Laboratory experiments add more evidence to the bradykinin storm theory of the viral pathogenesis of COVID-19

A new paper has been published in Nature Communications Adds more evidence to Bradykinen’s stormy theory of the 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 supercomputer to analyze lung cell gene expression data from COVID-19 patients. Their research suggested that genes related to some of the body’s systems responsible for controlling blood pressure, fluid balance and inflammation appear to be excessively dysregulated or impaired in the lung cells of people infected with the virus. In a paper published in eLife, the team predicted that the overproduction of bradykinin – ; The compound that dilates the blood vessels and makes them permeable -; Symptoms of COVID-19 such as excessive fluid buildup in the lungs, fatigue, nausea, and decreased cognitive function can be the source of symptoms.

This theory is further supported in a new study by Jacobson and colleagues in the Departments of Biological Sciences, Computational Science and Engineering, and Neutron Scattering at ORNL in collaboration with Soichi Wakatsuki, Professor of Photon Science at Stanford University’s SLAC National Accelerator Laboratory. Wakatsuki’s team was able to experimentally demonstrate that a major virus protease, 3CLpro, binds to the NF-κB Essential Modulator, or NEMO. Post-cleavage of NEMO means that it leads to a dysregulation of NF-κB, a protein complex that helps regulate the immune system’s response to infection -; And the dysregulation could contribute to the bradykinin storm, just as the ORNL team’s pathogenesis model predicted.

“This is the culmination of a lot of work coming from many different angles,” Jacobson said. “We are a computational systems biology group, so our previous work was really based on large-scale data analysis. This takes all of that computational work into the wet lab to create new data sets to confirm enzymatic activity and structural interactions. It’s incredibly exciting to see all these lines More evidence is gathered and then validated – and that whatever our previous work expected to be the case in reality.”

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

We now have evidence at the atomic and biochemical level that confirms the hypothesis that they bind and cleave just as we expected.”

Dan Jacobson, ORNL Systems Biologist

This cross-lab collaboration at ORNL and SLAC came through the National Virtual Biotechnology Laboratory, or NVBL, a Department of Energy program funded by the Coronavirus Aid, Relief, and Economic Security Act of 2020, which has encouraged national labs in the fight against COVID-19. Wakatsuki and Jacobson met after Jacobson gave a presentation at a virtual NVBL session and asked collaborators to help prove Bradykinen’s storm theory through structural biology experiments.

“We went looking for people to do the next step with us, and Soichi spoke at a meeting and said, ‘Yes, let’s go.'” And here we are with a nice, high-impact paper. I think this is a real benefit of the collaborative approach that NVBL has been working on with national labs together, and I’d like to see more of it,” Jacobson said.

As part of this effort, ORNL computational systems biologist Erica Pratts, then a postdoctoral researcher and now a staff member in the Department of Biological Sciences, coordinated a team that includes ORNL’s Omer Demerdach, Julie Mitchell and Stefan Earle. They have conducted extensive molecular dynamics work at Summit using both quantum mechanics and machine learning methods to look at the binding affinity of NEMO and 3CLpro in humans and other species and to look at structural models derived from other sequences. Corona Viruses.

“Erica plays an important role in what we call structural systems biology to connect computational efforts in the fields of systems biology and structural biology,” Jacobson said.

This team’s research will lead to a better understanding of the effects of different viruses, including zoonoses, which are human diseases that arise from animals, in different host species. This knowledge will be vital in efforts to predict or even prevent the next pandemic.

“Our work on COVID continues, but a large part of our focus has shifted toward epidemic prevention,” Jacobson said. “We have new funding that has been obtained in collaboration with a number of other research institutions that are really focused on dynamic prevention and trying to understand the bases of zoonotic diseases and the impacts, for example, climate change and how they lead to zoonotic spillovers.”

Jacobson and colleagues partner with Johns Hopkins University, Cornell University and others to conduct a wide range of studies and field assays to analyze interactions between viral and host proteins, and to create the datasets needed for computational models that will serve to predict viruses across entire ranges of species.

“Why do viruses live happily in some non-pathogenic species but become pathogens when zoonotic disease spreads? How do they jump between different host species and be non-pathogenic to infect humans?” Jacobson said. “The rules behind zoonoses are not well understood, and we have some really exciting work in progress as we build predictive models to understand the variables in the environment that could lead to these spillover events.”

The teams’ research was also funded in part by ORNL’s Laboratory-Driven Research and Development Program, which has supported conceptual work on NEMO cleavage in animal models of COVID-19 pathology. This work utilized DOE Office of Science user facilities including the Command Computing Facility at Oak Ridge, the neutron fragmentation source and the High Flow Isotope Reactor, all at ORNL, and the Stanford Synchrotron Radiation Lightsource at SLAC.

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


Journal reference:

Hamidi, MA, et al. (2022) Structural and functional characterization of Nemo cleavage by SARS-CoV-2 3CLpro. Nature Communications.

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