Cell-free assay technologies for the identification of active compounds

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This project resulted in the development high throughput screens for the targets Cbl-b and tyrosyl-DNA phosphodiesterase-2 in collaboration with Drs. Stanley Lipkowitz and Yves Pommier (CCR). The PCMBS, in collaboration with the laboratory of Dr. Lipkowitz (WMB) is developing a high throughput screen (HTS) of both synthetic compounds and natural products extracts for the discovery and characterization of Cbl-b specific biochemical inhibitors. The WMB has been at the forefront of characterizing and understanding the biochemistry of Cbl-b ubiquitin ligase activity and has established the framework for a cell-free screening assay that the PCMBS has been able to adapt for use in an HTS. As a dimeric RING finger E3 ubiquitin ligase, Cbl-b coordinates the interaction between an ubiquitin-containing E2 enzyme and the final target protein to be ubquitinated (the substrate). While Cbl-b itself does not transfer ubiquitin, it is the single component of the ubiquitination cascade that confers substrate specificity. Therefore, Cbl-b is an attractive target for pharmacologic intervention The structure of Cbl-b contains seven different motifs, including an ubiquitin-associated (UBA) domain which has been shown to have a high affinity and specificity for polyubiquitin chains. The ubiqiuitin ligase reaction is performed in assay plates pre-coated with the Cbl-b UBA, to allow for binding and retention of the polyubiquitinated (and hence biotinylated) reaction products.We anticipate that the use of these two agents will reduce the detection of false positive results from aggregating or non-specific protein binding compounds. In collaboration with Dr. Yves Pommier (DTB) a chromogenic assay for discovery of natural products based inhibitors of Tdp2 activity was redesigned from an assay developed by Ogilvie et al.). The assay was designed to measure the inhibition of Tdp2 activity by measuring the decrease in the generation of p-nitrophenol from a substrate, 4-NPPP. The absorbance based assay would employ clear, untreated 384-well plates for detection at 405nm, the absorption maxima of p-nitrophenol. The decrease in absorbance signal would correlate directly with the potency of putative inhibitors. Secondary assays with a larger tyrosinylated DNA construct are taking place in the DTB. DTB provided the TTRAP/Tdp2 enzyme construct (produced by Protein Expression Laboratory, NCI at FNL, Frederick, MD) and all initial enzyme quality assurance was evaluated at the MTL. The Tdp2 activity against the 4-NPPP substrate was mapped to similar values of Vmax, Km, and Kcat as that of the the Manchester group. Our assay concentration of 4-NPPP was set below the observed Km value (Km= 115 mM) primarily due to detector saturation at concentrations 100mM or above and to lengthen the time of the assay conditions beyond 20 minutes. Currently, we have screened all available MTL pure compound and synthetic libraries totaling 69,793 compounds with an initial hit rate of 0.22% and a pre fractionated natural product library which provided a hit rate of 0.82% (hit requirement of 50% inhibition activity). HTS is completed and the evaluation of CBL-b and Tdp2 inhibitory compounds is ongoing. Additional collaborations on DNAJ-PKA and Rpn2/Rpn13 are also underway with Drs. Ping Zhang and Kylie Walters. These assays use a variety of techniques including fluorescence polarization, differential scanning fluorometry and kinetic assays. In addition, we have recently begun a project using a thermal melt assay to identify potential inhibitors of the metabolic enzyme Irg1 with Dr. Daniel McVicar and the cancer target glypican-3 with Dr. Freddy Escorcia. We have also initiated COVID-19 related projects with Eugene Valkov and Yves Pommier.