OpenEye Scientific, Santa Fe, New Mexico 87508, United States.
Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States.
J Chem Inf Model. 2022 Apr 25;62(8):1891-1904. doi: 10.1021/acs.jcim.1c01540. Epub 2022 Apr 14.
Passive permeability of a drug-like molecule is a critical property assayed early in a drug discovery campaign that informs a medicinal chemist how well a compound can traverse biological membranes, such as gastrointestinal epithelial or restrictive organ barriers, so it can perform a specific therapeutic function. However, the challenge that remains is the development of a method, experimental or computational, which can both determine the permeation rate and provide mechanistic insights into the transport process to help with the rational design of any given molecule. Typically, one of the following three methods are used to measure the membrane permeability: (1) experimental permeation assays acting on either artificial or natural membranes; (2) quantitative structure-permeability relationship models that rely on experimental values of permeability or related pharmacokinetic properties of a range of molecules to infer those for new molecules; and (3) estimation of permeability from the Smoluchowski equation, where free energy and diffusion profiles along the membrane normal are taken as input from large-scale molecular dynamics simulations. While all these methods provide estimates of permeation coefficients, they provide very little information for guiding rational drug design. In this study, we employ a highly parallelizable weighted ensemble (WE) path sampling strategy, empowered by cloud computing techniques, to generate unbiased permeation pathways and permeability coefficients for a set of drug-like molecules across a neat 1-palmitoyl-2-oleoyl--glycero-3-phosphatidylcholine membrane bilayer. Our WE method predicts permeability coefficients that compare well to experimental values from an MDCK-LE cell line and PAMPA assays for a set of drug-like amines of varying size, shape, and flexibility. Our method also yields a series of continuous permeation pathways weighted and ranked by their associated probabilities. Taken together, the ensemble of reactive permeation pathways, along with the estimate of the permeability coefficient, provides a clearer picture of the microscopic underpinnings of small-molecule membrane permeation.
药物样分子的被动渗透率是药物发现早期阶段评估的关键性质,它可以告诉药物化学家一种化合物能够穿过生物膜(如胃肠道上皮或限制器官屏障)的程度,从而使其能够发挥特定的治疗功能。然而,仍然存在的挑战是开发一种方法,无论是实验方法还是计算方法,该方法既能确定渗透速率,又能提供对传输过程的机制见解,以帮助合理设计任何给定的分子。通常,有以下三种方法之一用于测量膜的通透性:(1)作用于人工或天然膜的实验渗透测定法;(2)基于通透性或一系列分子相关药代动力学性质的定量构效关系模型,用于推断新分子的这些性质;(3)根据斯莫卢霍夫斯基方程估算通透性,其中从大规模分子动力学模拟中获取沿膜法向的自由能和扩散分布作为输入。虽然所有这些方法都提供了渗透系数的估计值,但它们几乎没有提供指导合理药物设计的信息。在这项研究中,我们采用了一种高度可并行化的加权集合(WE)路径采样策略,该策略由云计算技术提供支持,以生成一组类似药物的分子在纯 1-棕榈酰-2-油酰基-甘油-3-磷酸胆碱双层膜中的无偏渗透途径和渗透率。我们的 WE 方法预测的渗透率系数与 MDCK-LE 细胞系和 PAMPA 测定法的实验值相比,对一组不同大小、形状和柔韧性的类似药物胺的预测值非常吻合。我们的方法还产生了一系列连续的渗透途径,按其相关概率加权和排序。总之,反应性渗透途径的集合以及渗透率的估计值,为小分子膜渗透的微观基础提供了更清晰的认识。