Targeting PDE4A for therapeutic potential: exploiting drug repurposing approach through virtual screening and molecular dynamics

Abstract

cAMP-specific 3′,5′-cyclic phosphodiesterase 4 A (PDE4A) holds a pivotal role in modulating intracellular levels of cyclic adenosine monophosphate (cAMP). Targeting PDE4A with novel therapeutic agents shows promise in addressing neurological disorders (e.g. Alzheimer’s and Parkinson’s diseases), mood disorders (depression, anxiety), inflammatory conditions (asthma, chronic obstructive pulmonary disease), and even cancer. In this study, we present a comprehensive approach that integrates virtual screening and molecular dynamics (MD) simulations to identify potential inhibitors of PDE4A from the existing pool of FDA-approved drugs. The initial compound selection was conducted focusing on binding affinity scores, which led to the identification of several high-affinity compounds with potential PDE4A binding properties. From the refined selection process, two promising compounds, Fluspirilene and Dihydroergocristine, emerged as strong candidates, displaying substantial affinity and specificity for the PDE4A binding site. Interaction analysis provided robust evidence of their binding capabilities. To gain deeper insights into the dynamic behavior of Fluspirilene and Dihydroergocristine in complex with PDE4A, we conducted 300 ns MD simulations, principal components analysis (PCA), and free energy landscape (FEL) analysis. These analyses revealed that Fluspirilene and Dihydroergocristine binding stabilized the PDE4A structure and induced minimal conformational changes, highlighting their potential as potent binders. In conclusion, our study systematically explores repurposing existing FDA-approved drugs as PDE4A inhibitors through a comprehensive virtual screening pipeline. The identified compounds, Fluspirilene and Dihydroergocristine, exhibit a strong affinity for PDE4A, displaying characteristics that support their suitability for further development as potential therapeutic agents for conditions associated with PDE4A dysfunction.

Communicated by Ramaswamy H. Sarma

Keywords:

• cAMP-specific 3′,5′-cyclic phosphodiesterase 4A
• drug repurposing
• virtual screening
• fluspirilene
• dihydroergocristine

Authors contributions

Mohd Shahnwaz Khan: Writing-original draft, Data Analysis, Investigation; Nojood Altwaijry: Visualization, software, Data validation, writing-original draft, Moyad Shahwan: Visualization, software, Writing-review and editing; Nageeb Hassan: Data curation, Writing-review and editing; Moyad Shahwan: Data Curation, Data Validation, Anas Shamsi: Conceptualization, Software, Data Curation, Methodology, Resources, formal analysis, Project Administration.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

M.S.K. acknowledges the generous support from the Research Supporting project (RSP2024R352) by the King Saud University, Riyadh, Kingdom of Saudi Arabia. A.S. is grateful to Ajman University, UAE for supporting this publication.