Researchers from the faculties of Medicine (FMRP) and Dentistry (FORP) of University of São Paulo (USP), Ribeirão Preto campus, identified one of the factors that made the new variant more infectious. coronavirus SARS-CoV-2, B.1.1.7, originally from the United Kingdom and with two cases confirmed in Brazil by the Adolf Lutz Institute.
Through the application of bioinformatics tools, they found that the protein spike of the new viral strain – which forms the crown structure that gives its name to the coronavirus family – establishes greater molecular interaction strength with the ACE2 receptor, present on the surface of human cells and with which SARS-CoV-2 binds to make viable the infection.
The increase in molecular interaction strength of the new strain is caused by a mutation already identified in amino acid residue 501 of the protein spike of SARS-CoV-2, called N501Y, which gave rise to the new variant of the virus, the researchers noted.
The results of the work, supported by FAPESP, were published on the platform bioRxiv, in article still without peer review.
“We saw that the interaction between the protein spike of the new strain of coronavirus with the N501Y mutation is much larger than that presented by the first strain of the virus isolated in Wuhan, China, ” FAPESP Agency Geraldo Aleixo Passos, professor at FMRP and FORP-USP and project coordinator. Another author of the study, who carried out the bionformatic analysis, is Jadson Santos, who is doing a doctorate at FMRP-USP under the guidance of Passos.
With the appearance of the B.1.1.7 strain in the United Kingdom, the researchers raised the hypothesis that the N501Y mutation present in the protein spike of the new variant, resulting from the replacement of an amino acid asparagine (N501) by one of the tyrosine type (N501Y), could be one of the factors responsible for the high contagiousness of the new line of the coronavirus.
That’s because N501 had already been identified as a crucial amino acid residue in protein binding affinity spike to the human ACE2 receptor and, consequently, implicated in the infectivity of the new coronavirus. In addition, previous studies have also pointed out that the N501Y mutation found in the B.1.1.7 strain covers one of the six key contact amino acid residues within the protein spike.
“There are other mutations in the genome of this strain that we have not analyzed. We focus on N501Y because it is involved in protein binding spike with ACE2 ”, explains Passos.
In order to test the hypothesis that the high infectivity of strain B.1.1.7 could be due to changes in the interaction strength between the protein spike mutant and the ACE2 receptor, protein structures were used spike SARS-CoV-2 isolated in Wuhan and strain B.1.1.7, deposited in a protein database, the Protein Data Bank.
Through public domain software, called PyMOL, it was possible to visualize the interaction between amino acid residue 501 of the protein spike of SARS-CoV-2 with the Y41 residue of the human ACE2 protein and simulate and analyze the interactions resulting from the N501Y mutation found in the B.1.1.7 line with the cell receptor.
“This software allows visualizing images of these molecular structures with an approximation of 3.5 angstroms in the field, much larger than the images generated even by an ultramicroscope”, compares Passos.
Through other public domain software, called PDBePISA, it was possible to compare the interaction of proteins spike the wild-type strain of SARS-CoV-2 and the mutant with the human ACE2 receptor.
The analysis results showed that the N501Y mutation in the protein spike of the new variant of the coronavirus establishes greater interaction with the ACE2 receptor compared to the wild strain of the virus. The interactions were predominantly non-covalent – weaker – the researchers noted.
“The sum of several weak links between the protein spike mutant of the new variant of the coronavirus with the human ACE2 receptor results in stronger molecular interactions, which allow the virus to enter cells more easily and trigger the replication system ”, explains Passos.
The study also revealed that the N501Y mutation causes a change in the spacing between the amino acid residues of the spike protein, allowing it to establish even more interactions with the ACE2 receptor.
“Together, these changes confirmed the hypothesis that the protein spike strain B.1.1.7 interacts more strongly with the ACE2 receptor, ”says Passos.
According to the researcher, the results of the study done through computer simulations in silico will allow guiding new experiments in vitro, aimed at evaluating in the laboratory the infectivity of the new coronavirus variant in human cell cultures.
Amazing evolution
According to the researchers, the rapid spread of SARS-CoV-2 among humans is driving their molecular evolution. So far, the virus has accumulated mutations at a rate of up to two nucleotides per month, and recent isolates show at least 20 nucleotide changes in their genomes compared to the wild strain, isolated in January 2020. Most of the mutations are located in protein spike.
The line B.1.1.7., Detected in early September and described in December 2020 by the COVID-19 Genomics UK Consortium, in the United Kingdom, and already registered in 17 other countries, including Brazil, represents an example, among several others, the rapid molecular evolution of the new coronavirus. However, it surprised scientists by accumulating 17 mutations, of which eight are located in the gene that encodes the protein spike on the surface of the virus.
“This new strain accumulates many mutations. A smaller number is observed in other viral strains ”, compares Passos.
As the description of this new variant is recent, it is not yet possible to evaluate the phenotype in more detail, that is, whether it is more or less pathogenic, explains the researcher.
The animation (below) shows the interaction of the protein spike of the new viral strain with the ACE2 receptor.
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