Vanderbilt Chemical Biology Interface Training Program

2023 Trainees

We received twenty-four nominations and selected five students. The V-CBI program aims to maintain a 50/50 ratio of trainees between chemistry and biological departments. The V-CBI proudly introduces these new trainees to training grant this year.

The following are the trainees appointed to the V-CBI training grant in 2023:

Paul Kastner (Bachmann, PMI)

This research project seeks to investigate the potential of caves as sources of novel secondary metabolites from microorganisms associated with karst features and cave crickets. Secondary metabolites are organic compounds that have diverse biological activities and applications in medicine and biotechnology. Caves are geographically isolated and oligotrophic environments, factors that historically have proven conducive to the evolution of unique adaptations. Insect-associated microbes, a relatively unexplored group of organisms, represent a promising source of secondary metabolites with diverse functions in microbe-host and microbe-microbe interactions. We hypothesize that cave microorganisms, particularly those found on cave crickets and active speleothems, exhibit distinct secondary metabolic profiles and capabilities compared to their epigean counterparts. To test this hypothesis, we will characterize the microbial diversity and composition of karst features and/or cave crickets using metagenomic analysis, isolate and identify cultivable microorganisms from these hypogean samples and screen them for their ability to produce secondary metabolites, and purify and elucidate the structure and bioactivity of new secondary metabolites from selected cave isolates. This project will contribute to the understanding of cave microbiology and ecology, as well as the discovery of new natural products with potential therapeutic value.

Valentina Guidi (Kim, Chemistry)

The purpose of my research is to develop a proximity labeling approach to glycan bioconjugation by exploiting biological molecular recognition relationships between carbohydrates and small molecules. While protein-ligand and DNA-ligand relationships have been thoroughly studied and understood, carbohydrate-ligand interactions have often been overlooked. Nevertheless, like proteins or nucleic acids, carbohydrates consist of higher order structures which are dynamic in nature, even though these dynamic conformations are still being actively studied. Analogously to protein or DNA ligands, the small molecule pradimicin A has the lectin-like property of recognizing and binding to D-mannopyranosides in the presence of a Ca2+ ion. Traditionally, site-selective transformations on carbohydrates have been difficult to achieve. Regioselectivity is a primary concern because monosaccharides are composed of several chemically similar hydroxyl groups and nearly identical C-H bonds. Nevertheless, regioselectivity on sugar scaffolds may be modulated via noncovalent interactions and remote functionalization. Pradimicin A takes advantage of these phenomena by instigating a Ca2+-mediated hydrogen bond network with a D-mannopyranoside. We are synthesizing a catalyst based on pradimicin A and, via photoredox catalysis, using it as a driving force for regioselective carbohydrate modifications.

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 virus transmission frequently occurs between animal and human hosts raising the risk for spread of existing viral pathogens and emergence of new infectious diseases. The zoonosis is driven in part by rapid evolution of the viral genome, allowing for adaptation to the changing cellular environment in different host species. Synonymous mutations are mutations that do not affect the amino acid sequence and are commonly used for live-virus attenuations in vaccine development, suggesting that these mutations may not be neutral despite the belief that they do not influence viral fitness. However, several recent studies have indicated that synonymous mutations may affect translational speed, ribosomal quality control, and co-translational folding. To identify how protein quality control affects viral fitness, my research aims to use quantitative mass spectrometry to determine how the recoded foot-and mouth disease virus (FMDV) affects the co-translational proteostasis interaction network in a host-dependent manner. FMDV is a severe and highly contagious pathogen in hoofed animals posing a threat to agriculture. Porcine and kidney cells will be transfected with FLAG-tagged WT P1 and recoded variants, which contain codon-deoptimized sequences, and interactors will be captured using in situ cross linking. P1 cross-linked complexes will be purified using FLAG affinity purification. Proteostasis interaction partners will be identified for each P1 variant using mass spectrometry-based proteomics. Translation speeds will be measured by our collaborator and correlated to protein interactions. We hypothesize that increased interactions with translation machinery and co-translational chaperone components will occur because of ineffective codon usage and slowed translation speed. However, excessive chaperoning resulting from increased interactions could possibly engage degradation pathways prematurely, leading to negligible stoichiometries of FMDV structural proteins that could be the cause of virus attenuation. Results of this study have the potential uncover how viruses are able to evolve in a species-specific manner based on dependencies on the proteostasis machinery.

Sydney Thompson (Niswender, IGP)

The focus of the current project is to profile and analyze the newly designed novel compound, VU0634703 (VU703).  Compound VU703 is a negative allosteric modulator (NAM) that functions as a group III metabotropic glutamate (mGlu) receptor-specific compound. This project involves a combination of in vitropharmacological studies such as an assessment of signal bias and identification of the compound’s binding site on the receptor. The overarching goal is to analyze the activity of this compound for various metabotropic glutamate receptors via conducting in vitro assays such as calcium mobilization assays and thallium flux through GIRK channels. Concentration-response curves are created for analysis to measure the efficacy of NAM VU703 on various group III metabotropic glutamate receptors, and future studies will involve site-directed mutagenesis and potential radioligand binding experiments. The study of this compound is intriguing and important because group III mGlu receptors have previously been considered good therapeutic targets for various diseases such as Rett syndrome, Parkinson’s disease, and anxiety; therefore, increasing our knowledge of how this group III mGlu receptor specific NAM, VU703, functions is anticipated to open potential new therapeutic avenues for drug development.