A great challenge for NP discovery in the post-genomic era is to develop innovative methods to unlock the full NP biosynthetic potential of a large strain collection and produce NPs in sufficient quantities for chemical, biological, and clinical investigations. Strategies for strain prioritization have become increasingly important for targeted NP discovery due to the large number of microbial strains available. We are currently taking two complementary strategies to leverage the strain collection and unlock its biosynthetic potential for NP and drug discovery.
Structure-centric approach to NP discovery: Exploitation of genome data to prioritize strains based on pharmacophores or scaffolds of the targeted NPs. We are running a pilot program to demonstrate the feasibility of sequencing the entire collection, which will enable the establishment of NP BGC data bank to rank them according scaffold, function, or both for targeted NP discovery.
Function-centric approach to NP discovery: Exploitation of activities to prioritize strains based on targets or modes of action of the targeted NPs. We have made ~46,000 crude extracts from ~12,000 actinobacteria, of which ~2,366 have been subjected to large scale fermentation and C-18 chromatography, affording ~28,700 partially purified fractions, and ~158,000 crude extracts from ~23,000 fungi, of which ~2,000 have been subjected to large scale fermentation and C-108 chromatography, affording ~25,000 partially purified fractions. Together with ~600 purified NPs, this library of ~258,000 samples is presented in 384-well format with all materials dissolved in DMSO (1 mM for pure compounds and 50 mg/mL for fractions and extracts), compatible with most of the HTS platforms. We are running multiple pilot projects with biology collaborators and partners to prioritize diseases, pathways, and targets, HTS the library of crude extracts and fractions, and rank the leads for NP discovery and follow up in vitro and in vivo studies.