Ebola is an acute disease causing hemorrhagic fever marked with high mortality rate. The patients who suffer from Ebola only receive palliative care because there is no available drug which can consistently cure this disease. To date, no cure has been found to treat this disease. Bioinformatics and computer-aided drug discovery and development (CADDD) are employed to utilize the readily available genomic and proteomic data and enhance the hit rate of the novel and repurposed drug for Ebola therapy. Additionally, the time and cost of wet laboratory experiments can be drastically reduced by the support of bioinformatics approach. Our laboratory has succeeded not only in creating the bioinformatics research pipeline but also screening and developing the drug candidate to cure Ebola. Through pharmacophore-based virtual screening and molecular docking simulations, we discovered that about three Indonesian natural product compounds have noteworthy molecular interactions against EBOV VP35 protein, which are responsible for the RNA synthesis of the Ebola. These compounds can be reevaluated further through advances in in silico simulation and in vitro experiments.