Method for including the dynamic fluctuations of a protein in computer-aided drug design

We have recently presented a new pharmacophore design method that allows fo r the incorporation of the inherent flexibility of a target active site. Th e flexibility of the enzymatic system is described by collecting many confo rmations of the uncomplexed protein: this ensemble of conformational states can come from a molecular dynamics (MD) simulation, multiple crystal struc tures, or many NMR structures. Binding sites for functional groups that com plement the active site are determined throu,oh multiple-copy calculations. These calculations are conducted for each protein conformation, providing a large collection of potential binding sites. The Cartesian coordinates fr om each protein conformation are overlaid through RMS fitting of essential catalytic residues, and the pharmacophore model is described by binding reg ions that are conserved over many protein conformations. Previously, we dev eloped a "dynamic" pharmacophore model for HIV-1 integrase using 11 conform ations of the protein from an MD simulation; the MUSIC procedure was used t o calculate binding positions for methanol molecules in each configuration of the active site. Here we present "static" pharmacophore models developed with a single conformation of the protein from two new crystal structures (standard protocol for multiple-copy methods). The static models do not per form as well as the previous dynamic model in fitting known inhibitors of H IV-1 intergrase. To test the applicability of the dynamic pharmacophore met hod and the assumption that any reliable source of protein conformations is applicable, we have now developed a second dynamic pharmacophore model bas ed on the two crystal structures also used for the development of the stati c models. Though the dynamic model based on the two crystal structures does not fit as many known inhibitors as the previous: dynamic model, it is a s ignificant improvement over the static models. Even better performance is e xpected with the addition of new crystal structures as they become availabl e. However, it is notable that using only two structures leads to great imp rovement in the models.