Parkinson’s disease(PD) has been identified as the second most common neurodegenerative disease which affects almost 1% of the world population. Even after decades of research, there is still no known cure for Parkinson’s disease (PD), and available treatments primarily focus on symptom management. BDNF (Brain-derived neurotrophic factor) is the connecting link between Central nervous system (CNS) and Parkinson’s Disease (PD). It plays an important role in nervous system development by maintaining cell differentiation, neuronal development, neurogenesis, and synaptic plasticity. This is the reason for the urgent need to identify the methods to increase the level of BDNF in CNS as a therapeutical tool for neurological diseases. Probiotics can be roughly defined as live microorganisms that can be delivered through food, supplements, drugs and formula. They provide health benefits when administrated in adequate frequency and strength. In silico studies are growing a widely acceptable technique that uses software to capture, analyze and integrate diverse medicinal and biological data from various sources. Here, the already available structure of BDNF interacted with metabolites of 3 different probiotics which are Lactobacillus casei, Bacillus subtilis, Escherichia coli using HEX DOCK. The results obtained show the best-interacted probiotic with BDNF is Escherichia coli with a Total Energy value of −802.33 Cal/mol.