t-SNE is a nonlinear dimension reduction method, and more information is lost based on the number of descriptors used. These results underscore the significant structural diversity offered by natural products, suggesting their potential as a rich source for the discovery of novel compounds in drug development. NPs have historically played a crucial role in the development of many therapeutic agents, accounting for a substantial percentage of drugs currently in use. This diversity not only provides a vast array of unique scaffolds but also facilitates the identification of compounds with distinct biological activities. Furthermore, recent advances in techniques such as high-throughput screening and cheminformatics have enhanced our ability to explore the vast chemical space represented by natural products, leading to the identification of promising candidates for various therapeutic targets and different neglected and emerging diseases.