Researchers at Stanford University School of Medicine have identified aspects of the novel acute coronavirus 2 (SARS-CoV-2) novel that have few mutations and therefore could be important targets for prophylactic agents against infection coronavirus 2019 (COVID-19).
Drugs targeting the “less volatile” regions are more likely to be effective against future changes of SARS-CoV-2 because they remain unchanged or “preserved” as the virus reacts. movement and growth.
Daria Mochly-Rosen and her colleagues identified the divisions using a database of nearly 190,000 individual virus strains from patients worldwide, thus revealing the natural evolution of the virus.
The team focused on data for the viral spike protein – the main structure the virus uses to get to host cells. The receptor binding domain (RBD) of the spike protein binds to the human receptor angiotensin-converting enzyme 2 (ACE2) as the first step in the infectious process.
Currently, much of the effort to develop prophylactic agents as therapies for COVID-19 is focused on targeting this spike protein to inhibit its interaction with ACE2.
Now, Mochly-Rosen and colleagues suggest that it may be beneficial to develop tolerant and active vaccines that target the RBD, rather than the whole spike protein.
They also suggest that it may be useful to exploit small area-like molecules known as the linoleic acid (LA) binding site. In addition, they say that drugs that target a relatively well-preserved and exposed area on the surface of the protein (spanning residue 541-612) may have a prophylactic benefit.
A pre-printed version of the paper is available on the bioRxiv * server while the article is under peer review.
Functional regions in S protein and RBD-ACE2 interaction site. a) The number of variations for each position over a complete sequence of S proteins, highlighting specific functional areas. b) Spike homotrimer with orally colored ribbons, attached to ACE2 (red). Black dotted illustration shown in c. c) RBD-ACE2 interface. d) RBD-ACE2 interface illuminates residues in RBD within 4.5Å from ACE2. e) The number of variations for each position across RBD land.
SARS-CoV-2 infection process
As part of the SARS-CoV-2 infection process, proteases secrete the spike protein into two subunits. In subsurface 1 (S1) the RBD is in a closed (inactive) concordance that does not allow viral binding or an open (active) concordance that enables binding. When the RBD in the conjunctiva is exposed, subunit (S2) enables the virus to enter the host cell membrane.
Methods of prophylaxis include inhibition of proteolytic transport of S1, competing with RBD binding, generating antibodies against the spike protein or RBD (tolerant vaccines), and stimulating an immune response to the spike protein (active vaccines).
In addition to the RBD, other areas such as the spike trimer interface and the LA binding site tend to play an important role in maintaining the structural integrity of SARS-CoV-2, entry and transmission, say Mochly-Rosen and colleagues.
The researchers assumed that these regions of the spike protein would be more conserved and that other regions would have fewer changes.
What did the researchers do?
To identify segments in the least variable spike protein, the team used the spike protein database created by the Singapore Institute of Bioinformatics.
Mar 11 Novth, 2020, the database contained 189,704 individual strains of the natural virus isolated from many patients worldwide.
All variants observed in the spike protein were uploaded to the PROVEAN software engine and compared to the spike protein amino acid series from the Wuhan reference (EPI_ISL_402124) received in February 2020.
What did they find?
Compared to the reference series, the spike protein was found to contain 4,517 strains (including 1,273 amino acids).
Each amino acid condition in the protein sequence caused four average changes. However, some categories had ten types at each location, while others did not. Regions with no more than two variants of each amino acid condition were more common in the structural diagnostic trimer interface (38%), the LA binding site (65%), and the RBD (37%).
The researchers say the trimer interface is less accessible so drugs are unlikely to be targeted. However, the LA binding site could be a potential target for treatment with small molecules that stabilize the spike protein in its closed, inactive concentration.
“The acid-binding pore acid in the S inactive condensate. [spike] proteins are retained in other coronaviruses and 82% of the variants among the 20 amino acids that make up this pocket are expected to have a neutral effect, ”the team wrote.
What about the RBD?
The study found that RBD contains ten insoluble amino acids (331-524 amino acids), and the PROVEAN engine predicted that only 7% of RBD mutations were expected to be destructive. in terms of structure or function.
“Therefore, drugs targeting the RBD are expected to be effective prophylactics for most SARS-CoV-2 mutations,” the researchers wrote.
The team also identified another less variable or so-called “hot” section spanning the residue of amino acid 541-612.
The researchers say that, within this category, the amino acid at position 564 has been suggested to be a “latch” that stabilizes the spike protein in the joint. closed agreement.
The team suggests that this hot section could be involved in membrane fusion.
“Determining the location of this unstable region is important, as targeting treatment against SARS-CoV-2 may be another Achilles heel,” wrote Mochly-Rosen and the team.
What is the impact of the study?
The researchers say the findings could guide the development of effective prophylactic agents to prevent the spread of COVID-19 pandemics.
“Our data suggest that it may be beneficial to develop passive and active vaccines that target the RBD, rather than the S protein as a whole, as well as small molecules that lock in the closed conjunctiva. , such as those who imitate LA, ”they write.
“Finally, drugs and antibodies targeting the 541-612 area, a relatively well-preserved and exposed area on the protein surface, may have a prophylactic benefit,” the team concluded.
* Important message
bioRxiv publish preliminary scientific reports that are not peer-reviewed and, therefore, should not be seen as final, guiding health-related clinical practice / behavior, or be treated as information established.