Identification of potential small molecule allosteric modulator sites on IL-1R1 ectodomain using accelerated conformational sampling method

• Published in: PloS one 2015-02, Vol.10 (2), p.e0118671-e0118671
• Main Author: Yang, Chao-Yie
• Format: Article
• Language: English
• Subjects: Allosteric properties; Allosteric Regulation; Antibodies; Binding sites; Cluster analysis; Crystal structure; Cytokines; Immune response; Immune system; Inflammatory diseases; Inhibitors; Innate immunity; Interleukin 1; Interleukin 1 receptors; Ligands; Medical screening; Molecular biology; Molecular chains; Molecular dynamics; Molecular Dynamics Simulation; Peptide mapping; Phenols; Physics; Principal Component Analysis; Protein Conformation; Protein interaction; Proteins; Receptors, Interleukin-1 Type I - chemistry; Receptors, Interleukin-1 Type I - metabolism; Sampling methods
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0118671

The interleukin-1 receptor (IL-1R) is the founding member of the interleukin 1 receptor family which activates innate immune response by its binding to cytokines. Reports showed dysregulation of cytokine production leads to aberrant immune cells activation which contributes to auto-inflammatory disorders and diseases. Current therapeutic strategies focus on utilizing antibodies or chimeric cytokine biologics. The large protein-protein interaction interface between cytokine receptor and cytokine poses a challenge in identifying binding sites for small molecule inhibitor development. Based on the significant conformational change of IL-1R type 1 (IL-1R1) ectodomain upon binding to different ligands observed in crystal structures, we hypothesized that transient small molecule binding sites may exist when IL-1R1 undergoes conformational transition and thus suitable for inhibitor development. Here, we employed accelerated molecular dynamics (MD) simulation to efficiently sample conformational space of IL-1R1 ectodomain. Representative IL-1R1 ectodomain conformations determined from the hierarchy cluster analysis were analyzed by the SiteMap program which leads to identify small molecule binding sites at the protein-protein interaction interface and allosteric modulator locations. The cosolvent mapping analysis using phenol as the probe molecule further confirms the allosteric modulator site as a binding hotspot. Eight highest ranked fragment molecules identified from in silico screening at the modulator site were evaluated by MD simulations. Four of them restricted the IL-1R1 dynamical motion to inactive conformational space. The strategy from this study, subject to in vitro experimental validation, can be useful to identify small molecule compounds targeting the allosteric modulator sites of IL-1R and prevent IL-1R from binding to cytokine by trapping IL-1R in inactive conformations.