Predicting relative binding free energies of tacrine-huperzine A hybrids as inhibitors of acetylcholinesterase

The binding of the 9-methyl derivative of tacrine-huperzine A hybrid to Tor pedo californica; acetylcholinesterase (AChE) has been studied by computati onal methods. Molecular dynamics simulations have been performed for the AC hE-drug complex considering two different ionization states of the protein and two different orientations of the drug in the binding pocket, which wer e chosen from a previous screening procedure. Analysis of structural fluctu ations and of the pattern of interactions between drug and enzyme clearly f avor one binding mode for the tacrine-huperzine A hydrid, which mixes effec tively some of the binding features of tacrine and huperzine A. The differe nces in inhibitory activity for a series of related derivatives have been s uccessfully predicted by free energy calculations, which reinforces the con fidence in the binding mode and its usefulness for molecular modeling studi es. The same techniques have been used to make de novo predictions for a ne w 3-fluoro-9-ethyl derivative, which can be used to verify a posteriori the goodness of the binding mode. Finally, we have also investigated the effec t of replacing Phe300 in the Torpedo californica enzyme by Tyr, which is pr esent in the human AChE. The results indicate that the Phe330-->Tyr mutatio n is expected to have little effect on the binding affinities. Overall,the whole of results supports the validity of the putative binding model to exp lain the binding of tacrine-huperzine A hybrids to AChE.