Parkinson’s disease is a neurodegenerative disorder characterized by the degeneration of dopaminergic neurons, resulting in multiple motor and cognitive impairments. Among the hypotheses proposed for its etiology, oxidative stress mediated by the enzyme monoamine oxidase B (MAO-B) stands out, as it is directly associated with dopamine metabolism. In this context, the search for molecules with potential antiparkinsonian activity and low toxicity, particularly those of natural origin, has been extensively investigated using computational approaches. In the present study, a pharmacophore-based virtual screening was carried out on molecules belonging to the alkaloid and flavonoid groups, followed by the evaluation of their pharmacokinetic, toxicological, and biological activity profiles, as well as ligand–receptor interaction analysis through molecular docking. The results indicated that palmatine, genistein, ZINC00597214, and ZINC72342127 exhibited superior performance compared to the other analyzed structures, considering all evaluated criteria. Therefore, this study, through in silico methodologies, demonstrated the antiparkinsonian potential of several chemical structures, attributable to their inhibitory activity on the MAO-B enzyme. Further experimental investigations, both in vitro and in vivo, are necessary to more comprehensively characterize the properties of these molecules, with the ultimate goal of developing new therapeutic strategies for the treatment of Parkinson’s disease.