In the world, Huntington’s disease, Parkinson’s disease, and Alzheimer’s disease are reported as the most deadly diseases to issue common disorders for human beings. In state-of-the-art works, it is well studied that Huntington’s disease (HD) and Parkinson’s disease (PD) are affected by genetic factors and common motor system disorder, respectively. On the other hand, Alzheimer’s disease (AD) is a neurodegenerative disorder which is categorized by age-related dementia, behavioral changes, and memory loss, etc. In the literature, it is also identified that lots of similar genetic factors are interrelated among these diseases. In this paper, our key objective is to screen out the most significant common gene targets among HD, PD, and AD diseases. Here, the analysis attempts to discover efficient drug design for reactive genes by analyzing the topological properties of protein–protein interaction (PPI) networks. Initially, the analysis is started by reducing the number of total reactive genes (around 37 common genes) through preprocessing and cross-linkage. Afterward, we have identified five most significant hub proteins among these three diseases based on degree value. Moreover, a gene regulatory network has been designed to explain molecular mechanisms that significantly help to discover drugs for targeted genes.