Recently, Deep Learning has been applied to many medical domains, such as medical image analysis, bioinformatic, biochemistry, drug design, and so forth, to improve the performance that is superior to traditional computational approaches; especially in computer-aided drug design. Many AI-driven drug discovery startups have utilized deep learning methodology to achieve the significant improvement of searching candidate compounds, predicting functions, and so forth. Therefore, using AI to facilitate drug design is the trend in the coming future. In this study, a comprehensive review of the current state-of-the-art in Computer-Aided Drug Design using deep learning methods is presented. Meanwhile, the challenges and potential of these methods are also highlighted.