Evolving Libraries of Bivalent Compounds

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DESCRIPTION (provided by applicant): Six libraries of at least 15 compounds each will be prepared such that every compound in the library is present in 1 -2 g amounts. The compounds in the library are all designed to be ¿-turn mimics, and their side chain pharmacophores will be designed to correspond to the natural amino acids that are found most frequently at hot spots for protein-protein interactions. We have developed a method that allows monovalent compounds to be joined to give bivalent molecules. This method does not require coupling agents and is applicable to compounds with unprotected side chain functional groups. Libraries of bivalent molecules can be formed from monovalent ones simply by mixing (micropipette) solutions of the two with potassium carbonate. Thus one library of 15 monovalent compounds could be assembled into 105 bivalent ones (total library size = 105 + 15 = 120). However, the number of bivalent compounds that can be made increases steeply as the number of monovalent compounds (n) increases {number of bivalent compounds = n(n - l)/2}. A library of 90 (corresponding to the 6 sets of 15 compounds proposed) monovalent building blocks could give 4005 bivalent compounds. Logistically, it is difficult to make the amounts of monovalent compounds required to assemble much more than 4,000 bivalent compounds; characterization issues become prohibitively time consuming and inventories of this many samples are not easy to keep. Consequently, we propose the concept of "evolving libraries" to keep the numbers manageable (1,000 - 3,000) while still exploring favorable regions of diversity space. This is based on formation of the bivalent compounds in sets of about 100 - 200 each, selection of the monovalent compounds that led to bivalent hits, addition of analogs of these to explore structure activity relationships, and formation of a second library of bivalent compounds from the lead monovalent compounds, their analogs, and a new set of monovalent compounds. All the bivalent compounds produced will be fluorescently labeled. This will make it possible to screen the libraries via direct binding assays; these have considerable advantages over the competitive binding assays that are often used for protein-protein interaction targets. First, labeled proteins are not required. This is important because many labeled proteins are so expensive that high throughput screens become impossible. Second, weak binders can be detected because they are not in competition with the native ligand. Another major advantage of this approach is that labeled compounds are selected from the assays that might be used as pharmacological probes. The approach could easily be adapted to include other types of label, or even a third small molecule. Bivalent molecules are valuable because they can bind two hot spots at a protein-protein interface. Strategies are proposed to optimize the linker dimensions required to join two small molecules together to achieve this. This information will emerge with little extra effort as the libraries of bivalent compounds are formed.