Trainees

The V-CBI program aims to maintain a 50/50 ratio of trainees between chemistry and biological departments. In general, we receive between 15-20 nominations per year, and select four or five students to participate in the training grant.

2025 Trainees

Tori Federico

PI: David Cliffel and Steven Townsend, Chemistry
Human milk oligosaccharides (HMOs) play an integral role in shaping the infant gut and developing the infant immune system. Previous Research has implicated HMOs in an inhibitory role of the inflammatory effects mediated by key immune system modulators, including cytokines such as IL-1β, suggesting that HMOs could potentially be used in a therapeutic role in inflammatory-related diseases and conditions. An electrochemical biosensor specific for measuring IL-1β can be utilized to assess the impact of HMOs on IL-1β levels in THP-1 macrophages. Other cytokines, including pro-inflammatory cytokines, can also be measured with the use of electrochemical biosensors specific to them. This will ultimately enable a broader exploration of the effects of HMOs on the inflammatory immune response mediated by specific cytokines, potentially leading to the development of a new line of defense against inflammatory-related disorders and diseases.
Will Harrison

PI: Doug Mitchell, CPB
The World Health Organization’s 2024 Bacterial Priority Pathogens list highlights the critical threat of multi- and extensively drug-resistant Gram-negative bacteria that evade available antibiotics via their formidable outer membrane. Therefore, this project targets the essential outer membrane protein (OMP) BamA (β-barrel assembly machinery A); as a protein vital for OMP assembly, its external location bypasses intracellular drug delivery challenges [Cottom et al., 2023]. The natural product darobactin validates BamA inhibition but is synthetically intractable, underscoring the need for tractable inhibitors targeting this essential OMP [Imai et al., 2019]. Using an iterative cycle of computational design, chemical synthesis, and biological evaluation, my project will develop tractable darobactin analogues that preserve potent BamA inhibition.
Samantha Kasbohm

PI: Maria Hadjifrangiskou, IGP
For my graduate research in the Hadjifrangiskou laboratory, I plan to test small-molecule inhibitors of cytochrome bd, a terminal oxidase encoded by Escherichia coli that is critical for the virulence of uropathogenic E. coli (UPEC) strains. Previous work in the lab has shown that deletion of cytochrome bd affects motility, prevents intracellular replication, and diminishes the pathogen’s ability to respond to stressors and form biofilms. Based on these findings, we hypothesize that inhibitors of cytochrome bd could be used to treat resistant or recurrent urinary tract infections. In collaboration with the Vanderbilt Institute for Chemical Biology (VICB), several derivatives of known cytochrome bd inhibitors—such as Ilicicolin B, Aurachin C, Aurachin D, and CK-2-63—have been synthesized. While these natural compounds have primarily been tested in vitro, CK-2-63 has shown promise in combating Mycobacterium tuberculosis infections. Initial testing of the derivatives has identified Compound 09, a CK-2-63 derivative, as the most active molecule based on lag phase extension assays performed on live bacteria treated with single doses of each compound. A UPEC mutant lacking all other quinol oxidases except cytochrome bd served as a control to demonstrate the specificity of the most active inhibitors. My thesis will focus on testing additional molecules synthesized by the VICB to determine the most potent UPEC respiration inhibitors, characterizing their interactions with purified cytochrome bd complexes through binding and oxygen-consumption assays, and assessing the cytotoxicity of each compound in urothelial cell lines. Additionally, I will optimize the compounds’ ability to traverse the bacterial outer membrane to reach their target in the inner membrane, and ultimately evaluate the most promising inhibitors on UPEC biofilms and bladder epithelial cells in vivo, followed by testing in a mammalian model to determine whether they are effective independently or in combination with established antibiotics.
Lindsey Weissman

PI: Lauren Buchanan, Chemistry

2024 Trainees

Maxwell Hughes

PI: Alex Schuppe, Chemistry
Terpenes are a diverse class of small molecule natural products that possess a broad range of biological activities including antimicrobial, anticancer, and anti-inflammatory properties. With over 50,000 known structures, their stereochemically rich and in many examples, polycyclic frameworks present both a synthetic challenge and an opportunity for drug discovery. While cationic and radical cyclization methods can be used to rapidly access trans-6-membered scaffolds from simple linear precursors, they are not applicable for more complex, rearranged architectures like that of mitchellene B. My goal is to resolve this retrosynthetic gap by developing a hydroboration-carbonylation protocol to assemble these challenging frameworks. Currently, I am working on the application of this method to the first total synthesis of mitchellene B and once complete, will be used to generate analogs for biological evaluation and structure–activity relationship studies.
John “Jack” Olson

PI: Lars Plate, CPB
Cystic fibrosis (CF) is a lethal genetic disorder affecting approximately 85,000 individuals globally [McDonald et al., 2023]. It is caused by a variety of loss-of-function mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Mutations lead predominantly to protein misfolding and degradation of the CFTR protein, an epithelial anion channel. Recent advancements have led to the development of small molecule correctors and potentiators that enhance CFTR expression and function, significantly improving treatment outcomes for about 90% of patients, particularly those carrying the ΔF508 CFTR mutation common among Caucasians. However, these therapies are less effective for approximately 10% of patients with rare and diverse CFTR mutations, creating a therapeutic gap for these individuals, particularly in non-white populations. The challenge lies in the limited throughput of existing methods to identify and characterize novel drug compounds to treat these rare mutations.
This proposal outlines a novel approach integrating computational and biochemical techniques to enhance drug discovery efforts for CF. N1303K, the third most common mutation in CF, is prone to both endoplasmic reticulum-associated autophagy and proteasomal degradation, which current correctors fail to adequately address [DeStefano et al., 2018]. Previous work from the Plate Lab identified a critical binding pocket in proximity to N1303K within the NBD2, influencing the TMD1 intercellular loop 2 (ICL2) and closely interacting with the N-terminus of the Q-loop (residues 1284-1291). This pocket is shaped by nearby residues, including R1358, a key contributor to a hydrogen bond network essential for stabilizing the interaction between N1303K and Q1291 in the NBD2 crystal structure [Vernon et al., 2017]. We first aim to conduct virtual high-throughput drug screening using Rosetta’s REvolveD (Rosetta Evolutionary Docking) program, specifically targeting the N1303K CFTR variant at this pocket. Given that the N1303K variant remains unresponsive to conventional therapeutic strategies, including temperature correction, the lysosomal cysteine protease inhibitor E-64, and the autophagy inhibitor tubacin, yet shows positive reactions to a combination of Type-I and Type-II correctors (C18 and C4 respectively), we believe it is reasonable to explore this binding pocket for potential new corrector compounds [Rapino et al., 2015].
Following a comprehensive drug screen, we will employ time-resolved proteomics in CF human bronchial epithelial (CFBE) cells treated with novel correctors to assess if these compounds can effectively rescue the N1303K variant from degradation pathways. Several time-resolved proteomic methods are under pursuit in the Plate Lab, such as an mRNA-based flash cap system, halo-tag labeling, and whole-cell unnatural amino acid labeling with a click reaction. This integrated approach will accelerate the discovery and development of effective therapies for CFTR variants currently lacking effective treatment options, thereby expanding the therapeutic landscape, and improving outcomes for a wider array of CF patients. Successful outcomes from these experiments will potentially lead to groundbreaking treatments for over 1,500 patients homozygous for this mutation worldwide.
Kelly O’Rourke

PI: Doug Kojetin, Biochemistry
Nuclear receptor-related 1 protein (Nurr1) is a transcription factor essential for the development and maintenance of dopamine neurons in the mammalian midbrain. By regulating a gene program that controls enzymes involved in dopamine biosynthesis and dopamine reuptake pathways, Nurr1 plays a protective role over the neurons essential for movement. Nurr1 is capable of activating transcription as a monomer, homodimer, or as a heterodimer with retinoid X receptor ɑ (RXRɑ). Our lab has proposed a model of ligand-mediated Nurr1-RXRɑ transcriptional activation, where RXRɑ acts as a tether to repress monomeric Nurr1 at its DNA response element. My project aims to further explore the molecular basis of Nurr1-RXRɑ activation by (1) Identifying small molecules to modulate the Nurr1-RXRɑ heterodimerization and (2) Defining the co-regulator interactome of Nurr1.
Megan Ward

PI: Jeff Spraggins, CPB
The Spraggins research group integrates multimodal molecular imaging technologies, bringing together matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) with various forms of microscopy and spatial transcriptomics to understand the molecular drivers of important diseases such as diabetic nephropathy and chronic kidney disease. My research project will expand on these development efforts by enabling, for the first time, functional information to be layered onto untargeted lipid imaging data. I will develop a multimodal imaging workflow to reveal the relationship between lipidomic profiles and membrane fluidity. This project encourages interdisciplinary skills in the areas of analytical chemistry, cell biology, bioinformatics, and renal pathology. The opportunity to develop novel technologies and apply them to problems like diabetic nephropathy offers the potential to directly impact human health and provide me with training in cutting-edge bioanalytical techniques.

2023 Trainees

Paul Kastner

Bachmann, PMI
The urgent need for new antibiotics and cancer treatments highlights the importance of natural products, which have historically provided a significant portion of small molecule drugs used in the clinic. Bacteria from the phylum Actinomycetota, especially the extensively-studied soil genus Streptomyces, have been a prolific source of these life-saving compounds. However, the rate of discovering novel natural product scaffolds has slowed, partly due to the rediscovery of known compounds from these well-trodden sources. We hypothesize that unique, understudied environments like caves, with their distinct aphotic, oligotrophic, and isolated conditions, may harbor novel Actinomycetota with untapped secondary metabolic potential. Our research will explore these hypogean environments to discover new microbial secondary metabolites using a comprehensive metagenomic and culturomics approach.
Valentina Guidi

Kim, Chemistry
Aminoglycosides are a class of potent, broad-spectrum antibiotic molecules used clinically for the treatment of severe bacterial infections. Plazomicin, a therapeutic agent against urinary tract infections, is of particular interest because unlike other aminoglycosides, it is resistant to most aminoglycoside-modifying enzymes, thus lowering its susceptibility to bacterial resistance. My project takes a total synthesis approach to plazomicin, a traditionally semisynthetic molecule, by separately targeting its three core fragments, an unsaturated aminomonosaccharide residue, C4-methylated aminoarabinopyranoside residue, and 2-deoxystreptamine core, and linking them via two glycosylation reactions.
Raleigh Jonscher

Jones, Neuroscience
Over the last two decades, small molecule ligands that directly or indirectly enhance acetylcholine neurotransmission have been developed to ameliorate or normalize the deficits associated with cognitive decline observed in aging and dementia patients. Preclinical and early proof-of-concept clinical studies have provided strong evidence that activators of specific muscarinic acetylcholine receptors (mAChRs) (M1 and M4) subtypes are effective in animal models for cognitive enhancement and in the treatment of behavioral disturbances and some cognitive symptoms in patients with Alzheimer’s disease. While early attempts to develop selective mAChR agonists provided important preliminary findings, these compounds have ultimately failed in clinical development due to a lack of true subtype selectivity and subsequent dose-limiting adverse effects. In recent years, we have made major advances in the discovery of highly selective activators for the different mAChR subtypes with suitable properties for optimization as potential candidates for clinical trials. One novel strategy has been to identify ligands that activate a specific receptor subtype through actions at sites that are distinct from the highly conserved ACh-binding site, termed allosteric sites. These allosteric activators, both allosteric agonists (ago) and positive allosteric modulators (PAM), of mAChR subtypes demonstrate unique mechanisms of action, high selectivity in vivo, and may provide innovative treatment strategies for AD. We have now identified several selective allosteric M1 and M4 ago/PAM and pure PAMs, represented by early-stage tool compounds VU0453595 and VU0467154, respectively. These ligands exhibit low nanomolar potency, greater than 100-fold selectively relative to the other mAChR subtypes, and suitable DMPK properties for in vivo testing. My graduate research project is focused on the chemical optimization of selective allosteric modulators of the M1 and M4 mAChRs as mediators of cholinergic regulation of cognition, with the aim of elucidating novel therapeutic strategies for the treatment of cognitive deficits in aging and dementia populations. Until recently, the technologies for exploring how our novel allosteric modulators facilitate chemical signaling in the brain have been limited. However, with the application of innovative fiber photometry techniques, I can assess real-time changes in acetylcholine signaling across different brain regions in awake free-moving young and aging rodents, while these animals are performing different cognitive tasks. However, because acetylcholine signaling decreases with aging and dementia, it remains unclear what will be the desirable chemical properties for effective M1 and/or M4 mAChR allosteric modulators to boost this declining acetylcholine tone, specifically whether an ago/PAM or pure PAM will provide more efficacy. Thus, working in collaboration with the medicinal chemistry and DMPK teams within the WCNDD, my ongoing work is to understand how fundamental changes in the SAR of different chemical series of M1 and/or M4 mAChR allosteric modulators can alter not only the potency, selectivity, and DMPK properties of different molecules but also their in vivo acetylcholine signaling in preclinical models of aging and dementia.
Molly Sullivan

Plate, CPB
RNA viruses mutate rapidly, facilitating their adaptation to diverse environments and increasing the need for effective therapies against RNA viruses to prevent ‘spillover’ events between host species. One promising strategy involves incorporating synonymous mutations into viral genomes by disrupting codon bias to attenuate RNA viruses that still produce a robust host immune response. While synonymous mutations do not alter the amino acid sequence of the encoded protein, recent studies have shown that they influence several cellular processes, such as mRNA structure and folding, mRNA splicing and stability, and cotranslational folding. Here, we have introduced deoptimized synonymous mutations into the foot-and-mouth disease virus (FMDV) capsid coding region as a model to study how synonymous mutations affect viral protein folding and interactions with critical cellular machinery. Characterization of how synonymous mutations influence interactions with these cellular factors with provide insights into the function of synonymous mutations during viral host adaptation.
Sydney Thompson

Nobis, Neuroscience
Investigate the function and identify the mechanism of action of novel anti-seizure medication Fenfluramine as a treatment to improve epilepsy patient survival and decrease risk of Sudden Unexpected Death in Epilepsy (SUDEP). This research aims to directly assess the therapeutic efficacy of Fenfluramine and investigate the precise mechanism of action underlying the decrease in Seizure -Induced Respiratory Dysfunction (SIRD) and SUDEP.

2022 Trainees

Xavier Streety

Chemistry, PI Steve Townsend
"Synthesis and Biological Evaluation of Tranvalencin A and Truncated Fragments"
Initially isolated from a clinical strain of Nocardia transvalensis, transvalencin A is a non-ribosomally encoded peptide and zinc chelator with antifungal and antibacterial activity. Despite its initial promise, no work has been published on the molecule since the elucidation of its structure in 2004. Transvalencin A features unique oxazoline, thiazoline, and thiazolidine moieties with challenging stereochemistry as well as two stereospecific oxidations. In the process of total synthesis, establishing conditions for the stereospecific modification of the constituent peptides composing tranvalencin A addresses a clear gap in knowledge. We have planned a modular approach in the construction of the molecule as we hypothesize that there is some minimal structure needed to achieve bioactivity and that variation in the number of Lewis basic sites will result in different metal cation affinity. The desired result would be the first reported total synthesis of transvalencin A along with tests for antibiotic activity against Gram-positive bacteria, Gram-negative bacteria, the ESKAPE pathogens, and pathogenic fungi. In addition, the same bioactivity experiments are to be performed on fragments of tranvalencin A. The ultimate positive result would be that tranvalencin A and its fragments all have antibiotic activity but act by disrupting the homeostasis of different metal cations in vivo thus yielding several compounds that can be further developed and optimized as antibiotics as well as probe the role of metals in various cellular processes.
Hanna Thurman

Cell and Developmental Biology, PI Jonathan Irish
"Tools in Single Cell Chemical Biology"
Hannah’s research at Vanderbilt started with her identifying candidate ‘hits’ from a screen and using quantitative analysis to choose which would move forward into secondary assays for validation and deeper characterization. Hannah analyzed the results of a pilot screen of >600 small molecules screened in millions of human cells and identified a subset of compounds for follow-up based on cell biological activity of interest (selective inhibition of one mTOR pathway target, 4EBP, and not another, S6). She went on to show that one of the molecules selected was not only active and potent in follow-up experiments, but also that the molecule had vastly different impacts depending on cell type. In cancer cells, it quickly led to death through intrinsic apoptosis, but in all non-malignant cells, it had no cell killing activity over a long time course and across a range of doses. The molecule Hannah studied is a rocaglate, and working with a collaborator’s group, we have now obtained a library of rocaglate structural variants suitable for studies comparing structure and biological activity. In an initial test, several rocaglates repeated the initial finding (specific killing of cancer cells). In contrast, a different subset of rocaglates triggered activation signaling and proliferation of a specific subset of blood leukocytes. These observations form the basis of Hannah’s chemical biology project focused on structure activity relationships in this rocaglate family and the development of machine learning tools to characterize screening results based on differential cell type activity. Hannah aims to develop a machine learning approach for identifying cell type specific activity of molecules grouped based on structure. She also aims to dissect the relationship between molecular structure and cellular bioactivity for the rocaglate chemotype and identify mechanisms of differential activity in cancer vs. healthy cells.
Chris Juric

Chemistry, PI John Yang
"Developing RosettaQM-based Kinetic Scoring to Evaluate the Impact of Mutation on Halide Methyltransferase Substrate Specificity"
Chris’ thesis emphasizes advancing computational tools for automatic enzyme design and discovery. His short-term research goal is the development of a novel kinetic scoring function to aid in designing co-factor dependent enzyme mutants for transforming non-native substrates. The scoring function will utilize calculations from the RosettaQM framework to characterize the mutation effects on kinetic parameters (i.e., kcat and KM) via explicitly considering quantum mechanical effects, including charge transfer and non-native substrate–co-factor interactions. As a proof of concept, he will endeavor to demonstrate the utility of kinetic scoring function through application to a halide methyltransferases (HMT) enzyme. HMT allows one-step recycling of S-adenosyl methionine (SAM) from S-adenosyl-L-homocysteine (SAH). Although HMT mutants have been engineered to synthesize alkyl-SAM analogues using site-saturated mutagenesis, the specificity towards bulkier substrates (e.g., phenyl, propargyl, etc.) remains low. This presents a big roadblock to leverage HMT platform for broader chemical biology applications. To address this challenge, he proposes to test kinetic scoring functions in the task of predicting beneficial mutations for generating ethyl-SAM analogues based on reported experimental data. He will then apply the kinetic scoring function to identify beneficial HMT mutations to generate propargyl-SAM analogues. Through a collaborator, we will then synthesize these mutant HMTs and measure their ability to generate non-native SAM analogues for late-stage functionalization of drug molecules. The kinetic score function will establish a quantum mechanics (QM)-based in silico tool in the chemical biology community to predict mutations effects for enhanced enzyme specificity towards non-native substrates. This work will serve as a proof of concept and inspire the development of new QM-augmented approaches for biocatalytic applications. This effort will be aided by the co-mentorship of Prof. Jens Meiler, a major contributor to the Rosetta Community, and Prof. John Yang, an expert in the high-throughput and multiscale modelling of organic and enzymatic systems.
Adam Ebert

Cell and Developmental Biology, PI Jason A. MacGurn
"Mechanism by which myriocin extends cellular longevity using yeast as a model system"
The MacGurn group’s current hypothesis is that sphingolipid accumulation in mitochondrial membranes contributes to chronological aging in eukaryotic cells. This hypothesis is based on the following preliminary data: (i) during chronological aging, mitochondria undergo a dramatic change in morphology that involves “swelling” of the inner member and/or intermembrane space, an effect which is prevented by treating cells with myriocin, (ii) chronological aging is associated with loss of mitochondrial inner membrane potential, which is also prevented by treatment with myriocin, and (iii) levels of mitophagy decline during chronological aging, but are actually increased during aging of myriocin-treated cells. Adam’s thesis project will build on these preliminary findings and systematically test the hypothesis that mitochondria accumulate sphingolipids during aging. Specifically, Adam will use quantitative mass spectrometry approaches to define how both protein and lipid composition of mitochondria change during aging and with myriocin treatment. Adam will also perform imaging experiments to localize sphingolipids in aging yeast cells and genetic experiments to define pathways involved in remodeling mitochondria during aging.

2021 Trainees

Crissey Cameron

Chemistry, PI Lars Plate
Understanding protein interaction networks can give insight into the inner workings of systems biology, linking seemingly unrelated pathways to one another and deepening our understanding of the cellular processes controlled by protein interactions. Many approaches have been used in the literature to tease out static interactions of important proteins, but most fail to account for the dynamics and transient nature of many protein complexes and fail to map interactions with time resolution. Because of this, only a snapshot of the protein interactions at one point in time are accessible, painting an incomplete picture of the interactome. Chemical genetic probe molecules designed specifically to rescue a protein of interest from degradation by the proteosome allow for controlled accumulation of proteins in the cell, therefore allowing time-resolved study of a protein of interest. My research has designed a system in which a protein of interest is linked to a mutant dihydrofolate reductase (dDHFR) domain that is marked for degradation by the proteosome. This dDHFR can be rescued from degradation and allowed to accumulate in the cell using the small molecule trimethoprim. A cysteine mutation has been made near the active site in position L28, which allows for nucleophilic attack and covalent linking to nearby electrophiles. A probe molecule made up of a trimethoprim moiety, a terminal alkyne Click-chemistry handle, and an electrophile allows for rescue of the protein of interest, bioorthogonal derivatization of the probe using a fluorophore or biotin for visualization or isolation, and covalent linking of the protein of interest and the probe. This system has been validated using yellow fluorescent protein (YFP) as a model, showing time-dependent accumulation of YFP and the ability to isolate YFP from cell lysates. Further validation of this system is currently being conducted to study the time-resolved interactome of the proteins KRas and coronavirus nonstructural proteins. Mutations in KRas are associated with colorectal cancer and nonstructural proteins of coronaviruses SARS1, SARS2, and MHV are involved in organelle remodeling or immune suppression, making their interactomes relevant for investigation. By combining quantitative proteomics using TMT-tags with this time-resolved system, the sequential protein interactions can be studied.
Payton Stone

Chemical and Biomolecular Engineering, PI John Wilson
Cancer immunotherapy has displayed the potential to overcome the limited therapeutic efficacy of traditional cancer treatments such as surgery, radiation, and chemotherapy. Specifically, delivery of a retinoic acid-inducible gene I (RIG-I) agonist such as 5’ triphosphate double-stranded RNA (5’ppp-dsRNA) to the tumor site can elicit a downstream signaling cascade resulting in the enhanced production of pro-inflammatory cytokines and anti-viral interferons. This in turn allows for the reprogramming of the tumor microenvironment (TME) to a more tumoricidal phenotype capable of more effectively eradicating tumor cells. However, 5’ppp-dsRNA displays poor tumoral delivery in vivo due to nuclease degradation, rapid clearance from the body, and limited access to the cell cytosol. Therefore, our lab has designed pH-responsive polymeric nanoparticles capable of encapsulating 5’ppp-dsRNA for improved delivery to the tumor site. Our lab has previously reported the ability of polymer vesicles (polymersomes) fabricated from poly(ethylene glycol)-block-[2-diethylamino)ethyl methacrylate-co-butyl methacrylate] (PEG-bl-[DEAEMA-co-BMA]) copolymers to effectively improve cytosolic delivery of drug cargo. However, this strategy has not yet been explored for delivery of 5’ppp-dsRNA. The goal of this work is to optimize a facile and highly scalable flash nanoprecipitation (FNP) method for loading of RNA into endosomolytic polymersomes. To accomplish this, we will evaluate the effect of polymer block ratio and composition on polymer self-assembly and the loading of diverse hydrophilic drug cargo, including RNA.
Jenny Tran

Biochemistry, PI Breann Brown
Hemoglobin is a tetrameric protein essential to the oxygenation of the body by transporting oxygen from the lungs to other tissues. To perform its functions, it relies on heme, an iron-containing porphyrin that is a cofactor for each hemoglobin subunit, allowing for oxygen binding. The enzymatic pathway starts in mitochondria with the condensation of succinyl coenzyme A (sCoA) and glycine to produce 5’-aminolevulinic acid (ALA), an important heme intermediate. This reaction is catalyzed by 5’-aminolevulinic acid synthase (ALAS) and is the rate-limiting step in heme biosynthesis. Vertebrates have two isoforms of ALAS, the erythroid-specific ALAS2 and the ubiquitous ALAS1. Heme biosynthesis is strictly regulated, and under- or over-production can cause human disease. Upregulation of human ALAS1 is seen in acute hepatic porphyrias (AHPs), which encompasses four inherited diseases relating to heme biosynthesis. Since ALAS1 is a housekeeping enzyme, its function is important for basic cellular tasks, therefore mutations in ALAS1 may affect other heme-mediated processes, such as cytochrome P450 or myoglobin production. The ubiquitous quality of ALAS1 makes it a prime therapeutic target, particularly for AHPs since treatment for acute attacks is centered around reducing hepatic ALAS1 activity. Under the direction of Dr. Breann Brown, my thesis research is focused on determining a structure for ALAS1, identifying potential protein-protein interactions, and studying the biomedical implications. Furthering research on the ALAS1 structure will provide the necessary insight on its function and may introduce new opportunities for drug design.
Boden Vanderloop

Interdisciplinary Graduate Program, PI Borden Lacy
TBD
Sarah Zelle

Chemical and Physical Biology, PIs Hassane Mchaourab and Kevin Schey
Organelles in ocular lens fiber cells are degraded after differentiation to maintain transparency and focus light onto the retina without scattering. Therefore, it is important to preserve the clarity and correct refractive index of the lens for the entire lifetime of individuals so that vision is not affected. However, as a result of the aging process, proteins accumulate post-translational modifications and shift towards nonnative states and form hydrophobic aggregates, potentially forming cataracts. Previous work in the Mchaourab lab has studied the effect of oxidative stress on cataract formation using zebrafish lens models. Nrf2, a transcription factor that is important in the oxidative stress response, was mutated in the lens so that the fish could not respond to stress properly. These fish were crossed with knock-out crystallin fish and phenotyped. In the lens, crystallin is a highly soluble and stable protein that acts as a molecular chaperone and binds destabilized protein. My research will focus on quantifying the protein in these mutant zebrafish lenses and I will be involved in the development and optimization of the targeted mass spectrometry assay. Ultimately, the goal of this proteomics project is to investigate how the lens maintains proteostasis and reveal mechanistic clues as to how cataracts can form. A separate goal of my thesis project is to optimize an assay to measure heat shock protein activity in zebrafish lens lysate using a client protein. Once optimized, this assay can be used to quantify the binding activity of mutant zebrafish lens lines and study cataract formation.

2020 Trainees

Katherine Clowes

Biochemistry, PI Charles Sanders
Long QT syndrome (LQTS) is a disorder characterized by the prolongation of the latter portion of the electrocardiogram signal (the QT interval) that increases risk of arrythmias and cardiac arrest. The most common form of LQTS, type 1 long QT syndrome (LQT1), is caused by mutations in the voltage gated potassium channel protein KCNQ1. While over 250 LQT1-associated mutations in KCNQ1 have been identified, the impacts of these mutations on the channel’s structure and function are still largely unexplored. The Sanders lab’s goal is to investigate how these mutations lead to protein dysfunction. Previous studies of mutations in the KCNQ1 voltage sensing domain found that many were destabilized and exhibited reduced cell surface trafficking. This led to the hypothesis that mistrafficking due to protein destabilization is a common cause of KCNQ1 loss of function in LQT1. I plan to determine if this theme is common to mutations in other domains of KCNQ1 by characterizing a selection of mutations in the KCNQ1 pore domain for their impact on protein expression, trafficking, stability, and function. I also plan to test the hypothesis that protein destabilization is the most common cause of mistrafficking by conducting high throughput screening for molecules that bind KCNQ1 and restore trafficking by stabilizing the protein.
Henry Schares

Chemical & Physical Biology, PI Brian Bachmann
Modern drug discovery screening campaigns screen small molecule libraries that are usually limited to characterized chemical space and rarely include natural product (NP) scaffolds, even though each year NPs make up a large proportion of newly FDA approved drugs. In addition, these screens often focus on a single target or a simplified readout of bioactivity (eg. Cytotoxicity). This can lead to investigators overlooking compounds with novel therapeutic mechanisms and spending time and resources fruitlessly advancing leads with nonspecific activity. Our lab, in collaboration with Dr. Jonathan Irish and Dr. Brent Ferrell, previously developed the Multiplexed Activity Metabolomics (MAM) platform, a fluorescence cell barcoding and multiplexed immunoassay that allows for simultaneous assessment of multiple phenotypes such as cell type, apoptosis, cell cycle status, DNA Damage, and various cell signaling markers to paint a more nuanced picture of compound bioactivity at the single cell level. In collaboration with the NCI Natural Product Division (NCI-NPD), my project uses the MAM platform to screen a library consisting of pre-fractionated plant and marine invertebrate extracts against Acute Myeloid Leukemia (AML) cells. This library was curated by the NCI-NPD as an effort to make NP discovery compatible with high throughput screening. Because the contents of each library well are a mixture of NPs unknown in structure and number, my screening efforts are able to investigate uncharacterized chemical space, but each “hit” requires identification of the bioactive compound within the extract fraction. To do this I use the MAM platform in which the assay is preceded by fractionating and dispersing the compounds in the “hit” extract across assay wells while collecting chromatographic data to create a well-content specific chromatographic map via HPLC-MS. This aids in rapid dereplication of known compounds and rapid activity-guided isolation of unknown compounds that will go on to structure elucidation using 2D NMR techniques, target identification, assessment in primary samples, and mechanistic investigation in the context of AML therapy development.
Ruben Torres

Chemistry, PI Sandra Rosenthal
"Single Particle Tracking of Disease-linked Neuronal Signaling Membrane Proteins Using Fluorescent Nanocrystals"
The dopamine transporter (DAT) is a transmembrane protein that modulates dopamine (DA) signaling amplitude and duration in the brain by driving rapid DA reuptake into the presynaptic nerve terminal. Several lines of evidence indicate that missense mutations, in particular A559V, result in DAT dysfunction that is linked to neuropsychiatric disorders, such as bipolar disorder, attention deficit hyperactivity disorder, and autism spectrum disorder. Our goal is to link transporter surface mobility with function. What is still unknown is how protein partner interactions influence DAT A559V lateral diffusion and the degree to which DAT, and its mutant variants, diffuse and cluster in vivo. Semi-conductor nanocrystal quantum dots (QDs) offer advantageous photophysical properties such as remarkable photostability and narrow emission spectra for single particle tracking (SPT) using optical microscopy. QDs are biofunctionalized with antagonist drug derivatives for specific DAT labeling. My research project encompasses both diffusion dynamics characterization of DAT A559V with respect to agonism/antagonism of speculated protein partners, such as the DA receptor as well as probe optimization for SPT of endogenous DAT at presynaptic nerve termini in acute striatal mouse brain slices to evaluate different diffusional states. If disturbed DAT diffusion dynamics can be linked to the central cause of the previously stated diseases, then novel diffusion recovery therapeutics can be investigated, potentially supplementing classical agonist/antagonist drug targeting.
Jennifer Wurm

Quantitative & Chemical Biology, PI Lars Plate
The CDC estimates 2.8 million people are infected each year with antibiotic-resistant bacterial infection. Without changes in current therapeutic approaches, these diseases will eventually become incurable. During my research in The Vanderbilt Laboratory for Biosynthetic Studies (VLBS), directed by Dr. Brian Bachmann, I am investigating everninomicin—an antibiotic effective against gram-positive antibiotic-resistant bacteria, produced by the organism Micromonospora carbonacea. Everninomicin inhibits bacterial protein translation by interacting with the ribosomal protein (rProtein uL16) in a binding pocket on the 50S ribosome. I analyze this structure-activity relationship by investigating how structural changes made to the everninomicin scaffold would affect binding affinity and translation inhibition. Structural analogs can be generated through use of the organism’s biosynthetic mechanisms. Of particular interest is structural biology of multiple orthoester functional groups throughout the everninomicin structure that interact with the ribosome. Additional possible engineering sites involving these orthoesters can be identified through mechanistic and biochemical studies of orthoester synthase by identifying the substrates through knockout methods and studying the enzyme-substrate interactions through metabolomics.