UC Berkeley

From the original medicinal plants to the modern formulation laboratories, natural products have played a central role in pharmaceutical science. As technologies have improved from crude extraction to product isolation, and then to heterologous expression and chemical and semi-synthesis, the field of natural product chemistry has expanded greatly. It has produced potent antibiotics, immunosuppressants and anti-cancer drugs. But central to drug discovery is derivitization and the development of new drugs. This can be accomplished by discovering and characterizing new natural product biosynthetic pathways or by developing individual biocatalysts for the alteration of chemical scaffolds. Included in this work are examples of both strategies and each lends new insight and new tools to metabolic engineering and biocatalysis.

The complete characterization of the 15-membered ring depsipeptide neoantimycin biosynthetic gene cluster establishes a biosynthetic route to producing a potent anti-cancer natural product scaffold. Moving this to a heterologous host allowed further engineering of that assembly line with the potential for producing novel neoantimycin derivatives. To demonstrate this, two separate engineering strategies were carried out, and eventually combined, to generate novel analogs. This engineerable hosts suggests that the bioproduction of a small library of neoantimycin analogs for drug discovery may be possible. Additionally, the characterization of a ring expanded antimycin assembly line, provides the necessary knowledge of future study and engineering of the entire family of antimycin depsipeptides.

To address the use of individual biocatalysts in natural product production, two enzymes from the cyclohexylcarbonyl-CoA biosynthetic pathway were fully characterized. The first, a shikimate-CoA synthetase, was shown to be highly promiscuous toward a wide range of small, cyclic carboxylic acids. This has the potential to contribute to drug discovery through the generation of novel thioesters for incorporation into natural product scaffolds. Similarly, an acyl-CoA dehydrogenase was shown to in fact be an acyl-CoA dehydratase that could lead to a new precursor supply of novel thioesters. Together, this work contributes significant new knowledge to the field of biosynthesis and biocatalysis. It provides two new enzymes to the metabolic engineering toolbox, and establishes a system for producing a bioactive scaffold for anti-cancer drug discovery.