13 octobre 2021

[Nanomedicine] – Computing at the frontiers of nanomedicine.

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Viruses kill millions around the world each year. « In addition to the novel coronavirus, leading viral killers include hepatitis, HIV, HPV, » said Lela Vukovic, Assistant Professor of Chemistry, University of Texas at El Paso.

Researchers are constantly trying to figure out new therapeutics that will help prevent infection or act therapeutically to reduce symptoms for one virus at a time. « Another strategy, » Vukovic said, « would be to find therapies that are broad spectrum and simultaneously act on a number of different viruses. »

Many viral infections start with the virus binding to heparan sulfate molecules on the host cell’s surface. Working with experimentalists led by Francesco Stellacci of the Swiss Federal Institute of Technology Lausanne (EPFL), and in collaboration with Petr Král at the University of Illinois at Chicago, Vukovic helped to investigate nanoparticles with solid cores and ligands attached that mimic the heparan sulfate molecules and their microscopic action on several viruses.

They found that nanoparticles with certain ligands can attach to the viruses, which soon after may disintegrate.

« Such virus-destructing materials can be prepared, » Vukovic said at a recent seminar at the Texas Advanced Computing Center (TACC). « The question is: Are there hints we can get from computational modeling to design new, better materials and understand the mechanism that causes the virus capsid to break? »

Since nanoparticles are minute, they can’t be imaged clearly at the atomic level and microsecond timescales at which the reactions happen. So Vukovic created models of the atomic structure of virus, as well as the nanoparticles with ligands of various lengths attached.

Using TACC supercomputers, she simulated how the viral proteins and nanoparticles interact with each other. She found that the virus binds and makes numerous contacts with longer ligands.

Not only that. The nanoparticles bind at the junction of two proteins and, like a wedge, increase the distance between viral proteins, breaking the contacts and disintegrating the virus. The initial findings research were published in Nature Materials in 2018 (« Broad-spectrum non-toxic antiviral nanoparticles with a virucidal inhibition mechanism »), and new results, obtained by the student Parth Chaturvedi, have been posted on bioRxiv (« Computational modeling of virucidal inhibition mechanism for broad-spectrum antiviral nanoparticles and HPV16 capsid segments »).

 

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