Shedding Light on the Inhibitory Mechanisms of SARS-CoV-1/CoV-2 Spike Proteins by ACE2-Designed Peptides

Abstract

Angiotensin-converting enzyme 2 (ACE2) is the host cellular receptor that locks onto the surface spike protein of the 2002 SARS coronavirus (SARS-CoV-1) and of the novel, highly transmissible and deadly 2019 SARS-CoV-2, responsible for the COVID-19 pandemic. One strategy to avoid the virus infection is to design peptides by extracting the human ACE2 peptidase domain α1-helix, which would bind to the coronavirus surface protein, preventing the virus entry into the host cells. The natural α1-helix peptide has a stronger affinity to SARS-CoV-2 than to SARS-CoV-1. Another peptide was designed by joining α1 with the second portion of ACE2 that is far in the peptidase sequence yet grafted in the spike protein interface with ACE2. Previous studies have shown that, among several α1-based peptides, the hybrid peptidic scaffold is the one with the highest/strongest affinity for SARS-CoV-1, which is comparable to the full-length ACE2 affinity. In this work, binding and folding dynamics of the natural and designed ACE2-based peptides were simulated by the well-known coarse-grained structure-based model, with the computed thermodynamic quantities correlating with the experimental binding affinity data. Furthermore, theoretical kinetic analysis of native contact formation revealed the distinction between these processes in the presence of the different binding partners SARS-CoV-1 and SARS-CoV-2 spike domains. Additionally, our results indicate the existence of a two-state folding mechanism for the designed peptide en route to bind to the spike proteins, in contrast to a downhill mechanism for the natural α1-helix peptides. The presented low-cost simulation protocol demonstrated its efficiency in evaluating binding affinities and identifying the mechanisms involved in the neutralization of spike-ACE2 interaction by designed peptides. Finally, the protocol can be used as a computer-based screening of more potent designed peptides by experimentalists searching for new therapeutics against COVID-19.

Systematic virtual screening in search of SARS CoV-2 inhibitors against spike glycoprotein: pharmacophore screening, molecular docking, ADMET analysis and MD simulations

“…Further, compound A possesses nitro-aryl features imparting the potential risk of mutagenicity due to interaction of nitro group with DNA [ 63 ]. Peptides identified by de Oliveira et al [ 30 ] and Baig et al [ 31 ] may not have sufficient oral bioavailability as compared to identified small molecules ( 1 – 17 ) due to degradation of these peptides under the acidic environment of stomach and peptidase enzymes [ 64 ].…”

“…2 ) as potent anti-viral agent with IC 50 of 28.1 µM against vero-E6 cells incubated with SARS CoV-2 [ 29 ]. Three different peptide fragments composed of N -terminal amino acid residues of α 1 helix of ACE2 peptidase domain have been reported by de Olivera and co-workers as effective agents to inhibit the binding of SARS CoV-2 spike protein with human ACE2 as identified through molecular modelling [ 30 ]. Further, Baig et al identified the 13-amino acid peptide (FLDKFNHEAEDLF) as spike protein inhibitor with minimal inhibition (40% at 100 µM concentration) of ACE2-spike protein–protein interactions through enzyme-linked immunosorbent (ELISA)-dependent inhibitory assay [ 31 ].…”

Engineering mesenchymal stromal cells with neutralizing and anti-inflammatory capability against SARS-CoV-2 infection

“…19,21 De novo protein design and computer-based peptide design have also been applied for engineering native soluble ACE2 to generate potential SARS-CoV-2 entry blockers. [22][23][24] These studies highlight the importance of ACE2-based therapeutics for treating COVID-19. However, whether cell therapy can be used for the delivery of ACE2-based therapeutics is unclear.…”

ACE2 Peptide Fragment Interaction with Different S1 Protein Sites

“…All these works were also dealing with in silico peptide modelling and screening of their binding with the RBD of the spike protein. In addition, the specificity pattern of this interaction was specified (Kuznetsov and Järv 2020b ) and the structural basis of the molecular recognition mechanism of these peptides was described (Freitas et al 2021 ). However, there is still no experimental data characterizing kinetics of interaction of these peptide fragments with the RBD on SARS-CoV-2 spike protein.…”