Bioactive conformations of two seminal delta opioid receptor penta-peptides inferred from free-energy profiles

Abstract

Delta-opioid (DOP) receptors are members of the G protein-coupled receptor (GPCR) sub-family of opioid receptors, and are evolutionarily related, with homology exceeding 70%, to cognate mu-opioid (MOP), kappa-opioid (KOP), and nociceptin opioid (NOP) receptors. DOP receptors are considered attractive drug targets for pain management because agonists at these receptors are reported to exhibit strong antinociceptive activity with relatively few side effects. Among the most potent analgesics targeting the DOP receptor are the linear and cyclic enkephalin analogs known as DADLE (Tyr-D-Ala-Gly-Phe-D-Leu) and DPDPE (Tyr-D-Pen-Gly-Phe-D-Pen), respectively. Several computational and experimental studies have been carried out over the years to characterize the conformational profile of these penta-peptides with the ultimate goal of designing potent peptidomimetic agonists for the DOP receptor. The computational studies published to date, however, have investigated only a limited range of timescales and used over-simplified representations of the solvent environment. We provide here a thorough exploration of the conformational space of DADLE and DPDPE in an explicit solvent, using microsecond-scale molecular dynamics and bias-exchange metadynamics simulations. Free-energy profiles derived from these simulations point to a small number of DADLE and DPDPE conformational minima in solution, which are separated by relatively small energy barriers. Candidate bioactive forms of these peptides are selected from identified common spatial arrangements of key pharmacophoric points within all sampled conformations.

Keywords: molecular dynamics; opioids; peptides.

Figure 1. Free-energy surface of DADLE in solution

Free-energy reconstructed from the bias-exchange metadynamics simulations of DADLE. Free-energy differences from the lowest energy minimum A are reported in kJ/mol. Representative structures (cluster medoids) for minima A, A′, B, B′, and C are reported in red, pink, dark blue, light blue, and green, respectively. The location on the map of representative, putative bioactive conformations is indicated with a six- or a five-point star for Clusters 1 and 2, respectively.

Figure 2. Free-energy surface of DPDPE solution

Free-energy reconstructed from the bias-exchange metadynamics simulations of DPDPE in water. Free-energy differences from the lowest energy minimum A are reported in kJ/mol. Representative structures (cluster medoids) for minima A and A′ are reported in orange and light gold, respectively. The location on the map of representative, putative bioactive conformations is indicated with a six- or a five-point star for Clusters 1 and 2, respectively.

Figure 3. Overlap of the pharmacophoric parameters calculated for DADLE and DPDPE

2D projections of the 6D free-energy functions (in light and dark blue, for DADLE and DPDPE, respectively) epitomizing the pharmacophoric model. Dark red points correspond to regions where free-energies are non negligible for both peptides.

Figure 4. Graphical sketch of the pharmacophoric model

Values of the pharmacophoric parameters of the most populated cluster (Cluster 1) for DADLE (in Panel A) and DPDPE (in Panel B).