Exploration of novel aryl binding sites of farnesyltransferase using molecular modeling and benzophenone-based farnesyltransferase inhibitors

Most non-thiol CAAX-peptidomimetic farnesyltransferase inhibitors bear nitr ogen-containing heterocycles in place of the terminal cysteine which are su pposed to coordinate the enzyme-bound zinc. However, it has been shown that those nitrogen-containing heterocycles can be replaced by carbocyclic arom atic moieties which are unable to coordinate the zinc ion, a conclusion tha t resulted in the postulation of one or two hitherto unknown aryl binding s ites. No indication has been given about the spatial location of these nove l binding sites. Employing flexible docking of several non-thiol farnesyltr ansferase inhibitors known from the literature and some model compounds bas ed on our benzophenone scaffold as well as performing GRID searches, we hav e identified two regions in the farnesyltransferase's active site which we suggest being the postulated aryl binding sites. One aryl binding region is located in close proximity to the zinc ion and is defined by the aromatic side chains of Tyr 300 beta, Trp 303 beta, Tyr 361 beta, and Tyr 365 beta. The second aryl binding site is defined by the side chains of Tyr 300 beta, Leu 295 beta, Lys 294 beta, Lys 353 beta, and Lys 356 beta. This second ar yl binding site has been used for the design of a non-thiol farnesyltransfe rase inhibitor (9c) with an IC50 of 35 nM.