Enzymatic transition state structures can be experimentally solved by a combination of intrinsic kinetic isotope effects (KIEs) and computational quantum chemistry. This approach provides experimental boundaries for transition states with reference to the chemical reactants. Bond geometry and electrostatic potential maps of transition states provide chemical-mechanistic insights as well as blueprints for transition state analog design. Femtomolar to picomolar analogs for several N-ribosyltransferases have resulted from this approch. These are among the most powerful enzyme inhibitors. Several are in clinical use, clinical trials or in preclinical studies. Here we extend this approach to human DNA methyltransferase and methionine S-adenosyltransferase. A third goal is to develop a new approach to extend the theory of transition state design principles toward drug discovery. Transition path sampling incorporates an unbiased computational approach to obtain the enzyme catalytic site geometry at the moment of the transition state. Transition path sampling finds the three- dimensional contacts between enzyme and reactants at the transition state. The privileged enzyme geometry at the transtion state has a lifetime on the fsec time scale and can be treated as an inhibitor design element. Drug candidates designed to stablize the protein geometry of the transition state will be powerful inhibitors. Transition state structures for two S-adenosylmethionine-dependent methyltransferases were solved in the past grant period. Both have SN2-like transition states, with the S-adenosylmethionine methyl donor a common element and the methyl-group recipient as a variable chemical element. Transition state analog design will be complemented with design of chemically unique inhibitors based on the enzymatic cavity at the moment of the transition state. DNA methyltransferase (DNMT1) is a validated anti-cancer drug target but current drugs are incorporated into cellular DNA, are mutagenic and therefore of limited application. Chemically stable analogs based on the transition state are intended to improve the theraputic approach to DNMT1 inhibition by providing non-mutagenic, tight-binding transition state analogs. Lead compounds provide proof-of-concept for the validity of a transition state approach. Methionine S-adenosyltransferase (MAT2A) is a genetically validated anticancer target by synthetic-lethal analysis in experimental cancer models. Transition state and virtual screening approaches will be used to obtain analogs to specifically target this cancer-related enzyme. Enzymatic cavity structure, based on transition path sampling,will provide an alternative inhibitor design approach for both targets. Transition state chemistry, transition state analog design and the fundamental properties of enzymatic catalysis will be advanced by these projects.
Drug design based on enzymatic transition state features improves the efficiency of drug development. Two targets for drug design expand this approach to new classes of drug targets. A new approach will use the protein geometry of enzyme targets at the few femtoseconds of the enzymatic transition states to design novel inhibitors. Drug design based on transition state structure continues to be a developing tecnology. Several drug candidates based on transition state information have reached clinical practice, clinical trials, or preclinical development, demonstrating the value of transition state information. Understanding catalytic sites at the instant of chemical catalysis has the potential to provide a novel advance in drug design.
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