Balancing target flexibility and target denaturation in computational fragment-based inhibitor discovery

• Published in: Journal of computational chemistry 2012-09, Vol.33 (23), p.1880-1891
• Main Authors: Foster, Theresa J., MacKerell Jr, Alexander D., Guvench, Olgun
• Format: Article
• Language: English
• Subjects: Binding sites; Binding Sites - drug effects; Computer simulation; computer-aided drug design; Crystallography, X-Ray; Drug Discovery; immunosuppression; Inhibitor drugs; interleukin-2; Interleukin-2 - antagonists & inhibitors; Interleukin-2 - chemistry; lead optimization; Ligands; Models, Molecular; Molecular Dynamics Simulation; molecular dynamics simulations; Pharmacology; Protein Denaturation - drug effects; protein-protein interactions; Proteins; Software; Structure-Activity Relationship
• ISSN: 0192-8651; 1096-987X
• DOI: 10.1002/jcc.23026

Accounting for target flexibility and selecting “hot spots” most likely to be able to bind an inhibitor continue to be challenges in the field of structure‐based drug design, especially in the case of protein–protein interactions. Computational fragment‐based approaches using molecular dynamics (MD) simulations are a promising emerging technology having the potential to address both of these challenges. However, the optimal MD conditions permitting sufficient target flexibility while also avoiding fragment‐induced target denaturation remain ambiguous. Using one such technology (Site Identification by Ligand Competitive Saturation, SILCS), conditions were identified to either prevent denaturation or identify and exclude trajectories in which subtle but important denaturation was occurring. The target system used was the well‐characterized protein cytokine IL‐2, which is involved in a protein–protein interface and, in its unliganded crystallographic form, lacks surface pockets that can serve as small‐molecule binding sites. Nonetheless, small‐molecule inhibitors have previously been discovered that bind to two “cryptic” binding sites that emerge only in the presence of ligand binding, highlighting the important role of IL‐2 flexibility. Using the above conditions, SILCS with hydrophobic fragments was able to identify both sites based on favorable fragment binding while avoiding IL‐2 denaturation. An important additional finding was that acetonitrile, a water‐miscible fragment, fails to identify either site yet can induce target denaturation, highlighting the importance of fragment choice. © 2012 Wiley Periodicals, Inc. Site Identification by Ligand Competitive Saturation (SILCS) is a computational method capable of detecting noncrystallographic (cryptic) binding sites through the creation of fragment‐binding maps (FragMaps). Here, a SILCS FragMap corresponds with a cryptic binding site in interleukin‐2 not present in the apo crystal structure, but seen in crystal structures with bound inhibitors (lines).