Rodrigues Filipe E P, Darbre Tamis, Machuqueiro Miguel
BioISI─Instituto de Biossistemas e Ciências Integrativas Faculdade de Ciências, Universidade de Lisboa, Lisboa 1749-016, Portugal.
Department of Chemistry Biochemistry and Pharmaceutical Sciences, University of Bern, Bern 3012, Switzerland.
J Chem Inf Model. 2024 Apr 22;64(8):3430-3442. doi: 10.1021/acs.jcim.4c00018. Epub 2024 Apr 8.
Peptide dendrimers are a type of branched, symmetric, and topologically well-defined molecule that have already been used as delivery systems for nucleic acid transfection. Several of the most promising sequences showed high efficiency in many key steps of transfection, namely, binding siRNA, entering cells, and evading the endosome. However, small changes to the peptide dendrimers, such as in the hydrophobic core, the amino acid chirality, or the total available charges, led to significantly different experimental results with unclear mechanistic insights. In this work, we built a computational model of several of those peptide dendrimers (MH18, MH13, and MH47) and some of their variants to study the molecular details of the structure and function of these molecules. We performed CpHMD simulations in the aqueous phase and in interaction with a lipid bilayer to assess how conformation and protonation are affected by pH in different environments. We found that while the different peptide dendrimer sequences lead to no substantial structural differences in the aqueous phase, the total charge and, more importantly, the total charge density are key for the capacity of the dendrimer to interact and destabilize the membrane. These dendrimers become highly charged when the pH changes from 7.5 to 4.5, and the presence of a high charge density, which is decreased for MH47 that has four fewer titratable lysines, is essential to trigger membrane destabilization. These findings are in excellent agreement with the experimental data and help us to understand the high efficiency of some dendrimers and why the dendrimer MH47 is unable to complete the transfection process. This evidence provides further understanding of the mode of action of these peptide dendrimers and will be pivotal for the future design of new sequences with improved transfection capabilities.
肽树枝状大分子是一类分支状、对称且拓扑结构明确的分子，已被用作核酸转染的递送系统。一些最有前景的序列在转染的许多关键步骤中表现出高效率，即在结合小干扰RNA（siRNA）、进入细胞和逃避内体方面。然而，肽树枝状大分子的微小变化，如疏水核心、氨基酸手性或总可用电荷的变化，会导致显著不同的实验结果，且作用机制尚不明确。在这项工作中，我们构建了其中几种肽树枝状大分子（MH18、MH13和MH47）及其一些变体的计算模型，以研究这些分子的结构和功能的分子细节。我们在水相以及与脂质双层相互作用的情况下进行了恒定pH分子动力学（CpHMD）模拟，以评估构象和质子化在不同环境中如何受到pH的影响。我们发现，虽然不同的肽树枝状大分子序列在水相中不会导致实质性的结构差异，但总电荷，更重要的是总电荷密度，是树枝状大分子与膜相互作用并使其不稳定的能力的关键。当pH从7.5变为4.5时，这些树枝状大分子会带上大量电荷，而高电荷密度的存在对于引发膜不稳定至关重要，对于可滴定赖氨酸少四个的MH47来说，其电荷密度会降低。这些发现与实验数据非常吻合，有助于我们理解一些树枝状大分子的高效率以及为什么树枝状大分子MH47无法完成转染过程。这一证据进一步加深了我们对这些肽树枝状大分子作用方式的理解，对于未来设计具有改进转染能力的新序列至关重要。
