Secondary metabolites are plant products that occur usually in differentiated cells, generally not being necessary for the cells themselves, but likely useful for the plant as a whole. Neurodegeneration can be found in many different levels in the neurons, it always begins at the molecular level and progresses toward the systemic levels. Usually, alterations are observed such as decreasing cholinergic impulse, toxicity related to reactive oxygen species (ROS), inflammatory "amyloid plaque" related processes, catecholamine disequilibrium, etc. Computer aided drug design (CADD) has become relevant in the drug discovery process; technological advances in the areas of molecular structure characterization, computational science, and molecular biology have contributed to the planning of new drugs against neurodegenerative diseases. This review discusses scientific CADD studies of the secondary metabolites. Flavonoids, alkaloids, and xanthone compounds have been studied by various researchers (as inhibitory ligands) in molecular docking; mainly with three enzymes: acetylcholinesterase (AChE; EC 3.1.1.7), butyrylcholinesterase (BChE; EC 3.1.1.8), and monoamine oxidase (MAO; EC 1.4.3.4). In addition, we have applied ligand-based-virtual screening (using Random Forest), associated with structure-based-virtual screening (docking) of a small dataset of 469 alkaloids of the Apocynaceae family from an in-house data bank to select structures with potential inhibitory activity against human AChE. This computer-aided drug design study selected certain alkaloids that might be useful in further studies for the treatment of neurological disorders such as Alzheimer's and Parkinson's disease.