My research surrounds the design and synthesis of natural compounds, as well as CNS ligands with potential pharmacologic activity through investigation of the SAR between compounds and the CNS.
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.
Angelo Andres - NIH Trainee
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.
Although important in biological processes, ions can become harmful to organisms when ingested in excess and cause serious environmental contamination issues. For example, a number of different ions, especially oxoanions, are particularly problematic in nuclear waste cleanup. Anions have traditionally posed difficult targets for sensing and separations due to the diffuseness of their charge and high solvation energies. The burgeoning field of supramolecular chemistry instead focuses on the chemistry of non-covalent, potentially powerful interactions, such as hydrogen bond and pi-pi interactions. These interactions have proved to be an important tool for anion recognition and binding. I study supramolecular host-guest chemistry targeting anions and using building blocks such as pyrazine and 4,4’-bipyridine. By targeted design and functionalization, these molecules can provide hosts for anions, cations, or both. Varying the functional groups within the molecules modifies the hydrophilicity and selectivity of the compounds for specific ions. Ultimately, I hope to build versatile hosts for both sensing and separation of anions.
Melissa Denler - NIH Trainee
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.
There is a critical need to understand and prevent the emergence of antibiotic resistance in pathogenic bacteria and to develop new antibiotics. Our group is interested in a type of cell-cell communication called quorum sensing that plays a vital role for some bacteria during interspecies competition. Many bacterial genes which encode antibiotic production and resistance have not yet been characterized, and their regulation is poorly understood. My research seeks to identify novel quorum sensing-controlled antibiotics and antibiotic resistance mechanisms and understand how quorum sensing control of these genes is important for bacterial competition.
Siderophores are macromolecules responsible for iron scavenging within a cell. In opportunistic pathogens like Pseudomonas areginosa, 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 hydroxyornithine 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.
Martin Leon - NIH Trainee
My research is focused on the development of novel chemical probes and therapeutics, called mimotopes, to induce antigen-specific immune tolerance in the mouse model of experimental autoimmune encephalomyelitis (EAE), which is a validated model for multiple sclerosis. A mimotope is a synthetic peptide that mimics a peptide antigen epitope, but that skews the immune response (i.e. towards immune tolerance). Multiple studies have indicated that co-administration of mimotopes with an immunosuppressant will induce antigen-specific immune tolerance. By conjugating drugs to our mimotope it may induce immune tolerance and reverse autoimmune diseases that are caused by autoreactive B cell and auto-antibodies. The proposed mimotope-drug conjugate will be used in the EAE model, in an attempt to yield an antigen specific regulatory immune response.
Cindy Yang Ly
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.
Jeff McFarlane - NIH Trainee
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 pseudopaline 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.
Targeted delivery of metal-based conjugates enables therapeutic and diagnostic applications for the treatment of cancer. Dr. Laurence’s lab works with a metal binding tripeptide known as the claMP Tag, which can be incorporated into a targeting protein to create a bioconjugate for the delivery of transition metals. To effectively deliver a bioconjugate, stability must be achieved in the circulating environment, yet degradation must occur inside of diseased cells for metal release. Proteases are a main concern, causing unwanted degradation in the circulating plasma. Characterization of the proteolytic susceptibility of the claMP Tag will determine the use of the claMP Tag as a targeted delivery system.
The 90 kDa heat shock proteins (Hsp90) are chaperones responsible for the maturation of approximately 200 protein substrates (clients), many of which are involved in cell signaling pathways essential for maturation and survival. This unique profile makes Hsp90 an attractive inhibition target and affords the opportunity to simultaneously inhibit multiple oncogenic pathways. 17 molecules which bind to the Hsp90 N-terminal ATP-binding site have undergone clinical evaluation, however, these molecules exhibit pan-inhibitory activity for all four Hsp90 isoforms. Isoform selectivity is required to reduce risk of toxicity and the number of client proteins affected. The endoplasmic reticulum localized isoform (Grp94) affects maturation of proteins responsible for cancer motility, and is a target for decreasing cancer metastasis without producing toxicity as Grp94 is nonessential for cell survival. The mitochondrial isoform of Hsp90 (Trap1) folds client protein B-Raf. B-Raf is the instigator of aggressive melanomas, a target which develops resistance to current FDA improved inhibitors, which could be overcome with selective isoform inhibition of Trap1. My research focuses on developing isoform selective inhibitors for Grp94 and Trap1.
Yssa Rodriguez - NIH Trainee
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.
Kelci Schilly - NIH Trainee
Katelyn Soules - NIH Trainee
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.
Sam Williamson - NIH Trainee
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.