For more accurate prediction of native-like protein-ligand poses, the pharmacophore-based matching and scoring scheme, PharmPose, was extended into a docking program, named PharmDock. The docking program further optimizes the top-ranked binding poses predicted from PharmPose and re-scores the optimized binding poses with a widely used empirical scoring function. An open-source graphical user interface (GUI) adapted to PyMOL was devised for PharmDock for eased use of the docking software by the scientific community. In addition, we developed two new features allowing the users to guide the docking process towards specific residues identified from previous experimental data.
To improve the docking performance, we addressed two major issues in standard docking methods:
Water molecules in the binding site of proteins are important for molecular recognition as they can either bridge interactions between protein and ligand, or can be displaced by the bound ligand. Both mechanisms contribute enthalpically and entropically to the binding free energy. The explicit consideration of water molecules has gained increasing attention in drug-design projects over the last decade. To elucidate the thermodynamic profile of individual water molecules and their potential contribution to ligand binding, we developed a hydration site analysis program WATsite together with an easy-to-use graphical user interface based on PyMOL. WATsite identifies hydration sites from a molecular dynamics simulation trajectory with explicit water molecules. The free energy profile of each hydration site is estimated by computing the enthalpy and entropy of the water molecule occupying a hydration site throughout the simulation.
All previous hydration-site related studies neglected the conformational transition of the protein upon ligand binding. Thus, the use of hydration site information from a single protein conformation is most likely incorrect for ligand binding. Therefore, we recently developed two methods to dissect the changes in location and free energy of hydration sites upon protein conformational change. We are currently incorporating the hydration site information into PharmDock to include water-mediated interactions in the docking procedure and protein desolvation as part of a more accurate scoring procedure.
Flexibility and dynamics are protein characteristics that are essential in the process of molecular recognition. Studies from our and other groups have demonstrated that protein conformational changes are frequently induced by the bound ligand. To sample protein conformations that are relevant for binding structurally diverse ligands, we introduced the methodology Limoc, the new concept of a hypothetical ligand model: a virtual ligand that binds to the protein and dynamically changes its shape and properties during sampling of protein conformations. In this method, MD simulations are performed with a dynamically changing set of restrained functional groups in the binding site of the protein, essentially representing a large hypothetical ensemble of different chemical species binding to the same target protein. Beginning with an individual apo or holo structure of the protein, the ligand-model approach can be used to derive an ensemble of protein structures (EPS) used for identifying energetically feasible protein-ligand configurations. This EPS is used to represent alternative, pre-generated protein conformations in docking to efficiently sample feasible protein-ligand configurations.