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When people get vaccinated or get infected by a pathogen, their bodies fight the foreign substance by producing antibodies. They also create memory cells to remember the foreign invasion, so that future infections can be readily fought by the body by quickly producing the right antibodies. Each human being has different antibodies because an individual’s body remembers the unique vaccines and infections he or she was exposed to over the years.
Through a National Science Foundation RAPID Award, researchers at FIU’s College of Engineering & Computing (CEC), College of Arts, Sciences & Education and Herbert Wertheim College of Medicine (HWCOM) are investigating whether it’s possible that antibodies people carry from other viral infections are fighting COVID-19.
This research could explain why some countries, such as New Zealand, may have beaten the coronavirus and why other countries have been more impacted with cases still rising at drastic rates.
Giri Narasimhan, professor in the School of Computing and Information Sciences (SCIS) and principal investigator on the grant, explains his inspiration in this study.
“Scientifically, it’s challenging to look at this pandemic and ask how I can contribute with my training,” said Narasimhan. “There are numerous theories as to why it took so long for COVID-19 to catch on in Asia and why some densely populated countries were spared. Could it all be explained based on the different measures each government took or is the reason more internal? Can the reason be found within our bodies?”
Molecular mimicry, defined as a theoretical possibility that proteins from SARS-CoV-2 mimic proteins from other pathogens, thus initiating immunity in some individuals, is what the researchers will be looking for during their one-year study. SARS-CoV-2 is the virus that causes COVID-19.
“We’re asking if the protein binding is happening in such a way that it is getting tricked by the SARS-CoV-2 protein, thinking it’s something else,” adds Narasimhan.
The multi-disciplinary COVID informatics team—with expertise in bioinformatics, machine learning, evolutionary biology, infectious diseases, high-performance computing and software engineering—has divided the project into two main parts, with the goal that at the end, there will be a better understanding of the severity of the additional waves of pandemics and how communities can manage future infections. Seven collaborators and members are part of FIU’s Biomolecular Sciences Institute.
“This project illustrates how multidisciplinary collaborations promoted by BSI could bring our expertise together to achieve better understandings and breakthroughs,” said Yuk-Ching Tse-Dinh, director of the Biomolecular Sciences Institute.
The first phase involves extracting useful features from structures of known complexes available from public databases such as the Protein Data Bank (PDB).
Prem Chapagain, an associate professor of physics in the College of Arts, Sciences & Education and associate director of the Biomolecular Sciences Institute who specializes in computational modeling and simulations of biomolecules, is studying how these protein molecules fix and bind with each other.
The second component of the award involves using machine learning to understand how the molecular mimicry is taking effect. Narasimhan, in collaboration with computer science faculty members, Ananda Mondal and Trevor Cickovski, is building machine learning models to be able to detect molecular mimicry in SARS-CoV-2.
Kalai Mathee, professor at HWCOM, and Jessica Liberles, an assistant professor of biological sciences in the College of Arts, Sciences and Education, both serve as advisors, guiding the computer science professors on evolutionary aspects and what useful features can be extracted to incorporate in the machine learning models.
Charles Dimitroff, executive associate dean for research at HWCOM, is studying sugars on molecules, such as those structures on viral proteins. Dimitroff’s research focuses on understanding how sugars regulate immune cell functions to help cure cancer and inflammatory diseases.
Phases of the NSF RAPID Project
Through the award, the National Science Foundation is offering Narasimhan and collaborators access to a cloud computing platform called Chameleon, which is located at the University of Illinois and the University of Texas. This will allow access to high-performing computing resources to run molecular dynamics simulations within the machine learning framework.
The machine learning framework will result in reusable models of molecular mimicry and is expected to assist with future vaccine development.
“We’re able to make a difference from home,” said Narasimhan. “We don’t need samples from people who’ve had COVID-19, and we don’t need to be in a lab.”
The one-year grant started on July 1s and will support three Ph.D. students. The team envisions a future project where the results can be tested in a lab.
