Department of Chemistry, The University of Chicago, 5735 S Ellis Avenue, Chicago, Illinois 60637, United States.
Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Unité Mixte de Recherche n◦7019, Université de Lorraine, B.P. 70239, 54506 Vandœuvre-lès-Nancy Cedex, France.
J Phys Chem B. 2024 Jan 25;128(3):795-811. doi: 10.1021/acs.jpcb.3c06765. Epub 2024 Jan 16.
According to the pH-partition hypothesis, the aqueous solution adjacent to a membrane is a mixture of the ionization states of the permeating molecule at fixed Henderson-Hasselbalch concentrations, such that each state passes through the membrane in parallel with its own specific permeability. An alternative view, based on the assumption that the rate of switching ionization states is instantaneous, represents the permeation of ionizable molecules via an effective Boltzmann-weighted average potential (BWAP). Such an assumption is used in constant-pH molecular dynamics simulations. The inhomogeneous solubility-diffusion framework can be used to compute the pH-dependent membrane permeability for each of these two limiting treatments. With biased WTM-eABF molecular dynamics simulations, we computed the potential of mean force and diffusivity of each ionization state of two weakly basic small molecules: nicotine, an addictive drug, and varenicline, a therapeutic for treating nicotine addiction. At pH = 7, the BWAP effective permeability is greater than that determined by pH-partitioning by a factor of 2.5 for nicotine and 5 for varenicline. To assess the importance of ionization kinetics, we present a Smoluchowski master equation that includes explicitly the protonation and deprotonation processes coupled with the diffusive motion across the membrane. At pH = 7, the increase in permeability due to the explicit ionization kinetics is negligible for both nicotine and varenicline. This finding is reaffirmed by combined Brownian dynamics and Markov state model simulations for estimating the permeability of nicotine while allowing changes in its ionization state. We conclude that for these molecules the pH-partition hypothesis correctly captures the physics of the permeation process. The small free energy barriers for the permeation of nicotine and varenicline in their deprotonated neutral forms play a crucial role in establishing the validity of the pH-partitioning mechanism. Essentially, BWAP fails because ionization kinetics are too slow on the time scale of membrane crossing to affect the permeation of small ionizable molecules such as nicotine and varenicline. For the singly protonated state of nicotine, the computational results agree well with experimental measurements ( = 1.29 × 10 cm/s), but the agreement for neutral ( = 6.12 cm/s) and doubly protonated nicotine ( = 3.70 × 10 cm/s) is slightly worse, likely due to factors associated with the aqueous boundary layer (neutral form) or leaks through paracellular pathways (doubly protonated form).
根据 pH 分区假说，与膜相邻的水溶液是渗透分子在固定亨德森-哈塞尔巴尔赫浓度下的各种离解状态的混合物，使得每种状态都以其自身特定的通透性平行通过膜。另一种观点基于这样一种假设，即离解状态的切换速度是瞬时的，代表可电离分子通过有效玻尔兹曼加权平均势（BWAP）的渗透。这种假设用于恒定 pH 分子动力学模拟。非均匀溶解-扩散框架可用于计算这两种极限处理中每种的 pH 依赖性膜通透性。通过有偏向的 WTM-eABF 分子动力学模拟，我们计算了两种弱碱性小分子（尼古丁，一种成瘾药物，以及伐伦克林，一种治疗尼古丁成瘾的药物）的每种离解状态的平均力势和扩散系数。在 pH = 7 时，BWAP 有效通透性比 pH 分区法测定的通透性高 2.5 倍对于尼古丁，5 倍对于伐伦克林。为了评估离解动力学的重要性，我们提出了一个斯莫卢霍夫斯基主方程，其中明确包括质子化和去质子化过程以及跨膜的扩散运动。在 pH = 7 时，由于 explicit 离解动力学导致的通透性增加对于尼古丁和伐伦克林都可以忽略不计。这一发现通过布朗动力学和马尔可夫状态模型的组合模拟得到了证实，这些模拟用于估计尼古丁的通透性，同时允许其离解状态发生变化。我们的结论是，对于这些分子，pH 分区假说正确地捕捉到了渗透过程的物理性质。尼古丁和伐伦克林去质子化中性形式渗透的小自由能势垒在建立 pH 分区机制的有效性方面起着至关重要的作用。基本上，BWAP 失败是因为在膜穿透时间尺度上，离解动力学太慢，无法影响像尼古丁和伐伦克林这样的小可电离分子的渗透。对于尼古丁的单质子化状态，计算结果与实验测量值（ = 1.29 × 10 cm/s）非常吻合，但与中性（ = 6.12 cm/s）和双质子化尼古丁（ = 3.70 × 10 cm/s）的吻合稍差，可能是由于与水相边界层（中性形式）或通过细胞旁途径泄漏（双质子化形式）相关的因素所致。
