Polyketide natural products represent excellent lead molecules for drug discovery and development. Biosynthetic engineering to optimise polyketide lead molecules in a medicinal chemistry-type approach is used to generate novel analogues which may be difficult to attain by semi-synthetic chemistry. Examples include inhibitors of Hsp90, mTOR and novel targets in angiogenesis. It is our experience that small changes in structure can have a profound influence on biological activity. For example borrelidin is a potent inhibitor of both angiogenesis and spontaneous metastasis. Using semi-synthetic derivatives of borrelidin and an inactive analogue as chemical probes for the affinity biopanning of a phage display library of colon tumor cell cDNAs a novel spliceosome-associated protein has been identified as a potential molecular target of borrelidin. Borrelidin is believed to act as a modulator of alternative splicing via disruption of specific protein:protein interactions. In support of this idea, borrelidin, and it’s more selective analog BC194, bound tightly to purified recombinant target protein. They also altered the ratio of vascular endothelial growth factor (VEGF) isoforms in retinal pigmented endothelial cells in favour of anti-angiogenic isoforms. Further, transfection with the protein target altered the ratio in favour of pro-angiogenic isoforms, and this effect was inhibited by BC194. These data implicate the protein target in the regulation of alternative splicing and suggest the potential of borrelidin analogs as tools to deconvolute key steps in spliceosome function. BC194 is one of a library of borrelidin analogues generated by mutasynthesis.