Unveiling the Molecular Mechanisms of Squalene Epoxidase Inhibition by Flavonoids from Erythrina speciosa: Integrative Computational and Experimental Insights

Elsayed, Rasha H. ORCID: https://orcid.org/0000-0003-3284-4227, Mahmoud, Ayman M ORCID: https://orcid.org/0000-0003-0279-6500, El-Toumy, Sayed A. ORCID: https://orcid.org/0000-0002-4699-1562, Ahmed, Sayed A. ORCID: https://orcid.org/0000-0001-5384-2621, Salah, Bashir ORCID: https://orcid.org/0000-0003-2709-760X, Lamsabhi, Al Mokhtar ORCID: https://orcid.org/0000-0002-1509-2513 and Kamel, Emadeldin M ORCID: https://orcid.org/0000-0002-1279-9564 (2025) Unveiling the Molecular Mechanisms of Squalene Epoxidase Inhibition by Flavonoids from Erythrina speciosa: Integrative Computational and Experimental Insights. Revista Brasileira De Farmacognosia, 35. pp. 599-618.

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Abstract

Squalene epoxidase is a key enzyme in the cholesterol biosynthesis pathway, making it a promising therapeutic target for cholesterol-related disorders. In this study, we integrated computational and experimental approaches to investigate the inhibitory potential of flavonoids isolated from Erythrina speciosa Andrews, Fabaceae, against squalene epoxidase. Molecular docking revealed strong binding affinities for apigenin and vitexin, driven by hydrophobic and electrostatic interactions with critical residues in the squalene epoxidase active site. Molecular dynamics simulations confirmed their binding stability, with low root mean square deviation values, consistent hydrogen bonding, and distinct conformational states supported by potential energy landscape analysis. Interaction energy calculations and binding free energy calculations using MM/PBSA highlighted their favorable binding free energies, underscoring their high affinity for squalene epoxidase. Absorption, distribution, metabolism, and excretion–toxicity analysis demonstrated that both apigenin and vitexin possess favorable drug-like properties, including high bioavailability and compliance with Lipinski’s rule of 5. Experimental validation through in vitro assays confirmed these findings, with apigenin and vitexin exhibiting low IC<inf>50</inf> values (4.70 ± 0.09 and 3.13 ± 0.23 µM, respectively). Enzyme kinetics revealed distinct inhibition mechanisms: apigenin as a mixed inhibitor (Ki = 2.32 µM) and vitexin as a noncompetitive inhibitor (Ki = 3.18 µM). This study highlights apigenin and vitexin as potent squalene epoxidase inhibitors, presenting them as promising lead compounds for further pharmacological development. Moreover, the alignment between computational predictions and experimental results underscores the reliability of the employed computational pipeline, paving the way for future structure-based drug design targeting squalene epoxidase and related enzymes.