CONCERTS: dynamic connection of fragments as an approach to de novo ligand design

Abstract

We have implemented and tested a new approach to de novo ligand design, CONCERTS (creation of novel compounds by evaluation of residues at target sites). In this method, each member of a user-defined set of fragments is allowed to move independently about a target active site during a molecular dynamics simulation. This allows the fragments to sample various low-energy orientations. When the geometry between proximal fragments is appropriate, bonds can be formed between the fragments. In this fashion, larger molecules can be built. The bonding arrangement can subsequently be changed-breaking bonds between chosen fragment pairs and forming them between other pairs-if the overall process creates lower energy molecules. We have tested this method with various mixes of fragments against the active sites of the FK506 binding protein (FKBP-12) and HIV-1 aspartyl protease. In several cases, CONCERTS suggests ligands which are in surprisingly good agreement with known inhibitors of these proteins.