Researchers recently used advanced computational simulations to investigate a tiny molecule's efficacy in treating COVID-19.
As indicated in a SciTechDaily report, many treatments for coronavirus focus on the spike protein used by the virus to attach to human cells.
Whereas such treatments are effective on the original COVID-19 variant, they may not be as effective on future ones. For instance, the Omicron strain has numerous spike mutations.
Professor Juan de Pablo of Pritzker School of Molecular Engineering, together with his group, has employed advanced computational simulations to study further a protein essential to the replication of the virus and remains comparatively consistent through different coronavirus variants.
Researchers recently used advanced computational simulations to investigate a tiny molecule's efficacy in treating COVID-19.
The Nsp13 Protein
The protein identified as Nsp13 is part of a class of enzymes called "helicases," playing a role in a manner the virus duplicates.
Through this research, the study authors have uncovered different compounds that can bind to Nsp13 and hinder replication of the virus.
Given the helicase sequences' consistency across COVID-19 variants, such inhibitors could function as a "valuable starting point" for designing drugs that target helicases for them to be able to treat COVID-19.
De Pablo explained, currently, there's only one treatment for COVID-19, and as there is a mutation of the virus, there is a need to target various building blocks aside from the spike protein.
The professor also said their study, published in the Science Advances journal, has shown how tiny molecules can modulate an attractive target's behavior in replication of the virus and has revealed that "existing molecular scaffolds" are potential candidates for COVID-19 treatment.
Computational Replications to Study Proteins
For the last two decades, as earlier mentioned, de Pablo's team has used computational replications to examine proteins that enable the virus that causes COVID-19 to duplicate or infect cells.
Such simulations, which need months of tremendously demanding computations with powerful algorithms, eventually show how the virus is working at the molecular level.
In this research, the collaborators investigated the Nsp13 protein, unwinding two-stranded DNA into two single strands, a crucial step in duplication.
Earlier, researchers knew that Nsp13 did this unwinding, although did not have a good insight of the process's complicated dynamics, a related University of Chicago News report specified.
Moreover, the simulations showed how several domains within the protein communicate with each other and function in concert to employ the proper forces for the unwinding.
The researchers also discovered that the moment an external molecule binds to specific areas of the protein, it disrupts such a communication network.
Meaning, the protein can no longer wind down or slow down the DNA effectively, and it turns more difficult for the virus to duplicate.
Information from Simulations Used to Develop New Drug
The research team has even used the information from their simulations to develop a new drug for COVID-19 treatment, which they hope to publish within the next couple of months.
De Pablo explained, they, in the team, continue to examine drugs that impact different virus parts, different proteins and then use investigational data to verify their effectiveness.
He added, there is now a series of candidates, and the team's newly designed drugs could be game-changers for COVID-19 treatment and novel coronaviruses later on.
Related information about COVID-19 treatment is shown on MedCram's YouTube video below:
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