Secondary metabolites produced by plants are valuable for their essential roles in food, medicine, and agrochemicals. Several of them have positive effects on health, such as reducing the risks of many chronic diseases like cardiovascular diseases, diabetes and cancer. They also show a wide range of pest control activities and have long been used to produce pesticides. However, the information about the classification of secondary metabolites and their known protein targets in human diseases is scattered in many publications. Furthermore, large data of published findings are available, which needs to be analyzed and managed for the best use and efficacy of the available products. Chemoinformatics techniques can use the vast chemical and bioactivity experimental data of various compounds and convert it into valuable knowledge for drug or lead design. Chemoinformatics tools and other in-silico drug designing software play an important role in designing novel drugs with no or fewer side effects and other drug interactions. We performed chemoinformatic analysis for ligand-based drug designing from secondary metabolites of plants. The analysis revealed that several bioactive compounds could serve as scaffolds for developing novel drugs, which can be analyzed further by experimental methods. Lipinski’s “Rule of Five” approach was quickly adopted in the field of agrochemical discovery and led to the establishment of rules for pesticide-likeness. The challenges identified in this study will serve as a useful reference for future intensive research in drug and pesticide discovery.

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