The present work aims to cover different aspects of computational tools, particularly focusing on structure-based methods. A general description of these methods precedes the first chapter, which focus on the evolution and current state-of-the-art of molecular docking method, in particular, when challenged in docking small molecules to nucleic acids. Successively, two case studies are presented. The first ‘protein target' study presents the rational investigation of a nanomolar compound (49c), which has been discovered to inhibit a novel class of aspartic proteases, namely Toxoplama gondii aspartyl protease 3 and Plasmodium falciparum plasmepsin IX-X, that are crucial for the respective obligate parasite. The second study presents a combination of in silico and phenotypic approach discovering PK4C9 small molecule modulator targeting TSL2, an RNA motif implicated in the pathogenesis of spinal muscular atrophy. PK4C9 employs its therapeutic effect correcting the splicing and restoring the lacking levels of SNM protein.