Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran.
PLoS One. 2021 Feb 19;16(2):e0247396. doi: 10.1371/journal.pone.0247396. eCollection 2021.
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.
在各种疫苗和药物传递系统中，细胞穿透肽（CPPs）因其能够穿透细胞膜并将某些类型的货物递送到细胞内而被认为是一种有效的传递系统。一些 CPPs 在病毒的蛋白质组中被发现，例如源自人类免疫缺陷病毒-1（HIV-1）的 Tat 和源自单纯疱疹病毒-1（HSV-1）的 VP22。在当前的研究中，使用计算机分析在 SARS-CoV-2 的蛋白质组中鉴定了广泛的 CPPs，SARS-CoV-2 是冠状病毒家族的新成员。这些 CPPs 可能在病毒高穿透细胞和感染宿主方面发挥主要作用。首先，我们将 SARS-CoV-2 的蛋白质组提交给 CellPPD 网络服务器，得到了大量长度为十个残基的 CPP。 之后，我们将预测的 CPP 提交给 C2Pred 网络服务器，以评估每个肽的概率。 然后，使用 CPPred-RF 和 MLCPP 网络服务器研究每个肽的摄取效率。 接下来，使用 protparam 和 pepcalc 工具计算预测的 CPP 的理化性质，包括净电荷、理论等电点（pI）、两亲性、分子量和水溶性。 此外，使用 APD3 网络服务器、D 因子和 TMHMM 网络服务器通过 Boman 指数估计每个 CPP 的膜结合潜力和细胞定位。 另一方面，使用各种网络服务器预测 CPP 的免疫原性、毒性、变应原性、溶血效力和半衰期。 最后，使用 PEP-FOLD3 和 Heliquest 网络服务器分别预测一些 CPP 的三级结构和螺旋轮投影。这些 CPP 分为：a）包含肿瘤归巢基序（RGD）和/或肿瘤穿透基序（RXXR）的 CPP；b）具有最高 Boman 指数的 CPP；c）在哺乳动物细胞中半衰期长（~100 小时）的 CPP；d）带+5.00 净电荷的 CPP。基于这些结果，我们发现了大量具有各种特征的新型 CPP。其中一些 CPP 具有肿瘤特异性基序，可用于癌症治疗。此外，源自 SARS-CoV-2 的新型有效 CPP 可单独使用或与核定位序列（NLS）等序列缀合，用于疫苗和药物传递。
