A Molecular Dynamics Study of Vasoactive Intestinal Peptide Receptor 1 and the Basis of Its Therapeutic Antagonism

Abstract

Vasoactive intestinal peptide receptor 1 (VPAC1) is a member of a secretin-like subfamily of G protein-coupled receptors. Its endogenous neuropeptide (VIP), secreted by neurons and immune cells, modulates various physiological functions such as exocrine and endocrine secretions, immune response, smooth muscles relaxation, vasodilation, and fetal development. As a drug target, VPAC1 has been selected for therapy of inflammatory diseases but drug discovery is still hampered by lack of its crystal structure. In this study we presented the homology model of this receptor constructed with the well-known web service GPCRM. The VPAC1 model is composed of extracellular and transmembrane domains that form a complex with an endogenous hormone VIP. Using the homology model of VPAC1 the mechanism of action of potential drug candidates for VPAC1 was described. Only two series of small-molecule antagonists of confirmed biological activity for VPAC1 have been described thus far. Molecular docking and a series of molecular dynamics simulations were performed to elucidate their binding to VPAC1 and resulting antagonist effect. The presented work provides the basis for the possible binding mode of VPAC1 antagonists and determinants of their molecular recognition in the context of other class B GPCRs. Until the crystal structure of VPAC1 will be released, the presented homology model of VPAC1 can serve as a scaffold for drug discovery studies and is available from the author upon request.

Keywords: G protein-coupled receptors; GPCR activation; GPCRM; PACAP; VIP; VIPR1; VPAC1; agonist; antagonist; gut hormone receptors; homology modeling; molecular dynamics; vasoactive intestinal peptide receptor 1.

Figure 1

(a) Comparison of extracellular domains in experimental structures of glucagon receptor (GCGR, blue, PDB id: 5IQZ), glucagon-like peptide-1 receptor (GLP-1R, grey, PDB id: 5VAI), parathyroid hormone receptor PTHR1 (red, PDB id: 6NBF) and calcitonin gene-related peptide receptor (CGRP, green, PDB id: 6E3Y). The least diverse are regions of a helix H1 and a β-sheet 1. The most structural diversity (a black arrow) between these ECD domains of class B GPCRs can be observed in the region of a helix H2 and a loop 4, which is involved in the binding of peptide agonists (b). Similar helical conformations of peptide analogs of GCG, GLP and PTH were shown with the ‘lines’ representation while a different conformation of CGRP agonist (dark green) was shown with the ‘cartoons’ representation. The helical part of the CGRP agonist is located perpendicularly to other class B agonists because of additional interactions with receptor activity-modifying protein (RAMP).

Figure 2

Details of interactions between vasoactive intestinal peptide receptors (VPAC receptors) and vasoactive intestinal peptide (VIP). (a) Comparison of ectodomain binding sites for VIP in VPAC1 (orange) and VPAC2 (grey). Most of residues involved in the peptide binding are non-polar or aromatic. (b) The upper part: C-terminal VIP residues which are involved in the interactions with ECD. Most of them are hydrophobic residues. The bottom part: the transmembrane domain binding site of N-terminal VIP residues. A hydrogen bond between Asp3 of the peptide and Arg188 of the receptor was observed (a yellow dashed line), similarly to the reported site-directed mutagenesis data [24]. Figures refer to the VPAC1 model (including VIP) based on the 5VAI template structure.

Figure 3

Two series of small-molecule antagonists of VPAC1 described in Harikrishnan et al.: (a) compound 31, Z = 3,4-dimethyl; 3-Cl; naphthyl (3,4-fused); 3-SMe; naphthyl (2,3-fused); 3-OMe; 3-Ph; 3-Me; 4-Cl; 4-Me; 3-NMe₂; H; 4-Ph; 4-F; 2-OMe; 4-OMe; 2-Ph; 3-CN; 3-CF₂; 2-Me (b) compound 41, R = phenylethyl; cyclohexyl; cyclopentyl; (4-methoxyphenyl)ethyl; (4-methylphenyl)ethyl; (3-methoxyphenyl)ethyl; (3-methylophenyl)ethyl; (4-chlorophenyl)ethyl; phenylmethyl; cyclobutyl; isobutyl; (2-benzo[b]thiophene)methyl; cyclopropyl; isopropyl; 2-(2,3-dihydrobenzofuran)ethyl; phenoxymethyl; (2-methylphenyl)ethyl; Et; 3-tetralin; Me; Phe; 2-indane; 2-indolemethyl. Here, tested derivatives were sorted in the ascending cAMP IC50 order (the first one—the highest potency for VPAC1).

Figure 4

The MD-refined pose 1 (a) of compound 31 (b) containing the two-tyrosines gate (c) blocking the VIP binding (d).

Figure 5

A two-tyrosines gate as the molecular basis of the VPAC1 antagonism. The peptide-bound, open conformation of VPAC1 (yellow) closes upon the antagonist binding (grey). In the closed conformation of ECD, two tyrosines: Tyr118 and Tyr39, form a gate or a steric hindrance that prevents the VIP binding.

Figure 6

The MD-refined pose 1 (a) of compound 41 (b) containing two tyrosine residues Tyr39 and Tyr39 (c) in conformations that prevent the peptide binding (d).