Vanderbilt Chemical Biology Interface Training Program

2017 Trainees

Alex Allweil (Chemistry, PI Sulikowski)

Synthesis and Biological study of a Novel Eicosonoid
Hemiketal E2(HKE2) is an unusual eicosanoid produced from arachadonic acid (AA), identified by the Schneider group (Vanderbilt) as a product of a cross-over of 5-LOX (AA to 5S-HETE) and COX-2 (5S-HETE to HKE-2 and HKD-2) enzymatic reactions. Like many metabolites from the arachadonic acid cascade it is hypothesized that HKE2may play an important role in various inflammatory process. Many diseases result in a chronic inflamed state, such as cancer, diabetes, and some neurodegenerative diseases. With this in mind it is important to fully understand physiological consequences of HKEproduction in relation to the inflammation process. However, nly nanogram quantities of HKE-2 have been produced using an in vitro enzymatic procedure. To resolve the HKE2supply issue in order to enable its biological study the first phase of my research project is to develop a rigorous and reproducible chemical synthesis route to HKE2. This will enable evaluation its biological evaluation in collaboration with the Schneider group.

Schulyer Chambers (Chemistry, PI Townsend)

Ellagic Acid Congeners as Antibiotic Adjuvants against
Staphylococcus Aureus
Antibiotic resistance within bacterial species such as Staphylococcus Aureuspresents an ever-growing hurdle for total synthesis and drug discovery.  This evolution of resistance is fueled by the cells ability to form a protective biofilm, which prevents antibiotics from successfully reaching cells. Isolation studies have demonstrated that glycosylated derivatives of ellagitannin natural products have notable impacts on biofilm disruption and formation within S. Aureus, but currently the precise structures of these compounds remains unknown.  By utilizing total synthesis, we hope to create a variety of glycosylated derivatives of ellagic acid, which can then be tested within S. Aureussystems for their specific impacts on biofilm formation and disruption.  Subsequently these compounds could have high potential for use as antibiotic adjuvants to help restore current antibiotic efficacy.

Jennifer Gribble (Pathology Microbiology Immunology, PI Denison)

Structure, Diversity, and Functions of Coronavirus Defective RNAs
Coronaviruses (CoVs) are a family of positive-sense RNA viruses that cause human colds and severe and potentially pandemic diseases such as SARS, and a new emerging zoonotic disease in humans – MERS. However no antivirals or vaccines are available for any human or zoonotic CoV. We are focusing on the biochemical and genetic determinants of inhibitors of CoV replication. Specifically, we are pursuing the development of defective viral genomes (DRNAs) as potential therapeutics as well as investigating whether DRNAs can function as stable, and adaptive inhibitors of coronavirus replication.  Though DRNAs have been described for numerous viruses, including CoVs, relatively little is understood about the roles of these incomplete, genetically rearranged, and frequently abundant mini-genomes both in the viral biochemical machinery and the balance between pro- and anti-viral states in the host. DRNAs have been shown to interfere with parental virus replication, possibly through direct biochemical competition or through activation of host antiviral defenses. However, their ultimate effects on viral survival at the environmental level are more complex than mere negative interference as the capacity for generation for DRNAs has been retained across time and viral taxa. Therefore, this work will encompass the discovery, chemical biology, diversity, and functional characterization of CoV DRNAs and testing for their capacity to function as pharmacologic inhibitors of CoVs.

Nicole Kendrick (Biochemistry, PI Olivares)

Study and Characterization of Torsin: Potential Therapeutic Target
Torsin belongs to the family of AAA+ (ATPases Associated with various cellular Activities) macromolecular remodeling enzymes proteins that utilize ATP to perform mechanical work, such as protein unfolding and degradation.  The physiological function of torsin is unclear, but it has been suggested through previous studies that it remodels nuclear envelope proteins, such as LINC (Linker of Nucleoskeleton and Cytoskeleton) components. The Olivares lab is interested in understanding how the LINC complex senses and uses mechanical forces to affect nuclear membrane position, alter chromosome dynamics, and control gene expression.  My research will be focused on how torsin remodels the LINC complex using biochemical methods, single molecule optical trapping, and through the development of small molecule agonists against torsin enzymatic and cellular function.  This will help to develop therapeutics for several diseases that have been linked to torsin mutations, such as early-onset torsin dystonia, a hereditary movement disorder that is characterized by repetitive and involuntary muscle contractions.

Benjamin Reisman (MSTP, PI Bachmann)

Identification and characterization of cell-type selective cytotoxic microbial metabolites as potential therapies for Acute Myeloid Leukemia
Microbial secondary metabolites have proved a rich source of bioactive natural products over the last century and form the basis of our modern pharmacopeia of chemotherapeutics and chemical probes. All natural products are intrinsically bioactive at some level – having evolved to modulate interactions between the producing organism and its ecosystem, however identifying the few metabolites which able to modulate human cellular physiology to achieve a therapeutic goal remains a key challenge to translating active extracts to new medicines. Previous work in our laboratory, in collaboration with Jonathan Irish (Cancer Biology) and Brent Ferrell (Hematology/Oncology), led to the development of Multiplexed Activity Metabolomics (MAM), an approach for identifying bioactive metabolites using HPLC fractionation and multiplexed, multiparametric flow cytometry on metabolite treated cells. Compared to traditional approaches, MAM allows for a broad definition of bioactivity, permitting simultaneously assessment of apoptosis, DNA damage, cell cycle, and intracellular signaling markers at the single cell level. Additionally, since bioactivity is determined on a per-well basis, these “bioactivity chromatograms” can be correlated to the mass chromatograms obtained during HPLC purification to putatively assign bioactivity to metabolites without the need for chemical purification.  The goals of my project are to extend the MAM approach to: 1) identify cell-type selective cytotoxic secondary metabolites which spare healthy immune cells and augment antitumor immunity, and 2) dissect the biological mechanism by which anthracyclines and other microbial metabolites modulate antitumor immunity in acute myeloid leukemia (AML) using fluorescence and mass cytometry on metabolite treated primary human tumor samples.

Megan van der Horst (Chemistry, PI Wright)

Next Generation Tuberculosis Diagnostics
Tuberculosis (TB) remains a major global health problem; one particular challenge is diagnosis in low resource settings, where TB is widespread. The goal of my research is to develop a simple, low-cost rapid diagnostic test (RDT) for M. tuberculosislipoarabinomannan (LAM), a biomarker for TB, utilizing microvirin. Microvirin (MVN) is a small lectin that shows high specificity for Manα(1-2)Manαmoieties which are present in the mannose caps of M. tuberculosisLAM. Another major problem is the rapid identification of drug resistant TB strains. My research involves developing a simple staining methodology to visualize the presence of the major drug mutations. DNA-functionalized dendrimers will be used to probe for the mutations followed by treating with tetramethyl orthosilicate to drive a silicon dioxide condensation reaction to form a silica shell. These aggregated silicon dioxide nanoparticles will be readily visible by bright field microscopy.