Exploration of the antagonist CP-376395 escape pathway for the corticotropin-releasing factor receptor 1 by random acceleration molecular dynamics simulations

Abstract

Corticotropin-releasing factor receptor 1 (CRF₁R), a member of class B G-protein-coupled receptors (GPCRs), plays an important role in the treatment of osteoporosis, diabetes, depression, migraine and anxiety. To explore the escape pathway of the antagonist CP-376395 in the binding pocket of CRF₁R, molecular dynamics (MD) simulations, dynamical network analysis, random acceleration molecular dynamics (RAMD) simulations and adaptive biasing force (ABF) calculations were performed on the crystal structure of CRF₁R in complex with CP-376395. The results of dynamical network analysis show that TM7 of CRF₁R has the strongest edges during MD simulation. The bent part of TM7 forms a V-shape pocket with Gly356^7.50. Asn283^5.50 has high hydrogen bond occupancy during 100 ns MD simulations and is the key interaction residue with the antagonist in the binding pocket of CRF₁R. RAMD simulation has identified three possible pathways (PW1, PW2 and PW3) for CP-376395 to escape from the binding pocket of CRF₁R. The PW3 pathway was proved to be the most likely escape pathway for CP-376395. The free energy along the PW3 pathway was calculated by using ABF simulations. Two energy barriers were found along the reaction coordinates. Residues Leu323^6.49, Asn283^5.50 and Met206^3.47 contribute to the steric hindrance for the first energy barrier. Residues His199^3.40 and Gln355^7.49 contribute to the second energy barrier through the hydrogen bonding interaction between CP-376395 and CRF₁R. The results of our study can not only provide useful information to understand the interaction mechanism between CP-376395 and CRF₁R, but also provide the details about the possible escape pathway and the free energy profile of CP-376395 in the pocket of CRF₁R.