A new paper published in nature communication adds further evidence to the bradykinin storm theory of viral pathogenesis of COVID-19 – a theory put forward two years ago by a team of researchers at the Department of Energy’s Oak Ridge National Laboratory.
At the height of the pandemic, ORNL systems biologist Dan Jacobson and his team used ORNL’s Summit supercomputer to analyze gene expression data from lung cells from COVID-19 patients. Their research suggested that genes related to some of the body systems responsible for controlling blood pressure, fluid balance and inflammation appear to be overly dysregulated or impaired in the lung cells of people infected with the virus. In a publication in eLifeThe team predicted that an overproduction of bradykinin – the compound that dilates blood vessels and makes them leaky – could be the cause of COVID-19 symptoms such as excess fluid buildup in the lungs, fatigue, nausea and decreased cognitive function.
This theory was further supported in a new study conducted by Jacobson and colleagues in ORNL’s Biosciences, Computational Sciences and Engineering, and Neutron Scattering departments in collaboration with Soichi Wakatsuki, a professor of photon science at Stanford University’s SLAC National Accelerator Laboratory . Wakatsuki’s team experimentally demonstrated that the virus’s main protease, 3CLpro, binds to the NF-κB essential modulator, or NEMO. Subsequent cleavage of NEMO means that it dysregulates NF-κB, a protein complex that helps regulate the immune system’s response to infection – and its dysregulation may contribute to a bradykinin storm, just as the ORNL team’s pathogenesis model predicted would have.
“This is the culmination of a lot of work coming from many different angles,” Jacobson said. “We’re a computational systems biology group, so our work so far has really been based on large-scale data analysis. This brings all that computational work to the wet lab to generate new datasets to confirm enzymatic activity and structural interactions. It’s incredibly exciting to see all of this evidence coming together and then being validated – that everything our previous work has predicted is in fact true.”
At SLAC, Wakatsuki’s team was able to use viral 3CLpro proteins (made by ORNL senior scientist Andrey Kovalevsky) and peptides to image the cleavage sites in NEMO. The team then used X-ray crystallography to show the structural interaction between the two. In addition, a team at ORNL led by former ORNL researcher Stephanie Galanie was able to demonstrate biochemically that 3CLpro can cleave NEMO at physiologically relevant concentrations.
“We now have evidence at the atomic level and biochemistry that supports the hypothesis that it binds and cleaves exactly as we expected,” Jacobson said.
This cross-laboratory collaboration between ORNL and SLAC originated through the National Virtual Biotechnology Laboratory, or NVBL, a DOE program funded by the 2020 Coronavirus Aid, Relief and Economic Security Act that encouraged national laboratories to fight COVID-19. Wakatsuki and Jacobson met after Jacobson pitched at one of the virtual NVBL sessions and asked for collaborators to prove his bradykinin storm theory through structural biology experiments.
“We were looking for people to take that next step with us, and Soichi spoke up at one of the meetings and said, ‘Yeah, let’s go.’ And here we are with a nice high impact paper. I think that’s a real benefit of the collaborative approach that the NVBL has had the national labs work on, and I’d love to see more of that,” said Jacobson.
As part of this effort, ORNL bioinformatician Erica Prates, then a postdoctoral fellow and now early-career researcher in the Department of Life Sciences, coordinated a team that included ORNL’s Omar Demerdash, Julie Mitchell and Stephan Irle. They performed extensive molecular dynamics work on Summit, using both quantum mechanics and machine learning methods to study the binding affinity of NEMO and 3CLpro in humans and other species, and to consider the structural models derived from the sequences of other coronaviruses.
“Erica plays an important role in what we call structural systems biology, bridging the computational efforts in systems biology and structural biology,” Jacobson said.
This team’s research will lead to a better understanding of the effects of different viruses, including zoonotic diseases, which are human diseases that originate from animals in different host species. This knowledge will be crucial to predict or even prevent the next pandemic.
“Our COVID work continues, but a large part of our focus has shifted to pandemic prevention,” Jacobson said. “We have obtained new funding in collaboration with a number of other research institutions that are really focused on dynamic prevention, trying to understand the rules of zoonosis and the effects of things like climate change and how they drive new zoonotic spillover events.”
Jacobson and his colleagues are collaborating with Johns Hopkins University, Cornell University and others to conduct a wide range of field studies and assays to analyze the interactions between viral proteins and host proteins and create the datasets required for the computational models , hitting the virus predictions for all whole species diversity.
“Why do viruses live happily and apathogenically in some species, but become pathogens when zoonotic spillover occurs? How do they hop between different host species and remain apathogenic until they meet humans?” Jacobson said. “The rules behind zoonosis are very poorly understood, and we have some really exciting work underway building predictive models to understand the variables in the environment that can lead to these spillover events.”
The teams’ research was also partially funded by ORNL’s laboratory-driven research and development program, which supported conceptual work on NEMO cleavage in animal models of COVID-19 pathology. This work used user facilities from the DOE Office of Science, including the Oak Ridge Leadership Computing Facility, the Spallation Neutron Source and High Flux Isotope Reactor, all at ORNL, and the Stanford Synchrotron Radiation Lightsource at SLAC.
Funding for the conceptualization of human pathogenesis was provided by a grant from the National Institutes of Health.
Learn more about ORNL research in the fight against COVID-19.
UT-Battelle manages ORNL for DOE’s Office of Science, the largest single funder of basic research in the physical sciences in the United States. The DOE’s Office of Science works to address some of the most pressing challenges of our time. For more information, see https://energy.gov/science.
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