Revenue growth and market capitalization of pharmaceutical firms have plunged over the past 10 years. Why? An important factor is that the engine for growth in drug discovery has come to a standstill. Historic reliance on synthetic organic chemistry and more recent innovations in combinatorial chemistry, randomer libraries and high-throughput screening have individually and collectively failed to meet expectations, as measured by the annual number of new drug approvals. These more recent innovations have yet to be validated in the marketplace, and the cost of conventional block-and-tackle drug development has begun to outweigh returns. Two of the most substantial areas of venture capital/private equity investment in life sciences over the past five years include biomedical applications of nanotechnology and next-generation sequencing (NGS). Investment in NGS is rapidly shifting from technology development to new applications. Until recently, the universal goal of NGS was rapid whole genome sequencing (<$1000/genome). We believe we are the first to use NGS for cancer drug discovery using synthetic nucleic acid and nucleotide-encoded chemical libraries. This proposal focuses on Lab-on-BeadTM enabled Ion Torrent sequencing (ITS) as a high-throughput way to decode single-sequence-per-bead DNA-encoded libraries. Micron-sized beads arrayed in millions of microelectronic wells are used to simultaneously sequence and then functionally select candidate molecules. Our project combines programmable DNA-encoded macrocycle synthesis, Lab-on-Bead processing and NGS to identify new ligands that modulate tyrosine kinase signaling (e.g., cytoplasmic Src kinase) by members of the erbB family of receptors (e.g., Her2) that are overexpressed in breast, prostate and ovarian cancers. Synthetic macrocycles represent an attractive class of drug candidates compared to their linear counterparts in terms of potency, solubility, lipophilicity, specificity, multivalent binding, metabolic stability, bioavailability and membrane permeability. To date, most of the >100 approved macrocycle drugs are derived or modified from natural sources rather than de novo synthesis. Massively parallel macrocycle synthesis can now be achieved by DNA templating, each macrocycle created with a DNA tag that both directs synthesis and encodes candidate identity. The bottleneck in encoded library-based discovery is the need for rapid, efficient screening and selection methods to reduce cost, time, labor and required amounts of library and target. NanoMedica is in the business of helping customers'""""""""discover more with less."""""""" Our competitive advantage in NGS-based drug discovery includes a first-mover opportunity and a strong, preemptive patent portfolio. Benefits include 1) cost-, time- and labor-efficiency through single-cycle selection sans the iterative rounds and subcloning of in vitro evolution;2) only femtomoles of target/library needed per run;3) versatility in selecting DNA- or PNA-encoded molecules, peptides and backbone-modified RNA and DNA aptamers;and 4) potential for in situ determination of target-binding dissociation rates of candidate molecules.

Public Health Relevance

The aims of this proposal are to 1) apply a novel, encoded macrocycle library screening and candidate molecule selection method to discovery of new anticancer drug candidates and 2) harness, develop and market Lab-on-Bead enabled next generation sequencing services capitalizing on programmable synthesis and selection of macrocycles for cancer drug discovery and development. This next-generation Lab-on-Bead sequencing and selection method is designed to discover more with less, as it only requires tiny amounts of target molecules and library candidates and may ultimately be able to screen up to 108 drug candidates in less than a day.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Small Business Innovation Research Grants (SBIR) - Phase I (R43)
Project #
Application #
Study Section
Special Emphasis Panel (ZRG1-OTC-T (10))
Program Officer
Fabian, Miles
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Nanomedica, LLC
United States
Zip Code
Dutta, Samrat; Rivetti, Claudio; Gassman, Natalie R et al. (2018) Analysis of single, cisplatin-induced DNA bends by atomic force microscopy and simulations. J Mol Recognit 31:e2731
Liu, YuYing; Guthold, Martin; Snyder, Matthew J et al. (2015) AFM of self-assembled lambda DNA-histone networks. Colloids Surf B Biointerfaces 134:17-25
Riley, Kathryn R; Gagliano, Jason; Xiao, Jiajie et al. (2015) Combining capillary electrophoresis and next-generation sequencing for aptamer selection. Anal Bioanal Chem 407:1527-32