Design and Synthesis of DNA-Encoded Libraries of Unnatural Peptides to Discover Specific Chemical Probes

设计和合成 DNA 编码的非天然肽文库以发现特定的化学探针

• 批准号: 2440404
• 金额: --
• 依托单位: Newcastle University
• 依托单位国家: 英国
• 项目类别: Studentship
• 财政年份: 2020
• 资助国家: 英国
• 起止时间: 2020 至 无数据
• 项目状态: 未结题
• 来源: https://gtr.ukri.org/projects?ref=studentship-2440404
• 关键词: Design; Synthesis; DNA; Encoded; Libraries

Project SummaryVast libraries of encoded peptides, including cyclic systems, can be synthesised using biological methods, such as ribosomal expression systems, and can be screened by affinity selection to produce high affinity protein ligands. However, the scope of the aforementioned biological methods is usually limited to proteinogenic amino acids and their close analogues. The incorporation of unnatural moieties would allow for the more specific targeting of selected proteins classes, potentially leading to compounds with greater proteolytic stability and cell permeability. The aim of the proposed project is to develop synthetic approaches to realise this goal by developing chemical, rather than biological, techniques for peptide library synthesis. These techniques lack the requirement of identification by biological machinery and can, therefore, incorporate a far wider range of building blocks. In a second strand, hybrid methodology will be developed which allows the incorporation of unnatural warheads for selected protein classes into biologically displayed peptide libraries.Chemical Synthesis of Encoded Peptide LibrariesDELs are a technology for the synthesis and screening of a large number of molecules. Each DEL is a collection of these molecules, which are comprised of an organic moiety linked to a DNA oligonucleotide. The "genotype" (the DNA tag) serves as an amplifiable identification bar code for the displayed "phenotype" (the small organic molecule).Peptoids are oligomers of N-alkylated glycines; a peptoid monomer is an amino acid with the side chain connected to the nitrogen of the backbone, rather than the alpha carbon. Peptoids offer certain advantages to peptides as drugs, incl. resistance to proteolytic degradation due to the tertiary amide, improved cell-permeability relative to peptides due to the absence of the amide NH for H-bonding, and side chain diversity as they can be theoretically synthesised from any given primary amine.Peptoids are most often synthesised via a solid-supported submonomer method, using bromoacetic acid and then a primary amine. This is an issue, as an ?-halo carbonyl is a powerful electrophile, so will alkylate the DNA, so this method is incompatible with DEL synthesis.Initial work will focus on the off-DNA synthesis of peptoid monomers and the optimisation of multiple routes towards these building blocks. Consequently, optimised conditions will be applied to a variety of amines (to afford a range of peptoid monomers) and the scope of the reactions elucidated. Concurrently, the on-DNA coupling of peptoid monomers will be established using micellar conditions. This will be developed to realise the scope of the couplings by testing the coupling of the aforementioned synthesised peptoid monomers on-DNA.This will develop, in further work, to the synthesis of a range of peptoid-containing libraries, beginning with a small linear peptoid library, comprised of a range of the synthesised monomers. Extension of this will lead to the incorporation of building blocks that allow for the control of peptoid conformation, developing into the inclusion of conformational locks and cyclic structures.Hybrid Biological and Chemical SynthesisBiological techniques allow for the synthesis of even larger libraries than DELs, pushing the limit of library size to near 1013. The associated work in this strand will revolve around the incorporation of unnatural motifs into cyclic peptide libraries from ribosomal expression. These unnatural motifs, such as a single bromophenylalanine residue, will allow for the coupling of partners, e.g. boronates for Suzuku coupling, with known motifs that bind to certain target proteins. The work will involve the synthesis of said peptide libraries, the coupling of the specific binding motifs, and the subsequent testing of the diverse cyclic peptide libraries.

大量的编码肽库，包括环状系统，可以使用生物学方法合成，如核糖体表达系统，并可以通过亲和选择进行筛选，以产生高亲和力的蛋白质配体。然而，上述生物学方法的范围通常限于蛋白质氨基酸及其类似物。掺入非天然部分将允许更特异性地靶向所选蛋白质类别，潜在地导致具有更大蛋白水解稳定性和细胞渗透性的化合物。拟议项目的目的是开发合成方法，以实现这一目标，通过开发化学，而不是生物，肽库合成技术。这些技术不需要通过生物机制进行识别，因此可以包含更广泛的构建模块。在第二条链中，将开发杂交方法，该方法允许将选定蛋白质类的非天然弹头掺入生物展示肽库中。编码肽库的化学合成DELs是一种用于合成和筛选大量分子的技术。每个DEL是这些分子的集合，其由连接到DNA寡核苷酸的有机部分组成。“基因型”（DNA标签）作为显示的“表型”（小有机分子）的可重复识别条形码。类肽是N-烷基化甘氨酸的寡聚体;类肽单体是侧链连接到主链的氮而不是α碳的氨基酸。类肽为肽作为药物提供了某些优势，包括。由于叔酰胺而对蛋白水解降解具有抗性，由于不存在用于H-键合的酰胺NH而相对于肽具有改善的细胞渗透性，以及侧链多样性，因为它们理论上可以从任何给定的伯胺合成。这是一个问题，作为一个？卤代羰基是一种强有力的亲电试剂，因此会烷基化DNA，因此这种方法与DEL合成不相容。最初的工作将集中在类肽单体的脱DNA合成和对这些结构单元的多种路线的优化上。因此，优化的条件将被应用于各种胺（以提供一系列的类肽单体）和反应的范围阐明。同时，将使用胶束条件建立类肽单体的DNA上偶联。这将通过测试上述合成的类肽单体在DNA上的偶联来实现偶联的范围。在进一步的工作中，这将发展到合成一系列含有类肽的文库，从一个小的线性类肽文库开始，由一系列合成的单体组成。扩展这将导致纳入积木，允许控制类肽构象，发展到包括构象锁和环状结构。杂交生物和化学合成生物技术允许合成甚至比DEL更大的库，将库大小的限制推到接近1013。这条链的相关工作将围绕着将非天然基序掺入核糖体表达的环状肽文库。这些非天然基序，例如单个溴苯丙氨酸残基，将允许配偶体（例如用于Suzuku偶联的硼酸酯）与结合某些靶蛋白的已知基序偶联。这项工作将涉及所述肽文库的合成，特异性结合基序的偶联，以及随后对不同环肽文库的测试。