Pocket-based drug design: exploring pocket space

Abstract

The identification and application of druggable pockets of targets play a key role in in silico drug design, which is a fundamental step in structure-based drug design. Herein, some recent progresses and developments of the computational analysis of pockets have been covered. Also, the pockets at the protein-protein interfaces (PPI) have been considered to further explore the pocket space for drug discovery. We have presented two case studies targeting the kinetic pockets generated by normal mode analysis and molecular dynamics method, respectively, in which we focus upon incorporating the pocket flexibility into the two-dimensional virtual screening with both affinity and specificity. We applied the specificity and affinity (SPA) score to quantitatively estimate affinity and evaluate specificity using the intrinsic specificity ratio (ISR) as a quantitative criterion. In one of two cases, we also included some applications of pockets located at the dimer interfaces to emphasize the role of PPI in drug discovery. This review will attempt to summarize the current status of this pocket issue and will present some prospective avenues of further inquiry.

Fig. 1

The scheme of two case studies in this review

Fig. 2

Illustration of the relationship between intrinsic specificity and conventional specificity as well as the corresponding energy spectrum. a The conventional definition of specificity is the difference(s) or discrimination(s) in affinity of the target receptor against other receptors binding to the same ligand; b the definition of intrinsic specificity is the difference(s) or discrimination(s) in binding energies of native (lowest) binding mode or site against other non-native binding modes (pockets) for a ligand binding to a receptor. The giant receptor here can be considered as the combination of many smaller receptors connected by certain linkers. When the giant receptor is large enough to cover all the possible ligand–protein interactions, the definition of intrinsic specificity is equivalent to the definition of conventional specificity. The receptors are colored blue; the yellow ball represents the ligand

Fig. 3

Potential ligand binding sites identified on the Ras conformational ensembles. The site is colored orange, and the GTP is shown as ball and stick model

Fig. 4

The heat map clustering of the binding pocket on the Ras protein. The horizontal axis labels are colored by properties of pockets (red for volume, green for depth, polarity, and NPLA; for further details, see the “Methods” section). Major pockets are indicated by the orange labels and corresponding marginal dendrograms

Fig. 5

The binding pockets of four representative conformations of the Ras protein. The negative image of the pockets formed by the probes and the PLAs are shown as colored surface on the right; the Ras protein is shown as surface model containing the GTP (ball and stick model) and the cofactor Mg²⁺ (green dot) as well as the water molecules interacting with the magnesium ion (red dot) on the left. The orange rectangle indicates the positioning of these binding pockets on the Ras protein

Fig. 6

The binding pockets at the interfaces of Ras proteins with SOS, GAPs, RalGDS, Raf, and PI3K, respectively. The cycling between the active and inactive states of the Ras protein controlled with GEF (SOS) and GAP proteins is described, then the complexes containing five proteins previously mentioned are shown as a cartoon model (grey) and placed at the corresponding positions. The GTP on the Ras protein as an indicator is shown as ball and stick model, the centers of predicted pockets are labeled using the colored spheres (for further details, see the “Methods” section), the centers of predicted pockets at the interfaces are highlighted (green circle)

Fig. 7

Potential ligand binding sites identified on the Src kinase conformational ensembles. The allosteric site is colored green, and the native ATP-binding site is colored orange. From the structural point of view, the allosteric site can be considered as a periphery of the ATP-binding site

Fig. 8

The ATP-binding sites of four representative conformations of the Src kinase. The Src protein is shown as a cartoon model, the negative image of the pockets and PLAs are shown as colored surfaces, and the corresponding PP1 is shown as a ball and stick model

Fig. 9

The allosteric sites of four representative conformations of the Src kinase. The Src protein is shown as a cartoon model, the negative image of the pockets and PLAs are shown as colored surfaces, and the corresponding PP1 is shown as a ball and stick model