A latest paper published in Nature Communications adds further evidence to the bradykinin storm theory of COVID-19’s viral pathogenesis -; a theory that was posited two years ago by a team of researchers on the Department of Energy’s Oak Ridge National Laboratory.

At the peak of the pandemic, ORNL systems biologist Dan Jacobson and his team used ORNL’s Summit supercomputer to research gene-expression data of lung cells from COVID-19 patients. Their research suggested that genes related to among the body’s systems which can be accountable for controlling blood pressure, fluid balance and inflammation seem like excessively dysregulated, or impaired, within the lung cells of those infected with the virus. In a paper published in eLife, the team predicted that overproduction of bradykinin -; the compound that dilates blood vessels and makes them permeable -; might be the source of COVID-19 symptoms comparable to excessive accumulation of fluid within the lungs, fatigue, nausea and decreased cognitive function.

That theory has been further supported in a latest study conducted by Jacobson and his colleagues in ORNL’s Biosciences, Computational Sciences and Engineering, and Neutron Scattering Divisions in collaboration with Soichi Wakatsuki, a professor of photon science at Stanford University’s SLAC National Accelerator Laboratory. Wakatsuki’s team was in a position to prove experimentally that the virus’s principal protease, 3CLpro, binds to the NF-κB Essential Modulator, or NEMO. The next cleavage of NEMO means it dysregulates NF-κB, which is a protein complex that helps regulate the immune system’s response to infection -; and its dysregulation can contribute to a bradykinin storm, just because the ORNL team’s pathogenesis model had predicted.

“That is the culmination of numerous work coming from numerous different angles,” Jacobson said. “We’re a computational systems biology group, so our previous work was really based on large-scale data evaluation. This takes all of that computational work into the wet lab to generate latest datasets to substantiate the enzymatic activity and structural interactions. It’s incredibly exciting to see all these lines of evidence come together after which be validated -; that every thing our previous work was predicting to be the case is actually true.”

At SLAC, Wakatsuki’s team was in a position to use viral3CLpro proteins (produced by ORNL senior scientist Andrey Kovalevsky) and peptides to represent the cleavage sites in NEMO. The team then used X-ray crystallography to point out the structural interaction between the 2. Moreover, a team at ORNL led by former ORNL researcher Stephanie Galanie was in a position to show, biochemically, that 3CLpro can cleave NEMO at physiologically relevant concentrations.

We now have atomistic-level evidence and biochemistry confirming the hypothesis that it binds and cleaves just how we expected it to.”

Dan Jacobson, ORNL systems biologist

This cross-lab collaboration at ORNL and SLAC got here about through the National Virtual Biotechnology Laboratory, or NVBL, a DOE program funded by the Coronavirus Aid, Relief and Economic Security Act in 2020, that encouraged national labs within the fight against COVID-19. Wakatsuki and Jacobson met after Jacobson made a pitch at one in all the NVBL virtual sessions and asked for collaborators to assist prove his bradykinin storm theory through structural biology experiments.

“We went searching for people to do that next step with us, and Soichi spoke up at one in all the meetings and said, ‘Yes, let’s go.’ And here we at the moment are with a pleasant high-impact paper. I feel that is an actual good thing about the collaborative approach that the NVBL had the national labs work together on, and I would really like to see more of it,” Jacobson said.

As a part of this effort, ORNL computational systems biologist Erica Prates, then a postdoctoral researcher and now an early profession staff member within the Biosciences Division, coordinated a team that included Omar Demerdash, Julie Mitchell and Stephan Irle of ORNL. They conducted extensive molecular dynamics work on Summit by utilizing each quantum mechanics and machine-learning methods to have a look at the binding affinity of NEMO and 3CLpro in humans and other species and to contemplate the structural models derived from the sequences of other coronaviruses.

“Erica is playing a very important role in what we’re calling structural systems biology to bridge across the computational efforts within the fields of systems biology and structural biology,” Jacobson said.

This team’s research will result in a greater understanding of the results of various viruses, including zoonotic diseases, that are human diseases that originate from animals, in several host species. This information might be vital in the trouble to predict and even prevent the following pandemic.

“Our COVID work continues, but a giant a part of our focus has shifted toward pandemic prevention,” Jacobson said. “We have now latest funding obtained in collaboration with a lot of other institutions for research that is admittedly focused on dynamic prevention and trying to know the foundations of zoonosis and the results, for instance, of climate changes and the way they’re driving latest zoonotic spillover events.”

Jacobson and his colleagues are partnering with Johns Hopkins University, Cornell University and others to conduct a big selection of field studies and assays to research the interactions between viral proteins and host proteins, creating the datasets needed for the computational models that can make virus predictions across whole ranges of species.

“Why do viruses happily live in some species nonpathogenically but turn into pathogens when zoonosis spillover occurs? How do they hop between different host species and be nonpathogenic until they hit humans?” Jacobson said. “The principles behind zoonosis are very poorly understood, and we’ve got some really exciting work underway wherein we’re constructing predictive models to know the variables within the environment that may lead to those spillover events.”

The teams’ research was also partially funded from ORNL’s Laboratory Directed Research and Development Program, which supported the conceptual work on the NEMO cleavage in animal models for COVID-19 pathology. This work used DOE Office of Science user facilities including the Oak Ridge Leadership Computing Facility, the Spallation Neutron Source and the High Flux Isotope Reactor, all at ORNL, and the Stanford Synchrotron Radiation Lightsource at SLAC.

Funding for human pathogenesis conceptualization was provided by a grant from the National Institutes of Health.

Source:

Oak Ridge National Laboratory

Journal reference:

Hameedi, M.A., et al. (2022) Structural and functional characterization of NEMO cleavage by SARS-CoV-2 3CLpro. Nature Communications. doi.org/10.1038/s41467-022-32922-9.