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: 8392046
• 负责人: Keith D Bonin
• 金额: $ 35万
• 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 2014-10-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8392046
• 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; 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; 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（由申请人提供）：过去10年来，制药公司的收入增长和市值大幅下降。为什么？为什么？一个重要的因素是，药物发现的增长引擎已经停止。历史上对合成有机化学的依赖，以及最近在组合化学、随机库和高通量筛选方面的创新，无论是单独还是共同地都未能达到预期，这一点可以通过每年批准的新药数量来衡量。这些最新的创新尚未在市场上得到验证，传统的阻断和解决药物开发的成本已经开始超过回报。在过去五年中，生命科学领域风险资本/私募股权投资的两个最重要领域包括纳米技术的生物医学应用和下一代测序。对NGS的投资正迅速从技术开发转向新的应用。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进行癌症药物发现的人，使用合成核酸和核苷酸编码的化学文库。该提案侧重于Lab-on-BeadTM启用离子激流测序（ITS）作为高通量方式来解码每个珠DNA编码库的单个序列。排列在数百万个微电子威尔斯孔中的微珠用于同时测序，然后功能性地选择候选分子。我们的项目结合了可编程的DNA编码的大环化合物合成，珠上实验室处理和NGS来鉴定调节酪氨酸激酶信号传导的新配体（例如，胞质Src激酶）通过受体的erbB家族成员（例如，Her 2）在乳腺癌、前列腺癌和卵巢癌中过表达。与线性对应物相比，合成大环化合物在效力、溶解度、亲脂性、特异性、多价结合、代谢稳定性、生物利用度和膜渗透性方面代表了一类有吸引力的候选药物。迄今为止，超过100种已批准的大环化合物药物中的大多数是从天然来源衍生或修饰的，而不是从头合成的。大规模并行大环化合物合成现在可以通过DNA模板化来实现，每个大环化合物用DNA标签创建，所述DNA标签既指导合成又编码候选物身份。基于编码文库的发现中的瓶颈是需要快速、有效的筛选和选择方法来减少成本、时间、劳动力以及文库和靶的所需量。NanoMedica的业务是帮助客户“用更少的钱发现更多的东西。“我们在基于NGS的药物发现方面的竞争优势包括先发机会和强大的先发制人的专利组合。益处包括1）通过单循环选择的成本、时间和劳动效率，而没有体外进化的迭代轮和亚克隆; 2）每次运行仅需要飞摩尔的靶/文库; 3）在选择DNA-或DNA-的多功能性; 4）在选择DNA-或DNA-的多功能性。 PNA编码的分子、肽和主链修饰的RNA和DNA适体;和4）原位测定候选分子的靶结合解离速率的潜力。