This project involves the application of the """"""""one-bead one-compound"""""""" encoded small molecule combinational library method and chemical microarray technique to study functional proteomics. Five enormous libraries of small molecule ligands (a total of over 1 million compounds) will be generated and screened against whole cell extracts derived from a B lymphoma cell line (Ramos). Billions of possible molecular interactions will be examined concurrently. Beads containing compounds that bind to cellular proteins or protein complexes will be isolated and the compound chemical structure determined by our novel decoding method. Selected small molecule ligands will be resynthesized on Sepharose beads and used as affinity matrix to capture the binding proteins or protein-complexes. The identity of the bound proteins will then be determined by protein separation and mass spectroscopy. Based on the chemical structure of these ligands, a small molecule microarray (approximately 1000 compounds) will be developed to probe the functional state of the whole cell extract. Our hypothesis is that with the above experimental scheme, we can systematically select a finite number of small molecule ligands and use them as capturing agents to probe the functional state of a B lymphoma cell. We further hypothesize that some of the ligands that bind to unique protein targets in lymphoma cell can be used as lead compounds for the development of anti-lymphoma agents. Once validated in a large number of lymphoid malignant cell lines, peripheral blood lymphocytes, and a limited number of primary malignant lymphoid tissues, this microarray technology can be applied to biopsy specimens obtained from a large number of patients with lymphoid malignancies. This technique, if successful, can readily be applied to other cancer types as well.
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