University of Minnesota: New application could lead to better treatments for diseases like cancer and COVID-19

A team led by University of Minnesota Twin Cities biomedical engineers has developed an application that can simulate complex molecular interactions, which will allow researchers to design better treatments for diseases like cancer and COVID-19.

The paper expands upon a study the researchers published in 2019 to simulate even more complex molecular interactions. Additionally, they made the application easy for non-experts to use and applied their findings to shed light on how the SARS-CoV-2 virus infects the body.

The study is published in Nature Communications. The app, called MVsim, is freely available to other researchers on GitHub.

The simulator predicts the strength, speed and selectivity of multivalent interactions, which involve molecules that have multiple binding sites and can be used to develop medicines for diseases.

Many cancer drugs not only bind to tumor cells but also to cells they aren’t meant to target, which often creates unwanted side effects for the patient. By optimizing the specificity of multivalent interactions using MVsim, researchers can design drugs that more specifically target the cells in a tumor while minimizing binding to other cells in the body.

“Multivalent drugs can target specific cells in a way that’s not possible with standard, monovalent drugs, but there are many variables to consider in their design and much of the work in the field to date has been done through experimental trial and error,” said Casim Sarkar, senior author of the paper and a professor in the U of M Department of Biomedical Engineering.

Another example is the SARS-CoV-2 virus. Scientists know that the virus is evolving to better infect our cells and evade our immune systems, but the molecular mechanisms behind how the virus does this are relatively unknown. Using their MVsim technology, the researchers were able to explore how the virus’s spike protein switches between a cell-infecting state and an immune-evading state.

The researchers have already identified potential ways to limit the infectivity of current and future SARS-CoV-2 variants, which they plan to test soon.

The research was funded by the National Institutes of Health and a COVID-19 Rapid Response Grant from the U of M’s Institute for Engineering in Medicine.