Aptamers are structured single-stranded oligonucleotides capable of highly specific target recognition. Shuhao Zhu, associate director, Archemix (www.archemix.com), noted that they are “an exciting new therapeutic modality.” His presentation focused on how Archemix is facilitating aptamer discovery.
Dr. Zhu noted that there is currently only one approved aptamer therapeutic, Macugen. Several more aptamers are in various stages of clinical development. “The aptamer lead-discovery process is enabled by a series of platform assays that allow for efficient measurement of aptamer-target affinities,” Dr. Zhu continued. “Aptamers are easily synthesized chemically, which allows for rapid screening assay turn-around and SAR analysis.”
Dr. Zhu described the use of SPR and 96-well flow cytometry-based assays to characterize, minimize, and optimize aptamers during the discovery stage and described how competitive ELISA and FACS assays have been used to prioritize aptamer hits.
“One challenge we are facing is that we have many discovery programs, and we need to screen a huge amount of aptamers targeting different biological molecules. To simplify the early-stage screening process, we need screening toolboxes to address the needs of different discovery programs. The SPR-based binding assay provides real-time measurement of on- and off-rate without labeling, and our plate-based FACS-binding assay provides a measurement of aptamer affinity toward the cell-presented targets. These platform-based screening assays used at the discovery stage can be easily translated for use in PK/PD assessment during downstream development.”
Recent technological advances have improved the speed and reliability of HTS, but the total number of compounds that can be assayed using these methods remains in the 106 range, said John W. Cuozzo, Ph.D., director, ELT lead discovery, GlaxoSmithKline (www.gsk.com)
“Aptamer-, phage-, and antibody-screening libraries have significantly greater diversity and can be rapidly queried for hits by selection.”
Encoded library technology (ELT) combines affinity-based enrichment with combinatorial chemistry to enable the rapid selection of hits from small molecule libraries containing up to several billion compounds. “Each ELT library molecule carries a unique DNA tag that encodes the chemical composition of the small molecule,” explained Dr. Cuozzo. “Libraries are selected against protein targets by affinity-based methods. Enriched binders are isolated, sequenced, and translated back into their corresponding chemical structures. The hit compounds are then synthesized without the DNA tag and assayed for activity against the target.”
“We focus largely on soluble protein targets—approximately half of our targets are soluble proteins,” said Robert Hertzberg, Ph.D., vp, screening and compound profiling. “Not all targets are amenable to this approach, e.g., ion channels are currently not. However, we are working to extend this technology.”
Drs. Cuozzo and Hertzberg agreed that key differentiators of ELT are the size of the library, currently some 10 billion compounds, against the key constants of economy and time. “Our primary goal is to increase the likelihood of quality hits,” noted Dr. Hertzberg. “We’re pushing to increase the number and diversity of compounds in the clinic.”