New methodology predicts SARS-CoV-2 virus mutation hotspots

Researchers in Sweden and China have published a new methodology for predicting the “hot spot” sites of mutations in Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2).

Within these hotspots, mutations cause small local changes within SARS-CoV-2 Spike protein Structure – The surface structure used by the virus to bind to and infect host cells.

This small change in the structure of the spiked protein will result in a large conformational change in the protein that alters its biological function.

As a proof-of-concept exercise, the team first demonstrated how the infamous spike variant D614G was predicted using a new methodology. This variant increases the infectivity of the virus and is currently the most prevalent strain in the world.

The team also presents other examples of hotspot residues that may be good candidates for mutation.

Researchers say that this methodology can be used to design effective drugs and antibodies against spike proteins, and more generally to search for and identify mutation hotspots.

Preprinted paper is available on the server bioRxiv*, While the article is undergoing peer review.

(Online color) The spike protein subunit S1 is composed of the N-terminal domain NTD and the receptor binding domain RBD. The subunit S2 consists of a fusion peptide FP, two heptapeptide repeats HR1 and HR2, a transmembrane domain TM, and a cytoplasmic domain tail CT.

Spike proteins are the focus of major research

Transmembrane spikes given their role in host cell binding and infection Glycoprotein What covers the surface of SARS-CoV-2 is of particular interest to researchers.

Proteins are made up of two subunits. Subunit 1 (S1) begins at the N-terminal domain (NTD; residues 14-305), which contributes to protein conformational changes during interaction with the host cell.

The NTD is followed by a receptor binding domain (RBD; residues 319-541), which initiates host cell invasion by binding to the host cell receptor angiotensin converting enzyme 2 (ACE2).

The RBD is followed by the junction region between S1 and subunit 2 (S2). The cleavage site within this segment is hydrolyzed by a host cell protease that primes the spike protein for fusion with the cell membrane.

The subunit 2 (S2) constitutes the rest of the protein and begins with a fusion peptide that spans residues 788-806 to initiate fusion. This is followed by two heptapeptide repeat (HR) sequences, HR1 at residue 912-984 and HR2 at residue 1163-121. These HR sequences form a 6-helix bundle that allows the virus to fuse with the cell and enter the cell.

Much effort to develop vaccines and therapies has focused on the RBD and HR1 / HR2 domains.

“But for durable antivirals, we need to know how to identify mutation-prone amino acids and how to predict the biological effects of potential mutations,” said Stockholm University. Antti Juhani-Niemi and Xubiao Peng of Beijing said. Research Institute.

“Conformations are crucial to protein function, so knowledge of hotspots is important to better understand how spike proteins work and can be neutralized.”

What did the researchers do?

Currently, the team has presented a methodology that helps predict the location of the spike along the Cα backbone. Changes in local topology can result in large conformational changes that alter protein activity.

Such changes in backbone topology only occur when structural branching occurs at critical sites. The prerequisite for this branch is the presence of flattening points.

Therefore, this methodology identifies potential mutation hotspots by graphing all sites proximal to the flattening point.

(Online color) a) The current total atomic structure of the spike protein near site 103. b) Substitution of A instead of 103G predicted by chimera [32].. There is no obvious steric hindrance for replacement.

The potential outcome of the mutation was predicted by comparing the residues to those present in the most matching high-resolution protein databank structure.

As a proof of concept, the team applied this methodology to the infamous D614G mutation site. This site was shown to be proximal to the flattening point, and the D → G substitution was correctly predicted.

Several topologically similar hotspot sites have been identified in the fusion core that forms the junction between NTD and HR1 and HR2.

Hotspot sites within the NTD turned out to be good candidates from mutations, but hotspot sites within the fusion core were more stable.

Researchers have identified, in particular, the fusion core residue 1080A as stable to mutations, but as it is close to the two flattening points, the local topology tends to change. It says it seemed.

“This makes residue 1080A an excellent target for the development of structure-based fusion inhibitors,” the team suggests.

What is the meaning of research?

Researchers say that identifying and analyzing these mutant hotspot sites in spike proteins can help predict their future evolution and help develop structure-based therapeutics and vaccines.

“This methodology can be used to design effective drugs and antibodies against spiked proteins, and can be used more commonly whenever protein mutation hotspots need to be searched and identified. “They write.

“Conformations are so important to protein function that topology should be the most effective tool in protein research,” the team concludes.

*Important Notices

bioRxiv Publish preliminary scientific reports that should not be considered definitive as they are not peer-reviewed, guide clinical / health-related behaviors, and should not be treated as established information.