Understanding, Predicting, and Engineering Membrane Permeability

描述（由申请人提供）：小分子进入细胞的能力是化学生物学药物制剂和工具开发的关键参数。大多数合成化合物通过膜的被动扩散进入细胞。这项提议的目的是增加我们对被动膜渗透的理解和预测能力。对这一认识的最终检验将是合理地修饰化合物以提高膜的渗透性。这里提出的工作建立在现有的膜渗透模型的基础上，但我们正在开发的模型与大多数实际使用的模型不同，因为它更直接地基于对被动膜渗透物理的理解。因此，它具有系统的可改进性，具有广泛的适用性。我们提议……实施和测试一个基于物理的被动膜渗透性模型。该模型的第一代已经在PI的一系列论文中进行了描述，并强调了构象柔韧性和形成内部氢键的能力在促进膜渗透中的作用。与文献数据和目标2和目标3中生成的新数据相比，我们将扩展该模型以包括物理学的其他关键方面，包括膜插入时的熵损失和膜内部的半有序疏水环境。2. 询问使用环肽膜渗透的关键方面，并利用这些知识来设计高渗透环肽。我们建议使用环肽作为一个具有挑战性的模型系统来研究被动膜渗透。制造环状肽的相对合成容易，有利于开发一系列在立体化学、刚性、大小、疏水性等方面定义明确的不同化合物。正如我们早期的工作一样，计算预测总是在实验测试之前进行，结果将探索膜渗透物理的特定方面。3. 利用非肽小分子探究膜渗透的关键方面，并在实际工作中使用这些知识来优化蛋白质抑制剂的化学性质。其中一个合作项目涉及改善寄生虫半胱氨酸蛋白酶抑制剂的膜通透性，这些抑制剂通常具有较差的生物利用度。该提案的核心要素是与化学家Scott Lokey （UCSC）和Adam Renslo （UCSF）合作，测试和应用计算模型。计算建模和实验测试之间的紧密耦合是该提案的核心，允许我们对被动膜渗透性的物理理解和封装该理解的计算方法进行迭代改进。这项工作的成功将使假设驱动的（“工程”）方法能够改善膜的渗透性。

DESCRIPTION (provided by applicant): The ability of small molecules to enter cells is a critical parameter in development of pharmaceutical agents and tools for chemical biology. Most synthetic compounds enter cells by passive diffusion across the membrane. The goal of this proposal is to increase our understanding of, and ability to predict, passive membrane permeation. The ultimate test of this understanding will be rationally modifying compounds to improve membrane permeation. The work proposed here builds on existing models of membrane permeation, but the model we are developing differs from most in practical use by being more directly based on an understanding of the physics of passive membrane permeation. As such, it is systematically improvable, and has broad applicability. We propose to 1. Implement and test a physics-based model for passive membrane permeability. A first generation of this model has been described in a series of papers by the PI, and has emphasized the role of conformational flexibility and the ability to form internal hydrogen bonds in promoting membrane permeation. We will extend this model to include other critical aspects of the physics, including entropic losses upon membrane insertion and the semi-ordered hydrophobic environment of the membrane interior, comparing to both literature data and new data generated in Aims 2 and 3. 2. Interrogate key aspects of membrane permeation using cyclic peptides, and use this knowledge to design highly permeable cyclic peptides. We propose to use cyclic peptides as a challenging model system for studying passive membrane permeation. The relative synthetic ease of creating cyclic peptides facilitates developing series of compounds that differ in well-defined ways, such as stereochemistry, rigidity, size, hydrophobicity, etc. As in our earlier work, computational predictions will always be made prior to experimental testing, and the results will probe specific aspects of the physics of membrane permeation. 3. Interrogate key aspects of membrane permeation using non-peptidic small molecules, and use this knowledge in practical efforts to optimize the chemical properties of protein inhibitors. One of the collaborative projects involves improving membrane permeability for inhibitors of parasite cysteine proteases, which have typically had poor bioavailability. A central element of this proposal is collaborations with chemists Scott Lokey (UCSC) and Adam Renslo (UCSF) to test and apply the computational models. Tight coupling between computational modeling and experimental testing is central to this proposal, allowing iterative improvement of our physical understanding of passive membrane permeability and computational methods that encapsulate that understanding. Success of this work will enable hypothesis-driven ("engineering") approaches to improving membrane permeability. PUBLIC HEALTH RELEVANCE: One important property of drugs is their ability to enter cells, especially for drugs that are taken orally. This proposal is concerned with developing new computer programs that can predict the ability of compounds to enter cells, and experimental testing of these methods. Success of this work has the potential to reduce the time and cost of early-stage drug discovery, such as the proposed project to develop improved drug candidates for "sleeping sickness", a serious parasitic disease common in Africa.