Specific Inhibition of an Conformationally Flexible t-RNA Modifying Enzyme by Ligands Synthesized by Combinatorial Chemistry

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The functional and conformational properties of tRNA modifyingenzymes, catalyzing the exchange reaction of bases in tRNA,will be studied by chemical probes synthesized in awell-planned strategy using the concepts of combinatorialchemistry. Different members of this enzyme family originatingfrom the three kingdoms of life operate on deviating ranges ofsubstrates. The differences in substrate recognition areachieved by conformational adaptations of the proteins and theinvolvement of a water molecule in ligand binding. Usingwell-tailored libraries of specific inhibitors, accessiblethrough combinatorial synthesis, we want to address thedifferent conformational states that demonstrate a surprisingversatility of substrate recognition intimately related to thefunctional role of these enzymes. The protein from Shigellaflexneri has been characterized as a target for a specificantibiotics therapy, thus potential leads could possibly servefor a subsequent drug development program. The present researchproposal uses a combined approach of chemical synthesis,molecular modeling, X-ray crystallography, site-directedmutagenesis and molecular dynamics simulations to give accessto specific molecular probes which address differentconformational states among the members of this enzyme class,required to accomplish their functional role. They will help tounderstand the enzymatic properties, in particular with respectto adaptability and substrate specificity.