NextGen Lab-on-Bead: Harnessing Ion Torrent Sequencing for Cancer Drug Discovery

NextGen Lab-on-Bead：利用 Ion Torrent 测序进行癌症药物发现

• 批准号: 8575337
• 负责人: Keith D Bonin
• 金额: $ 34.51万
• 依托单位: NANOMEDICA, LLC
• 依托单位国家: 美国
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-11-01 至 2016-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8575337
• 关键词: Address; Affinity; Antibodies; Antineoplastic Agents; Area; Binding; Biological Availability; Biological Sciences; Businesses; Capital; Cell Membrane Permeability; Code; Custom; DNA; DNA Sequence; Dissociation; ErbB Receptor Family Protein; Evolution; Fluorescein-5-isothiocyanate; Genome; Goals; Growth; Heterogeneity; High-Throughput Nucleotide Sequencing; In Situ; In Vitro; Individual; Investments; Ions; Label; Lead; Legal patent; Libraries; Ligand Binding; Ligands; Link; Malignant Neoplasms; Malignant neoplasm of ovary; Malignant neoplasm of prostate; Marketing; Massive Parallel Sequencing; Measurement; Measures; Metabolic; Methods; Nanotechnology; New Drug Approvals; Nucleotide aptamers; Nucleotides; Oligonucleotides; Organic Chemistry; Output; Peptides; Pharmaceutical Preparations; Pharmacologic Substance; Phase; Positioning Attribute; Process; Protein Tyrosine Kinase; RNA; Reliance; Running; Sampling; Scheme; Services; Signal Transduction; Solubility; Source; Specificity; Technology; Testing; Time; Vertebral column; aptamer; base; combinatorial chemistry; commercialization; cost; cost effective; design; drug candidate; drug development; drug discovery; expectation; genome sequencing; high throughput screening; innovation; lipophilicity; malignant breast neoplasm; meetings; member; next generation; next generation sequencing; novel; overexpression; prevent; public health relevance; research study; screening; small molecule libraries; src-Family Kinases; synthetic nucleic acid; technology development; therapeutic target

DESCRIPTION (provided by applicant): 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.

描述(申请人提供)：制药公司的收入增长和市值在过去10年里大幅下降。为什么？一个重要因素是，药物发现的增长引擎已经停滞不前。从每年批准新药的数量来看，历史上对合成有机化学的依赖以及组合化学、随机库和高通量筛选方面的更新创新，个别和共同未能达到预期。这些较新的创新尚未在市场上得到验证，传统的块状和整体式药物开发的成本已经开始超过回报。过去五年，生命科学领域风险资本/私募股权投资的两个最重要的领域包括纳米技术的生物医学应用和下一代测序(NGS)。对NGS的投资正迅速从技术开发转向新应用。直到最近，NGS的普遍目标是快速全基因组测序(1000美元/基因组)。我们相信，我们是第一个使用NGS利用合成核酸和核苷酸编码的化学库来发现癌症药物的公司。这项提案将重点放在启用了BeadTM上的Lab-on-BeadTM的离子激流测序(ITS)上，作为一种高通量的方法来解码每个珠单序列DNA编码库。微米大小的珠子排列在数百万个微电子井中，用于同时对候选分子进行测序，然后从功能上选择候选分子。我们的项目结合了可编程DNA编码的大周期合成、Lab-on-Bead处理和NGS来识别新的配体，这些配体通过在乳腺癌、前列腺癌和卵巢癌中过度表达的erb B受体家族成员(例如Her2)来调节酪氨酸激酶信号转导(例如细胞质Src激酶)。合成大环在效力、溶解性、亲脂性、特异性、多价结合、代谢稳定性、生物利用度和膜通透性等方面与线性大环相比是一类很有吸引力的候选药物。到目前为止，大多数&gt；100批准的大周期药物都是从自然来源获得或修改的，而不是从头合成。现在可以通过DNA模板来实现大规模并行大环合成，每个大环都创建了一个DNA标签，该标签既指导合成又编码候选身份。基于编码库的发现的瓶颈是需要快速、高效的筛选和选择方法来减少成本、时间、劳动力以及所需的库和目标的数量。NanoMedica的业务是帮助客户“用更少的资源发现更多的东西”。我们在基于NGS的药物发现方面的竞争优势包括先发制人的机会和强大的、先发制人的专利组合。好处包括：1)通过单周期选择省去了体外进化的迭代轮次和亚克隆；2)每次运行只需要靶分子/文库的毫微米分子；3)选择DNA或 PNA编码的分子、肽和骨架修饰的RNA和DNA适配子；以及4)原位测定候选分子的靶结合解离率的可能性。

项目成果

Combining capillary electrophoresis and next-generation sequencing for aptamer selection.

• DOI: 10.1007/s00216-014-8427-y
• 发表时间: 2015-02
• 期刊: ANALYTICAL AND BIOANALYTICAL CHEMISTRY
• 影响因子: 4.3
• 作者: Riley, Kathryn R.;Gagliano, Jason;Xiao, Jiajie;Libby, Kara;Saito, Shingo;Yu, Guo;Cubicciotti, Roger;Macosko, Jed;Colyer, Christa L.;Guthold, Martin;Bonin, Keith
• 通讯作者: Bonin, Keith