Postgraduate Institute of Science, University of Peradeniya, 20400 Peradeniya, Sri Lanka.
Department of Chemistry, University of Peradeniya, 20400 Peradeniya, Sri Lanka.
Comput Biol Chem. 2022 Jun;98:107679. doi: 10.1016/j.compbiolchem.2022.107679. Epub 2022 Apr 6.
In gene therapy utilising short interfering RNA (siRNA), delivery of the siRNA therapeutics to the target site is a major obstacle, due to low cellular uptake. Efficient delivery systems such as cell penetrating peptides (CPPs) are in the forefront for the development of efficient, safe, non-viral gene delivery. The C6 peptide series are a class of synthetic CPPs, developed specifically for the delivery of siRNA. This series of peptides are derivatives of the original C6 peptide, modified to increase cellular uptake and efficiency. In this study, multiscaled computational simulations of these peptides were performed in aqueous media, interrogating the relationship between the structure and behaviour. All atom molecular dynamic (MD) simulation results show that all CPPs show stable α-helical amphipathic secondary structures. Furthermore, docking calculations indicate that the C6 peptides can fit into the major groove of the siRNA double-helix, and once filled, could bind randomly along the minor grooves and to other, previously bound peptides. Coarse grained MD simulations were also used to generate free energy profiles for the dimerization of peptides, and binding of the peptide to siRNA. Simulation results confirm that all peptides favour binding to siRNA, they however, also favour dimerization. This affinity for aggregation may trigger the formation of larger complexes with siRNA and enhance the cellular uptake. These results indicate the capacity of C6 peptides as efficient delivery vehicles. As expected the amino acid sequence plays a crucial role in the helicity, peptide self-assembly, interaction of peptide with cell membrane and formation of stable siRNA-CPP complex.
在利用短干扰 RNA (siRNA) 的基因治疗中，由于细胞摄取率低，siRNA 治疗剂递送到靶位是一个主要障碍。高效的递送系统，如细胞穿透肽 (CPP)，是开发高效、安全、非病毒基因递送的前沿。C6 肽系列是一类合成的 CPP，专门用于 siRNA 的递送。该系列肽是原始 C6 肽的衍生物，经过修饰以增加细胞摄取率和效率。在这项研究中，对这些肽在水介质中的多尺度计算模拟进行了研究，探究了结构与行为之间的关系。全原子分子动力学 (MD) 模拟结果表明，所有 CPP 均表现出稳定的α-螺旋两亲性二级结构。此外，对接计算表明 C6 肽可以与 siRNA 双链体的大沟结合，一旦结合，就可以沿着小沟随机结合，并与其他先前结合的肽结合。粗粒 MD 模拟也用于生成肽二聚体和肽与 siRNA 结合的自由能曲线。模拟结果证实所有肽都有利于与 siRNA 结合，但它们也有利于二聚化。这种聚集的亲和力可能会引发与 siRNA 形成更大的复合物，并增强细胞摄取。这些结果表明 C6 肽作为有效的递药载体的能力。正如预期的那样，氨基酸序列在螺旋性、肽自组装、肽与细胞膜的相互作用以及形成稳定的 siRNA-CPP 复合物方面起着至关重要的作用。
