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Starting at the microscopic level: COVID-19 researchers at Brown combat viral proteins

Faculty, students use COVID-19 Research Seed Fund to investigate biology of disease, virus, drug candidates

With the assistance of the COVID-19 Research Seed Fund awards, several projects are diving in to investigate COVID-19 on the microscopic, molecular level.

How pharmaceuticals impact COVID-19

Members of the Brown Experimentalists Against COVID-19 research group, dubbed the BEACON group and led by principal investigator and Professor of Medical Science and Pathology and Laboratory Medicine Wafik El-Deiry, have traditionally dedicated their time to cancer research. But in March, they began studying the immune system’s response to COVID-19 and pharmaceutical drugs’ effects on the disease, The Herald previously reported

The COVID-19 Seed funding has helped the team push their experiments forward. They are investigating how to block the interaction between the “spike” protein on the virus’s surface and the ACE2 receptor on human cells. Fitting together like a lock and key, these two molecules allow the virus to pass into human cells. 

The researchers are testing the efficacy of singular drugs as well as combinations that they hope could block this entryway. Targeting the protease protein that enables infectivity by cleaving the spike protein could be one effective approach. 

But this approach is hardly the only option. Questions linger about whether some drugs may have the potential to elevate the response from T-cells, the body’s natural defenders, or to alleviate the “storm” of cytokine proteins that flood the body in response to infection — and may lead to respiratory complications in COVID-19 patients. These Brown researchers are seeking answers.

“At this point, we have a couple of candidates that look promising for suppressing the (ACE2) receptor” and lessening “the severity of the cytokine storm,” El-Deiry said. The researchers are also looking into how drugs affect the creation of this protein prior to its placement on the cell’s surface. 

BEACON’s focus on fostering teamwork extends from its members to its potential solutions to COVID-19: They are exploring how the coupling of different drugs may target the virus at multiple stages of its life cycle. 

Remdesivir — a drug that has been tested widely in the treatment of COVID-19 and one of the lab’s drug candidates — has shown promising results in other studies, reducing hospitalization stays among the “severely ill.” Still, the medication has not yet had an equal impact in significantly reducing deaths from the disease, El-Deiry said. 

Although remdesivir may prevent the virus from replicating, the BEACON researchers' preliminary data suggested that the drug could impact cellular factors and thereby actually increase infectivity before its beneficial effects against the virus kick in. To contend with this counterproductive initial consequence, they are working on pairing this medication with another drug that could first safely counter infection by COVID-19; remdesivir would then function as backup if the virus managed to evade the first drug. 

Those at the forefront of the lab’s COVID-19 research include Assistant Professor of Pathology and Laboratory Medicine Shengliang Zhang, Assistant Professor of Pathology and Laboratory Medicine Lanlan Zhou, Teaching Fellow in Medicine Ilyas Sahin, surgical research resident Cassandra Parker, Lindsey Carlsen GS and Kelsey Huntington GS.

“We want to contribute useful knowledge that affects how people think about the drugs and what may be possible to bring to the patients,” El-Deiry said. 

Correlating chitinase-like proteins with COVID-19

The potentially fatal transition from a persistent cough to pneumonia, resulting in a disproportionate number of deaths among the elderly have defined much fear of COVID-19 since the onset of the pandemic. A University study has been researching whether the root causes of this transition and trend may be linked in part to a specific chitinase-like protein

In humans, chitinase-like proteins bind present chitin molecules, and prior research has suggested that these proteins may thereby affect immunity, according to a 2011 study by Ober et al. Chitinase enzymes break down chitin, the material that composes the hard shells covering some insects, explained a principal investigator of the study and Professor of Molecular Microbiology and Immunology Chun Lee, who formerly studied chitinase independent of COVID-19.

Having higher chitinase-like protein levels, which is the case for older individuals and those with other diseases like high blood pressure, obesity, diabetes and cancer, could explain why some people have a higher susceptibility to COVID-19 and more extreme symptom severity, according to co-principal investigator, Senior Vice President for Health Affairs and Dean of Medicine and Biological Sciences Jack Elias, who has come across patients receiving lung-related critical care throughout his years as a pulmonary physician.

The team of University researchers is studying whether having a larger number of these proteins may have deleterious consequences by regulating the protease protein and the receptor molecule for SARS-CoV-2 on cells so in order to aid viral entry, Lee and Elias explained.

The researchers who also include co-principal investigators Assistant Professor of Molecular Microbiology and Immunology Bing Ma and Associate Professor of Medicine Bharat Ramratnam ’86 MD’93 are determining the exact relationship between the chitinase-like protein and vulnerability to the new virus through a series of experiments involving lung cells and animal models. 

“We set this whole system up to study cancer,” Elias said. “But the more we sat and talked to each other and read the literature (on COVID-19), the more we kept saying, ‘Oh, that’s like what we’re studying.’” 

Results from pilot experiments reassured the researchers that their hypotheses were worth pursuing. 

Their transgenic mice — mice which have been experimentally modified to express a gene of interest — have been altered to express the gene coding for the chitinase-like protein, which the researchers can regulate, turning “on” the gene has led to an “increase of expression of (the ACE2) receptor and protease,” Elias said — meaning that when more of these proteins are present, more receptors for COVID-19 are active. The receptor is also appearing on cells outside of the lungs upon the expression of this gene, and the researchers aim to identify the locations throughout the body where chitinase has a regulatory role. 

The team also plans to measure the quantity of the protein in human blood serum samples, Elias and Lee said. These people can then be followed to see whether they become infected and whether the COVID-19 patients recover quickly or end up in critical condition. The outcomes can be linked to their chitinase-like protein levels to analyze whether a correlation between the two exists.

If such a relationship is found, understanding this pattern could allow health care providers to use the protein measurements as biomarkers — indicators of how COVID-19 would likely run its course in different people, Lee and Elias said. 

The researchers are also testing drug efficacy and how strongly specific antibody molecules, which they have developed, can bind to their protein of interest. This route of investigation could lead to a means of preventing the chitinase enzyme from having such a negative effect in COVID-19 patients.

Lee added that the Seed funding has been “really instrumental … for initiating this unexpected project.”

Studying the structural proteins of COVID-19

While discussions about COVID-19 research have often hovered around the virus’s signature spike protein, another team of University researchers have instead been investigating the less-studied nucleocapsid “N” protein, a protein which the “viral genome wraps around,” now with the assistance of the COVID-19 Research Seed Fund. They intend to “leave no stone unturned,” said Assistant Professor of Molecular Pharmacology, Physiology and Biotechnology Mandar Naik, a co-principal investigator of the study who is familiar with coronaviruses from his prior work on SARS-CoV.

COVID-19 uses RNA to carry its genetic material and replicate. This RNA associates with the N protein, which contributes to the function, quality and packaging of the virus’s genome, according to Naik and Nicolas Fawzi, co-principal investigator and associate professor of molecular pharmacology, physiology and biotechnology.

“If we could understand ‘how does (the N protein) work?’ and ‘what might we do to disrupt that function?’, that would definitely be a potential avenue for therapeutic” agents, Fawzi said.

The principal investigators, several University graduate students and laboratory staff are now looking for compounds that could have the capability to become effective drugs for treating COVID-19 by inhibiting this protein. This disruption could interfere with the arrangement of the RNA and thereby impede its activity, or it may affect the proteins’ tendency to join together into larger molecules, Fawzi and Naik said.

Co-principal investigator and Associate Professor of Biology Gerwald Jogl compiled a list of hundreds of candidates from analyses using a computer software that indicates which molecules might successfully inhibit the N protein, which Naik intends to test using the N protein in the lab. Fawzi will then use these compounds to determine their effects on the RNA-protein interactions.

Professor of Medical Science and Neurology, Director of Cancer Signaling and Vice Chair of Molecular Biology, Cell Biology and Biochemistry Walter Atwood, also a co-principal investigator, will also apply his expertise in virology to contribute to experiments on the drug compounds’ activity within the actual COVID-19 virus. Any ensuing clinical trials on patients would likely involve further collaborations, Naik added. 

“The Brown response on all levels was amazing,” Jogl said. He added that all of the COVID-19-related research projects are coordinated and readily exchanging information, "giving us a feel that this is a community tackling” the issue.

The researchers are studying other proteins as well, such as the associated membrane “M” protein and the envelope “E” protein on the virus’s surface, Naik said. They are hopeful that this work will not only identify potential drug candidates for COVID-19 patients but also augment scientists' understanding of a broader category of viruses that rely on these proteins.

COVID-19 is “unfortunately not going to be the last virus that’s going to come around, so if we learn something about virus biology in general, then next time we (will be) better off,” Naik said. 


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