Researchers develop helix-hairpin miniproteins for inhibiting SARS-CoV-2 infection
New Delhi, July 07 th (India Science Wire): The COVID-19 pandemic has entered into the third year.
The scientists and experts the worldwide have toiled to discover the best possible measures to
prevent the pandemic from spreading its tentacles further. Their collective efforts have led to the
discovery of vaccines protecting against the SARS-CoV-2.
However, the emergence of the new strains of the virus is a challenge to the protective effect of
COVID-19 vaccines. This has necessitated alternate means to help fight the virus in a way that it
cannot spread further. The researchers at the Indian Institute of Science (IISc), Bengaluru, have
developed a new class of artificial peptides (small chains of amino acids which combine to form
protein) or miniproteins which can render COVID-19 virus inactive. The details of the research have
been published in the journal Nature Chemical Biology.
‘Protein-protein interaction is more like that of a lock and a key. The interaction can be hampered by
a lab-made miniprotein that acts, fights with, and stops the ‘key’ from binding to the ‘lock’, and vice
versa,’ the researchers noted.
The artificial peptides or miniproteins can block not only the entry of viruses like SARS-CoV-2 into
human cells but also have the potential to clump virions (virus particles) together, reducing their
capacity to infect.
‘To examine the effectiveness of one of the miniproteins, called SIH-5 (SARS Inhibitory Hairpin- 5) in
preventing the COVID-19 infection, the research team also tested it for toxicity in mammalian cells.
It was found to be safe’, says Dr. Jayanta Chatterjee, Principal Investigator and Associate Professor at
the Molecular Biology Unit (MBU), IISc, and the primary author of the study.
Next, SIH-5 was administered to the hamsters in the laboratory of Raghavan Vardarajan, a Professor
at the Molecular Biology Unit (MBU). The hamsters were then exposed to the SARS-CoV-2. It was
found that the hamsters showed no weight loss and had significantly decreased viral load with much
less cell damage in the lungs compared to hamsters exposed only to the virus and getting no dose of
the miniprotein.
The miniproteins can bind to, and block the spike (S) protein of the SARS-CoV-2, which helps it enter
and infect human cells. The binding was further characterised extensively by cryo-electron
microscopy (cryo-EM), carried out in the laboratory of Somnath Dutta, an Assistant Professor at
MBU and one of the corresponding authors of the study.
In addition to cryo-EM, the researchers used various biophysical tools like CD spectroscopy, size
exclusion chromatography, surface plasma resonance, and dynamic light scattering.
On the outcome of the methodology followed by his team, Dr. Chatterjee says, “Through this
methodology, we identified the role of the helix-hairpin molecule (miniprotein) in inhibiting the
SARS-CoV-2 virus entry into human cells.”
What, after all, is the mechanism by which miniproteins act in preventing the viral infection?
Chatterjee explained that miniproteins, which are helical, hair-pinned peptides, can pair up with
another of its kind, forming a dimer with two faces to interact with two target molecules. The spike
(S) protein of the SARS-Cov-2 virus binds to the ACE-2 (Angiotensin-Converting Enzyme-2) protein in
the human cells to gain entry into these cells. Each S protein is a complex of three identical peptides,
forming an S protein trimer. Each of these polypeptides has a Receptor Binding Domain (RBD) that
binds with the ACE-2 receptor on the host cell surface. This interaction facilitates viral entry into the
cells. Now, when a SIH-5 dimer encounters an S protein, one of its faces binds tightly to one of the
RBDs of the S protein trimer while the other face binds to an RBD from a different S protein.
This ‘cross linking’ allows the miniprotein to block both S proteins simultaneously. “In this way, the
dimeric helix-hairpin molecule (miniprotein) can bind to its target and hold it tight to form a
sandwich complex. This prevents the target (virus) from getting loose and engaging in its native
biological role,” Dr. Chatterjee explains.
Highlighting the significance and effectiveness of cross linking in blocking the action of S protein,
Jayanta Chatterjee says- “Several monomers can block their target. {But} cross-linking, also called
dimerisation, of S proteins block their action many times more effectively. This is called the avidity
effect.”
Under cyro-EM, the S protein targeted by miniproteins appeared to be attached head-to-head. “We
expected to see a complex of one spike trimer with SIH-5 peptide. But I saw a much more elongated
structure,” says Dr. Dutta.
The miniprotein was found to be thermostable by the researchers. This means that it can be stored
at room temperature without deteriorating. This property can make it a fitting candidate for
inhibiting the Covid-19 infection from spreading further.
What are the further recommendations emerging out of this study?
“The therapeutic efficacy of SIH-5 in hamsters demonstrates its promise in evolving into a normal
class of therapeutics against diseases like Covid-19 that require inhibition of protein-protein
interaction to stall the disease progression,” explains Dr. Chatterjee.
Although their study focussed on inhibiting the SARS-CoV-2, the researchers believe that with minor
manipulation and peptide engineering, this lab-made helix-hairpin miniprotein could inhibit other
protein-protein interactions as well.
Besides Jayanta Chatterjee, Raghavan Vardarajan and Somnath Dutta, the other members of the
research team included Bhavesh Khatri (first author of the study), Ishika Pramanick, Sameer Kumar
Malladi, Raju S. Rajmani, Sahil Kumar, Pritha Ghosh, Nayanika Sengupta, R. Rahusuddin, Narender
Kumar, S.Kumaran and Rajesh P. Ringe.