Parkinson’s disease is a progressive nervous system disorder characterized by motor, cognitive, sensory, psychiatric, and autonomic disturbances. While there is currently no cure for Parkinson’s Disease, medication can offer relief from its symptoms for many years. Although these medications are considered safe, they can present acute or chronic side effects and can become less effective over time. Thus, new medications are highly needed. In this regard, α-synuclein is a protein of great interest to Parkinson’s researchers because it is a major constituent of Lewy bodies, which are protein clumps being the pathological hallmark of Parkinson’s disease. However, current medications are not focused on the inhibition of α-synuclein oligomerization, and therefore, therapeutics preventing the formation of these bodies through the inhibition of α-synuclein oligomerization may play a role in the fight against this and other synucleinopathies. In this study, we used chemoinformatics tools and molecular docking simulations to analyze molecules that have been experimentally tested and bound to α-synuclein, causing neuroprotective or neurotoxic activity, and whose results have been used to select potential natural neuroprotective molecules. We identified 6 potential natural neuroprotective molecules that are similar in their chemical structure to neuroprotective molecules and have a high number of hydrogen bonds with α-synuclein. We expect that these molecules may lead to the design or discovery of new effective treatments for Parkinson’s disease.