January 11 | 2021
Scientists Working to Develop Clever Nasal Spray That Tricks the Coronavirus Out of the Body
Biochemist Longxing Cao is working with colleagues at the University of Washington on promising research to disable infectious coronavirus in a person's nose.
UW
Imagine this scenario: you get an annoying cough and a bit of a fever. When you wake up the next morning you lose your sense of taste and smell. That sounds familiar, so you head to a doctor's office for a Covid test, which comes back positive.
Your next step? An anti-Covid nasal spray of course, a "trickster drug" that will clear the once-dangerous and deadly virus out of the body. The drug works by tricking the coronavirus with decoy receptors that appear to be just like those on the surface of our own cells. The virus latches onto the drug's molecules "thinking" it is breaking into human cells, but instead it flushes out of your system before it can cause any serious damage.
This may sounds like science fiction, but several research groups are already working on such trickster coronavirus drugs, with some candidates close to clinical trials and possibly even becoming available late this year. The teams began working on them when the pandemic arrived, and continued in lockdown.
<p>This may sounds like science fiction, but several research groups are already working on such trickster coronavirus drugs, with some candidates close to clinical trials and possibly even becoming available late this year. The teams began working on them when the pandemic arrived, and continued in lockdown.</p><p>When the pandemic first hit and the state of California issued a lockdown order on March 16, postdoctoral researchers Anum and Jeff Glasgow found themselves stuck at home with nothing to do. The two scientists who study bioengineering felt that they were well equipped to research molecular ways of disabling coronavirus's cell-penetrating spike protein, but they could no longer come to their labs at the University of California San Francisco. </p><p>"We were upset that no one put us in the game," says Anum Glasgow. "We have a lot of experience between us doing these types of projects so we wanted to contribute." But they still had computers so they began modeling the potential virus-disabling proteins <em>in silico</em> using <a href="http://robetta.bakerlab.org/alascansubmit.jsp" target="_blank" rel="noopener noreferrer"><u>Robetta</u></a>, special software for designing and modeling protein structures, developed and maintained by University of Washington biochemist David Baker and his lab.</p>
<blockquote>"We saw some imperfections in that lock and key and we created something better. We made a 10 times tighter adhesive."</blockquote>
<p>The SARS-CoV-2 virus that causes Covid-19 uses its surface spike protein to bind on to a specific receptor on human cells called ACE2. Unfortunately for humans, the spike protein's molecular shape fits the ACE2 receptor like a well-cut key, making it very successful at breaking into our cells. But if one could design a molecular ACE2-mimic to "trick" the virus into latching onto it instead, the virus would no longer be able to enter cells. Scientists call such mimics receptor traps or inhibitors, or blockers. "It would block the adhesive part of the virus that binds to human cells," explains Jim Wells, professor of pharmaceutical chemistry at UCSF, whose lab took part in designing the ACE2-receptor mimic, working with the Glasgows and other colleagues.</p><p>The idea of disabling infectious or inflammatory agents by tricking them into binding to the targets' molecular look-alikes is something scientists have tried with other diseases. The anti-inflammatory drugs commonly used to treat autoimmune conditions, including rheumatoid arthritis, Crohn's disease and ulcerative colitis, rely on conceptually similar molecular mechanisms. Called TNF blockers, these drugs block the activity of the inflammatory cytokines, molecules that promote inflammation. "One of the biggest selling drugs in the world is a receptor trap," says Jeff Glasgow. "It acts as a receptor decoy. There's a TNF receptor that traps the cytokine." </p><p>In the recent past, scientists also pondered a similar look-alike approach to treating urinary tract infections, which are often caused by a pathogenic strain of <em>Escherichia coli</em>. An <em>E. coli</em> bacterium resembles a squid with protruding filaments equipped with proteins that can change their shape to form hooks, used to hang onto specific sugar molecules called ligands, which are present on the surface of the epithelial cells lining the urinary tract. </p><p>A <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7024335/" target="_blank" rel="noopener noreferrer"><u>recent study</u></a> found that a sugar-like compound that's structurally similar to that ligand can play a similar trick on the <em>E. Coli</em>. When administered in in sufficient amounts, the compound hooks the bacteria on, which is then excreted out of the body with urine. The "trickster" method had been also tried against the HIV virus, but it wasn't very effective because HIV has a high mutation rate and multiple ways of entering human cells.</p><p>But the coronavirus spike protein's shape is more stable. And while it has a strong affinity for the ACE2 receptors, its natural binding to these receptors isn't perfect, which allowed the UCSF researchers to design a mimic with a better grip. "We saw some imperfections in that lock and key and we created something better," says Wells. "We made a 10 times tighter adhesive." The team demonstrated that their traps neutralized SARS-CoV-2 in lab experiments and <a href="https://www.pnas.org/content/117/45/28046" target="_blank" rel="noopener noreferrer">published their study</a> in the Proceedings of the National Academy of Sciences.</p><p>Baker, who is the director of the Institute for Protein Design at the University of Washington, was also devising ACE2 look-alikes with his team. Only unlike the UCSF team, they didn't perfect the virus-receptor lock and key combo, but instead designed their mimics from scratch. Using Robetta, they digitally modeled over two million proteins, zeroed-in on over 100,000 potential candidates and identified a handful with a strong promise of blocking SARS-CoV-2, testing them against the virus in human cells. Their design of the miniprotein inhibitors <a href="https://science.sciencemag.org/content/370/6515/426" target="_blank" rel="noopener noreferrer"><u>was published in the journal <em>Science</em></u></a>. </p>
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Biochemist David Baker, pictured in his lab at the University of Washington.
UW
<p>The concept of the ACE2 receptor mimics is somewhat similar to the antibody plasma, but better, the teams explain. Antibodies don't always coat all of the virus's spike proteins and sometimes don't bind perfectly. By contrast, the ACE2 mimics directly compete with the virus's entry mechanism. ACE2 mimics are also easier and cheaper to make, researchers say. </p><p>Antibodies, which are long protein chains, must be grown inside mammalian cells, which is a slow and costly process. As drugs, antibody cocktails must be kept refrigerated. On the contrary, proteins that mimic ACE2 receptors are smaller and can be produced by bacteria easily and inexpensively. Designed to specs, these proteins don't need refrigeration and are easy to store. "We designed them to be very stable," says Baker. "Our computation design tries to come up with the stable proteins that have the desired functions."</p><p>That stability may allow the team to create an inhaler drug rather than an intravenous one, which would be another advantage over the antibody plasma, given via an IV. The team envisions people spraying the miniprotein solution into their nose, creating a protecting coating that would disable the inhaled virus. "The infection starts from your respiratory system, from your nose," explains Longxing Cao, the study's co-author—so a nasal spray would be a natural way to administer it. "So that you can have it like a layer, similar to a mask." </p><p>As the virus evolves, new variants are arising. But the teams think that their ACE2 protein mimics should work on the new variants too for several reasons. "Since the new SARS-CoV-2 variants still use ACE2 for their cell entry, they will likely still be susceptible to ACE2-based traps," Glasgow says. </p><p>Cao explains that their approach should work too because most of the mutations happen outside the ACE2 binding region. Plus, they are building multiple binders that can bind to an array of the coronavirus variants. "Our binder can still bind with most of the variants and we are trying to make one protein that could inhibit all the future escape variants," he says.</p><p>Baker and Cao hope that their miniproteins may be available to patients later this year. But besides getting the medicine out to patients, this approach will allow researchers to test the computer-modeled mimics end-to-end with an unprecedented speed. That would give humans a leg up in future pandemics or zoonotic disease outbreaks, which remain an increasingly pressing threat due to human activity and climate change. </p><p>"That's what we are focused on right now—understanding what we have learned from this pandemic to improve our design methods," says Baker. "So that we should be able to obtain binders like these very quickly when a new pandemic threat is identified."</p>
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Lina Zeldovich has written about science, medicine and technology for Scientific American, Reader’s Digest, Mosaic Science and other publications. She’s an alumna of Columbia University School of Journalism and the author of the upcoming book, The Other Dark Matter: The Science and Business of Turning Waste into Wealth, from Chicago University Press. You can find her on http://linazeldovich.com/ and @linazeldovich.
December 15 | 2020
Scientists Attempt to Make Human Cells Resistant to Coronaviruses and Ebola
Scientists are experimenting with turning certain genes on and off to make cells better fight viral infection.
By srady/Adobe
Under the electronic microscope, the Ebola particles looked like tiny round bubbles floating inside human cells. Except these Ebola particles couldn't get free from their confinement.
They were trapped inside their bubbles, unable to release their RNA into the human cells to start replicating. These cells stopped the Ebola infection. And they did it on their own, without any medications, albeit in a petri dish of immunologist Adam Lacy-Hulbert. He studies how cells fight infections at the Benaroya Research Institute in Seattle, Washington.
These weren't just any ordinary human cells. They had a specific gene turned on—namely CD74, which typically wouldn't be on. Lacy-Hulbert's team was experimenting with turning various genes on and off to see what made cells fight viral infections better. One particular form of the CD74 gene did the trick. Normally, the Ebola particles would use the cells' own proteases—enzymes that are often called "molecular scissors" because they slice proteins—to cut the bubbles open. But CD74 produced a protein that blocked the scissors from cutting the bubbles, leaving Ebola trapped.
<p>"When that gene turns on, it makes the protein that interferes with Ebola replication," Lacy-Hulbert says. "The protein binds to those molecular scissors and stops them from working." Even better, the protein interfered with coronaviruses too, including SARS-CoV-2, <a href="https://science.sciencemag.org/content/370/6513/241/tab-article-info" target="_blank" rel="noopener noreferrer"><u>as the team published in the journal <em>Science</em></u></a>.</p><p>This begs the question: If one can turn on cells' viral resistance in a lab, can this be done in a human body so we that we can better fight Ebola, coronaviruses and other viral scourges? </p><p>Recent research indeed shows that our ability to fight viral infections is written in our genes. Genetic variability is at least one reason why some coronavirus-infected people don't develop symptoms while others stay on ventilators for weeks—often due to the aberrant response of their immune system, which went on overdrive to kill the pathogen. But if cells activate certain genes early in the infection, they might successfully stop viruses from replicating before the immune system spirals out of control. </p>
<blockquote>"If my father who is 70 years old tests positive, I would recommend he takes interferon as early as possible."</blockquote>
<p>When we talk about fighting infections, we tend to think in terms of highly specialized immune system cells—B-cells that release antibodies and T-cells that stimulate inflammatory responses, says Lacy-Hulbert. But all other cells in the body have the ability to fight infections too via different means. When cells detect the presence of a pathogen, they release interferons—small protein molecules named so because they set off a genetic chain reaction that interferes with viral replication. These molecules work as alarm signals to other cells around them. The neighboring cells transduce these signals inside themselves and turn on genes responsible for cellular defenses.</p><p> "There are at least 300 to 400 genes that are stimulated by type I interferons," says professor Jean-Laurent Casanova at Rockefeller University.</p><p>Scientists don't yet know exactly what all of these genes do, but they change the molecular behavior of the cells. "The cells go into a dramatic change and start producing hundreds of proteins that interfere with viral replication on the inside," explains Qian Zhang, a researcher at Casanova's lab. "Some block the proteins the virus needs and some physically tether the virus." </p><p>Some cells produce only small amount of interferon, enough to alert their neighbors. Others, such microphages and monocytes, whose jobs are to detect foreign invaders, produce a lot, injecting interferons into the blood to sound the alarm throughout the body. "They are professional cells so their jobs [are] to detect a viral or bacterial infection," Zhang explains. </p><p>People with impaired interferon responses are more vulnerable to infections, including influenza and coronaviruses. In two recent studies published in the journal <em>Science</em>, Casanova, Zhang and their colleagues found that patients who lacked a certain type of interferon had more severe Covid-19 symptoms and some died from it. The team ran a genetic comparison of blood samples from patients hospitalized with severe coronavirus cases against those with the asymptomatic infections. </p><p>They found that people with severe disease had <a href="https://science.sciencemag.org/content/early/2020/09/29/science.abd4570" target="_blank" rel="noopener noreferrer"><u>rare variants in the 13 genes</u></a> responsible for interferon production. More than three percent of them had a genetic mutation resulting in non-functioning genes. And over ten percent <a href="https://science.sciencemag.org/content/early/2020/09/23/science.abd4585" target="_blank" rel="noopener noreferrer"><u>had an autoimmune condition</u></a>, in which misguided antibodies neutralized their interferons, dampening their bodies' defenses—and these patients were predominantly men. These discoveries help explain why some young and seemingly healthy individuals require life support, while others have mild symptoms or none. The findings also offer ways of stimulating cellular resistance.</p>
A New Frontier in the Making
<p>The idea of making human cells genetically resistant to infections—and possibly other stressors like cancer or aging—has been considered before. It is the concept behind the Genome Project-write or <a href="https://engineeringbiologycenter.org/" target="_blank" rel="noopener noreferrer"><u>GP-write project</u></a>, which aims to create "ultra-safe" versions of human cells that resist a variety of pathogens by way of "recoding" or rewriting the cells' genes.<br></p><p>To build proteins, cells use combinations of three DNA bases called codons to represent amino acids—the proteins' building blocks. But biologists find that many of the codons are redundant so if they were removed from all genes, the human cells would still make all their proteins. However, the viruses, whose genes would still include these eliminated redundant codons, would no longer successfully be able to replicate inside human cells. </p><p>In 2016, the GP-Write team successfully reduced the number of <a href="https://science.sciencemag.org/content/353/6301/819.full" target="_blank" rel="noopener noreferrer"><u><em>Escherichia coli's</em> codons from 64 to 57</u></a>. Recoding genes in all human cells would be harder, but some recoded cells may be transplanted into the body, says Harvard Medical School geneticist George Church, the GP-Write core founding member. </p><p>"You can recode a subset of the body, such as all of your blood," he says. "You can also grow an organ inside a recoded pig and transplant it." </p><p>Church adds that these methods are still in stages that are too early to help us with this pandemic.</p>LeapsMag exclusively interviewed Church in 2019 about his latest progress with DNA recoding:
<span style="display:block;position:relative;padding-top:56.25%;" class="rm-shortcode" data-rm-shortcode-id="69c0097cffe4901c23314f01f779e129"><iframe lazy-loadable="true" src="https://www.youtube.com/embed/IjjSg8ED0Jw?rel=0" width="100%" height="auto" frameborder="0" scrolling="no" style="position:absolute;top:0;left:0;width:100%;height:100%;"></iframe></span>The Push for Clinical Trials
<p>In the meantime, interferons may prove an easier medicine. Lacy-Hulbert thinks that interferon gamma might play a role in activating the CD74 gene, which gums up the molecular scissors. There also may be other ways to activate that gene. "So we are now thinking, can we develop a drug that mimics that actual activity?" he says.<br></p><p>Some interferons are already manufactured and used for treating certain diseases, including multiple sclerosis. Theoretically, nothing prevents doctors from prescribing interferons to Covid patients, but it must be done in the early stages of infection—to stimulate genes that trigger cellular defenses before the virus invades too many cells and before the immune systems mobilizes its big guns.</p><p>"If my father who is 70 years old tests positive, I would recommend he takes interferon as early as possible," says Zhang. But to make it a mainstream practice, doctors need clear prescription guidelines. "What would really help doctors make these decisions is clinical trials," says Casanova, so that such guidelines can be established. "We are now starting to push for clinical trials," he adds.</p>
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Lina Zeldovich has written about science, medicine and technology for Scientific American, Reader’s Digest, Mosaic Science and other publications. She’s an alumna of Columbia University School of Journalism and the author of the upcoming book, The Other Dark Matter: The Science and Business of Turning Waste into Wealth, from Chicago University Press. You can find her on http://linazeldovich.com/ and @linazeldovich.