Browsing by Subject "Drug discovery"

Now showing 1 - 3 of 3
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    Computational methods to explore chemical and genetic interaction networks for novel human therapies
    (2013-11) Deshpande, Raamesh
    Model organisms are often used as a test-bed for the development of new genomic technologies and computational approaches. For example, the yeast Saccharomyces cerevisiae was the first eukaryote to have its entire genome sequenced, paving the way for the sequencing of the human genome. Beyond genome sequencing, yeast and other model organisms have been extensively used for reverse genetics technology development. Reverse genetics is a general approach for studying biology where the genome is perturbed in precise ways (e.g. targeted gene deletion), to gain functional information about the perturbed genes from the resulting phenotypic changes. With developments of new genomic technologies, reverse genetics at a genome-wide scale has become a reality. This dissertation focuses on the development of several computational methods for scaling up the reverse genetics experiments in model organisms as well as for exploring the generated genomics data with the ultimate goal of understanding and translating these data for use in applications for human therapeutics. One such method I developed is COMPRESS-GI which compresses the deletion collection by 95% such that the compressed set still remains highly informative for drug discovery analyses. This compression is critical for conducting chemical genomics experiments on natural products available in extremely limited quantities. I also conducted a systematic comparison of different profile similarity measures for genetic interaction networks which was crucial in discovering dot product as one of the most robust similarity measure. Enabled by these methods, we have conducted chemical genomics experiments for more than 10,000 natural products in yeast and now aim to discover therapeutically interesting compounds for human diseases. For this problem and a more general problem of translating and comparing genomic data across species, we developed a computational method neXus. Furthermore, we have started working on applications that could benefit from discovery of large number of drug-targets. One application is discovery of cancer targets using synthetic lethal interactions; however, very few synthetic lethal interactions are known in human so we developed a novel approach of discovering cancer relevant synthetic lethal interactions by translating the wealth of genetic interactions in model organisms to human.
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    Discovery of Small Molecule Inhibitors of Hyaluronan Binding at Cell Receptor CD44
    (2015-06) Liu, Li-Kai
    Selective inhibitors of hyaluronan (HA) binding to the cell surface receptor CD44 will have value as probes of CD44-mediated signaling, and have potential as therapeutic agents in chronic inflammation, cardiovascular disease and cancer. Using biophysical binding assays, fragment screening, and crystallographic characterization of complexes with the CD44 HA binding domain, we have discovered an inducible pocket adjacent to the HA binding groove into which small molecules may bind. Fragment combination and iterations of structure-driven design has led to identification of a series of 1,2,3,4-tetrahydroisoquinolines as the first non-glycosidic inhibitors of the CD44-HA interaction. The affinity of these molecules for the CD44 HA binding domain parallels their ability to interfere with CD44 binding to polymeric HA in vitro. X-ray crystallographic complexes with lead compounds are described and compared to a new complex with a short HA tetrasaccharide, in order to establish the tetrahydroisoquinoline pharmacophore as an attractive starting point for lead optimization.
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    Fluorescence tools to identify Novel SERCA activators
    (2013-08) Gruber, Simon Joseph
    One of the universal hallmarks of heart failure is defective calcium cycling. The calcium concentration in a muscle cell must be high to cause contraction and low to allow relaxation, and most of the calcium removal is accomplished by the intracellular membrane pump known as the sarco-endoplasmic reticulum calcium ATPase (SERCA). When SERCA activity is too low in cardiac muscle, the heart does not fully relax and fill with blood, so the next contraction cannot pump enough blood through the body. The ubiquity of calcium cycling dysfunction in heart failure and other muscle diseases has made SERCA a major target for novel heart failure therapeutics since the late 1990s. All of the work presented in this thesis focuses on methods to activate SERCA as a treatment for heart failure. SERCA is regulated by phospholamban (PLB) in heart muscle, preventing the enzyme from being fully active all the time but allowing maximal activity when the body demands. Some methods of activating SERCA seek to remove the inhibitory effects of PLB, either partially or fully. In this thesis, PLB mutants are investigated as potential gene therapy vectors. PLB mutants that are less inhibitory but still bind to SERCA could allow the enzyme to be more active if they displace endogenous PLB. A FRET assay using genetically engineered fluorescent fusions of SERCA and PLB expressed stably in a human cell line was used to measure the ability of different mutants to compete for SERCA binding. Fluorescently labeled SERCA and PLB were also reconstituted in an in vitro lipid bilayer system to screen for small-molecule compounds that activate SERCA. Several compounds were found to decrease SERCA-PLB FRET and many of these turned out to be SERCA activators that improved myocyte contractility. However, none of the compounds were specific to the SERCA-PLB interaction. Finally, an intramolecular FRET assay was developed to detect changes in the relative distance between cytoplasmic domains within SERCA in living cells. This assay was used to screen a small-scale compound library to show that FRET between SERCA domains is sensitive to both activators and inhibitors of SERCA function. All of these FRET assays are being followed up in the Thomas lab to identify potential SERCA activators for heart failure and other diseases.