Cyclic peptide permeability

环肽可以实现针对具有挑战性的靶标的精细的生物化学效力和特异性， 蛋白质-蛋白质相互作用（PPI）。虽然大多数环肽的大小和极性不能满足Lipinski的 根据预测药物相似性的“5规则”，已经描述了越来越多的环肽，其表现出 小分子药物的ADME特性，包括高被动细胞渗透性和口服生物利用度。 这些例外的情况，其中包括天然产品，如环孢菌素A（CSA）以及各种 我们小组开发的模型系统，产生了热情的想法，大循环可能 在追求具有挑战性的细胞内靶点时，提供了小分子和生物制剂之间的“中间道路”。 然而，在环肽中实现药物样渗透性远非简单。简单地去除C- 并且单独的N-末端很少足以实现治疗相关的细胞渗透性。其他因素 联合收割机来确定环肽的性质，我的小组已经领导了阐明原理的努力 管理着这些财产。该提议旨在1）鉴定表现出以下特性的新颖的脂质体和钉合肽： 高被动膜渗透性; 2）开发筛选策略，用于筛选 基于侧基大环的净极性的环肽;和3）使用NMR和计算 方法研究模型脂质双层渗透性的详细机制。在目标1中，我们 合成基于LIFE和钉合肽设计的质量编码文库，并使用 让我的小组评估他们的渗透率研究结果将有助于深入了解结构渗透性 在这个化学空间的关系，以及为合成库提供原材料，旨在 生化靶向筛选。在目标2中，我们将开始合成一系列DNA标记的环状 肽测试系统，其中侧基大环的渗透性仅相差 在2个位置处的立体化学，跨越近两个对数单位。我们将测试各种分离方案，其中一些 已知其基于共价连接的小分子的极性分离核酸。我们 然后，将合成~108个肽的多样性文库，并基于固有的 连接肽的极性。选择前和选择后文库的深度测序将阐明 7-mer至11-mer大小范围内的环肽中的“渗透性景观”具有前所未有的范围， 宽度在目标3中，我们将使用1H和19 F 2-D NMR技术，结合先进的分子动力学 我们的合作者Sereina Riniker教授（ETH）进行了模拟，以研究详细的机制 潜在的被动膜通透性在环肽。我们将合成CSA的含氟衍生物 和其他模型系统，并研究它们在合成脂质体中的转运动力学， 与当前理论模型的对比。

Cyclic peptides can achieve exquisite biochemical potency and specificity against challenging targets such as protein-protein interactions (PPIs). Although the size and polarity of most cyclic peptides fail to meet Lipinski's "Rule of 5" for predicting drug-likeness, a growing number of cyclic peptides have been described that exhibit the ADME properties of small molecule drugs, including high passive cell permeability and oral bioavailability. These exceptional cases, which include natural products such as cyclosporine A (CSA) as well as a variety of model systems developed by our group, have generated enthusiasm for the idea that macrocycles may provide a “middle way” between small molecules and biologics in the pursuit of challenging intracellular targets. However, achieving drug-like permeability in cyclic peptides is far from straightforward. Simply removing the C- and N-termini alone is rarely sufficient for achieving therapeutically relevant cell permeability. Other factors combine to determine the properties of cyclic peptides, and my group has led the effort to elucidate principles that govern those properties. This proposal aims to 1) identify novel, lariat and stapled peptides that exhibit high passive membrane permeability; 2) develop selection strategies for filtering DNA-encoded libraries of cyclic peptides based on the net polarity of the pendant macrocycles; and 3) use NMR and computational methods to study the detailed mechanisms of permeability across model lipid bilayers. In Aim 1, we will synthesize mass-encoded libraries based on lariat and stapled peptide designs, and use methods developed in my group to evaluate their permeabilities en masse. The results will provide insights into structure-permeability relationships in this chemical space, as well as providing raw materials for the synthesis of libraries aimed at biochemical target-based screening. In Aim 2, we will begin by synthesizing a series of DNA-tagged cyclic peptide test systems in which the permeabilities of the pendant macrocycles, which differ only by stereochemistry at 2 positions, span nearly two log units. We will test a variety of separation schemes, some of which are known to separate nucleic acids based on the polarity of covalently attached small molecules. We will then synthesize a diverse library of ~108 lariat peptides and fractionate the library based on the intrinsic polarity of the attached peptides. Deep sequencing of the pre- and post-selection libraries will illuminate the “permeability landscape” in cyclic peptides in the 7-mer to 11-mer size range with unprecedented scope and breadth. In Aim 3, we will use 1H and 19F 2-D NMR techniques, combined with advanced molecular dynamics simulations performed by our collaborator, Prof. Sereina Riniker (ETH), to study the detailed mechanisms underlying passive membrane permeability in cyclic peptides. We will synthesize fluorinated derivatives of CSA and other model systems and study their transport kinetics across synthetic liposomes, and compare observations with current theoretical models.