Dec 2025

Equipment Criticality Analysis To Determine Asset Integrity Management System Scheme In Supporting Production Optimization Scenarios In The Aeging Field, Donny Andryanto, Donanta Dhaneswara

Journal of Materials Exploration and Findings

This research investigates the production decline and cost increase in the X&Y oil and gas fields from 2022 to 2023. Production fell by 34%, while production costs per barrel rose by 79%. To address these issues, a series of optimization processes are proposed. These aim to restructure and enhance the production facilities to reduce current production costs. The optimizations include reducing pressure at the PPP Platform in 2024. Additional steps include shutting down CPP-ORF 14” pipelines and most processes at CPP 2 Platform by 2027 to convert it into an accommodation platform. Further, the plan involves optimizing the release of …