New peptide derivatives that target the SARS-CoV-2 spike protein

By Lakshmi Supriya, PhD.Oct 26 2020

Using computer simulations, researchers have identified peptide derivatives that could inhibit the binding of the spike protein.  

The rapid spread of the COVID-19 pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to tremendous efforts to curb the disease. The spike protein of the virus plays a key role in infection and disease progression. The spike protein binds to the human angiotensin-converting enzyme 2 (ACE2), facilitating entry into the host cell, causing infection.

The SARS-CoV-2 virus is a single-stranded positive-sense RNA virus. It has a genome size of 26 to 32 kb. The genome encodes the four major structural proteins, the spike, the nucleocapsid, envelope, and membranes proteins. The envelope and membrane proteins are related to virus assembly.

The spike protein interacts with the peptidase domain of the ACE2 receptor to help the virus enter the host cell. Thus, preventing this interaction may be potentially useful in curbing the infection.

Apart from developing vaccines, many efforts have focused on drugs and therapy to limit infection in the early stage. These include antibodies from blood plasma in convalescent patients, repurposing existing drugs, and designing blocking peptides. Peptides are attractive to fight viral infections because they are close to natural peptide conformations.

In a new study published in the journal Cellular and Molecular Bioengineering, researchers report peptide derivatives, or peptidomimetics, based on the circle residues involved in the interaction of the spike protein and ACE2.

Structure of the SARS-CoV-2 spike glycoprotein, black background, 3D illustration credit: Volodymyr Dvornyk / Shutterstock

New peptide derivatives

Targeting peptides are advantageous as they have good structural compatibility with target proteins and can disrupt protein-protein interfaces.

Previously, the researchers had designed an 18 amino acid (18aa) peptide for SARS-CoV-2 inhibition. To make this peptide, they first obtained the crystal structure of the SARS-CoV-2-ACE2 complex and examined the residues involved in the interaction.

They found that a stretch of the ACE2 peptidase domain N-terminal region was the main portion interacting with the virus spike protein.

Then, they designed new peptide derivatives based on the inhibitory residues on the 18aa peptides. These peptide derivatives can bind to the receptor-binding domain (RBD) of the spike protein better than the peptide.

Using the pep:MMs: MIMIC server, they obtained about 200 conformations of the peptidomimetics. They ran a virtual screening of these 200 compounds using the Hig-Throughput Virtual Screening (HVTS) using the LibDock platform of the BIOVIA Discovery Studio.

The team then analyzed the compounds obtained using virtual molecular docking-based screening to get the best compounds that could stably bind to the spike protein. They looked for compounds that had the best docking pose, and interactions were similar to that of the binding sites of the 18aa peptide.

They obtained scores for all the compounds by comparing the uniformity of binding mode and energy scoring pattern of the final peptide derivative residues. From this list, they selected the top four compounds for further analysis.

Four promising compounds to target spike protein

The researchers further analyzed how the individual peptide derivatives interacted with the spike protein residues. All four compounds showed strong interaction and had non-covalent bonds such as hydrogen bonds, p-p interactions, and cation-p interactions. These non-covalent bonds stabilize the protein-ligand complex as well as the dynamics and thermodynamics of the system.

Further analysis showed the aliphatic chain regions attached to the aryl rings are important in the hydrogen bonding and p-p interactions with the spike protein.

None of the four compounds were toxic, as analyzed using the ‘ToxinPred’ server. The compounds were less lipophilic and had higher solubility. Computer simulations showed these compounds have a good binding affinity and suggest good potential for use in drugs.

Molecular Electrostatic Potential analysis showed the most electropositive and electronegative regions in the four compounds. In the compounds, the electropositive regions were in the areas with amine groups, and the electropositive region was in the regions with protonated groups and carbonyl groups.

The amount of peptides unbound in the plasma provides an understanding of pharmacokinetic properties and helps screen candidates early in drug discovery. The unbound fractions can bind to proteins to form complexes.

The four compounds have a predicted unbound fraction of between 0.4 and 0.6. The total clearance value, which is a combination of renal and hepatic clearance, of these compounds indicates the adaptive nature of their physiological environments.

A maximum recommended tolerated dose, which estimates the toxic dose threshold in humans, of 0.48 is considered low. The value obtained for these compounds is about 0.39, so they are non-toxic to humans. Thus, these compounds can be further experimentally tested in SARS-CoV-2 spike protein inhibition assays.