Decoding the proteome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) for cell-penetrating peptides involved in pathogenesis or applicable as drug delivery vectors

• Published in: Infection, genetics and evolution Vol. 85; p. 104474
• Main Authors: Hemmati, Shiva, Behzadipour, Yasaman, Haddad, Mahdi
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.11.2020
• Subjects: Antiviral Agents - pharmacology; Antiviral Agents - therapeutic use; Bioactive peptide; Cell-penetrating peptide; Cell-Penetrating Peptides - chemistry; Cell-Penetrating Peptides - metabolism; Computational Biology - methods; Coronavirus; COVID-19; Drug delivery; Drug Evaluation, Preclinical; Humans; Protein Folding; Protein Structure, Secondary; Proteome - drug effects; Research Paper; SARS-CoV-2; SARS-CoV-2 - drug effects; SARS-CoV-2 - metabolism; SARS-CoV-2 - pathogenicity; Support Vector Machine; Viral Proteins - chemistry; Viral Proteins - metabolism; Virus Replication; RTC; CPP; AMP; ERGIC; AH; SCV; Bioactive peptide; AIP; Drug delivery; NSP; CoV; ACP; COVID-19; COVID; SARS-CoV-2; Coronavirus; a.a; VLP; Cell-penetrating peptide
• ISSN: 1567-1348; 1567-7257; 1567-7257
• DOI: 10.1016/j.meegid.2020.104474

Synthetic or natural derived cell-penetrating peptides (CPPs) are vastly investigated as tools for the intracellular delivery of membrane-impermeable molecules. As viruses are intracellular obligate parasites, viral originated CPPs have been considered as suitable intracellular shuttling vectors for cargo transportation. A total of 310 CPPs were identified in the proteome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Screening the proteome of the cause of COVID-19 reveals that SARS-CoV-2 CPPs (SCV2-CPPs) span the regions involved in replication, protein-nucleotide and protein-protein interaction, protein-metal ion interaction, and stabilization of homo/hetero-oligomers. However, to find the most appropriate peptides as drug delivery vectors, one might face several hurdles. Computational analyses showed that 94.3% of the identified SCV2-CPPs are non-toxins, and 38% are neither antigenic nor allergenic. Interestingly, 36.70% of SCV2-CPPs were resistant to all four groups of protease families. Nearly 1/3 of SCV2-CPPs had sufficient inherent or induced helix and sheet conformation leading to increased uptake efficiency. Heliquest lipid-binding discrimination factor revealed that 44.30% of the helical SCV2-CPPs are lipid-binding helices. Although Cys-rich derived CPPs of helicase (NSP13) can potentially fold into a cyclic conformation in endosomes with a higher rate of endosomal release, the most optimal SCV2-CPP candidates as vectors for drug delivery were SCV2-CPP118, SCV2-CPP119, SCV2-CPP122, and SCV2-CPP129 of NSP12 (RdRp). Ten experimentally validated viral-derived CPPs were also used as the positive control to check the scalability and reliability of our protocol in SCV2-CPP retrieval. Some peptides with a cell-penetration ability known as bioactive peptides are adopted as biotherapeutics themselves. Therefore, 59.60%, 29.63%, and 32.32% of SCV2-CPPs were identified as potential antibacterial, antiviral, and antifungals, respectively. While 63.64% of SCV2-CPPs had immuno-modulatory properties, 21.89% were recognized as anti-cancers. Conclusively, the workflow of this study provides a platform for profound screening of viral proteomes as a rich source of biotherapeutics or drug delivery carriers. [Display omitted] •A total of 310 CPPs were identified in the proteome of SARS-CoV-2 called SCV2-CPPs.•SCV2-CPPs are entailed in viral replication, transcription, and pathogenesis.•The most optimal SCV2-CPPs for drug delivery are introduced by computational analyses.•Antimicrobial, anticancer, and anti-inflammatory SCV2-CPPs are determined.