National Supercomputing Center in Korea, KISTI, Joins Fight Against COVID-19

A research team in Korea Institute of Science and Technology Information (KISTI) have utilized the KISTI-5 called Nurion, the world 14th fastest supercomputer, to identify 43 drug candidates. These drugs’ efficacy against COVID-19 needs further experimental verification, and the preliminary results have been published on ChemRxiv.

COVID-19 was first identified in the Chinese city of Wuhan and has since spread around the world, quickly becoming a major global pandemic. Many research institutes and pharmaceutical companies across the globe have promptly responded to develop vaccines and treatments as a counteraction to the rapid spread of COVID-19. For example, researchers at the Department of Energy’s Oak Ridge National Laboratory (ORNL) were quick to react against COVID-19. They used its own supercomputer, Summit, the world’s fastest supercomputer, to carry out research exploring inhibitor candidates that could possibly inhibit activity of “spike” proteins on the envelop of the novel coronavirus.

Researchers in KISTI have used its own supercomputer, Nurion, to find drug candidates potentially usable as a cure for COVID-19 amongst 19,168 drug molecules from SWEELEAD library and ChEMBL database. Using the 3D structure of main protease (Mpro) of the novel coronavirus discovered by Germany researchers which is known as an essential enzyme used in the cloning of the novel coronavirus inside the host cell, KISTI researchers evaluated binding affinity between Mpro and the 19,168 compounds, and ranked these compounds based on the molecular docking score. After selecting 43 candidates, they conducted a molecular dynamics (MD) simulation to further investigate protein-drug interaction. Finally, 8 drug candidates were narrowed down and selected.

“Leveraging the power of supercomputer is a key to in-silico screening through tens of thousands of chemical compounds within days, which would, otherwise, take months using PC,” said Sangjae Seo, a KISTI researcher who has led this study.

“We plan to collaborate with Korea Institute of Chemical Technology (KRICT) and Seoul National University (SNU) to further assess the effectiveness of the selected drug candidates at the cellular and enzymatic level and will refine more extended drug discovery pipeline by adding in-vitro and in-vivo steps as well as AI-driven in-silico screening approaches,” added Soonwook Hwang, director of KISTI supercomputing center.

Keeping COVID-19 under control is a nation’s top priority, and KISTI, as a government-funded research institute, has a responsibility to take prompt measures in responding to this current national and global epidemic. To this end, KISTI has recently announced a call for project to which any Korean scientists, who want to join the combat against COVID-19, could a proposal for willing to tap into the KISTI-5 supercomputing resources in order to be able to be armed with better tools for their own fight. “This contingency call is exceptional in a sense that as opposed to a routine call requiring relatively long and time-consuming review process that occurs three times a year, nearly all applications will likely be accepted and approved with no special review process, once the application is proved to have a strong relevance to the fight against COVID-19. This program will be in operation tentatively for about up to six months”, said Hee-yoon Choi, president of KISTI.

The image illustrates how a candidate drug, located inside the orange circle, binds to the main protease (Mpro) of the novel coronavirus in blue and red.