Hydrophobic interaction-driven binding of ensifentrine stabilizes PDE3A: insights from X-ray crystallography and molecular dynamics

Abstract

Phosphodiesterase 3A (PDE3A) is a critical regulator of cyclic nucleotide signaling and a significant therapeutic target for cardiovascular and inflammatory airway diseases. Ensifentrine, recently approved as an inhaled dual PDE3 and PDE4 inhibitor for chronic obstructive pulmonary disease (COPD), promotes bronchodilation through PDE3A inhibition and reduces inflammation via PDE4 inhibition. However, the molecular basis for ensifentrine's interaction with PDE3A has remained unclear due to the absence of high-resolution structural data. Here, we combined high-resolution X-ray crystallography (2.1 Å) and extensive molecular dynamics (MD) simulations (200 ns) to elucidate the binding mechanism of ensifentrine to PDE3A. Structural analyses revealed critical hydrophobic interactions, particularly with residues Leu 910 and Phe 972, which contribute significantly to the binding affinity. MD simulations indicated substantial stabilization of flexible loops and increased structural compactness of PDE3A upon ligand binding. MM–PBSA calculations confirmed hydrophobic interactions as the dominant binding force (ΔG = −35.6 kcal mol⁻¹; >85% contribution). These multi-scale structural and dynamic insights provide the first comprehensive molecular picture of the PDE3A–ensifentrine interaction and guide future designs for selective phosphodiesterase inhibitors and synergistic bronchodilator therapies. Notably, this study highlights the potential for improving PDE3A selectivity and designing more effective and selective inhibitors for COPD and other respiratory conditions.