Small Glycols Discover Cryptic Pockets on Proteins for Fragment-Based Approaches

Area of Science:

• Structural Biology
• Computational Chemistry
• Drug Discovery

Background:

• Cryptic pockets are protein binding sites present only in ligand-bound states, making them difficult to identify and utilize for drug design.
• Classical drug design approaches struggle with proteins lacking accessible binding sites, necessitating novel methods to uncover potential targets.

Purpose of the Study:

• To investigate the potential of small glycols as probes for identifying cryptic pockets in proteins.
• To demonstrate the utility of small glycols in both experimental and computational fragment-based drug design strategies.

Main Methods:

• Crystallography experiments with ethylene glycol and propylene glycol to identify cryptic pockets.
• Explicit-solvent molecular dynamics (MD) simulations to analyze pocket stability and ligand interactions.
• Construction and analysis of a protein dataset with validated cryptic sites.

Main Results:

• Small glycols, including ethylene glycol and propylene glycol, successfully identified cryptic pockets in various proteins.
• MD simulations confirmed the instability of exposed cryptic pockets without ligands and the inability of water to open them.
• Ethylene glycol was observed to bind to cryptic sites in proteins like Bcl-xL and G-actin, which are revealed upon ligand binding.

Conclusions:

• Small glycols are effective probes for discovering cryptic pockets, expanding the druggable proteome.
• This approach offers a promising strategy for fragment-based drug design against challenging and previously undruggable protein targets.