Natural living organisms produce many natural compounds with diverse structures. They are one of the most productive sources of drug/bio-probe discovery and development, biosynthesis and enzymology, and organic synthesis. So far, more than 40% of current commercial drugs are natural products or natural product derivatives. However, given the highly selective modification site of natural products, de novo chemical synthesis and modification of natural products can be hard to design and sometimes problematic. To better exploit nature’s tool, I studied the structures of biosynthesizing enzymes for several potential drug leads by X-ray crystallography. Specifically, I studied the loop dynamics of TDP-rhamnose 3’-O-methyltransferase (Cals11), an enzyme in calicheamicin biosynthesis. I also characterized the structure and mechanism of decarboxylase (TtnD) as well as a non-heme FeII/α-ketoglutarate dependent hydroxylase (TtnM), both of which are involved in Tautomycetin biosynthesis. These results would provide us with guidance to engineering more efficient enzymes with different substrate specificity. Also, the impact of natural products in bioactive probe or drug lead discovery/development has faltered in the last decade due to an inability of natural products discovery technologies to keep pace with monumental advances in both screening and library synthesis platforms. Importantly, this de-emphasis in natural products discovery programs correlates with an overall reduction in new chemical entities/leads in the development pipeline. Thus, technological innovation is needed to realign natural product discovery with next generation technologies. The two most significant challenges in the discovery of new microbial natural products are: i) how to rapidly identify strains capable of novel chemistries (strain dereplication); and ii) how to expedite the subsequent structure determination of new natural products (structure elucidation). I propose a new paradigm for rapid unambiguous natural product structure elucidation, which will require very small amounts (g) of target natural product and, when merged with the rapid metabolomics-based dereplication process described herein, offers the potential to transform the natural products discovery process.