Cell Permeable Cyclic Peptide Library Generation for Target-Based Screening

市场上的大多数药物都是小分子的。虽然这些药物通常具有良好的口服生物利用度，但小分子药物并不总是对其靶标具有高选择性。这可能会导致脱靶效应带来的毒性增加。同样，小分子不能选择性地以具有大结合表面的蛋白质为靶标，例如那些参与蛋白质-蛋白质相互作用的蛋白质。大的生物制剂，如蛋白质和抗体，对这些靶标表现出非常高的选择性，但不是细胞渗透性的，因此只能结合到细胞外蛋白质上。此外，与合成分子相比，生物制品的制造成本很高。多肽位于小分子光谱和生物制品之间，具有很高的靶标选择性，能够通过靶向具有大结合表面的蛋白质探测更大的化学空间，并且生产成本相对较低，因此是一种很有前途的治疗药物。然而，多肽的细胞渗透性低、代谢速度快、口服生物利用度低的问题仍然存在，这是限制其作为治疗药物使用的主要因素。已观察到多肽的环化具有几个结构上的好处，如消除N-末端和C-末端以防止蛋白质降解、增加刚性和减少极表面面积以改善细胞通透性和代谢稳定性，从而提高口服生物利用度。目前已发现1000多种自然产生的环肽，其中一些已被开发成临床广泛使用的药物，如万古霉素、环孢菌素A和放线菌素D。然而，环化肽潜在的物理化学性质尚不清楚。小分子药物的设计遵循利平斯基规则5，该规则定义了药物必须具有口服生物利用度的物理化学性质。这些规则包括具有分子量500、对数P和5、氢键供体的数量和氢键受体的数量10。由于肽的尺寸较大，它们不符合这些规则，因此它们不能用于口服生物可用环肽的设计。本项目旨在阐明环肽细胞通透性背后的物理化学性质。通过确定这些性质，它们可以用作基于mRNA展示的环肽文库的筛选过滤器，以有效地识别针对目标蛋白的细胞通透性环肽。这有可能通过消除对Hit多肽的细胞渗透性的调节而极大地改善环肽药物开发的格局，这可能是非常耗时和困难的。随着这些文库的产生，它们可以接受针对靶点的筛选，以发现具有治疗潜力的细胞渗透肽。

Most drugs on the market are small molecules. Whilst these typically have good oral bioavailability, small molecule drugs do not always have a high selectivity for their targets. This can lead to increased toxicity from off-target effects. Likewise, small molecules are unable to selectively target proteins with large binding surfaces, such as those that are involved in protein-protein interactions. Large biologics such as proteins and antibodies exhibit very high selectivity for these targets but are not cell permeable and can thus only bind onto extracellular proteins. Furthermore, biologics are costly to manufacture compared to synthetic molecules. Peptides are promising therapeutics as they lie between the spectrum of small molecules and biologics whereby they have high selectivity for their targets, are able to probe a larger chemical space by targeting proteins with large binding surfaces and have relatively low production costs. However, the issue of low cell permeability, rapid metabolism and thus low oral bioavailability still persists for peptides and is a major limiting factor in their use as therapeutics.It has been observed that cyclisation of peptides has several structural benefits, such as eliminating the N- and C- termini to prevent proteolytic degradation, increasing rigidity and reducing the polar surface area to improve cell permeability and metabolic stability, leading to increased oral bioavailability.Over 1000 naturally occurring cyclic peptides have been discovered and some have been developed into widely used clinically available drugs, such as vancomycin, cyclosporin A and actinomycin D. However, the physicochemical properties underlying cyclic peptide cell permeability are unclear. The design of small molecule drugs is guided by Lipinski's Rule of 5 which defines the physicochemical properties that a drug should have to be orally bioavailable. Such rules include having a molecular weight <500, logP <5, number of hydrogen bond donors <5 and number of hydrogen bond acceptors <10. Due to the larger size of peptides, they do not conform to these rules and thus they cannot be used for the design of orally bioavailable cyclic peptides.This project aims to elucidate the physicochemical properties underlying the cell permeability of cyclic peptides. By ascertaining these properties, they can be used as screening filters in mRNA-display based cyclic peptide libraries to efficiently identify cell permeable cyclic peptide hits against target proteins of interest. This has the potential of vastly improving the landscape for cyclic peptide drug development by eliminating the need for modulating cell permeability of hit peptides, which can be highly time-consuming and difficult. Following the generation of these libraries, they can undergo screening against targets for the discovery of cell permeable peptides with therapeutic potential.