Advances in the Molecular Mechanism of Kappa Opioid Receptors Signaling and the Important Sampling Methods to Probe the Activation Landscape of GPCRs

The kappa opioid receptor (KOR) is one of class A G-protein-coupled receptors (GPCRs), playing important roles in pain sensation. The unique analgesic activity of KOR requires KOR activation that recruits downstream effectors. It is noted that KOR primarily couples to the G_i/o family proteins in the process of KOR signaling that contain the conventional (G_i1, G_i2, G_i3, G_oA, and G_oB) and nonconventional (G_z and G_g) subtypes. The molecular mechanisms governing KOR signaling—particularly its selectivity for G_i/o protein subtypes and the pathway specificity of its ligands—remain unclear. Furthermore, the structural and energetic sequence of events during the activation of KOR and its cognate G_i/o proteins is poorly understood. This lack of knowledge hinders the structure-based design of pharmacophores targeting the KOR/G_i/o complex. It suggests that further research and investigation are required to analyze the crystal structure of the agonists/KOR complexes and various intermediate states in the KOR activation pathway. Some improved enhanced sampling methods, such as umbrella sampling, metadynamics, and Markov State Model methods, can characterize the interaction between GPCRs and different G protein subtypes after specific ligands binding, and the free energy landscapes along the ligand binding pathway. In this review, we discuss the research advances in the molecular mechanisms of KOR signaling. We also present a brief overview of computational conformational sampling methods based on molecular dynamics, including the activation mechanisms, allosteric effects, and actions of biased ligands of GPCRs to describe their activation energy landscape. It can provide an insight into evaluate the convergence of free energy surfaces along coordinates of functional interest, which is helpful to understand the role of GPCR conformational ensembles in intracellular signal transduction.