In the last years, some studies showed the patho-genetic role of CXCR3 bound to its ligands in many human inflammatory diseases and cancers. Thus, the blockage of the CXCR3 interaction site to its ligands is seen as a possible therapeutic target for the treatment of cancer. The presence of flexible regions in the chemokine receptors determines their capability to develop specific mechanisms of action. We have recently focused on the features of the N-terminal region of human CXCR3 free in solution, where we demonstrate the presence of numerous conformational ensembles, dynamically stabilized by H-bonds. Since up to now no structure was experimentally determined for CXCR3, we decided to approach the study of its conformational behavior by molecular dynamics simulations, in a lipid bilayer, surrounded of water, at neutral pH and 300 K. Furthermore, we modeled the CXCR3/CXCL11 complex, where CXCL11 is one of its natural ligands. The aim of this work is to have a vision as realistic as possible in dynamic terms of the biological mechanism that drives the search for the ligand, its interaction and the formation of a stable complex between CXCR3 and CXCL11.
Overall, our approach has been able to describe the structural events which dynamically characterize the molecular mechanisms involved in the binding of CXCR3 to CXCL11 and the critical role exerted by its N-terminal region in “hunting” and capturing the ligand.