The COVID-19 pandemic challenged researchers to discover life-saving treatments at an unprecedented pace. While these researchers rose to the occasion by discovering drugs faster than ever before, variants continue to challenge the world in addressing COVID-19. New innovations in computer-aided drug discovery tools could dramatically accelerate the study of new variants.
Nanome, a virtual and augmented reality software company for scientific discovery, gives scientists the ability to explore molecules in 3D – powering scientific breakthroughs and fighting diseases. With the help of the Nanome platform, one laboratory at Oak Ridge National Laboratory is now on the verge of creating the first-ever publicly known COVID inhibitor designed in virtual reality.
Dr. Andrey Kovalevsky at Oak Ridge National Laboratory specializes in research that elucidates the structural features of SARS-CoV-2 main protease 3CL (Mpro), which plays a central role in viral replication. He and his team of researchers approach drug design differently from other groups. They combine data from cryogenic X-ray crystallography with room temperature crystallography and neutron crystallography to create the most accurate molecular structure of Mpro possible, down to hydrogen positioning. When dealing with these kinds of complex structures, the challenge lies in exhaustively comprehending the nuances of the data – fine details often lost in 2D visualizations.
There’s a simple answer to complex visualization: virtual reality.
Dr. Kovalevsky, Oak Ridge National Laboratory
Virtual reality meets these needs by enabling scientists to ‘walk’ into the protein and see things how the protein sees them. Using Nanome’s Med Chem Tool, scientists at Oak Ridge created a new chemical structure characterized by an extra chlorine atom that showed a greater ability to bind Mpro. They were able to look at the enzyme and design and test different chemical groups on molecules while examining how the modifications affected the binding.
Inside Nanome, the researchers built and edited chemical structures in real-time with the MedChem Tool. This process was guided by built-in plugins that minimized the energy of ligands, display potential clashes, and show protein-ligand interactions in real-time, providing scientists with immediate feedback while designing. The team also used the platform to communicate and collaborate in VR across geographical distances.
If the study from Oak Ridge National Laboratory succeeds, it will result in the first drug ever discovered in virtual reality, and a notable step in combating COVID-19. VR is making possible hands-on collaboration in molecular design possible at a level never before seen by scientists and researchers. Scientists have more opportunities for those ‘eureka’ moments that ensure further progression of medical discovery.
Pharma Mirror Requested Answers To A Few Questions From Nanome Regarding Their Success
How does the technology work?
- Nanome is an XR (VR/AR/MR) software platform that leverages off-the-shelf VR/MR hardware, such as (but not limited to) the Meta Quest, HTC Vive, Valve Index, or HP Reverb headsets.
- Nanome also is able to leverage state-of-the-art molecular simulation algorithms that are industry standard to let researchers leverage their existing workflow, all within these headsets.
- Lastly, Nanome has a real-time and asynchronous collaboration feature that lets research across the globe be in one virtual room to quickly get on the same page and make scientific breakthroughs.
What is the added value of VR here?
- Scientists that have been trying to gain an intuition for the structural nuances of their data are able to instantly gain meaningful insights they were otherwise missing. I.e. it makes complex molecular nuances “immediately obvious”.
- Oakridge is an example of how scientists came up with a novel compound for covid that they wouldn’t have come up with otherwise.
- Other Nimbus Therapeutics case study here.
- Video testimony here.
- Scientists within their own specialties often of “their own language” chemists and biologists often have communication barriers to prevent them from being 100% on the same page. This problem gets worse when scientists are trying to communicate with non-scientists such as stakeholders, managers, and investors. VR is able to completely eliminate this communication gap as there is zero ambiguity on what the data looks like, how these molecular interactions happen, etc.
- The status quo for this type of research often requires a dozen different computational algorithms and solutions, with this VR environment scientists are able to get all their data, simulation/informatics algorithms, and colleagues in one virtual environment.
How can drugs designed this way be tested?
- Given insilico drug discovery (using computers to theoretically design and simulate drugs) has been established for quite some time since the 1980s, these drugs would be tested in the clinic just like 92% of drugs that went to market between 2010-2016, list here.
- Full paper here.
Who else is using this technology?
- Over half of top 20 pharmaceutical companies, numerous smaller biotech and start-ups, and over 250 universities have downloaded Nanome.
What are future ways you expect companies to use this technology?
- More different molecular applications: batteries, solar cells, semiconductors, polymer chemistry, chemical engineering
- Further down the pipeline of biopharma research and clinical applications: personalized precision medicine via personalized proteomics.
