Medical Miners

The number of active coalmines is diminishing, but older mines may still have their uses. Specialists in “bioprospecting” – the search for new organisms and biochemistries that could be useful for making drugs – say they have made new versions of the antibiotic daptomycin, using a prenylating enzyme obtained from the smoke vents of a coalmine in Kentucky, USA. The enzyme – named PriB – was isolated from a soil bacterium and could be a useful biocatalysts for drug developers. Prenylating enzymes have been used to modify simple molecules before, but the benefit of PriB is that it can modify more complex drugs – like daptomycin.

We caught up with Jon Thorson, Director of the University of Kentucky’s Center for Pharmaceutical Research and Innovation (CPRI) and co-author of the study (1), to find out more about “bioprospecting.”

How did you get involved with this field of research?

A central theme in our research is the discovery and synthetic application of new enzyme-catalyzed transformations, with a particular emphasis on the biosynthetic pathways used by nature. A natural extension was to get involved in the actual natural product discovery process – so we launched an initiative as part of the new UK CPRI. Though the discovery of new bioactive natural products is a key deliverable of a program like ours, the effort also exposes potentially useful new biocatalysts and biosynthetic pathways. Coalmines and other subterranean environments are a great new place to look for unique biodiversity.

What exactly is PriB?

PriB is a highly permissive indole C-prenyltransferase, the gene for which was found by sequencing the genome of a microbe isolated from the Ruth Mullins underground coalmine and seam fire site. We previously reported that this particular microbe produces a series of new metabolites that contain a uniquely functionalized carbohydrate as part of their structures. Biochemical characterization of PriB revealed unusual permissivity in terms of the enzyme’s ability to use both a wide range of non-native prenyl acceptors and donors as substrates, including the complex natural product-based antibiotic daptomycin. These modifications were subsequently found to improve daptomycin’s antibacterial potency in vitro. The structure of PriB, determined by George Phillips Jr. and colleagues, presents a structural blueprint for understanding PriB ligand recognition and catalysis – and could potentially guide future catalyst engineering. Shanteri Singh also pioneered the surprising discovery that other previously characterized prenyltransferases could also modify daptomycin.

What does the research mean for drug companies?

Though prenylation improves the antibacterial potency of daptomycin, the impact on fundamental drug properties and in vivo efficacy remain to be determined. However, our work offers new enabling biocatalysts and corresponding genes for natural product analoging (via biochemical or strain engineering approaches) that could extend to a variety of drugs beyond daptomycin. Our CPRI natural product repository now contains more than 1000 distinct microbial strains and more than 300 pure microbial natural products (50 percent of which are exclusive to our collection) as a potential source for new industrial biocatalysts and/or new lead compounds. As a related example of biocatalyst discovery and development, our longstanding effort in small molecule glycosylation contributed to the discovery of lead structures that helped launch a new paradigm in antibody drug conjugate technology (currently under development by Centrose).

This glycosylation platform continues to present unique opportunities for improved formulation and targeted delivery.