Library Synthesis Core

文库合成核心

• 批准号: 7695399
• 负责人: Scott Edward Schaus
• 金额: $ 132.54万
• 依托单位: BOSTON UNIVERSITY (CHARLES RIVER CAMPUS)
• 依托单位国家: 美国
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-09-30 至 2013-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7695399
• 关键词: Accounting; Acids; Aldehydes; Alder plant; Aliquot; Architecture; Atlases; Benzaldehyde; Biological; Cataloging; Catalogs; Chemicals; Chemistry; Collaborations; Collection; Communities; Computer software; Computers; Custom; Cyclopropanes; DNA Sequence Rearrangement; Data; Databases; Development; Development Plans; Devices; Dimethyl Sulfoxide; Electronics; Ensure; Environment; Equipment and supply inventories; Evaluation; Evaluation Methodology; Event; Facility Construction Funding Category; Generations; Glass; Goals; High Pressure Liquid Chromatography; Human Resources; Image; Individual; Informatics; Information Storage; Information Systems; Internet; Java; Ketones; Knowledge; Laboratories; Letters; Libraries; Linux; Maintenance; Mediating; Metadata; Methodology; Methods; Microfluidics; Numbers; Organic Synthesis; Output; Phase; Physical condensation; Placement; Plant Resins; Plastics; Positioning Attribute; Postdoctoral Fellow; Procedures; Process; Protocols documentation; Published Comment; Reaction; Reagent; Relative (related person); Reporting; Research; Research Personnel; Resources; Robin bird; Sampling; Scandium; Scheme; Scientist; Screening procedure; Secure; Services; Shipping; Ships; Site; Social Network; Solid; Solutions; Specialist; Staging; Structure; Students; Subgroup; System; Techniques; United States National Institutes of Health; Validation; Vial device; Water; Week; Weight; Work; base; catalyst; cyclopropane; data management; day; design; detector; digital; instrumentation; interest; liquid chromatography mass spectrometry; mass spectrometer; member; method development; novel; outreach program; programs; rehearsal; repository; scaffold; seal; small molecule libraries; stereochemistry; tool

Q.1 Library Synthesis Core. Q.I7 Personnel: The continuing goal of the Library Synthesis Core (LSC) will be to develop and disseminate chemical methodology and synthesize chemical libraries as described in the project descriptions (section P). The LSC is subdivided between the three projects described in this proposal, though the interactions between project team members and methodology overlap will be quite extensive. Each project subgroup within the LSC will consist of one postdoctoral fellow and two graduate students. In the course of the library synthesis, the project subgroups will be responsible for methods development, library synthesis, and purity assessment. After library synthesis and purity assessment are completed, the libraries will be delivered to the Administrative and Compound Inventory Core (ACIC) for database entry and storage, and ultimately shipped to members of the Chemical Library Consortium (CLC). Within the LSC, the Assistant Director (Aaron Beeler) oversees the day-to-day management of all three projects, interacting with the postdoctoral students, graduate students, and technicians. He is also responsible for ensuring that the synthesis core accomplishes its stated goals, which include: (1) design of libraries for each project; (2) development and validation of methodologies and reaction protocols for generation and purification of chemical libraries; (3) interacting with the analytical services group for library analysis in the assessment of purity; (4) transferring the libraries to the ACIC for storage and maintenance; and (5) interacting with ACIC personnel to implement the biological and community outreach programs. The Organic Synthesis Specialists (OSS) will primarily implement library synthesis based on methodologies developed in the LSC. Information technology systems support within the Library Synthesis Core will be provided by Aruna Jain. This will mainly consist of oversight of the computers and databases used by the LSC. Dayle Acquilano, the Compound Curator, will continue to facilitate transfer of compound collections from the LSC to the ACIC. Placement of orders and other administrative duties will be provided by Paul Ferrari and Sarah Coenen. Q. 1.2 Library Synthesis: Our specific goals in library synthesis will focus on generation of discrete multimilligram quantities of compounds in pure form (>90% analytical purity). The development of a library synthesis plan will involve five stages (Figure 1). 1) Transfer and Validation Stage. In this stage, a postdoctoral fellow or graduate student responsible for methodology development will be paired with an Organic Synthesis Specialist (OSS) to adapt the methodology from the development stage to parallel synthesis. Strategies for this transition will vary depending on the chemistry involved, but will focus on evaluation of methodology scope and limitations, and utilization of supported reagents, scavengers, and purification techniques. Details of the overall workflow will be determined during this phase, including intermediate parallel work-up steps required (e.g. solid phase extraction (SPE)) and development of HPLC methods suitable for the compounds of interest. This first stage of library synthesis will rely heavily on small scale reaction blocks (48 position MiniBlock XT). This stage generally requires 4-8 weeks. 2) Synthesis of Scaffolds and Building Blocks. The synthesis of building blocks and scaffolds will be performed on scales suitable for the synthesis of 30 mg of each compound planned for library synthesis. Starting material and intermediates will be synthesized by the Organic Synthesis Specialists. The synthesis of scaffolds will be conducted in a low throughput/high output manner utilizing parallel reaction vessels capable of 50 - 200 ml reaction volumes (6 position MiniBlock XT, Syrris Atlas). In this regard, sufficient scaffold material will be prepared for library synthesis and storage of a stock amount for anticipated resynthesis efforts (2-5 g of each scaffold). Building blocks, including custom diversity reagents, will also be synthesized during this phase as required. This stage generally requires 3-7 weeks. 3) Library Rehearsal. Upon completion of scaffold and building block synthesis, we will rehearse a subset of the overall library. In order to minimize loss of custom scaffolds and building blocks, we have successfully employed analytical library rehearsal protocols involving piloting of reactions on approximately 10 jimol scale and analysis of reactions using HPLC/MS/ELSD. Library rehearsal will be conducted in 96-position reaction blocks and carried through the necessary work-up procedures. Each reaction will then be aliquoted for analysis using a Waters Acquity UPLC/UV/ELS/MS system and a Protasis MicroFlow Probe equipped with an autosampling system. Library rehearsal generally requires 1-2 weeks for completion. 4) Library Synthesis and Purification. The synthesis of preparative scale libraries will be carried out in 24 - 48 reaction arrays. Compounds will be synthesized on approximately 20-30 mg scale. Solution-phase parallel synthesis will be the main approach and will be accomplished using MiniBlock¿ XT and SynthArray-24 reaction blocks. In the event that solid supported reagents or scavengers are utilized, the library synthesis will be carried out using MiniBlock systems equipped with 20 mL reaction vessels. Solid reagents such as catalysts or resins will be weighed into appropriate reaction vessels using the AutoChem FlexiWeigh system. This system is capable of weighing all types of solid materials and weights from 1 - 200 mg. All library members will be purified by the Purification Specialist using mass directed preparative HPLC (Waters FractionLynx Autopurification system equipped with a Micromass ZQ quadrapole mass spectrometer, Waters 996 diode array, and Sedere Sedex 75 ELS detectors). While many library synthesis efforts will be carried out utilizing parallel reaction blocks, the AutoChem FlexiWeigh, and digital pipettors, we will begin to incorporate microfluidic synthesis as described in Project 3. Synthesis and purification of a library generally requires 2-4 weeks. 5) Library Analysis and Compound Management. Immediately following the purification process, each compound will be evaluated for purity using analytical LC/MS/UV/ELSD (Waters Acquity System). Compounds with less than 90% purity will be subjected to a second preparative HPLC purification. If a compound is not purified to greater than 90% purity after two purification attempts, it will be removed from the library. Once all compounds have been verified for purity, they will be subjected to structural verification using the Protasis 1 minute NMR system. Upon validation of compound purity and structure, each library member will be transferred (using a Zinnser Lissy2002) to 15 x 45 mm conical bottom glass vials with septa screw tops (each vial will have a barcode and will be pre-weighed using the AutoChem FlexiWeigh) and evaporated using a GeneVac HT-4. After the weight of each sample has been determined, structural, analytical, and storage information will be entered into a secure IDBS Activity Base database. Vials will be stored in 24-position racks situated in sealed containers with Drierite. The sealed plastic containers (four 24-position racks each) will be stored in -40 ¿C freezers. When compound libraries have been approved for submission to the NIH repository, samples will be dissolved in DMSO and transferred to vials provided by DPI using the Zinsser Lissy2002. New compound IDs will be entered into the database and compounds will be sent to the repository as dry samples or in DMSO as instructed. Each compound will be accompanied by electronic LC/MS. Building blocks and scaffolds will also be stored and catalogued for potential use in resynthesis efforts. Analysis of purified compounds, registration, and shipment will require two weeks. 0.1.3 Library Synthesis Core Informatics: The goal of the Synthesis Core Informatics initiative at the CMLD-BU is to develop an integrated electronic research environment software suite for all affiliated scientists. The software package will integrate synthetic procedures, compound registration, and biological data management into a single electronic data management resource. This project will be conducted in collaboration with ArtusLabs, Inc. (see letter of collaboration from Robin Smith). The project's scope will include the development of a social networking research environment that allows researchers to record their collaborative work in shared electronic laboratory notebooks. Through these shared notebooks, the software will greatly facilitate collaboration among scientific colleagues whether in the same lab or in different buildings. This tool is especially important for the CMLD-BU because key collaborations are being established with researchers at MIT. Academic or CLC collaborators will be easily accommodated in the group, and their contributions will facilitate the association of biological data to specific compounds or compound collections. The research planning software and database will maintain a large amount of information (documents, images, and spreadsheets) for compounds, reaction screens, projects, and studies. The information architecture will group related assets to individual compounds and establish connections between associated metadata, based on how people interact with the information (i.e. reaction development, catalyst, biological activity, analytical device). These metadata connections will allow researchers to track down important information more intuitively, through a variety of commonalities across contexts, rather than isolating information by study or project. The software suite will be programmed using Java and Ajax to ensure cross-platform compatibility (PC, Mac, and Linux). Individual researchers will be able to easily access their accounts and electronic laboratory notebooks via the Internet through any Web browser. Specific functionalities to be developed include an imbedded Java-based chemical drawing program, reaction planning capabilities, reaction screening using multidimensional processes, chemical library planning and construction, integration of ACD/Labs analytical software for instrumentation, and complete searching capabilities (e.g.. by keyword, substructure, reagent, scientist, etc.). Researchers will be able to associate biological data and add comments to that data as well as to compounds and procedures. This functionality is intended to facilitate and sustain collaborative research, as all researchers in the CMLD-BU and affiliated groups will have access to the electronic laboratory notebook. Through the development of this new collaborative research environment software suite, the CMLD-BU will continue to grow as a collection of scientists who operate synergistically to accomplish the goals of the CMLD program. The plan for development of the ArtusLabs software will take place from the summer of 2008 until the Spring of 2009. During the transition to the new electronic reaction planning software, the Symyx Reaction Planner will be used by researchers at the CMLD-BU. Q.1.4 Synthesis of Libraries Utilizing Current CMLD-BU Methodologies: The LSC will also be responsible for identifying methodologies developed in the CMLD-BU that have not yet been transferred to library synthesis. The following are methodologies that will be adapted to library synthesis by an Organic Synthesis Specialist. 1) Cyclopropanation of Alkynyl Isochromenes. Yamamoto and co-workers reported the synthesis of naphthyl ketones utilizing a cycloisomerization/Diels-Alder sequence starting with diyne benzaldehydes.' Inspired by these examples, we have utilized diyne benzaldehydes as potential substrates for tandem cycloisomerization processes to afford novel chemotypes. Initial studies revealed that upon treatment of diyne 1 with Cu(l), cycloisomerization occurred affording isochromene 2 (Scheme 1).2 The isochromene was readily transformed to fused cyclopropane 3 in the presence of PtCI2. pai-Acid mediated cyclopropanations of enynes have been reported,3 however, such reactions have not been reported to our knowledge utilizing isochromenes. Thus, the reaction will be further developed to incorporate a number of diversity sites which may be exploited for library synthesis (Scheme 1, inset). The fused cyclopropanes produced may also serve as substrates for further library synthesis through base-catalyzed rearrangement (Scheme 2). Enolization of 3 initiated an unanticipated rearrangement process to afford polycyclic ketone 6. In this manner, we intend to synthesize a library of 96 fused cyclopropanes of which 24 library members will be selected for synthesis of a sublibrary utilizing the base-mediated rearrangement. 2J Synthesis of indenoisoauinoline-derived libraries. An ongoing project in the CMLD-BU has focused on exploration of chemical transformations involving dihydroisoquinolines.4 We have demonstrated that in the presence of an aldehyde and scandium triflate as catalyst, dihydroisoquinoline 7 undergoes condensation to afford indenoisoquinoline 8. The relative stereochemistry of 8 was confirmed through an interesting annulation process to afford the bridged indenoisoquinoline 9. Efforts toward adaptation of this methodology to parallel synthesis will initiate with evaluation of potential diversity sites. At this point the design of a library of indenoisoquinolines will be conducted and the library synthesis completed to afford approximately 86 novel compounds. Several of the primary library members will be selected for the synthesis of a sublibrary through the bromination/annulation process. Representative library members are shown in Figure 3.

Q.1 文库综合核心。 Q.I7 人员：Library Synthesis Core (LSC) 的持续目标是开发和传播 化学方法学并合成化学库，如项目描述（P 部分）中所述。 LSC 被细分为本提案中描述的三个项目，尽管各项目之间的相互作用 项目团队成员和方法的重叠将相当广泛。 LSC 内的每个项目小组将由一名博士后研究员和两名研究生组成。 在库合成过程中，项目小组将负责方法开发， 文库合成和纯度评估完成后， 图书馆将被交付给管理和复合库存核心（ACIC）进行数据库输入和 存储，并最终运送给 LSC 内的化学图书馆联盟 (CLC) 成员。 助理总监（Aaron Beeler）负责监督所有三个项目的日常管理，并与 他还负责确保博士后、研究生和技术人员的工作。 综合核心实现其既定目标，其中包括：（1）为每个项目设计库；（2） 化学品生成和纯化的方法和反应方案的开发和验证 (3) 在纯度评估中与文库分析的分析服务小组进行互动； 将库移交给 ACIC 进行存储和维护；以及 (5) 与 ACIC 人员互动 有机合成专家 (OSS) 将实施生物和社区外展计划。 主要基于 LSC 开发的方法实现库合成。 图书馆综合核心内的信息技术系统支持将由 Aruna 提供 Jain. 这主要包括对 LSC 使用的计算机和数据库的监督。 化合物馆长将继续促进化合物收藏从 LSC 转移到 ACIC。 Paul Ferrari 和 Sarah Coenen 将负责下订单和其他行政职责。 Q. 1.2 文库合成：我们文库合成的具体目标将集中于离散多毫克的生成 大量纯化合物（>90% 分析纯度）的库的开发。 综合计划将涉及五个阶段（图1）。 1) 传输和验证阶段。 阶段，博士后研究员或研究生 学生负责方法论 发展将与有机相结合 综合专家（OSS）以适应 从开发阶段到方法论 这种转变的并行综合策略。 会根据所涉及的化学反应而变化， 但将侧重于方法评估 范围和限制以及利用 支持的试剂、清除剂和 整体净化技术细节。 工作流程将在此阶段确定， 包括中间并行处理步骤 需要（例如固相萃取 (SPE)） 并开发合适的 HPLC 方法 对于感兴趣的化合物。 文库合成将严重依赖于小 刻度反应块（48 位 MiniBlock XT）。这个阶段一般需要4-8周。 2) 支架和构件的合成。 积木和支架的合成 将在适合的规模上进行 每种化合物 30 mg 的合成 计划用于文库合成。 和中间体将由合成 有机合成专家。 脚手架将在低 吞吐量/高输出方式利用率 能够容纳 50 - 200 ml 反应体积的平行反应容器（6 位 MiniBlock XT、Syrris Atlas）。 在这方面，将准备足够的支架材料用于文库合成和储存量 预期的再合成工作（每个支架 2-5 克），包括定制多样性试剂。 也可根据需要在此阶段进行合成。此阶段一般需要3-7周。 3) 库排练 完成脚手架和构建块合成后，我们将排练一部分。 为了最大限度地减少定制脚手架和构建块的损失，我们成功地完成了整个库的设计。 采用分析库演练方案，涉及约 10 jimol 规模的反应试验 使用 HPLC/MS/ELSD 的反应分析将在 96 位反应中进行。 然后将每个反应进行等分以进行分析。 使用 Waters Acquity UPLC/UV/ELS/MS 系统和配备了 自动采样系统。图书馆排练一般需要1-2周才能完成。 4) 文库合成和纯化 制备型文库的合成将在 24 - 48 日进行。 反应阵列将以大约 20-30 mg 规模合成。 合成将是主要方法，并将使用 MiniBlock 来完成XT 和 SynthArray-24 如果使用固体支持的试剂或清除剂，则文库合成将进行。 使用配备 20 mL 反应容器的 MiniBlock 系统进行。固体试剂，例如催化剂。 或树脂将使用 AutoChem FlexiWeigh 系统称重到适当的反应容器中。 系统能够称重所有类型的固体材料，重量范围为 1 - 200 mg 所有图书馆成员都会。 由纯化专家使用质量定向制备型 HPLC（Waters FractionLynx 自动纯化系统配备 Micromass ZQ 四极杆质谱仪、Waters 996 二极管 阵列和 Sedere Sedex 75 ELS 检测器），而许多文库合成工作将利用该技术进行。 平行反应模块、AutoChem FlexiWeigh 和数字移液器，我们将开始整合 微流控合成如项目3所述。文库的合成和纯化一般需要2-4 几周。 5) 纯化过程之后立即进行文库分析和化合物管理。 将使用分析型 LC/MS/UV/ELSD（沃特世化合物分析系统）评估化合物的纯度。 如果化合物不合格，则纯度低于 90% 的化合物将进行第二次制备型 HPLC 纯化。 经过两次纯化尝试后纯化至纯度大于 90%，一旦全部从文库中删除。 化合物已经过纯度验证，将使用 Protasis 1 对其进行结构验证 分钟 NMR 系统验证化合物纯度和结构后，每个库成员都将被 转移（使用 Zinnser Lissy2002）至 15 x 45 mm 锥形底玻璃瓶，带有隔膜螺旋盖（每个 小瓶上有条形码，并使用 AutoChem FlexiWeigh 进行预称重，并使用蒸发器进行蒸发 GeneVac HT-4 确定每个样品的重量、结构、分析和储存后。 信息将被输入安全的 IDBS 活动数据库数据库，小瓶将存储在 24 个位置的货架中。 与 Drierite 一起放置在密封容器中。 塑料容器（每个 4 个 24 位置的架子）将 存储在-40°当化合物库有 C 冰箱时。 已被批准提交至 NIH 存储库， 将样品溶解在 DMSO 中并转移至 DPI 使用 Zinsser Lissy2002 提供的小瓶。 化合物 ID 将被输入数据库并 化合物将作为干样品发送到储存库 或按照说明在 DMSO 中。 配有电子 LC/MS 模块和 脚手架也将被存储和编目以供潜在的 用于纯化的再合成分析。 化合物、注册和运输需要两个 几周。 0.1.3 文库综合核心信息学：目标 CMLD-BU 的综合核心信息学计划是 开发集成电子研究环境 适用于所有附属科学家的软件套件。 软件包将集成合成程序、化合物 注册和生物数据管理一体化 单一电子数据管理资源。 项目将与 ArtusLabs 合作进行， Inc.（参见 Robin Smith 的合作信）。 项目范围将包括开发一个社会 网络研究环境允许 研究人员在共享中记录他们的协作工作 通过这些共享的电子实验室笔记本。 笔记本电脑，该软件将大大方便 科学界同事之间的合作，无论是在 同一实验室或不同建筑物中的该工具尤其适用。 对于 CMLD-BU 来说很重要，因为正在与麻省理工学院的研究人员建立关键合作。 学术或 CLC 合作者将很容易融入该小组，他们的贡献将促进 生物数据与特定化合物或化合物集合的关联 研究计划。 软件和数据库将维护大量信息（文档、图像和电子表格） 信息架构将相关资产分组到化合物、反应屏幕、项目和研究中。 基于人们互动的方式，各个化合物以及相关元数据之间的联系 与信息（即反应发展、催化剂、生物活性、分析设备）。 连接将使研究人员能够通过各种方式更直观地追踪重要信息 跨环境的共性，而不是通过研究或项目来隔离信息。 使用 Java 和 Ajax 进行编程，以确保跨平台兼容性（PC、Mac 和 Linux）。 研究人员将能够通过互联网轻松访问他们的帐户和电子实验室笔记本 待开发的具体功能包括基于 Java 的嵌入式化学物质。 绘图程序、反应计划功能、使用多维过程的反应筛选、 化学库规划和建设、ACD/Labs 仪器分析软件的集成，以及 完整的搜索功能（例如，按关键字、子结构、试剂、科学家等）。 能够关联生物数据并向该数据以及化合物和程序添加注释。 此功能旨在促进和维持协作研究，因为 CMLD-BU 的所有研究人员 通过此开发，附属团体将可以使用电子实验室笔记本。 新的协作研究环境软件套件 CMLD-BU 将继续发展成为一个集合 协同运作以实现 CMLD 计划发展计划的科学家。 ArtusLabs 软件的测试将于 2008 年夏季至 2009 年春季进行。 过渡到新的电子反应计划软件，Symyx Reaction Planner 将用于 CMLD-BU 的研究人员。 Q.1.4 利用当前 CMLD-BU 方法的文库合成：LSC 还将负责 识别 CMLD-BU 中开发的尚未转移到文库合成的方法。 以下是有机合成专家将适用于文库合成的方法。 1) 炔基的环丙烷化 山本和同事。 萘酮的合成报道 利用环异构化/Diels-Alder 以二炔苯甲醛开始的序列。 受这些例子的启发，我们利用 二炔苯甲醛作为串联的潜在底物 环异构化过程以提供新的化学型。 初步研究表明，用二炔 1 处理后 Cu(l)，发生环异构化，得到异色烯 2 (方案1).2 异色烯很容易转化为 在 PtCl 2 存在下稠合环丙烷 3 已被介导的烯炔的环丙烷化反应进行了。 据报道，3 然而，据我们所知，尚未有利用异色烯进行此类反应的报道。 反应将进一步发展，以纳入许多可用于图书馆的多样性位点 合成（方案 1，插图）。产生的稠合环丙烷也可以作为进一步的底物。 通过碱催化重排进行文库合成（方案 2）引发了意想不到的情况。 重排过程以提供多环酮6。通过这种方式，我们打算合成一个包含96个的文库 稠合环丙烷，其中 24 个文库成员将被选择用于利用以下方法合成子文库 碱基介导的重排。 2J 茚并异琥珀酸衍生文库的合成 CMLD-BU 正在进行的一个项目重点关注 涉及二氢异喹啉的化学转化的探索。4我们已经证明，在 在醛和三氟甲磺酸钪作为催化剂存在下，二氢异喹啉7缩合成 提供茚并异喹啉 8。8 的相对立体化学通过有趣的环化得到证实 提供桥联茚并异喹啉的工艺 9. 为使该方法适应并行化而做出的努力 合成将从评估潜在的多样性位点开始，此时设计一个库。 将进行茚并异喹啉并完成文库合成，以提供大约 86 个新颖的化合物 化合物的几个主要库成员将被选择用于通过合成子库。 典型的库成员如图 3 所示。