Innovations in marine toxicity testing: Fish embryo and mysid tests as replacements for larval test

Type: Undergraduate
Author(s): Katie Solomons Biology
Advisor(s): Marlo Jeffries Biology

Marine environments are at risk of contamination from oil refinery effluents, major oil spills, and wastewater runoff. To identify and mitigate such risks, the EPA requires toxicity testing of marine effluents. The larval growth and survival (LGS) test, featuring either sheepshead minnows (SHMs) or inland silversides (INS), is currently used to screen marine effluents for acute toxicity; however, the use of fish larvae represents an animal welfare concern, especially in light of legislation calling for adherence to the 3Rs of animal research. The fish embryo toxicity (FET) test and mysid growth and survival (MGS) test may represent viable alternatives to LGS tests as the FET test uses fish embryos (which are thought to experience less pain than older fish), while the MGS test uses invertebrates. The objective of this study was to determine if the FET and/or the MGS tests produce similar results as the LGS. To accomplish this, INS LGS, SHM LGS, INS FET, SHM FET, and MGS tests were run using phenanthrene, an environmentally-relevant component of crude oil. Results revealed that the LC50 values obtained from the MGS and INS LGS tests were comparable and that both were significantly lower than that of the other test types, suggesting that the MGS test may be a viable replacement for the LGS tests. This was further substantiated when growth metrics were evaluated. In contrast, the LC50 values obtained from both FET tests were significantly higher than those of the other test types indicating a relative lack of sensitivity. However, when hatchability was included as a test metric, the sensitivity of the INS and SHM FET was enhanced indicating that the inclusion of hatch may improve FET test performance.

Watershed Mapping of the Thule Defense Zone - Northwest Greenland

Type: Graduate
Author(s): Benjamin Strang Biology
Advisor(s): Matt Chumchal Biology

The Thule Defense Zone in Northwest Greenland is a region of ecological concern because of its sensitive Arctic tundra ecosystem. Anthropogenic-induced climate change and deposition of contaminants into these fragile systems has the potential to alter these ecosystems. Mercury is a toxin of global importance that is capable of contaminating landscapes far from its source of origin, including those in the high Arctic. Understanding levels of mercury contamination that persist across landscapes requires analysis of aquatic ecosystems, as these systems are where mercury is converted into its toxic form, methylmercury. In Summer 2023, the Aquatic Ecology Lab at Texas Christian University will be traveling to the Thule Defense Zone and testing six ponds for mercury contamination. To better understand how contaminants reach these ponds, nutrient inputs from the landscape need to be understood. To date, there is no available watershed map for the Thule Defense Zone that delineates the hydrological characteristics of these ponds. My project will use Geographic Information Systems (GIS) to create a formal delineation of these aquatic systems.

Taxonomic Re-evaluation of the Tropical Blueberries (Vaccinium L., Ericaceae) of Palawan and Mindanao Islands, Philippines

Type: Graduate
Author(s): Maverick Tamayo Biology Peter Fritsch Biology John Horner Biology
Advisor(s): John Horner Biology

Biodiversity, which is important to the health of ecosystems, is currently being lost to extinction at an alarming rate. Thus, cataloguing and documenting the biodiversity of the world has never been more critical. In this study, the diversity and taxonomy of the tropical blueberries (Vaccinium L., Ericaceae) of Palawan and Mindanao Islands, Philippines were revisited. A total of 27 species (23 from Mindanao and four from Palawan) were documented and recorded. Six novel species, two new island records, and clarification of three ambiguous species complexes were included. Two of the six novel species (V. jubatum and V. vomicum) were discovered among historical herbarium collections, while the rest (V. carmesinum, V. coarctatum, V. fallax, and V. gamay) were discovered during botanical excursions. Two previously island endemic blueberries, V. cebuense and V. banksii, were documented to have an extended distribution in Mindanao. Further, the V. barandanum, V. caudatum, and V. halconense species complexes were taxonomically explained. The nomenclatural status of these species was stabilized through assigning type specimens following specifications of the International Code of Nomenclature for algae, fungi, and plants (Shenzhen Code). We concluded that Mindanao Island is the center of Philippine Vaccinium diversity. This study underscores the crucial role of herbaria in understanding the floristic diversity of the world. This study also serves as a basis for taxonomical studies of the other blueberries in the Philippine Islands and the Southeast Asia.

The Effects of a Mediterranean Versus Western Diet in C57BL/6J Mice on Inflammation in the Brain

Type: Undergraduate
Author(s): Emily Van Dyck Biology Gary Boehm Psychology Paige Braden Kuhle Psychology Kelly Brice Psychology Michael Chumley Biology
Advisor(s): Michael Chumley Biology

Due to our rapidly aging population, 6.5 million Americans currently have Alzheimer’s disease (AD), and this is predicted to increase to almost 14 million in the next 40 years. AD is more prevalent in western societies, and researchers suggest that this may be due to the typical Western diet. In contrast, AD prevalence is lower in Mediterranean regions, where a healthier diet could be a contributing factor. Therefore, this research examined the neuroprotective potential of a Mediterranean diet against AD pathologies and inflammation in mice. Our lab designed two experimental rodent diets, one that mimicked a typical Western-style diet, and another that mimicked a typical Mediterranean diet. We examined the lifelong effects of diet on biological markers of AD, including amyloid beta, a protein that aggregates together to form plaques in the AD brain, and pro-inflammatory cytokines, which are associated with increased inflammation. We hypothesized that the Mediterranean diet has the potential to mitigate these AD pathologies and therefore, could potentially be used as a future preventative strategy for AD.

Regulatory effects of loss of ClpX on the msrA chromosomal gene in Bacillus anthracis

Type: Undergraduate
Author(s): Kelsey Waite Biology Voung Do Biology Salina Hona Biology Shauna M. McGillivray Biology
Advisor(s): Shauna M. McGillivray Biology

Bacillus anthracis is the causative agent of anthrax. Previously, our lab identified the clpX gene as critical for virulence in B. anthracis. The ΔclpX mutant exhibited decreased cell wall integrity and increased susceptibility to cell-envelope active antibiotics. ClpX is one component of the intracellular caseinolytic protease ClpXP that degrades multiple proteins including transcriptional regulators. To understand changes in gene expression in ΔclpX, a microarray comparing WT and ΔclpX was conducted. This project focuses on msrA, an upregulated gene in ΔclpX. MsrA is an antioxidant enzyme that reduces methionine-S-sulfoxide to methionine but also impacts cell wall strength in S. aureus. This study will determine if loss of the msrA gene impacts antibiotic susceptibility. We hypothesized that since ΔmsrA is upregulated in ΔclpX, ΔmsrA would exhibit the opposite phenotype. Surprisingly, we find that ΔmsrA has significant growth inhibition in the presence of penicillin. However, we do not find susceptibility with other antibiotics, such as daptomycin, nor does it appear to be more susceptible to other clpX-related stress responses such as heat or acid stress. Future research will test ΔmsrA susceptibility to additional antimicrobials, such as the antimicrobial peptide LL-37 and the antibiotic vancomycin, as well as ΔmsrA virulence in vivo with the Galleria mellonella infection model. We will also complement ΔmsrA to confirm the phenotypes are due to loss of the msrA gene. This research is important as it aids our understanding of bacterial defenses and may provide new drug targets to help combat rising antibiotic resistance.

Correlation between mercury accumulation in spiders and drought conditions in the Great Salt Lake

Type: Graduate
Author(s): Kimberlee Whitmore Biology
Advisor(s): Matt Chumchal Biology

The Great Salt Lake in Utah is an important stopover point for many migratory bird species. Birds that stop to breed or forage at the Great Salt Lake may be at risk of mercury contamination due to high levels of methylmercury that are found in the lake. The purpose of this study was to examine the transfer of mercury from the lake into the terrestrial food web using organisms at the base of the food web. During the summers of 2019-2022 western spotted orb weaver spiders (Neoscona oaxacensis) and, when possible, brine flies (Ephydra sp.) were collected from various sites on Antelope Island. These specimens were analyzed for total mercury content using a Nippon MA-3000. In addition, satellite imagery and GIS software were used to document the approximate distance from the collection sites to the water surface. We examine differences between years, study sites and spider body size. We also examined the correlation between mercury levels and environmental conditions.

Molding Melanin Magic Mentorship Program

Type: Undergraduate
Author(s): Hailey Williams Biology Madison Brown Psychology
Advisor(s): Matt Chumchal Biology

The Molding Melanin Magic mentorship program through TCU Pre-Health is geared to impact minority female student populations at the Texas Academy of Biomedical Sciences (TABS) in Fort Worth. The program provides small group mentorship as high school students are paired with a college student in their area of interest. Along with mentorship, workshops are utilized as a method of increasing confidence, exposure, and overall knowledge about college and STEM careers. By coupling workshops and mentorship, the Molding Melanin Magic program seeks to encourage mentees to serve as mentors along their educational journey, and apply for college and professional school to pursue a career in STEM.

Effects of Preservation on Mercury Concentration in Spiders

Type: Undergraduate
Author(s): Macyn Willingham Biology
Advisor(s): Matt Chumchal Biology

Spiders are sentinel species, organisms that serve to map the bioavailable fraction of contaminants in an ecosystem by retaining their contaminants in their tissues. For example, spiders in the families Tetragnathidae and Araneidae are frequently used as sentinels of mercury contamination of aquatic ecosystems. Spiders are frequently preserved in alcohol prior to contaminant analysis but the impact of contamination on mercury concentrations in spiders has not been assessed. The objective of the present study was to determine the effects of different preservation methods on mercury concentrations in tissues of spiders in the families Tetragnathidae and Araneidae. The spiders were collected along water sources using nets and gloved hands. The Tetragnathids were collected from grassy terrain or a bridge overhanging the water of Lake Weatherford. The araneids were collected from a boat dock overhanging Eagle Mountain Lake. On site, each spider was placed into its respective bottle of varying ethanol or Ziplock's for freezing. Individual spiders were placed into one of three different concentrations of ethanol (100%, 95% , 70%) or frozen. Following about two months of preservation, the spiders were dried and run through the DMA-80 collecting the data for data analysis. Data xxxx *insert conclusion info*

Role of ClpX in the stress response and virulence of Bacillus anthracis: protease or chaperone?

Type: Undergraduate
Author(s): Lillian Wilson Biology Vuong Do Biology
Advisor(s): Shauna McGillivray Biology

Understanding the Structure and Function of Protein Kinase C-epsilon using Site Directed Mutagenesis

Type: Undergraduate
Author(s): Mariana Zollinger Biology Dr. Giridhar Akkaraju Biology
Advisor(s): Giridhar Akkaraju Biology

This research is focused on gaining a better understanding of PKC-epsilon a calcium-dependent protein kinase involved in a wide range of cellular functions including cell proliferation, survival, and apoptosis. The interest in PKC-epsilon derives from the discovery of a de novo mutation in the PKC-epsilon gene in patients suffering from SHORT syndrome. This syndrome is a debilitating disorder characterized by short stature, hyperextensibility, ocular depression, Rieger anomaly, and teething decay. The project involved recapitulating the naturally occurring de novo mutation in vitro as well as determining if other mutations in PKC-epsilon could cause similar disease-state phenotypes. Using a technique known as Site Directed Mutagenesis mutations were introduced into the PKC-epsilon gene and the effects of these mutations on the protein expression were assessed. This mutational analysis will help identify the regions of PKC-epsilon that are vital for its function. This will help elucidate the effect of the same mutations in patients and could help predict the severity of disease. Obtaining a clearer picture of the different regions of the PKC-epsilon protein allows for future studies to focus on successfully fixing these regions when they become damaged and could therefore be used to help patients with SHORT syndrome.

Directed evolution of RimJ for N-terminal protein acetylation with broad substrate specificity

Type: Undergraduate
Author(s): Anastasia Bernal Chemistry & Biochemistry Youngha Ryu Chemistry & Biochemistry
Advisor(s): Youngha Ryu Chemistry & Biochemistry

N-terminal acetylation is essential for the stability, activity, and targeting of proteins in eukaryotes. However, most eukaryotic proteins are not acetylated when expressed in bacteria. Therefore, it is of practical significance to control N-terminal acetylation of recombinant proteins in bacteria. RimJ is an N-terminal acetyltransferase (NAT) known to acetylate many recombinant proteins with a narrow substrate specificity in E. coli. This project is aimed to increase the applicability of RimJ for the N-terminal acetylation of a broad range of recombinant proteins.
Based on the AlphaFold-predicted structure of E. coli RimJ, we predicted that six amino acids (Y35, E46, R49, Y106, Y170, and L171) may recognize substrate proteins in the active site. We created RimJ variants, in which one or two of these amino acids are changed to alanine, a small neutral amino acid, so that the active site becomes larger to accommodate substrate proteins containing bigger N-terminal amino acid residues. The RimJ variants were created using site directed mutagenesis, confirmed by DNA sequencing, and co-expressed with Z domain mutants that were not acetylated by the wildtype RimJ. The Z domain mutants were isolated by immobilized metal ion affinity chromatography and analyzed by mass spectrometry for their N-terminal acetylation patterns.

Making Drug Model Marcocycles that Adds Tert-Butoxycarbonyl Hydrazide Last that Block Protein, Protein Interactions

Type: Undergraduate
Author(s): Grace Bobo Chemistry & Biochemistry
Advisor(s): Eric Simanek Chemistry & Biochemistry

Nature and bacteria make molecules like cyclosporine and coricidin that pharmaceutical companies do not make. They are too big, too greasy, and should not be able to be taken orally, however, these big molecules can fold to become small enough to intact with active sights on proteins. To try to replicate molecules like these we are making drug models called macrocycles. We focus on macrocycles because they are made quickly and cheaply. These molecules are big enough to block protein, protein interactions making a new way to fight diseases and illnesses. The groups universal macrocycle is made it the order: tert-butoxycarbonyl hydrazide, amino acid, dimethylacetamide, then acetal. My project moves the tert-butoxycarbonyl hydrazide to the end making the order: acetal, amino acid, in this case valine, dimethylacetamide, and tert-butoxycarbonyl hydrazide. The goal of this is to see if a bioactive macrocycle can still be made with this method and if there is any benefits in making the macrocycles this way.

Characterization of Fe-Py2N2 Complexes as C-C Coupling Catalysts

Type: Undergraduate
Author(s): Jack Bonnell Chemistry & Biochemistry Magy Mekhail Chemistry & Biochemistry Katherine J. Smith Chemistry & Biochemistry
Advisor(s): Kayla Green Chemistry & Biochemistry

The goal of this project is to offer a more economic and environmentally friendly, alternative carbon-carbon coupling catalyst complex to what is used industrially today. Carbon-carbon coupling is a common reaction performed in the industrial production of organic materials through routes that use palladium and platinum catalysts. These metals, however, are both economically and environmentally costly to acquire. It has previously been demonstrated that iron containing complexes can be used as an alternative to the precious metal complexes. We have previously demonstrated the carbon-carbon coupling ability of iron PyN3 complexes and characterized the mechanism. Based on these results, we have developed a Py2N2 series and the iron congeners for C-C catalysis. We also characterized them in order to understand the relationship between the catalytic performance and the number of pyridine rings and pyridine substitution.

Impacts of Indole Moiety Location on Pyridinophane Activity

Type: Undergraduate
Author(s): Will Campa Chemistry & Biochemistry Christina Mantsorov Biology Shrikant Nilewar Chemistry & Biochemistry
Advisor(s): Kayla Green Chemistry & Biochemistry

Pyridinophane molecules have recently been shown to have both antioxidant and pharmacological properties suitable for therapeutic applications targeting neurodegenerative diseases, including Alzheimer’s. We have synthesized derivatives of the parent molecules with substitutions on the pyridine ring (L1) or on the ‘side’ of the macrocycle (L2) designed to increase the antioxidant activity beyond that of the parent molecule in hopes of producing a molecule suitable for pharmacological testing in animal models. The lab is currently working towards substituting on the ‘bottom’ of the macrocycle (L3) to characterize and compare substitutions at each of the three positions.

Exploring the impact that S-oxidation has on the conformation and solubility (logP) of methionine macrocycles

Type: Undergraduate
Author(s): April Cannon Chemistry & Biochemistry Liam Claton Chemistry & Biochemistry Casey Patterson-Gardner Chemistry & Biochemistry Eric Simanek Chemistry & Biochemistry
Advisor(s): Eric Simanek Chemistry & Biochemistry

Macrocycles are molecules containing at least one ring composed of 12 or more atoms. Macrocyclic drugs have been used clinically for decades. Many interfere with protein-protein interactions. Therapeutic intervention requires that macrocycles remain flexible to facilitate the adoption of different conformations. Specifically, small compact hydrophobic conformations are required to cross cell membranes. The ability of a macrocycle to perform these contortions is predicted by its octonal:water partition coefficient, its so-called logP. Macrocycles (as well as small molecule drugs) that are suitable for oral delivery have a logP value <5. In this study, methionine containing macrocycles are studied. The studies commence with the synthesis of a macrocycle with a dimethylamine auxiliary group that allows for solution-phase NMR analysis. Upon formation of the macrocycle, oxidation to sulfone and sulfoxide derivatives was executed. These macrocycles are of interest because the impact that oxidation has on log P values has not been reported. Additionally, S-oxidation could change the conformation of the molecules. Synthesis beings with substitution of trichlorotriazine with BOC-hydrazine, followed by treatment with methionine in basic conditions. The final substitution of the triazine installs the auxiliary group, dimethylamine (NMR). Amidation with 1,1-diethoxypropyl amine using a peptide coupling reagent yields the monomer. Cyclization using TFA yields the macrocycle. NMR spectroscopy confirms macrocyclization and gives insight into the solution conformation of the molecule. Oxidation strategies and the results of logP analysis will be developed.

Investigating the Effects of Variants of Unknown Significance on the Binding Interaction between BRCA1 and PALB2 for Breast Cancer Predisposition

Type: Undergraduate
Author(s): Precious Castillo Chemistry & Biochemistry Davis Martin Biology
Advisor(s): Mikaela Stewart Biology

Proper functioning of BRCA1 and PALB2 are essential in preventing tumor formation. Upon detection of DNA damage, BRCA1 binds to PALB2, leading to formation of the BRCA1-PALB2-BRCA2 DNA repair complex which is recruited to double-stranded break sites. Mutations in the genes coding for BRCA1 and PALB2 may disrupt this binding interaction, causing obstructions in DNA damage repair and increased breast cancer risk. Variants of unknown significance (VUS) found in breast cancer patients are genetic variants whose impact on the health of individuals are not yet known. Our study characterizes the effects of these VUS on the BRCA1-PALB2 binding interaction. Site-directed mutagenesis was used to generate BRCA1 and PALB2 VUS. It was found that the binding event between BRCA1 and PALB2 is enthalpic in nature and can be measured adequately via isothermal titration calorimetry (ITC). Thus, ITC was employed to identify whether the VUS disrupted binding. ITC data suggest that several PALB2 and BRCA1 VUS exhibit disruptions of the BRCA1-PALB2 binding interaction, but to varying degrees. We will share the data for variants tested thus far and emerging themes for prediction of the roles residues in both proteins play in the vital interaction.

“It Works Because It Works” - Necessary Foundations for Understanding Triazine-Rich Macrocycles

Type: Graduate
Author(s): Liam Claton Chemistry & Biochemistry
Advisor(s): Eric Simanek Chemistry & Biochemistry

Triazine rich macrocycles have been the focus of the Simanek group for the past 3 years after their accidental discovery while attempting to create new polymers. Macrocycles are commonly found in nature and show promise in a variety of applications, but have been a difficult target to produce synthetically. The Simanek group has developed a novel synthetic route to produce a large and diverse library of macrocycles at quantitative yield, but there are still questions as to why the synthetic phenomenon occurs. Acyclic models provide the foundational understanding of why these triazine-rich macrocycles are able to be made.

Pyclen Macrocycle Release from Mesoporous Silica as a Drug Carrier and Impact on Amyloid Beta-Peptide Aggregation

Type: Undergraduate
Author(s): Caroline Crittell Chemistry & Biochemistry
Advisor(s): Jeff Coffer Chemistry & Biochemistry

Alzheimer’s Disease (AD) affects over 6.5 million Americans over the age of 65. Previous research links AD with the aggregation of Amyloid-beta-40 (AB40) in the brain, which creates neurotoxic plaques, causing further development of AD in the brain. A potential therapeutic mechanism in the treatment of AD is using drugs that will prevent the formation of these plaques, which is possible with Metal Chelation Therapy.
Metal ion chelation ideally stops metal ions from aiding in the aggregation of AB40. However, to deliver metal chelating agents to the brain, a drug-delivery mechanism is required that will be able to deliver this medicine across the Blood-Brain Barrier. Porous silica is a potential drug delivery material due to its particle size, high loading capacity, tunability, and biocompatibility. Along with these characteristics, porous silica can create a “sustained” release of a given drug, allowing for a slow and steady release profile, reducing the risks of medication side effects.
This project seeks to establish the optimal loading capacities of a class of potential AD therapeutic molecules known as pyclens into porous silica, each with different pyridyl moieties and chemical functionalities along the rim of the molecule. Encapsulation efficiencies measurements for these pyclen derivatives reveal loading percentages in the 10-19% range, varying by pyclen identity. Additionally, release studies monitored diffusion over time to find which pyclen molecule achieved “sustained” release. All loaded pyclen species were able to show sustained release after 20 minutes. Additional release studies of these molecules in the presence of copper (Cu2+) remain to be completed to ascertain the ability of release drugs in the presence of Cu2+ to inhibit AB40 aggregation, followed by independent assays of AB40 solubility under such conditions.

Investigating the Effects of BRCA1 Threonine Phosphorylation on PALB2 Interaction

Type: Undergraduate
Author(s): Chloe Duvak Chemistry & Biochemistry
Advisor(s): Mikaela Stewart Chemistry & Biochemistry

Two proteins, BRCA1 and PALB2 are known to aid in DNA damage repair through homologous recombination. Both proteins are phosphorylated upon DNA damage, and we hypothesize that the phosphorylation of these proteins acts as an “on switch” to allow the proteins to interact and form the DNA repair complex. To test this hypothesis, we mimicked phosphorylation on the BRCA1 protein to test the binding affinity between BRCA1 and PALB2. Phosphomimicking mutants are created by mutating an amino acid with the ability to be phosphorylated and acquire a negative charge, such as threonine (T) or serine (S), to a negatively charged amino acid, such as glutamic acid or aspartic acid. Recent research has shown that specific phosphorylation sites, such as T1394 in BRCA1 are essential to DNA damage and repair in cells. We have created a phosphomimic mutant in this specific T1394 site by mutating threonine to glutamic acid. We are currently measuring the effect that this mutation has on the ability of BRCA1 to bind to PALB2 in vitro. The obtained data will reveal whether phosphorylation has an impact on the interaction between these two proteins or not.

Pyridine Substitutions on 12-Membered Tetra-Aza Macrocyclic Ligands Modulate the Reactivity of Manganese towards Disproportionation of Hydrogen Peroxide

Type: Graduate
Author(s): David Freire Chemistry & Biochemistry Hannah Johnston Chemistry & Biochemistry Sugam Kharel Chemistry & Biochemistry Magy Mekhail Chemistry & Biochemistry Kristof Pota Chemistry & Biochemistry Katherine Smith Chemistry & Biochemistry
Advisor(s): Kayla Green Chemistry & Biochemistry

Manganese complexes remain attractive as catalysts for oxidation reactions in biology and industry due to their abundance in nature and versatility to access different oxidation states. Macrocyclic ligands offer the advantage of substantially stabilize the metal center, hence allowing a handle to control their reactivity. Inspired by the manganese catalase enzyme, a biological catalyst for the disproportionation of H2O2 into water and O2, this work shows the impact of pyridine substitutions on the reactivity of the manganese center towards H2O2 disproportionation. Potentiometric titrations were used to study the ligand basicity as well as the thermodynamic equilibrium with Mn(II). Synthesis and isolation of the manganese complexes was followed by characterization using UV-vis spectroscopy, SC-XRD and cyclic voltammetry. Manganese complexes were also produced in situ and characterized using electrochemistry for comparison to the isolated species. Results from these studies and those with H2O2 reactivity showed a remarkable difference among the ligands studied, highlighting a distinction in the reaction mechanism from N4 and PyN3 vs. Py2N2. Moreover, electron-donating groups on the pyridine enhanced the reactivity of the manganese center for H2O2 disproportionation, demonstrating a handle for control of this type of reaction using the pyridinophane scaffold.

Opening the Door on New Drugs: Swapping an Oxygen for Nitrogen May “Grease” Hinge-like Molecule

Type: Undergraduate
Author(s): Nathan Kebler Biology
Advisor(s): Eric Simanek Chemistry & Biochemistry

To fight many diseases, pharmaceutical companies have historically prepared small molecules designed to bind to specific sites on proteins (enzymes) to stop a chemical reaction that the protein is a part of. Examples of this include penicillin for bacterial infections and tipranavir for HIV. However, there is another paradigm for interacting with proteins to fight diseases that has gone largely unexplored--blocking protein-protein interactions. To accomplish this, large molecules are needed to bind to large areas on the protein target. Unfortunately, large molecules present additional challenges that many small molecules do not face. Typically, large molecules are hard to synthesize and not water-soluble. These characteristics make the development of oral medications virtually impossible as the molecules cannot cross cell membranes. Nature has designed molecules like cyclosporin that should not work as drugs based on current understanding. These molecules fold to hide hydrophilic groups so that they can cross cell membranes. This research explores the ability of comparable large, ring-shaped molecules, so-called macrocycles, to behave similarly. We recently showed that our macrocycles fold like door hinges with a rate that depends on the groups attached to the ring. Here, we explore how changing one of the hinge components--substituting an oxime for a hydrazone—affects folding.

The effects of protonation and hydrogen bonding on templating efficient macrocyclization

Type: Undergraduate
Author(s): Lola Kouretas Chemistry & Biochemistry Benjamin Janesko Chemistry & Biochemistry Alexander Menke Chemistry & Biochemistry
Advisor(s): Eric E. Simanek Chemistry & Biochemistry

Macrocyclic drugs adopt multiple conformations--a behavior referred to as chameleonicity--to navigate hydrophobic cellular membranes and aqueous intracellular environments. The rules for understanding this behavior are beginning to emerge through studying existing drugs and the synthesis of model systems. Historically, one challenge to macrocycle synthesis is low yield reactions. To this end, dynamic covalent chemistry has been explored. Here, macrocycles are afforded readily by dimerization with the formation of two hydrazones.

The efficiency of the macrocyclization reaction led to the hypothesis that upon formation of the first hydrazone, the acyclic intermediate was preorganized to place the hydrazine and acetal in close proximity thereby reducing the likelihood of oligomeric or polymeric products. The preorganization could result from a network of hydrogen bonds. Moreover, in an acidic environment, wherein the triazine ring is protonated, the opportunity for bifurcated hydrogen bonds emerge. Computation has been used to identify sites for protonation and the energetic contributions of hydrogen bonding.

To explore templating and the role of protonation in the formation of hydrogen bonds, model systems were prepared that emulate ‘half’ of the macrocycle. The acetylated aminoacetal offers a well-resolved NMR spectrum. In contrast, hindered rotation about the triazine-N bond leads to a mixture of rotamers in the hydrazine component. However, upon condensation, a single rotamer is observed and resonances corresponding to the hydrogen bonded protons emerge downfield between 7-12 ppm. Computation provides estimates of the energetic contribution of the bifurcated hydrogen bond as well as the hydrogen bond formed in the absence of protonation. The results of titration and variable temperature NMR experiments will also be described.

Exploration of Radical Scavenging Reactivity in Substituted Pyridinophane Ligands

Type: Undergraduate
Author(s): Christina Mantsorov Chemistry & Biochemistry David Freire Chemistry & Biochemistry Magy Mekhail Chemistry & Biochemistry Kristof Pota Chemistry & Biochemistry Katherine Smith Chemistry & Biochemistry
Advisor(s): Kayla Green Chemistry & Biochemistry

The mis-regulation of reactive oxygen species and transition metal ions contributes to the onset of Alzheimer’s Disease. Reactive oxygen species are a natural byproduct of metal redox cycling that occurs within the body and are important in processes like homeostasis and various pathways of cell signaling. Two series of pyridinophane ligands were produced and evaluated for the ability to target the molecular features of Alzheimer’s Disease. The functionalized pyridinophanes were chosen to analyze their blood-brain barrier permeability and radical scavenging ability when included within a molecular scaffold. Preliminary results with the DPPH assay indicated a significant increase in radical scavenging activity for ligands containing electron-donating substitutions in comparison to the parent ligands. These results warrant further exploration into the mechanism of the activity observed.

Building the Petro-Informatics Chemical Structure Database

Type: Undergraduate
Author(s): Sydney Mazat Chemistry & Biochemistry
Advisor(s): Benjamin Janesko Chemistry & Biochemistry

Petroleum crude oil, unconventional crudes, and renewable bio-crudes are essential materials in our everyday lives. They fuel vehicles, heat buildings, provide electricity, and are used to produce a multitude of other materials, such as plastics and solvents. Crudes are highly complex chemical mixtures, estimated to contain between 100,000 and 100,000,000,000,000,000 unique molecules. Since 2015, single-molecule imaging has visualized hundreds of chemical structures, and historical literature has published thousands of proposed structures. This project builds an open database populated with published crude structures enabling data-driven analysis of these structures, and detailed workflows, allowing for easy future insertion of new molecules into the database. This database can be used to make calculations and predict characteristics of molecules, such as viscosity, density, and reactivity, which are all critical in refinery plants, transportation, and usage of these fuels. Performing queries on the molecules in the database to filter for specific characteristics allows scientists to develop more successful experiments by refining their hypotheses to account for the query results displaying possibilities of their desired outcome.  

Opening the Door on Molecular Hinges

Type: Undergraduate
Author(s): Joseph Mellberg Chemistry & Biochemistry
Advisor(s): Eric Simanek Chemistry & Biochemistry

This research aims to understand how to design and control molecular hinges. The molecular hinges of interest are nano-sized equivalents of door hinges. Such hinges could find applications in new materials or the design of new drugs.

The foundation for this research was the observation that a large, ring-shaped molecule - a so-called macrocycle – prepared by a colleague folded and unfolded rapidly at room temperature. Two research questions arose from this observation: was the hinge behavior unique to this molecule, and could the hinging rate be controlled?

Addressing these questions required the three-step synthesis of a related macrocycle. This new molecule had groups equivalent to putting grit around the hinge's pin. The difference in the rate of hinging motion due to the addition of these groups was observed using a technique called variable temperature NMR spectroscopy.

The results of this work revealed that hinging is a general phenomenon for some of these macrocycles. Second, the 'molecular dirt' designed into this new hinge reduced the rate of hinge motion from 2000 times per second to 20 times per second.

This work is being written up for communication to the Journal of the American Chemical Society based on the novelty of this molecular device and the scientific community's interest in molecular machines.