UTEP Researchers Using Supercomputers to Develop COVID-19 Vaccine

By Oliver Peckham

April 15, 2020

With COVID-19’s spread across the globe meeting a strong front of resistance from the world’s governments, the supercomputing community increasingly seems united in a single goal: stopping the pandemic. The latest player to highlight their role in the fight is the University of Texas at El Paso (UTEP), where researchers have leveraged supercomputing in their quest to develop a vaccine for the novel coronavirus.

Suman Sirimulla. Image courtesy of JR Hernandez/UTEP Communications.

The research is led by Suman Sirimulla, assistant professor of pharmaceutical sciences at UTEP. Like many others, Sirimulla is attacking COVID-19’s spike protein: the crucial, invasive protein that allows COVID-19 to hijack human cells and reproduce itself within them. The UTEP team is hunting both for small molecules that could serve to inhibit the spike protein and for inhibitors of COVID-19’s primary protease.

“The coronavirus targets the respiratory cell’s ACE2 and TMPRSS2 enzymes and uses the spike protein to attach itself to them,” Sirimulla said. “Once the virus gets into the cell, it begins to replicate. What we are trying to do is target the virus’ RNA-dependent RNA polymerases enzymes that are involved in replicating the virus.”

To analyze these small molecules and viral proteins, Sirimulla and his colleagues are leveraging the supercomputing resources of the Texas Advanced Computing Center (TACC), which is providing HPC services, visualization and data storage. Using these capabilities, the UTEP team is applying AI algorithms to help refine the small molecule selection for assailing the spike protein.

“These computer-aided approaches are common in pharmaceutical sciences research, and Dr. Sirimulla’s expertise is uniquely suited to make significant contributions to the fight against COVID-19,” said Marc B. Cox, a professor of biology and chair of the Pharmaceutical Sciences Department at UTEP. “His work and contributions toward solving this global public health crisis reaffirm UTEP’s status as an R1 institution, and validate the impact that scientific research has in our communities.”

The researchers know they have a long road ahead – optimistically, the entire process could take between 15 months and two years, they say. Even after they identify promising small molecules for inhibiting the spike protein, there are many stages of drug development to consider.

“If we find compounds able to inhibit the viral proteins, we will seek collaboration with laboratories outside UTEP that can work with the virus in order to test the antiviral efficacy of these compounds,” explained Manuel Llano, associate professor in the Department of Biological Sciences at UTEP. “If the compounds are effective against the virus, then we will find collaborators that can test the compounds in animals infected with the virus. If our compounds protect the animals from infection and do not cause toxicity to the animals, then clinical trials need to be conducted. Therefore, this is just the beginning of a long project that has the potential to obtain a therapeutic drug.”

In the interim, Sirimulla is calling on volunteers to contribute their own computing resources to TACC’s crowdsourced computing initiative, [email protected], which supplements TACC’s supercomputers. To learn more about that, click here.

To read more about this research, visit UTEP’s article here.

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