Trends in the Binding of Cell Penetrating Peptides to siRNA: A Molecular Docking Study

Abstract

The use of gene therapeutics, including short interfering RNA (siRNA), is limited by the lack of efficient delivery systems. An appealing approach to deliver gene therapeutics involves noncovalent complexation with cell penetrating peptides (CPPs) which are able to penetrate the cell membranes of mammals. Although a number of CPPs have been discovered, our understanding of their complexation and translocation of siRNA is as yet insufficient. Here, we report on computational studies comparing the binding affinities of CPPs with siRNA, considering a variety of CPPs. Specifically, seventeen CPPs from three different categories, cationic, amphipathic, and hydrophobic CPPs, were studied. Molecular mechanics were used to minimize structures, while molecular docking calculations were used to predict the orientation and favorability of sequentially binding multiple peptides to siRNA. Binding scores from docking calculations were highest for amphipathic peptides over cationic and hydrophobic peptides. Results indicate that initial complexation of peptides will likely occur along the major groove of the siRNA, driven by electrostatic interactions. Subsequent binding of CPPs is likely to occur in the minor groove and later on bind randomly, to siRNA or previously bound CPPs, through hydrophobic interactions. However, hydrophobic CPPs do not show this binding pattern. Ultimately binding yields a positively charged nanoparticle capable of noninvasive cellular import of therapeutic molecules.

Nucleic Acids Delivery Into the Cells Using Pro-Apoptotic Protein Lactaptin

“…Among various carriers, the CPP peptides are the potential delivery system for nucleic acids (Ignatovich et al, 2003; Järver et al, 2012; Shukla et al, 2014; Kizil et al, 2015). Forming protein-nucleic acid complex, CPPs can absorb on the surface of the double-stranded helix generally by electrostatic interaction, and such complexes can aggregate with size of up to 100 nm and have a positive charge (Rathnayake et al, 2017). CPPs were demonstrated as potential siRNA delivery systems for the suppression of gene expression.…”

“…Delivery molecules or vesicles help nucleic acids to cross biological barriers and prevent enzymatic degradation by endogenous nucleases. Besides the lipid-based delivery system, the polymer-based delivery system or inorganic nanoparticles, peptide carriers can be also used for nucleic acids transport into the cells (Zorko and Langel, 2005; Rathnayake et al, 2017). Among peptide carriers, the most promising are short amphipathic and cationic peptides, which translocate themselves across membranes and are collectively named as cell-penetrating peptides (CPP) (Hoyer and Neundorf, 2012; Morris and Labhasetwar, 2015).…”

Overcoming Barriers for siRNA Therapeutics: From Bench to Bedside

“…CPPs, also referred to as protein transduction domains (PTD), can penetrate the plasma membrane of a cell and facilitate the delivery of various cargoes. Moreover, the cytotoxicity of CPPs is relatively low [ 115 ]. For instance, Tanaka et al reported stearic acid conjugated a CPP demonstrated that injecting STR-CH 2 R 4 H 2 C peptide with siVEGF suppressed the tumor growth efficiently compared with naked siRNA or controlled group [ 116 ].…”

Cell Penetrating Peptides Used in Delivery of Therapeutic Oligonucleotides Targeting Hepatitis B Virus

“…To date, a great variety of delivery system for siRNAs has been investigated such as lipids, polymers, aptamers and cell penetrating peptides (CPPs) [ 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 ]. In this regard, CPPs appear as a new class of transporters, which increase intracellular uptake of biologically active molecules including siRNAs [ 45 ] ( Figure 2 ). Concerning hepatitis B virus infection, few or no studies are available currently on CPP-siRNAs targeting HBV.…”