Computational Insights Into New Portulaca oleracea Alkaloids as Potential SARS-CoV-2 PL^pro Inhibitors

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) papain-like protease (PL^pro) is a multifunctional enzyme essential for viral replication and immune evasion, representing a validated antiviral drug target. Natural alkaloids from Portulaca oleracea L. remain unexplored for their potential against this enzyme. This study provides the first computational evaluation of newly isolated P. oleracea alkaloids as prospective PL^pro inhibitors. Molecular docking revealed favorable binding affinities (-7.81 to -9.31 kcal/mol; K_i 0.15-1.89 µM). Among them, oleracone M, olerapyrimidine, oleracone Q, and olerapyridine showed values close to the co-crystallized inhibitor GRL0617 (-9.28 kcal/mol, K_i = 0.16 µM). Interaction analysis highlighted conserved pharmacophoric contacts, including hydrogen bonds with ASP164 and GLN269, and hydrophobic interactions with TYR264, TYR268, and TYR273. Absorption, distribution, metabolism, excretion, and toxicity (ADMET) predictions further prioritized oleracone M and olerapyrimidine, which satisfied drug-likeness filters and exhibited favorable pharmacokinetic profiles. These two compounds, alongside GRL0617, were subjected to 200 ns molecular dynamics simulations. Root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (R_g), H-bonds, radial distribution function (RDF), solvent-accessible surface area (SASA), probability density functions (PDFs), diffusion, dynamic cross-correlation matrices (DCCM), principal component analysis (PCA), and Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) analyses confirmed stable binding. Collectively, oleracone M may serve as a promising PL^pro inhibitor, whereas olerapyrimidine offers a flexible scaffold for optimization. All findings in this work are derived exclusively from in silico analyses; therefore, experimental validations (in vitro and in vivo) remain essential to confirm their therapeutic potential against coronavirus disease 2019 (COVID-19).