Over the last year, Riken’s Fugaku supercomputer (pictured in the header) has maintained the top spot on the Top500 thanks to a staggering 442 Linpack petaflops of computing firepower. The system sprung onto the scene nearly a year ahead of schedule for a very specific purpose: turbocharging COVID-19 research early in the pandemic. The system has hosted critical COVID-19 research virtually nonstop ever since, and now, the University of Tokyo and Fujitsu are teaming to use Fugaku to develop small molecules to fight COVID-19 infections.
The new research is an extension of a decade-long partnership between Fujitsu and the University of Tokyo’s Research Center for Advanced Science and Technology (RCAST). Through that partnership, the two institutions have worked to create small molecule compounds to fight a variety of diseases, including cancers. Specifically, they have aimed to create drugs that are orally ingestible, chemically synthesizable and low-cost.
The researchers see the extension of this work into COVID-19 therapeutics as crucial, given that – despite the many effective vaccines – the billions of unvaccinated people still remain susceptible to the devastating effects of the virus if infected, with no strongly effective therapeutics as-yet identified.
For the drug development work, they will, of course, be making extensive use of molecular dynamics simulations. The researchers aim to use docking simulations to investigate the potential of possible inhibitory compounds, producing a 3D structure model of each viral protein and candidate compound identified during the search.
Then, the researchers will use further molecular dynamics simulations to track the dynamic behavior of each protein-compound pair to ensure that, to the best of the simulations’ knowledge, they could exist in a staple bound state in the human body. Any compounds that pass these two stages will move on to further testing in the real world.
While drug development is the primary aim of the partnership, the researchers also have their sights set on another hot topic of the pandemic in 2021: variants and mutations. The team will set out to use Fugaku’s computing power to predict future mutations – and even new types of coronaviruses – by mutating various amino acid sequences within SARS-CoV-2’s viral proteins and observing the modified virus’ new behavior. This work will, in theory, allow for preemptive drug development for predicted strains of concern.
With a wide range of efforts underway by a variety of supercomputing institutions, it remains to be seen if any of them can successfully identify a therapeutic drug that is strongly effective in treating COVID-19. And, with the Top500 due to be refreshed in the coming week at ISC21, it remains to be seen whether Fugaku will retain its crown in the new year.
To learn more about Fugaku’s fight against COVID-19, read the stories below: