The Center has infrastructure to run medium- to high-throughput screening campaigns (96- and 384-well) and experienced personnel to miniaturize assays. We acquired libraries of small interfering RNAs (siRNAs) that specifically target the druggable human genome (8,000 targets). For each targeted transcript we have four individual, independent siRNAs (32,000). The library is arrayed in 96-well format and is spotted out into 384-well screening sets using our in-house robotics. Analogous overexpression screens can be run with arrayed cDNA libraries which are commercially available. These screens can be used not only to discover new targets, but also to interrogate mechanisms of action of drug candidates, since target depletion or overexpression modulates cellular susceptibility to the bioactive compounds. Genomic as well as small molecule/natural products library screens also can be extended to screens with isogenic pair cell lines. Comparative screening of certain knockout cells and parental cells for siRNAs and small molecules that specifically affect the target pathway could yield new drug targets and new therapeutic agents, respectively.
The CNPD3 also integrates whole-organism screening into its assay platform. In particular, the transparent free living nematode Caenorhabditis elegans is genetically tractable, and mutants and transgenic reporter strains are available for screening. Activity in this in vivo model is predictive of bioavailability. Infrastructure is being developed to accommodate various screening readouts, including luminescence, fluorescence and high-content imaging. Our multidimensional genomic assay platform is complemented by a powerful, focused chemical platform with emphasis on natural products and natural products-like libraries.
Approximately half of the current drugs are natural products or derivatives thereof, demonstrating the potential of natural resources for drug discovery. One reason for the suitability of natural products as therapeutics or at least as lead candidates for drug discovery is their biologically relevant chemical diversity. Natural products have evolved with and against their biological targets, which is oftentimes manifested in high affinity interactions. In addition to being a historically prolific source of drugs, Nature has also provided us with arguably the best tool compounds for chemical biology, such as rapamycin, FK506 and cyclosporin. These compounds likely represent only a fraction of what is awaiting discovery. Particularly the marine world represents a largely untapped resource, and we are only beginning to exploit chemical secrets found in marine organisms.
View recent news articles for updates on CNPD3 marine natural product compound discoveries and published findings.
A compound identified during the discovery program will serve as the starting point for development campaigns, including medicinal chemistry to establish structure‒activity relationships and improve drug-like properties of the compounds, ADME and PK studies as well as formulation, delivery, and pharmacology. The identification and monitoring of biomarkers is critical to interrogate target engagement and correlate with efficacy.
To fully harness the biosynthetic potential of the organisms that produce these natural products, the CNPD3 will obtain the genomic and metagenomic DNA. The focus here will be on microbes which appear to produce the richest chemical diversity, while 99 percent of them are still considered uncultivable. The standard screening methods are limited to organisms that can be cultured and/or whose biosynthetic operons are sufficiently expressed in nature (e.g., ocean) or under laboratory culture conditions to provide assayable amounts of active material. These intrinsic limitations reduce the rate of new discoveries, and the CNPD3 will leverage advances in synthetic biology to engineer model microorganisms for the production of natural products. Genomic and metagenomic DNA obtained from particularly unexplored marine microbes will be subjected to next-generation high-throughput sequencing, which will be the starting point for bioinformatic analysis.
In parallel, we are investigating natural products that have been used in diets, as dietary supplements or anecdotally for the purpose of conferring health benefits. We provide the scientific rationale and molecular basis for some of the reported health-promoting activities and link circumstantial anecdotic evidence to hard science.