Aptamers have emerged as one of the most promising classes of drug leads and diagnostic ligands presently available. Aptamers, nucleic acid ligands derived from large combinatorial libraries, typically have affinities and specificities that rival antibodies, yet they have a number of significant advantages for therapeutic and diagnostic applications. Unfortunately, the existing process for aptamer development is low-throughput and tedious as DNA or RNA libraries are screened against only a single target. This project focuses on developing the methods and tools to allow large combinatorial to be screened against arrays of thousands of proteins simultaneously. Such protein arrays are increasing available with content of high therapeutic and diagnostic value. The key to achieving this is developing the necessary steps to decipher which aptamers (once selected) correspond to which target. So-called "next generation" sequencing will greatly enable the proposed process coupled with the necessary "sequence-tagging" approaches developed in this project. Once our massively parallel aptamer selection process is developed, we will be in a position to create high affinity aptamer ligands to thousands of proteins in roughly 1 week. The developed ligands can then be further characterized as promising drug candidates, diagnostic labels, and other research applications perhaps eventually including personalized medicine.
A recent white paper by the US Federal Drug Administration finds that there exists a critical problem in bringing novel drugs to market, something the FDA describes as the 'pipeline problem'. According to this and other reports drug companies spend an average of $0.8-1.7 billion dollars on the discovery, development and approval of any one individual drug. To make matters worse, the time from the initial testing of a drug candidate and to its eventual marketing can take up to 20 years. Thus, the FDA report strongly urges the incorporation of novel quantitative predictive tools for the assessment of safety and efficacy of new drug leads and diagnostic ligands early in the drug development process. This project provides for the parallel development and evaluation of enormous combinatorial libraries of DNA or RNA 'aptamers'against of thousands of protein targets of potential 'druggable'interest. If successful, the technology could provide for unprecedented throughput of drug leads and diagnostic ligands.