Understanding ligand-protein interactions is a piece of molecular detective work and the difficulty of the task depends on what is available as a starting point. In some cases, a protein structure will be available; in others there might be a molecule, a chemotype or a piece of protein or DNA. Ultimately, the task is always the same: to work out how they fit together.
Crystallographic or cryo-EM structures provide important clues to the ligand’s bioactive conformation in the protein binding site. Even in this favourable scenario, a detailed analysis of the interactions is critical to obtain appropriate premises that will outline the next steps at initial stages of a project. This analysis transcends an insightful interaction map, opening to the possibility for a comprehensive study of the electrostatics and hydrophobicity governing these interactions, facilitated by a unique description obtained with Cresset’s XED force field.
Targeting the unknown
There are occasions were a good reliable binding mode of our reference ligand(s), or a precise definition of the binding site are not available (e.g. looking for potential allosteric sites). A meticulously designed molecular docking experiment can provide a good starting hypothesis for the bioactive conformation, whilst a Pocket Detection tool will not only determine putative binding sites but also help in the definition of the grid box for the docking. In cases where there is no structural data available for a specific protein a homology model can be built using a related protein as a template.
Accurate binding modes drive affinity prediction
A suitable definition of the binding mode for the reference ligands can be used to generate a binding hypothesis for additional ligands featured within the dataset. Depending on the purpose of the research and scope of the project, different approaches can be explored:
- Working with congeneric series, a precise ligand alignment allows for MM/GBSA binding free energy estimation, building a QSAR model, along with providing the starting point for Free Energy Perturbation (FEP) calculation.
- On the other hand, for a set of ligands encompassing higher chemical diversity the methods of preference might involve the use of customized dockings, XED-aided alignments, or a combination of both.
Furthermore, during the process of dataset processing a Protein-Ligand Interaction Fingerprint (PLIF) can be generated, comparing the results with the initial hypothesis drawn based on the assessment of the interactions.
