Due to the increasing number of proteins targets that are solved by X-ray crystallography, in silico structure-based ligand design is becoming a very attractive alternative to high throughput in vitro methods. The structure-based ligand design can be broken into two main stages. First it is necessary to estimate finely the binding mode of the small ligand (i.e. its position, orientation and conformation) on the protein surface. Second, this knowledge can be used to suggest rationally ligand modifications that can be expected to increase its affinity for the targeted macromolecule.
To address these problems, we designed the EADock docking program, which aims at determining theoretically the binding mode of a small ligand on a macromolecule surface (Proteins, 2007, 67, 1010). EADock is using a very accurate and universal scoring function providing a good description of molecular interactions from small fragments up to complete ligands. An efficient conformational search engine has been designed based on an evolutionary algorithm.
We are currently using a structure-based fragment-based approach for ligand design or modification. This approach consists mainly of three steps. In the first, positions and orientations for a series of molecular fragments are determined in the known structure of the macromolecular target. The EADock program is used for this. The fragments may correspond to molecular functions and frameworks that can be found frequently in organic molecules, or peptides.
In the second step, selected molecular fragments are connected to form putative ligands. The fragments may be connected directly, or through the use of an additional linker. In a first approximation, the connection of the fragments may be done based on simple geometric rules. However, we are also developing a new method that will take account of other physical parameters during the fragment connection, like solvation, and will also allow a dynamic modification of the linker nature as a function of its environment. At this stage, hundreds to many thousands candidate ligands can be obtained. In the final step, the ligand candidates are examined for synthetic feasibility and their free energies of binding are estimated to determine which of them are likely to have the strongest affinities for the target.