In Silico Evaluation of Diketopiperazine (DPK) Derivatives as Potential Inhibitors for G-Protein-Coupled Receptors (GPCRs)

Background: G-protein-coupled receptors (GPCRs) are a diverse group of membrane proteins that mediate critical physiological processes by converting extracellular signals into intracellular responses. The β2-Adrenergic Receptor (β2-AR), a key GPCR, plays a pivotal role in smooth-muscle relaxation, bronchodilation, and cardiovascular function, making it a therapeutic target for conditions such hypertension or asthma. Diketopiperazines (DPKs), as the simplest cyclic peptides, have emerged as promising scaffolds for inhibiting protein interactions and modulating receptor activity, offering a novel, appealing therapeutic approach with potentially fewer side effects compared to small-molecule inhibitors.

Methods: In this study, five DPK derivatives were obtained from PubChem and evaluated for their binding affinity to 3D structure of β2-AR (PDB ID = 2RH1) through molecular docking studies using Autodock 4.6 and MGLTools. Each compound’s binding energy and hydrogen bond formation were assessed to determine their interaction efficiency.

Results: Among the five compounds, tryptophan–proline diketopiperazine (compound 3) exhibited the highest binding affinity with a binding energy of -5.89 kcal/mol and formed two hydrogen bonds. The enhanced interaction is attributed to the aromatic nature of tryptophan, which promotes strong π-π stacking interactions, and the rigidity of proline, which allows for optimal fitting within the receptor's binding pocket. The hydrophobic interactions further stabilized the complex.

Conclusion: This study highlights that diketopiperazine (DPK) derivatives, particularly tryptophan–proline diketopiperazine, are promising inhibitors of the β2-Adrenergic Receptor (β2-AR), a key G-protein-coupled receptor (GPCR). The compound’s aromaticity and rigidity enhance receptor interaction, providing insights into the design of peptide-based inhibitors for β2-AR and other GPCR-related diseases, with potential for improved specificity and fewer side effects.