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Drug design is a research process with a goal of creating a chemical drug to produce the desired biological effect. Because of the long time and the high cost issues associated with traditional drug discovery, there is a need to develop new techniques and strategies to increase the diminishing effectiveness of traditional approaches. Ligand-Based Virtual Screening (LBVS) plays a vital role in the early stage of the drug discovery. It could constitute a possible solution to solve the time and cost problems. Subsequently, the researchers are looking for new methods to find new active compounds and bring them to market in a short time. LBVS can be enhanced by different methods and strategies such as Machine Learning and Deep Learning. In this paper, a Deep Convolutional Neural Network method is proposed to enhance the performances of Ligand-Based Virtual Screening process (DCNNLB). Two main contributions are presented in this paper, The first contribution consists of designing a model based on Deep Convolutional Neural Network (DCNN) for LBVS. We propose several topological network models to find the one that gives the best performance such as accuracy and recall. For this, many network topology configurations have been proposed, and a variety of parameters have been taken into account. Furthermore, our proposed model is trained on all compounds of all activity classes of the Drug Data Report Database (MDDR). Thus, it presented a mean accuracy of 0.98 for all three MDDR Datasets. The second contribution is to generate a new learning representation in order to better represent chemical compound. This representation is based on the extraction of the automatic features learning from the weights of our proposed model. Consequently, it is very efficient in calculating molecular similarity and performances of the LBVS process. The obtained results with the three different datasets drawn from the MDDR and the performance evaluation with ANOVA test, have proved the superiority in performance of our proposed method compared to the different conventional methods. [Display omitted] • New molecular representations obtained by the proposed deep convolutional model. • Enhancement in effectiveness of similarity searching with DCNNLB method in LBVS. • Decreasing in training time by using the molecular learning representation. • The proposed DCNNLB method significantly outperforms the conventional TAN method. [ABSTRACT FROM AUTHOR]