High-Throughput Functional Annotation of Natural Products by Integrated Activity Profiling

Determining mechanism of action (MOA) is one of the biggest challenges in natural products discovery. Here, we report a comprehensive platform that uses Similarity Network Fusion (SNF) to improve MOA predictions by integrating data from the cytological profiling high-content imaging platform and the gene expression platform FUSION, and pairs these data with untargeted metabolomics analysis for de novo bioactive compound discovery. The predictive value of the integrative approach was assessed using a library of target-annotated small molecules as benchmarks. Using Kolmogorov–Smirnov (KS) tests to compare in-class to out-of-class similarity, we found that SNF retains the ability to identify significant in-class similarity across a diverse set of target classes, and could also find target classes that were not detectable in either platform alone. This confirmed that integration of expression-based and image-based phenotypes can accurately report on MOA. Furthermore, we integrated untargeted metabolomics of complex natural product fractions with the SNF network to map biological signatures to specific metabolites. Three examples are presented where SNF coupled with metabolomics was used to directly functionally characterize natural products and accelerate identification of bioactive metabolites, including the discovery of the novel azoxy-containing biaryl compounds parkamycins A and B. Our results support SNF integration of multiple phenotypic screening approaches along with untargeted metabolomics as a powerful approach for advancing natural products drug discovery. Significance statement New data-driven methods to aid in the discovery and biological characterization of natural products are necessary to advance the field. Assigning the mechanism of action (MOA) to novel bioactive compounds is an essential step in drug discovery and a major challenge in chemical biology. Despite technological advances in isolation, synthesis and screening strategies that make many bioactive substances readily available, in most cases their biological targets remain unknown. Additionally, a major bottleneck in natural products discovery efforts is de-replication of the large number of known compounds that predominate in crude extracts and fraction libraries. Advances in metabolomics has provided a better understanding of the constituents present in these libraries, but is not sufficient in itself to drive the discovery of novel biologically active metabolites. Here we describe an unbiased, data-driven strategy which integrates phenotypic screening with metabolomics into a single platform that provides rapid identification and functional annotation of natural products. This approach can be applied to any cohort of uncharacterized chemicals and represents a strategy that could significantly accelerate the process of drug discovery.