This book presents applications of metabolomics and integrated computational systems modeling in the bioprospecting of novel chemical entities (NCEs) and active pharmaceutical ingredients (APIs) from diverse natural sources. It bridges the gap between basic computational skills and advanced software development. The volume comprises original research articles, experimental protocols, case studies, and comprehensive reviews on computational approaches, including targeted and untargeted metabolomics, network pharmacology, molecular docking, density functional theory, and advanced molecular dynamics simulations, among others. An introduction to computational tools, algorithms, and databases relevant to systems biology and their applications in bioprospection A discussion of advanced approaches for the discovery of new bioactive compounds and therapeutic agents Insights into how systems biology simulations of cellular pathways can assist in identifying potential drug targets and bioactive compounds with precise therapeutic effects Reviews of strategic advances in the characterization and application of secondary metabolites derived from plants, microbes, animals, and endophytes Mapping of unexplored target spaces for therapeutic bioprospection This book is intended for researchers and students in bioengineering, natural products development, phytopharmacology, plant biotechnology, drug discovery and development, phytotherapeutics, and metabolomics. .