Analyzing the Molecular Effects of Endomorphin-2 Degradation on Stabilizing Interactions at the μ-Opioid Receptor

Background: Endogenous opioids, such as endomorphin-2, are key regulators of the body’s pain pathways and mediate analgesia by engaging the μ-opioid receptor. This class of opioids are distinguished by their transient activation of the μ-opioid receptor, which is attributed to rapid enzymatic degradation. Methods: To understand how degradation of endomorphin-2 by the enzyme DPP IV affects its interaction with the μ-opioid receptor, we analyzed the ligand–receptor conformational dynamics and interaction patterns of molecular dynamics simulations data of morphine, fentanyl and endomorphin-2 and one degradation product Phe-Phe-NH2, using molecular fingerprints and the mathematical framework ISOKANN. Results: Our analyses revealed that both the clinically relevant opioids, morphine and fentanyl, as well as the endogenous opioid endomorphin-2, adopt a set of recurring binding conformations within the μ-opioid receptor binding pocket, maintaining overlapping interaction motifs throughout the simulations. In contrast, Phe-Phe-NH2 failed to maintain a persistent binding mode over the simulated timescale. This instability arises from the dipeptidyl peptidase IV mediated cleavage of endomorphin-2, which generates Phe-Phe-NH2 and removes critical proline and tyrosine residues, thereby leading to the loss of stabilizing hydrophobic contacts with receptor residues Tyr1503,33, Val2385,43 and Val3026,55. Conclusion: By mapping structural interaction motifs essential for stable μ-opioid receptor binding, this study provides mechanistic insights into how endogenous degradation reshapes ligand–receptor interactions.