Molecular Basis of Class B GPCR Selectivity for the Neuropeptides PACAP and VIP

Abstract

The related neuropeptides PACAP and VIP, and their shared PAC1, VPAC1 and VPAC2 receptors, regulate a large array of physiological activities in the central and peripheral nervous systems. However, the lack of comparative and molecular mechanistic investigations hinder further understanding of their preferred binding selectivity and function. PACAP and VIP have comparable affinity at the VPAC1 and VPAC2 receptor, but PACAP is 400–1,000 fold more potent than VIP at the PAC1 receptor. A molecular understanding of the differing neuropeptide-receptor interactions and the details underlying the receptor transitions leading to receptor activation are much needed for the rational design of selective ligands. To these ends, we have combined structural information and advanced simulation techniques to study PACAP/VIP binding selectivity, full-length receptor conformation ensembles and transitions of the PACAP/VIP receptor variants and subtypes, and a few key interactions in the orthosteric-binding pocket. Our results reveal differential peptide-receptor interactions (at the atomistic detail) important for PAC1, VPAC1 and VPAC2 receptor ligand selectivity. Using microsecond-long molecular dynamics simulations and the Markov State Models, we have also identified diverse receptor conformational ensembles and microstate transition paths for each receptor, the potential mechanisms underlying receptor open and closed states, and the interactions and dynamics at the transmembrane orthosteric pocket for receptor activation. These analyses reveal important features in class B GPCR structure-dynamics-function relationships, which provide novel insights for structure-based drug discovery.

Pituitary Adenylate Cyclase-Activating Polypeptide (PACAP) in Physiological and Pathological Processes within the Gastrointestinal Tract: A Review

“…The multifarious physiological effects of PACAP are mediated through binding to different G protein-coupled receptors, including PAC1 (PAC1-R), VPAC1 (VPAC1-R) and VPAC2 (VPAC2-R) receptors [35] (Figure 1). PAC1-R exerted a 100-fold higher affinity for PACAP than for VIP, whereas VPAC1-R and VPAC2-R exhibit a comparable affinity to PACAP and VIP [36]. Molecular studies identified diverse receptor conformational ensembles and microstate transition paths for each receptor and revealed differential peptide-receptor interactions (at the atomistic detail) for each receptor important for PAC1, VPAC1 and VPAC2 receptor ligand selectivity [37].…”

“…The PAC1-R has various variant transcripts (Null, Hip, Hop1, Hop2, Hiphop1, Hiphop2, short and very short isoforms), which lead to the activation of two different signaling pathways: increasing the intracellular level of cyclic AMP (cAMP) by adenylyl cyclase (AC) and the stimulation of phospholipase C (PLC) [36,38]. Activation of VPAC1-R and VPAC2-R stimulate AC and some other cAMP-independent signaling cascades [39].…”

Essential Dynamics Ensemble Docking for Structure-Based GPCR Drug Discovery

“…Most of the neural and peripheral tissues known to date contain the PAC1null or PAC1hop isoforms that includes a 21-amino acid insert in the ECD (Figure 1), which is missing in available PAC1R structures in the PDB (May and Parsons, 2017). This ECD insert was found highly dynamic in our previous modeling studies (Liao et al, 2017;Liao et al, 2021), but its role in regulating PAC1R remains unknown. While PAC1R antagonists are being developed as potential treatments for stress-related disorders, the agonist-bound cryo-EM structures are not directly applicable to computational design or screening of PAC1R antagonists.…”

Delineating the activation mechanism and conformational landscape of a class B G protein-coupled receptor glucagon receptor

“…Class B GPCRs (the secretin peptide receptors) play a crucial role in maintaining hormonal homeostasis in the human body. The structure of class B GPCRs consists of an extracellular domain (ECD) and a seven-transmembrane domain (TMD) [22] , [23] , [24] , [25] , [26] , [27] . The human glucagon receptor (GCGR) is a prototypical class B GPCR.…”