Interleukin (IL)-33, the newest member of the IL-1 family, plays a pivotal role in inflammatory and autoimmune diseases through its protein-protein interaction (PPI) with the ST2 receptor. Targeting this interaction holds promise for disease management. Although the IL-33/ST2 complex crystal structure has been resolved for nearly a decade, no comprehensive investigations into the druggability of IL-33 have been conducted. Furthermore, while several IL-33 inhibitors have been reported, their binding mechanisms have predominantly relied on rudimentary molecular docking approaches. In this study, we sought to identify possible druggable sites on the IL-33 surface using mixed-solvent molecular dynamics (MixMD) simulations and propose the possible mechanism of action of a reported IL-33 inhibitor using extensive-MD simulations. MixMD is an advanced MD technique that not only captures the protein's flexibility but also considers its interactions with small chemical probes. Our findings revealed five potential druggable sites on the IL-33 surface, two of which overlaid well with the interface of the ST2 receptor. The three remaining sites were investigated for their allosteric potential via all-atom normal mode analysis in the presence of pseudoligands. The current results suggested that interaction with these binding sites could exert possible dynamical change compared to the apoprotein conformation and serve as starting points for IL-33 allosteric modulation. Additionally, the binding modes of an orthosteric IL-33 inhibitor were also extracted and analyzed using the results from a 5-microseconds simulation. Our study can pave the way for future studies aiming to modulate the PPI of IL-33/ST2 employing both orthosteric and allosteric approaches.
IL-33 is a protein that in humans is encoded by the IL33 gene. IL-33 is a member of the IL-1 family of cytokines, which are molecules that regulate immune and inflammatory responses. IL-33 is present in the cell nucleus and is released into extracellular spaces, where it acts as an alarmin by binding to the receptor ST.
ST2 is a protein that in humans is encoded by the IL1RL1 gene. ST2 is a member of the IL-1 receptor family, which are molecules that mediate the effects of IL-1 cytokines. ST2 is expressed on various immune cells, such as Th2 cells, mast cells, and innate lymphoid cells. ST2 forms a heterodimeric receptor complex with the IL-1 receptor accessory protein (IL-1RAP) and transduces the signals of IL-3.
MixMD is a cosolvent simulation technique for identifying binding hotspots and specific favorable interactions on a protein’s surface. MixMD studies have the ability to identify these biologically relevant sites by examining the occupancy of the cosolvent over the course of the simulation. MixMD uses a mixture of water and organic solvent molecules, such as methanol, ethanol, or acetonitrile, to probe the protein surface and reveal the druggable sites.
Extensive-MD simulations are long-duration molecular dynamics simulations that allow the exploration of the conformational space and the binding modes of a protein and its ligands. Extensive-MD simulations can provide detailed insights into the structural and energetic aspects of protein-ligand interactions, such as binding affinity, binding kinetics, and binding mechanism.
IL-33 is a protein that in humans is encoded by the IL33 gene. IL-33 is a member of the IL-1 family of cytokines, which are molecules that regulate immune and inflammatory responses. IL-33 is present in the cell nucleus and is released into extracellular spaces, where it acts as an alarmin by binding to the receptor ST.
ST2 is a protein that in humans is encoded by the IL1RL1 gene. ST2 is a member of the IL-1 receptor family, which are molecules that mediate the effects of IL-1 cytokines. ST2 is expressed on various immune cells, such as Th2 cells, mast cells, and innate lymphoid cells. ST2 forms a heterodimeric receptor complex with the IL-1 receptor accessory protein (IL-1RAP) and transduces the signals of IL-3.
MixMD is a cosolvent simulation technique for identifying binding hotspots and specific favorable interactions on a protein’s surface. MixMD studies have the ability to identify these biologically relevant sites by examining the occupancy of the cosolvent over the course of the simulation. MixMD uses a mixture of water and organic solvent molecules, such as methanol, ethanol, or acetonitrile, to probe the protein surface and reveal the druggable sites.
Extensive-MD simulations are long-duration molecular dynamics simulations that allow the exploration of the conformational space and the binding modes of a protein and its ligands. Extensive-MD simulations can provide detailed insights into the structural and energetic aspects of protein-ligand interactions, such as binding affinity, binding kinetics, and binding mechanism.
