Exploring novel and potent cell penetrating peptides in the proteome of SARS-COV-2 using bioinformatics approaches

Abstract

Among various delivery systems for vaccine and drug delivery, cell-penetrating peptides (CPPs) have been known as a potent delivery system because of their capability to penetrate cell membranes and deliver some types of cargoes into cells. Several CPPs were found in the proteome of viruses such as Tat originated from human immunodeficiency virus-1 (HIV-1), and VP22 derived from herpes simplex virus-1 (HSV-1). In the current study, a wide-range of CPPs was identified in the proteome of SARS-CoV-2, a new member of coronaviruses family, using in silico analyses. These CPPs may play a main role for high penetration of virus into cells and infection of host. At first, we submitted the proteome of SARS-CoV-2 to CellPPD web server that resulted in a huge number of CPPs with ten residues in length. Afterward, we submitted the predicted CPPs to C2Pred web server for evaluation of the probability of each peptide. Then, the uptake efficiency of each peptide was investigated using CPPred-RF and MLCPP web servers. Next, the physicochemical properties of the predicted CPPs including net charge, theoretical isoelectric point (pI), amphipathicity, molecular weight, and water solubility were calculated using protparam and pepcalc tools. In addition, the probability of membrane binding potential and cellular localization of each CPP were estimated by Boman index using APD3 web server, D factor, and TMHMM web server. On the other hand, the immunogenicity, toxicity, allergenicity, hemolytic potency, and half-life of CPPs were predicted using various web servers. Finally, the tertiary structure and the helical wheel projection of some CPPs were predicted by PEP-FOLD3 and Heliquest web servers, respectively. These CPPs were divided into: a) CPP containing tumor homing motif (RGD) and/or tumor penetrating motif (RXXR); b) CPP with the highest Boman index; c) CPP with high half-life (~100 hour) in mammalian cells, and d) CPP with +5.00 net charge. Based on the results, we found a large number of novel CPPs with various features. Some of these CPPs possess tumor-specific motifs which can be evaluated in cancer therapy. Furthermore, the novel and potent CPPs derived from SARS-CoV-2 may be used alone or conjugated to some sequences such as nuclear localization sequence (NLS) for vaccine and drug delivery.

Inactivation of HIV-1 in Polarized Infant Tonsil Epithelial Cells by Human Beta-Defensins 2 and 3 Tagged with the Protein Transduction Domain of HIV-1 Tat

“…Second, hBD-2 PTD and hBD-3 PTD may be released from newly formed vesicles into cytosol and subsequently enter existing vesicles, including those that contain HIV-1 (Figure 12). CPP may be released from endosomes into cytoplasm [82][83][84] and enter other vesicles [33][34][35]69]. PTD-mediated release of HIV-1 Tat from endosomes into cytosol has also been shown [85].…”

“…It is well known that HIV-1 Tat PTD-derived CPP can rapidly deliver various cargo, including proteins, DNA, RNA, and drug molecules, to cells via the plasma membrane in vitro and in vivo [64][65][66][67][68]. The molecular mechanism of these peptides' penetration of cells varies significantly according to their properties, including physiochemical features, dose, incubation time, and cell type [33][34][35]69]. The internalization of Tat PTD-based CPP via cell membranes may occur by various mechanisms, such as clathrin-and caveolin-dependent or independent endocytosis, macropinocytosis, or direct penetration [28,31,32,52,53,56,[70][71][72][73][74][75][76][77].…”

In silico identification and experimental validation of cellular uptake and intracellular labeling by a new cell penetrating peptide derived from CDN1

“…Once screening and identification have been completed, every peptide must be examined for its potential cell-penetrating activity, which is a time-consuming and laborious cycle (Manavalan et al, 2018 ). Few papers (Hu et al, 2020 ; Kardani and Bolhassani, 2021 ) published showed that bioinformatic tools were used to predict CPP, however, they did not predict the CPP systematically such as CPP prediction, penetration efficiency, structural, peptide-membrane interaction, physical-chemical properties, and wet-lab experiment validation. We found that peptide P2 has higher penetration efficiency than MT23 but lower than TAT, hPP10 and Dot1l.…”

Cell-Penetrating Peptides Predicted From CASC3, AKIP1, and AHRR Proteins

“…The availability of large databases has made the discovery and characterization of new CPPs and, more importantly, the design of multifunctional peptides feasible. For example, many CPPs have been predicted and characterized from SARS-COV-2 using bioinformatics approaches ( Kardani and Bolhassani, 2021 ).…”

“…As a control, a known CPP, Tat 48-60 , was included. The prediction of new CPPs is becoming a more relevant tool for pre-screening of protein sequences, with a recent example of SARS-COV-2 proteome screening ( Kardani and Bolhassani, 2021 ).…”