A novel peptide analogue of spike glycoprotein shows antiviral properties against SARS-CoV-2

Abstract

At the very beginning of the new decade, the COVID-19 pandemic has badly hit the globe. SARS-CoV-2, the causative agent of COVID-19 carries dozens of new mutations in its genome. Multiple countries are now in the race to find a defined treatment and vaccine against COVID-19. Herein, we made an effort to find antiviral peptides against SARS-CoV-2. Gladly, with the help of Machine Learning algorithms and Supported Vector Machine, we have found three potential antiviral peptides against SARS-CoV-2. Antiviral peptides namely, Seq12 and Seq12m showed very low cytotoxicity. All antiviral peptides were able to block the RBD of the spike glycoprotein. Besides, antiviral peptides retain their properties even in case of in silico multi-point mutant models (Rosetta and FoldX based) of RBD. Moreover, Seq12, Seq12m, and Seq13m can bind with the viral membrane protein (M) and eventually interfere with viral re-packaging. In conclusion, this study suggests Seq12, Seq12m, and Seq13m holds the potential for possible therapeutics use after formal clinical trials. Besides, these antiviral peptides could aid a new diagnostic tool.

Recent Patents and FDA-Approved Drugs Based on Antiviral Peptides and Other Peptide-Related Antivirals

“…AMPs with antiviral activity or antiviral peptides (AVPs) have turned into a research hotspot and already show tremendous potential to become pharmaceutically available antiviral medicines. AVPs have shown great potential in inhibiting viruses by rupturing the viral capsid, directly inhibiting the virus, and targeting various stages of the viral life cycles (Dutta 2020;Feng et al 2020;Rider et al 2011). Some disadvantages of AMPs such as expensive synthesis, time-consuming production, high degradability in some physiological conditions, low stability, immunogenicity, and cytotoxicity have limited their use in the clinic (Kang et al, 2014;Rinanda 2019).…”

Nanoscale Pathogens Treated with Nanomaterial-Like Peptides: A Platform Technology Appropriate for Future Pandemics

“…Dutta studied the genome sequences of SARS-CoV-2 and used some bioinformatic tools to understand the behavior of these amino acid sequences [118]. He studied the genetic sequences of the spike glycoproteins of the virus before starting to do any lab work.…”

“…Then he predicted three antiviral peptides whose amino acid sequences aligned with the viral spike glycoprotein, as shown in Figure 4. The three analogous antiviral peptides to the viral spike glycoproteins are Seq12, Seq12m and Seq13m [118]. The molecular dynamics process was used to study the physicochemical properties between these antiviral peptides and the binding pocket.…”

“…Lan et al identified the RBD of the spike glycoproteins for the ACE2 cell receptor [120]. Supplementary Table 3 shows the types of amino acids that constitute the RBD Additionally, it has been suggested that SARS-CoV can future science group 10.2217/nnm-2020-0447 Reproduced with permission from [118], licensed with CC BY 4.0.…”

“…These sequences have some common amino acids as represented with an asterisk. Reproduced with permission from[118], licensed with CC BY 4.0.…”