Outstanding challenges in protein–ligand docking and structure‐based virtual screening

Crystal structures of a selection of cyclin‐dependent kinase 2 (CDK2) inhibitors from the Protein Data Bank (PDB), exemplifying how a diverse range of chemotypes bind to the ATP‐binding site. For clarity, only a single receptor structure is shown (cream carbon atoms), with a solvent accessible surface colored by electrostatic potential.

The six ligands with reported K_i values <4 µM against the β2 adrenergic receptor.168

X‐ray structure of the β2‐adrenergic receptor (PDB code: 2RH1), with the ligand carazolol highlighted in spheres.

Structure and anti HIV‐1 activity data for the three hits found by virtual screening against HIV‐1 reverse transcriptase.164

X‐ray structure of compound 4163 showing the hydrogen bonds between the ligand and the protein as yellow dashed lines. Note also the face‐to‐face stacking interaction between the nitro‐bearing phenyl ring and the tryptophan beneath it.

Chemical structures of compounds derived from virtual screening hits.163

Chemical structures of IDD594 and the two most potent hits identified by virtual screening using the X‐ray structure of aldose reductase.162

The four Pim‐1 kinase hits identified by virtual screening at Vertex.161

Use of ROC curves as a metric of virtual screening performance. A high enrichment rate is exemplified by the blue curve (rapid retrieval of actives; all actives retrieved relatively quickly), a poorer enrichment by the pink curve (slow initial retrieval; late retrieval of all actives), and a random retrieval rate by the green line. The ROC curve is defined as a plot of selectivity versus specificity across the entire ranked dataset, where sensitivity is the fraction of actives retrieved and specificity the fraction of inactives discarded. Enrichment can be quantified by the area under the curve (AUC = 1 for perfect retrieval of actives; AUC = 0.5 for a random retrieval rate).

Example of clustering a virtual screening dataset in terms of the volume overlap of the docked poses. The figure shows three representative clusters, which contain ligands of diverse structure but with a similar 3D shape in the binding site. The example is based on a virtual screen to identify hinge binders to a protein kinase (hinge region shown in brown).

Illustration of distribution of docking scores in a virtual screening experiment. Left: The ideal scenario, where the small number of actives (blue) are well separated from the much larger number of inactives (red) – ranking on docking score readily separates the majority of the actives with little contamination from inactives. Right: The more usual situation encountered in VS applications: the actives significantly overlap with the highest‐scoring inactives. In this case, ranking gives an enrichment of actives but not complete separation.

Crystal structure of p38 MAP kinase in complex with a naphthalene‐urea (PDB code: 2PUU). The contact to the hinge (gray ribbon) is unusually achieved through mediation of a water molecule. (Hydrogen atoms added using Maestro from Schrödinger, Inc.)

Crystal structure of scytalone dehydratase in complex with two different ligands. (Left): A water‐mediated interaction of the ligand with the two tyrosine residues (PDB code: 1STD). (Right): The water has been replaced by a nitrile group that interacts with both tyrosines (PDB code: 3STD). (Hydrogen atoms added using Maestro from Schrödinger, Inc.)

Examples of backbone and side‐chain flexibility in protein kinases. Left: In the Protein Kinase B X‐ray structure 2JDR (green carbons), Phe163 (ball‐and‐stick) folds into the binding site to gain lipophilic contacts with the ligand, whereas in 2JDO (pink carbons), Phe163 is directed out of the binding site, leaving a lipophilic pocket under the P‐loop, which is occupied by a chlorophenyl group on the ligand. Right: In p38 MAP kinase, movement of the DFG motif away from its usual binding site (pink) to a ‘DFG‐out’ conformation (orange) reveals a lipophilic pocket occupied by the ligand BIRB‐796 (green).

Schematic of a typical workflow in docking and virtual screening.