Comparative Structure-Based Prioritisation of Daniellia oliveri Metabolites Against PBP2a of Staphylococcus aureus and PBP2x of Streptococcus pneumoniae

Background/Objectives: The therapeutic durability of β-lactams is increasingly threatened by penicillin-binding proteins (PBPs) that retain cell-wall transpeptidase activity under antibiotic pressure. This study computationally evaluated 221 Daniellia oliveri metabolites against penicillin-binding protein 2a (PBP2a) of methicillin-resistant Staphylococcus aureus (MRSA) and penicillin-binding protein 2x (PBP2x) of Streptococcus pneumoniae, using amoxicillin and cefotaxime as reference standards. Methods: Molecular docking and interaction analysis prioritised quercitrin, apigetrin, quercetin 3-rutinoside and acid methyl ester for PBP2a, and amyrin, columbin, apigetrin, quercetin 3-rutinoside and N-(2H-tetrazol-5-yl)benzamide for PBP2x. The candidates were further assessed through pharmacokinetic and drug-likeness prediction, 160 ns molecular dynamics (MD) simulations, molecular mechanics/generalised Born surface area (MM/GBSA) analysis and density functional theory (DFT). Results: Quercetin 3-rutinoside emerged as the highest-priority computational dual-target candidate, with the numerically most favourable within-protocol MM/GBSA estimates for PBP2a (−58.51 kcal mol−1) and PBP2x (−55.92 kcal mol−1) among the tested compounds and controls. The compound also had the lowest PBP2a root-mean-square deviation (RMSD; 1.64 Å) and root-mean-square fluctuation (RMSF; 1.26 Å), indicating lower global deviation and residue-level fluctuation in the PBP2a simulation. Against PBP2x, quercetin 3-rutinoside exhibited a higher RMSD (4.98 Å) but a relatively low RMSF (1.75 Å), consistent with greater global protein reorganisation alongside comparatively limited residue-level fluctuation. DFT descriptors of quercetin 3-rutinoside indicated moderate electronic responsiveness, whereas pharmacokinetic profiling revealed high molecular weight, rule-of-five violations, low predicted gastrointestinal absorption and P-glycoprotein liability. Conclusions: Overall, quercetin 3-rutinoside was the highest-ranked computational dual-PBP candidate from D. oliveri; this prioritisation does not establish PBP inhibition and requires structural optimisation and biochemical, antibacterial, safety and in vivo validation.