Researchers at the Indian Institute of Science (IISc) Bangalore have designed a new class of artificial peptides or mini proteins that they say can render viruses like SARS-CoV-2 inactive.

According to the study, published in the journal Nature Chemical Biology, the mini proteins can not only block virus entry into our cells but also clump virus particles together, reducing their ability to infect. The researchers noted that protein-protein interaction is often like that of a lock and a key.

This interaction can be hampered by a lab-made mini protein that mimics, competes with, and prevents the 'key' from binding to the 'lock', or vice versa, they said. The team used this approach to design mini proteins that can bind to, and block the spike protein on the surface of the SARS-CoV-2 virus, which helps it to enter and infect the human cells.

This binding was further characterised extensively by cryo-electron microscopy (cryo-EM) and other biophysical methods. These mini proteins are helical, hairpin-shaped peptides, each capable of pairing up with another of its kind, forming what is known as a dimer. Each dimeric bundle' presents two faces' to interact with two target molecules.

The researchers hypothesised that the two faces would bind to two separate target proteins locking all four in a complex and blocking the targets' action. "But we needed proof of principle," said Jayanta Chatterjee, Associate Professor in the Molecular Biophysics Unit (MBU), IISc, and the lead author of the study.

The team decided to test their hypothesis by using one of the mini proteins called SIH-5 to target the interaction between the spike protein of SARS-CoV-2 and ACE2 protein in human cells. The spike protein is a complex of three identical polypeptides, each of which contains a Receptor Binding Domain (RBD) that binds to the ACE2 receptor on the host cell surface, facilitating viral entry into the cell.

The SIH-5 mini protein was designed to block the binding of the RBD to human ACE2. When a SIH-5 dimer encountered an S protein, one of its faces bound tightly to one of the three RBDs on the S protein trimer, and the other face bound to an RBD from a different S protein.

This cross-linking allowed the mini protein to block both S proteins at the same time. "Several monomers can block their targets. (But] cross-linking of S proteins blocks their action many times more effectively," said Chatterjee.

Under cryo-EM, the S proteins targeted by SIH-5 appeared to be attached head-to-head, the researchers said. We expected to see a complex of one spike trimer with SIH-5 peptides. But I saw a structure that was much more elongated, said Somnath Dutta, Assistant Professor at MBU and one of the corresponding authors of the study.

Dutta and others realised that the spike proteins were being forced to form dimers and clumped into complexes with the mini protein. This type of clumping can simultaneously inactivate multiple spike proteins of the same virus and even multiple virus particles.

The mini protein was also found to be stable for months at room temperature without deteriorating. To test if SIH-5 would be useful for preventing COVID-19 infection, the team first tested the mini protein for toxicity in experimental models in the lab and found it to be safe.

The researchers noted that with minor modifications and peptide engineering, this lab-made mini protein could inhibit other protein-protein interactions as well.