Protein-RNA interactions, as drug targets, are interesting and at the same time challenging. The interface of these interaction sites are different from other conventional drug target both physico-chemically and geometrically. That's why my research is focused on using non-traditional approach for the search of potential inhibitors of these targets. To be specific, my research is focused on developing a computational algorithmic pipeline that combines generation of in-silico library of chemical compounds -that are biased towards binding RNA-binding proteins- with ligand-based virtual screening and experimental validation in an attempt to find potent inhibitors of Protein-RNA interaction sites.
Signal transduction pathways of human cells are vital for intercellular signaling and processes such as cellular death (apoptosis). These pathways are initiated by cell surface receptor peptides with unique transmembrane sequences that allow for their insertion into the membrane of the cell. By creating artificial cell surface receptors, we seek to control specific signal transduction pathways involved in cellular dysfunction and apoptosis. My research focuses on the synthesis and evaluation of synthetic transmembrane (TM) peptides and their spontaneous insertion into the cellular membrane. Development of synthetic TM peptides will enable the study of artificial receptors and their potential role in modulating signal transduction pathways.
My research focuses on the development of novel biological probes. We are particularly interested in utilizing sultam moieties, as they are not found in nature and posses unique chemical properties. We strive to develop Michael accepting sultam scaffolds for the covalent modification of cysteine-activated enzymes. We believe our probes will be of great use in studying cell-signaling processes critical for human health, such as ubiquitination and phosphorylation.
In nature, manganese-dependent enzymes in bacteria and higher organisms have the ability to catalyze substrate oxidation reactions using molecular oxygen as an oxidant. The oxidation products of these reactions often serve as carbon sources, which are important for growth in nature. Two examples of such systems include manganese-dependent dioxygenase (MndD) and quercetin dioxygenase, which break down catechol and flavonoid species respectively. Recent evidence has established a peroxomangansese intermediate for MndD that forms when dioxygen reacts with the active-site manganese-catechol complex. My research uses synthetic models to explore these types of transformations as a means of advancing our understanding of the enzyme mechanisms. The complexes I study are supported by polypyrazolbylborate ligands, which serve as molecular vises, keeping the metal ion in a tridentate grip. This mimics what is seen in the active site of natural enzymes, leaving the rest of the coordination sites open for chemical operations. To study these systems, I use a combined approach of spectroscopic characterization with methods such as electronic absorption, electron paramagnetic resonance and reactivity studies with dioxygen.
My PhD research involves design, synthesis, and reactivity profiling studies for the investigation of diverse macrocycles bearing electrophilic warheads. Our interest in the synthesis of these macrocycles was originated from the naturally occurring bioactive polyketide macrolides possessing 1,3 anti-diol subunits. Our current efforts towards the synthesis of these macrocycles involves pot-economical and library amenable approaches which utilize (i) differentially-protected polyol subunits to selectively generate various ring sizes employing selective deprotection and coupling reactions; (ii) chemoselective derivatization of the stereogenic carbinol centers that enable functional group and stereochemical attenuation; and (iii) late-stage variable warhead installation offering a wide range of attenuated C-, S-, and P-based electrophilic warheads. Reactivity profiling studies of all systems are being carried out in order to elucidate structure-reactivity patterns to further our understanding of complex biological pathways involved in human health and disease.
I work in the Michael Johnson lab in the Chemistry Department. Our main focus is looking at how diseased states of the brain affect the chemicals in the brain. We use fast scan cyclic voltammetry to probe levels of dopamine, serotonin, and hydrogen peroxide in different models of disease in rats, mice, and zebrafish. My project focuses on in vivo and ex vivo detection of dopamine and hydrogen peroxide and correlating that with behavioral measurements in chemotherapy treated rats. Looking at both the neurochemical and behavioral sides allows us to better understand chemotherapy induced cognitive impairment (chemobrain). We also investigate some rescue methods such as novel synthetic compounds and commonly used drugs for other conditions. We are expanding into looking that the transcritome (using RNA seq) of chemotherapy treated mice. All of these different experiments allow us to understand a multifaceteddisease that does not look the same in all patients.
Bacterial antibiotic resistance is recognized by the World Health Organization as a global health threat. Despite this, very few antibiotics have been developed over the past two decades, resulting in an urgency to discover new treatment options for bacterial disease. This health threat has spurred efforts to identify new classes of antibiotics that operate through alternative and novel modes of action. Filamenting Temperature-Sensitive Mutant Z (FtsZ) is a prokaryotic tubulin homolog that is necessary for bacterial cell division and is conserved among all bacteria, making it a potential antibacterial target. The aim of my doctoral research is to identify a new class of antibiotics that prevent bacterial cell division by inhibiting FtsZ polymerization.
I am a graduate student in the Department of Chemistry at KU, and am a member of the Blakemore laboratory. In my research, I am focusing on the preparation and study of metal complexes that undergo light-driven carbon monoxide (CO) release. CO is a toxic gas when released in an uncontrolled fashion, but when released in a controlled manner CO has been implicated in cellular signaling pathways, has anti-inflammatory properties, and has anti-apoptotic effects. I am working on mechanistic studies of light-driven CO release in order to provide design rules for useful therapeutics capable of releasing CO in vivo. [Mn(CO)3] complexes are my current target compounds, as we have found that they can be readily modified to release CO in the right place and at the right time. In my work, I use a variety of techniques available at KU, including ultrafast laser spectroscopy in collaboration with Prof. Chris Elles. Additionally, our team recently carried out studies of my compounds with time-resolved X-ray absorption spectroscopy at Argonne National Laboratory, providing new insight into the transient intermediates involved in CO release.
AraC transcriptional activators are found in 70% of sequenced bacterial genomes and regulate genes involved in metabolism, stress response, and virulence. Our lab focuses on RhaR and RhaS, two AraC family members found in E.coli. Structural analysis obtained from the crystal structure of the RhaR N-terminal domain and a full-length RhaR computational model suggests a mechanism of allosteric signaling between the N-terminal domain and DNA-binding domain in RhaR. In several other AraC family transcriptional activators, it is hypothesized that interdomain contacts are important for the protein’s transition to and from its activating to non-activating state, controlling the protein’s allosteric regulation. My dissertation research in particular focuses on testing the importance of interdomain contacts in RhaR and ToxT, another AraC family member found in V. cholerae.
The microtubule-associated protein tau promotes the stabilization of the axonal cytoskeleton in neurons; however, in disease tau has been found to dissociate from microtubules and form pathological aggregates. These aggregates are a common hallmark of a group of neurodegenerative diseases known as tauopathies, including Alzheimer’s disease. My research focuses on identifying natural products isolated from the fungi Aspergillus nidulans that are able to inhibit in vitro tau aggregation as well as further modify and characterize derivatives with the hope of increasing potency.
In the Berkland laboratory, my studies focus on synthesizing novel antigen-toxin conjugates to selectively target insulin-specific B cells (IBCs) for the treatment of Type I Diabetes (T1D). B cell depletion using Rituximab has emerged as a viable treatment for T1D. Although effective in humans, the risks associated with global B cell deletion limit clinical use in juvenile T1D. While autoreactive B lymphocytes play a critical role as producers of pathogenic autoantibodies in other autoimmune disorders, in T1D these autoreactive cells appear to function differently. It has been shown that autoantibodies are the best predictors of development of T1D, but interestingly, secreted antibody is dispensable, indicating that B cells may instead contribute to disease by antigen presentation and/or cytokine production. Deactivating or deleting IBCs may offer a safe intervention for these patients. Our strategy is to identify molecular constructs that selectively bind to IBCs and deliver a toxic payload, thereby killing the cells.
Siderophores are macromolecules responsible for iron scavenging within a cell. In opportunistic pathogens like Pseudomonas aeruginosa, pyoverdin is just one of the siderophores made. The enzymatic biosynthesis of these molecules is characterized by “assembly line” production through nonribosomal peptide synthetases (NRPS). One portion of this molecule is an ornithine derivative that has been modified by PvdA and PvdF enzymes. So far it is believed that PvdF catalyzes the conversion of hydroxyomithine to formyl hydroxy ornithine. Besides this hypothesis, enzymatic catalysis and mechanism of this reaction remains elusive. My research encompasses functional determination of PvdF through the discovery of a functional assay as well as establishing a potential structure-function relationship.
Dynorphin A (Dyn A) is an opioid peptide that is found in nervous system tissue. The peptide is metabolized to smaller peptide fragments that have lesser-known and different activities. It is necessary to separate and detect these peptides in biological samples in order to characterize how the peptides behave in vivo. Dyn A binds the kappa opioid receptor and has been shown to be involved in both peripheral pain and drug addiction. Therefore, better methods for determining Dyn A and its metabolites in vivo will help in our understanding of the neurochemistry of drug addiction and withdrawal, which are major societal problems. My research currently focuses on developing a capillary electrophoresis-electrospray ionization mass spectrometry method for separating and detecting dynorphin peptides. I will then develop a microchip electrophoresis-miniaturized mass spectrometry system combined with on-line microdialysis sampling to monitor dynorphin transport and metabolism in rat models. This will provide a better understanding of the role of dynorphin peptides and dynorphin analogs in drug addiction and pain.
Currently in Dr. Davido’s lab my research focuses on understanding virus-host interactions in the herpes simplex virus 1 (HSV-1) life cycle. HSV-1 is a common human pathogen infecting about 80% of the world’s population. The virus establishes a life-long latency in the neuronal cells and upon activation can cause a variety of diseases such as cold sores, ocular infections, and encephalitis. One major area of interest is to delineate mechanisms by which a major viral regulatory factor destabilizes host cell proteins while contributing to viral replication and pathogenesis. Another part of my thesis will focus on identifying novel compounds that impair HSV-1 growth. Aside from research, an important goal of mine is to continuously encourage and expand the sciences within the community. I actively participate in outreach programs that entail teaching young students about different science topics to advocating minorities and woman to pursue science in higher education.
Increasing antibiotic resistance among major pathogens underscores the need to identify new targets for antimicrobial therapy. Pseudomonas aeruginosa and Staphylococcus aureus are opportunistic pathogens causing severe infections with high mortality rates. Critical to their pathogenesis is the need to acquire essential metals such as iron and nickel. In order to meet this requirement, bacteria biosynthesize small molecules known as metallophores that scavenge metals required for growth. Recently, a novel metallophore biosynthetic pathway conserved between P. aeruginosa and S. aureus, has been identified. The enzymes in this pathway produce small molecule opine metallophores named pseudopine and staphylopine. The production of these macromolecules contributes to virulence in mouse model infections for both species. We are interested in the structural and kinetic analysis of the enzymes responsible for the production of these metallophores. This work will provide the foundational knowledge to guide future drug design efforts directed at these novel antimicrobial targets.
Research in my lab focuses on diabetic peripheral neuropathy. Previous results have shown that heat shock protein (HSP) 90 inhibitors improve neuronal function in diabetic mice. Diabetically-stressed cells seem to change the composition of the Hsp90 complex and have no effect on non-diabetic control mice. KU-596, an Hsp90 inhibitor, improves mitochondrial bioenergetics and decreases oxidative stress in diabetic sensory neurons. We hypothesize that diabetes changes the Hsp90 complex, which helps KU-596 discern affected complexes from house-keeping proteins. My project uses biotinylated KU-596 as an affinity probe to pull down the Hsp90 complex and identifying co-chaperones in diabetic and non-diabetic samples. Hsp90 and its co-chaperons are promising targets for the development of both neuroprotective and anti-cancer agents.
Nonribosomal peptide synthetases (NRPSs) are one approach used by microbes to generate bioactive peptides. These bioactive peptides are not only used as secondary metabolites (toxins, pigments, siderophores – iron scavenging molecules), but have found their way into the clinic as antibiotics, anticancer drugs, and immunosuppressants. To elicit their unique bioactivity, these peptides must be tailored. Natural product chemists, metabolic engineers, and researchers in biochemistry and biotechnology work to exploit the biosynthesis of these secondary metabolites in order to generate new compounds for clinical use. My research focuses on understanding the structure-function relationship of epimerases and methyltransferases that are incorporated into these assembly lines. Structural biology and mechanistic enzymology can provide novel insight and assist natural product investigations, protein engineering projects, antimicrobial development, and other therapeutic design.
My research focus encompasses the interactions between proteins and carbohydrates in pathogenesis. Carbohydrate-protein interactions are implemented in the initiation and propagation of many cancers and infectious diseases. For example, numerous viruses utilize the interaction between carbohydrates and proteins to bind to the outside of host cells, thus initiating infection. My work aims to develop a new way to treat influenza with the use of novel compounds that concomitantly bind to the hemagglutinin protein on the Influenza envelope and recruit the immune system (i.e., antibodies) to neutralize the virus. From our work, we aim to provide a new strategy to treat influenza in a manner that would target a wide breath of Influenza strains.
Alzheimer’s disease (AD) is a devastating condition about which much is still not understood. It is believed that during AD, β-amyloid plaques activate microglia, the immune cells of the brain, to produce cytotoxic molecules such as reactive nitrogen and oxygen species (RNOS), thereby inducing neurodegeneration. In addition, analysis of AD brain tissue has shown increased protein nitration that is indicative of peroxynitrite-related activity. An effective method for detecting these RNOS species will be beneficial to better understanding the balance between oxidants and antioxidants that affects neurodegenerative disease states. The goal of my project in the Lunte group is to develop a microchip electrophoresis with electrochemical detection method to detect nitric oxide and peroxynitrite directly in microglial cells that have been stimulated by various inflammatory agents. This method will ultimately allow for the individual analysis of microglia of different phenotypes in order to probe RNOS production from each type of cell. This will help us to better understand the origin and role of different substances in the development of the inflammatory response in the brain that can lead to protein nitration and cell death.
Chlamydia trachomatis leading cause of infectious blindness worldwide, as well as the most common sexually transmitted infection in the United States. Despite its impact on public health, and because of its obligate intracellular nature, there are still many gaps in our understanding of the basic biology of the organism. One of my research focuses is on the characterization of the role and mechanism of activation of specific transcription and sigma factors in Chlamydia. Additionally, I am testing novel synthetic compounds for use as Chlamydia-specific antibiotics targeting an enzyme in the futalosine pathway for menaquinone synthesis.
Advancing small molecule discovery for the identification of covalent modulators that can further our understanding of complex biochemical is the aim of this project. In particular, we aim to design, synthesize, and develop electrophilic scaffolds as potential small molecule modulators of protein function. Naturally occurring disulfides are a particular type of electrophilic chemotype that exists within a number of bioactive natural products and peptides. In proteins, these privileged architectures have innate properties that improve both chemical and biological stability, contribute to maintaining native structure even under extreme environments, and play a role in the regulation of protein activity. These properties have greatly enhanced their potential for probes design that can ultimately lead to drug candidates
Research in our lab focuses mostly on the k-Opioid receptor (KOR). Specifically, our efforts involve synthesizing analogs of the natural product salvinorin A . Our approach to this is currently two-fold: 1.) utilizing salvinorin A extracted from the leaves of Salvia divinorin as a scaffold for developing semi-synthetic analogs in order to understand the structure-activity relationship (SAR) between salvinorin analogs and the KOR and 2.) development of a synthetic procedure that allows us to synthesize analogs that would otherwise be inaccessible via semi-synthesis from salvinorin A with the goal of understanding how molecular simplification of the complex structure of Salvinorin A can retain activity at KOR or potentially at other opioid receptors. The ultimate goal of our research is to develop molecules with superior pharmacological and physiological properties that show promise as novel therapeutics for the treatment of drug abuse as well as development of novel analgesics.
Cell-surface receptors (transmembrane receptors), are receptors that are anchored in the cell membranes and composed of three domains: extracellular domain, transmembrane domain and intracellular domain. By binding to ligands at the extracellular domain, it transduces multiple signaling cascades inside the cells. Mutations that inactivate cell surface receptors cause a wide range of cellular dysfunction. When the receptor is damaged by mutation, few non-genetic options exist to reactivate signaling pathways. Our team is working on synthesis of peptides that can mimic the biological functions of normal cell membrane receptors. In this project, we are hoping to obtain the first synthetic cell surface receptor that works effectively in activating signal transduction pathway.