IISc researchers develop way to inactivate SARS-Cov-2

The researchers of the Indian Institute of Science (IISc) have developed an alternative mechanism to inactivate viruses such as SARS-CoV-2, IISc’s official statement said Monday.

In a study published in Nature Chemical Biologythe researchers report the design of a new class of artificial peptides or mini-proteins that can not only block viruses from entering our cells, but also clump virions (virus particles) together, reducing their ability to infect.

A protein-protein interaction is often like that of a lock and a key. This interaction can be hindered by a lab-made mini-protein that mimics the ‘key’, competes with it and prevents it from binding to the ‘lock’, or vice versa.

In the new study, the team used this approach to design mini-proteins that can bind to and block the peak protein on the surface of the SARS-CoV-2 virus. This binding was further extensively characterized by cryo-electron microscopy (cryo-EM) and other biophysical methods.

These mini-proteins are spiral, hairpin-shaped peptides, each of which is able to mate with another of its kind, forming a so-called dimer. Each dimeric ‘beam’ presents two ‘faces’ to interact with two target molecules. The researchers hypothesized that the two faces would bind to two separate target proteins, locking all four into a complex and blocking the targets’ action.

“But we needed proof of principle,” says Jayanta ChatterjeeAssociate Professor in the Unit Molecular Biophysics (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 (S) protein of SARS-CoV-2 and ACE2 protein in human cells.

The S protein is a trimer – a complex of three identical polypeptides. Each polypeptide contains a Receptor Binding Domain (RBD) that binds to the ACE2 receptor on the surface of the host cell. This interaction facilitates the entry of viruses into the cell.

The SIH-5 miniprotein is designed to block the binding of the RBD to human ACE2. When an SIH-5 dimer encounters an S protein, one of its faces is tightly bound to one of the three RBDs on the S protein trimer and the other face to an RBD of another S protein.

This ‘crosslinking’ enabled the mini-protein to block both S proteins at the same time. “Different monomers can block their targets,” Chatterjee says. “(But) cross-linking of S proteins blocks their action many times more effectively. This is called the avidity effect.”

Under cryo-EM, the S proteins targeted by SIH-5 appeared to be attached head-to-head. “We expected to see a complex of one spike-trimer with SIH-5 peptides. But I saw a structure that was much longer,” says Somnath DuttaAssistant Professor at MBU and one of the corresponding authors.

Dutta and the others realized that the spike proteins were forced to form dimers and clumped together into complexes with the mini-protein. This type of clumping can simultaneously inactivate multiple spike proteins from the same virus and even multiple virus particles. “I have previously worked with antibodies raised against the spike protein and observed them under a cryo-EM. But they never made dimers of the spikes,” Dutta says.

The mini-protein was also found to be thermostable – it can be stored for months at room temperature without deteriorating.

The next step was to ask whether SIH-5 would be helpful in preventing Covid-19 infection. To answer this, the team first tested the mini-protein for toxicity in mammalian cells in the lab and found it safe. Then, in experiments conducted in the laboratory of Raghavan VaradarajanProfessor at MBU, hamsters were dosed with the mini-protein followed by exposure to SARS-CoV-2. These animals showed no weight loss and had a greatly reduced viral load and much less cell damage in the lungs, compared to hamsters exposed to the virus alone.

The researchers believe that this lab-created mini-protein with minor modifications and peptide engineering could also inhibit other protein-protein interactions.

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