Cyclic peptide permeability

环肽可以针对具有挑战性的靶标，如 蛋白质-蛋白质相互作用(PPI)。尽管大多数环肽的大小和极性都不能满足利平斯基的 为了预测药物的相似性，越来越多的环肽被描述出来 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。 这些例外情况包括天然产物，如环孢素A(CsA)以及各种 我们团队开发的模型系统激发了人们对大周期可能 在追求具有挑战性的细胞内靶点的过程中，在小分子和生物制品之间提供一条“中间路线”。 然而，在环肽中实现类药物渗透性远非一帆风顺。简单地去掉C- 仅有N-末端很少足以实现与治疗相关的细胞通透性。其他因素 结合来确定环肽的性质，我的团队领导了阐明原理的努力 来管理这些财产。这项建议旨在1)确定新的、套索和装订的多肽 高被动膜通透性；2)开发筛选DNA编码文库的选择策略 基于悬挂大环的净极性的环肽；以及3)使用核磁共振和计算 方法研究模型脂双层透过性的详细机制。在目标1中，我们将 基于套索和装订的多肽设计合成大量编码的文库，并使用 我的团队来评估他们的整体渗透性。这些结果将为深入了解结构渗透性提供依据。 在这一化学空间中的关系，以及为合成旨在 基于生化靶点的筛查。在目标2中，我们将从合成一系列DNA标记的环开始 多肽测试系统，其中悬挂大环的渗透率只有不同 立体化学在2个位置，跨越近两个对数单位。我们将测试各种分离方案，其中一些 已知的是根据共价连接的小分子的极性来分离核酸。我们 然后将合成一个由~108个套索多肽组成的多样化文库，并根据内在的 结合的多肽的极性。对选择前和选择后的文库进行深度测序将阐明 在7-聚体至11-聚体大小范围内的环肽中的“渗透性景观”具有前所未有的范围和 广度。在目标3中，我们将使用1H和19F二维核磁共振技术，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 环肽中潜在的被动膜通透性。我们将合成CsA的氟化衍生物 和其他模型体系，研究它们在合成脂质体中的转运动力学，并比较 用目前的理论模型进行观测。

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.