ICHEC announces details of COVID-19 research projects currently active on KAY.
ICHEC has announced details of two promising Covid-19 research projects which are currently active on KAY, the national high-performance computer.
Dr Elisa Fadda, Department of Chemistry Maynooth University and her team are examining the molecular interaction of the coronavirus 2 spike (CoV2-s) with the cell surface receptor ACE2.
"The first step of infection in COVID19 is triggered by the molecular interaction of the coronavirus 2 spike (CoV2-S) with the cell surface receptor ACE2. The CoV2-S is a viral envelope glycoprotein, which means a protein expressed on the surface of the virus, heavily functionalized with complex carbohydrates (or glycans). Glycans are biomolecules inherently and inextricably linked to the spike's structure and function, thus to the viral pathogenicity. The glycans' chemical nature makes them extremely flexible and dynamic, so hard or impossible to characterise (observe) experimentally," Dr Fadda said.
Commenting on the use of high-performance computing in this critical research, Dr Fadda said: "We use ICHEC's supercomputer kay to study these glycans by molecular simulations and to understand their role in COVID19 viral pathogenicity. Our research provides very important (and missing) insight at the atomistic level of detail that will help us understand the key mechanistic first steps of viral entry and that can aid in devising therapeutic strategies, such as the development of vaccines, antibodies and small molecules drug-based therapeutics."
Dr. Donal MacKernan, UCD School of Physics, is developing immunoassay based POC tests for COVID 19 disease using a protein based molecular switch that is designed to greatly reduce false positives and false negatives, a difficulty that plagues other POC tests currently available.
"The most widely used tests for COVID 19 currently target the nucleic acid sequences characteristic of virus to detect infection and generally integrate PCR in the measurement process. As a consequence, the machines used are generally large and laboratory based and required skilled technicians, so that the turnaround time from sampling to result and cost of testing is significant. The WHO has, as a consequence, indicated that the immediate priority for COVID-19 diagnostics research is the development of diagnostic tests and detection at the point-of-care (POC) such as doctors offices, clinics, ambulances and even more widely, such as in pharmacies and the home,” he said.
Commenting on the importance of these tests he said, "These tests are needed not only to limit the spread of infection but also to most effectively treat patients suffering from a serious infection. Instead of detection of the RNA of the virus, it is possible to measure proteins that are also present in the complex, such as spike proteins using suitable antibodies that bind specifically to them. Such immunoassay based diagnostic tests can be utilised to both measure acute current infection and past infections/immunity.”
Commenting on the role of HPC in this research, Dr MacKernan said, “This design has already been validated experimentally at the UCD Conway Institute of molecular biology and molecular medicine to detect upregulated epidermal growth factor receptor which plays a key role in cancer research. That design emerged entirely through simulation that was in part supported by the EU E-CAM Centre of ExcellenceConsortium (both ICHEC/NUIG and UCD are members) associated with CECAM, with Irish HPC resources provided by ICHEC. The design is now being modified using advanced molecular simulation methods to target COVID 19, with HPC resources again being provided by ICHEC.
The simulation part of the team includes Dr Donal MacKernan (lead inventor of the molecular switch design), Shrinath Kumar, and Ali Zeinlabadin Jaafar all at the UCD School of Physics.
Dr. Goar Sánchez, Computational Scientist and National Service Programme Manager, ICHEC said, “We hope that the fast-track access to HPC we announced in March will help these projects to advance their COVID-19 research. The calibre of the projects above, hosted on Kay, highlights the world-class research being conducted by researchers in Irish third-level institutions. From ICHEC and particularly the National Service team, we are happy to support the Irish HPC ecosystem during this time. We look forward to seeing the results of Dr Fadda and Dr MacKernan’s research, furthering the understanding of the molecular structure of COVID-19 and improving testing for it.