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Playing with molecules in VR

It may look like a video game but it may help researchers to find the right drug. To figure out how to block a bacteria’s attempt to create multi-resistance to antibiotics, a researcher grabs a simulated ligand (binding molecule) — a type of penicillin called benzylpenicillin (red) — and interactively guides that molecule to dock within a larger enzyme molecule (blue-orange) called β-lactamase, which is produced by bacteria in an attempt to disable penicillin (making a patient resistant to a class of antibiotics called β-lactam). Credit: University of Bristol

In the past fifteen years the amazing progress in computation capabilities has made possible to address very demanding computational problems. One of them is the protein folding, an area that was already identified as demanding huge computational capabilities back in the early nineties.

Understanding protein folding is crucial in health care. Our body is made of proteins and their interaction with one another is makes like tick. Tampering with these interaction as well as altering these proteins can lead to health problem and this is what happens as consequence of an infection by bacteria and viruses as well as with presence of toxins and other substances that alter the proteins.  Bacteria, viruses, toxins and more interact with proteins like Lego bricks. They plug in onto specific parts of a protein and by doing so they can modify the folding (the shape) of the protein and/or can disrupt interactions by blocking the access to a specific part of the protein.

This same basic mechanism of coupling a molecule onto a part of a protein thus blocking the access to that part can, and is used, by drugs. As an example a drug may attach to a part of bacteria or virus that would normally attache to one of our protein and effectively block the action of that bacteria/virus on our proteins.

In the past researchers and doctors where moving blindly trying to find, by pure chance, a substance that would block a bacteria. Now that the chemical process is understood they can work to design a substance, a drug, that can serve that purpose. This is revolutionising pharma decreasing cost and increasing effectiveness.

The design remains extremely complex and the computational problem requires supercomputer power to simulate the folding of a single protein.

Starting in the middle of the last decade tools for helping the study of protein folding and for simulation of protein bonding have started to appear using computer graphics and haptic interfaces.

These tools are an example of a symbioses between a researcher brain (which means its knowledge, experience, skill and imagination) and a computer. The computer would present the 3D image of a protein and the researchers use their hands to touch the protein atoms, “feel” how strong their mutual bonds are, how sticky (or repulsive) they can be to other molecules.  The work is like building a puzzle. You have several pieces already in place and you try several other pieces one by one trying to have them locking in place.

At the university of Bristol, UK, a team has developed a virtual environment that can be explored using VR goggles letting researchers to look at a protein folding in 3D and try to place another molecular structure on the protein and see where and how it would fit (see the clip). Several researchers can work around the virtual molecule at the same time trying the bonding with several other molecules.

The possibility of working in parallel is very important since the bonding of just one molecule alters the overall protein folding and has an impact on the bonding in other parts.

The complexity is still there but we are seeing the emergence of tools that help in managing it. We might expect a real revolution in drugs design in the next decade, something that will be sorely needed as we move from general drugs to customised drugs, effectively multiplying the number of drugs that will be needed.

About Roberto Saracco

Roberto Saracco fell in love with technology and its implications long time ago. His background is in math and computer science. Until April 2017 he led the EIT Digital Italian Node and then was head of the Industrial Doctoral School of EIT Digital up to September 2018. Previously, up to December 2011 he was the Director of the Telecom Italia Future Centre in Venice, looking at the interplay of technology evolution, economics and society. At the turn of the century he led a World Bank-Infodev project to stimulate entrepreneurship in Latin America. He is a senior member of IEEE where he leads the Industry Advisory Board within the Future Directions Committee and co-chairs the Digital Reality Initiative. He teaches a Master course on Technology Forecasting and Market impact at the University of Trento. He has published over 100 papers in journals and magazines and 14 books.