ACE2 : S1 RBD Interaction-Targeted Peptides and Small Molecules as Potential COVID-19 Therapeutics

Abstract

The COVID-19 pandemic that began in late 2019 continues with new challenges arising due to antigenic drift as well as individuals who cannot or choose not to take the vaccine. There is therefore an urgent need for additional therapies that complement vaccines and approved therapies such as antibodies in the fight to end or slow down the pandemic. SARS-CoV-2 initiates invasion of the human target cell through direct contact between the receptor-binding domain of its Spike protein and its cellular receptor, angiotensin-converting enzyme-2 (ACE2). The ACE2 and S1 RBD interaction, therefore, represents an attractive therapeutic intervention to prevent viral entry and spread. In this study, we developed a proximity-based AlphaScreen™ assay that can be utilized to quickly and efficiently screen for inhibitors that perturb the ACE2 : S1 RBD interaction. We then designed several peptides candidates from motifs in ACE2 and S1 RBD that play critical roles in the interaction, with and without modifications to the native sequences. We also assessed the possibility of reprofiling of candidate small molecules that previously have been shown to interfere with the viral entry of SARS-CoV. Using our optimized AlphaScreen™ assay, we evaluated the activity and specificity of these peptides and small molecules in inhibiting the binding of ACE2 : S1 RBD. This screen identified cepharanthine as a promising candidate for development as a SARS-CoV-2 entry inhibitor.

Receptor-binding domain-anchored peptides block binding of severe acute respiratory syndrome coronavirus 2 spike proteins with cell surface angiotensin-converting enzyme 2

“…With the help of computation of RBD-ACE2 interactions, the Baker’s team generated mini-proteins of 56–64 residues with inhibitory concentrations of 24–35 nM for RBD-ACE2 binding ( Cao et al, 2020 ). On the contrary, also based on analysis of motifs or amino acids involved in RBD-ACE2 interaction, Chitsike proposed six peptides (20–29 aa) mimicking S-RBD fragment or hACE2 fragment but found that their IC50 for inhibiting RBD-ACE2 binding in experiments varied from 27 to 363 μM ( Chitsike et al, 2021 ). For us, the direction of our future study would be to use the current C6 SEAL peptides as the core sequences and to develop them into larger molecules (e.g., mini-protein) or other types of peptides (e.g., circular peptides) that would have a better chance to block RBD-ACE2 binding ( Pomplun, 2020 ).…”

Computer-aided discovery, design, and investigation of COVID-19 therapeutics

“…3 peptide-mimics [P8-10 in Table 1 ] were found to be able to block SARS-CoV-2 pulmonary cell infection with an inhibitory concentration (IC50) of within nanomolar range [ 71 ]. For screening of peptides, Chitsike et al designed several candidate peptides [ 72 ] from motifs in ACE2 and spike protein RBD by analyzing a crystal complex structure (PDB: 6LZG). Peptides with and without modifications (indicated with # in Table 1 ) to the native sequences were screened for their inhibitory potential to ACE2-RBD binding with a proximity-based AlphaScreen™ assay [ 72 ].…”

“…For screening of peptides, Chitsike et al designed several candidate peptides [ 72 ] from motifs in ACE2 and spike protein RBD by analyzing a crystal complex structure (PDB: 6LZG). Peptides with and without modifications (indicated with # in Table 1 ) to the native sequences were screened for their inhibitory potential to ACE2-RBD binding with a proximity-based AlphaScreen™ assay [ 72 ]. The sequence between the 21 th amino acid to the 45 th amino acid of ACE2 is commonly found in the results from different research groups to interact with SARS-CoV-2 spike protein RBD and should be an important consideration for future peptide drug design.…”

Current status and future challenges in extraction, purification and identification of Cepharanthine (a potential drug against COVID-19)

“…WHO reported that as of July 7, 2022, there have been 550, 218, 992 confirmed cases of COVID-19 worldwide, including nearly 6, 343, 783 deaths [7] . Despite the successful developments and relatively widespread applications of COVID-19 vaccines ( Fig.1 ), the emergence of new variants of SARS-CoV-2, which escape the immunity that comes from vaccinations, poses severe challenges for COVID-19 surveillance and control [7] , [8] , [9] . Moreover, people in some areas of the world have not been vaccinated due to issues related to hesitancy, unavailability or compromised immune systems, which could undermine efforts to end the pandemic through vaccines [8] .…”