Category: Coronavirus

Antiviral proteins block coronavirus infection in the lab

Today we report in Science [PDF] the design of small proteins that protect cells from SARS-CoV-2, the virus that causes COVID-19. In experiments involving lab-grown human cells, the activity of the lead antiviral candidate produced (LCB1) was found to rival that of the best-known SARS-CoV-2 neutralizing antibodies. LCB1 is currently being evaluated in rodents. 

Coronaviruses are studded with so-called Spike proteins that latch onto human cells, leading to infection. Drugs that interfere with this process may treat or even prevent infection. Researchers at the IPD used computers to design new proteins that bind tightly to SARS-CoV-2 Spike protein, interfering with its ability to infect cells. Beginning in January, over two million candidate Spike-binding proteins were designed on the computer, and over 118,000 were produced and tested in the lab.

“Although extensive clinical testing is still needed, we believe the best of these computer-generated antivirals are quite promising. They appear to block SARS-CoV-2 infection at least as well as monoclonal antibodies but are much easier to produce and far more stable, potentially eliminating the need for refrigeration.”

Longxing Cao, postdoctoral scholar at the IPD

The researchers created antiviral proteins using two approaches. First, a segment of the ACE2 receptor, which SARS-CoV-2 naturally binds to, was incorporated into a series of small protein scaffolds. Second, completely synthetic proteins were designed from scratch. The latter method produced the most potent antivirals, including LCB1, which is roughly six times more potent on a per mass basis than the most effective monoclonal antibodies reported thus far.

This work was conducted by scientists from the University of Washington School of Medicine and Washington University School of Medicine in St. Louis.

“Our success in designing high-affinity antiviral proteins from scratch is further proof that computational protein design can be used to create promising drug candidates,” said senior author and HHMI Investigator David Baker, director of the IPD.

To confirm that the new antiviral proteins attached to the coronavirus Spike protein as intended, the team collected snapshots of the two molecules interacting using cryo-electron microscopy. These experiments were performed by researchers in the laboratories of David Veesler, assistant professor of biochemistry at the University of Washington School of Medicine, and Michael S. Diamond, the Herbert S. Gasser Professor in the Division of Infectious Diseases at Washington University School of Medicine in St. Louis.

This work was supported by the National Institutes of Health, Defense Advanced Research Projects Agency, The Audacious Project at the Institute for Protein Design, Eric and Wendy Schmidt by recommendation of the Schmidt Futures program, Open Philanthropy Project, an Azure computing resource gift for COVID-19 research provided by Microsoft, and the Burroughs Wellcome Fund.

De novo nanoparticles as vaccine scaffolds

IPD researchers have developed a new vaccine design strategy that could confer improved immunity against certain viruses, including those that cause AIDS, the flu, and COVID-19. Using this technique, viral antigens are attached to the surface of self-assembling, de novo designed protein nanoparticles. This enables an unprecedented level of control over the molecular configuration of the resulting vaccine. This research, which includes collaborative pre-clinical evaluation of initial vaccines in animals, is detailed in three new papers published on August 4.

The first paper, published in the journal eLife, describes the overall vaccine design strategy and how it was used to create vaccine candidates for three important viruses: HIV, RSV, and influenza.

“One of the things we found in this study was that putting the same viral antigen on different nanoparticles alters which regions antibodies can see. This can be used to bias the immune response towards certain regions of an antigen that confer greater protective immunity.” 

George Ueda, lead author and IPD translational postdoctoral scholar.

The second paper, published in PLOS Pathogens, looks at how one of the new HIV vaccine nanoparticles performed in rabbits. A team led by Aleks Antanasijevic and Andrew Ward at Scripps Research found that repeated immunization of the vaccine resulted in a higher proportion of neutralizing antibodies compared to immunization with the same antigen not displayed on the nanoparticle.

The third paper, published in npj Vaccines, looks at how one of the HIV vaccine nanoparticles circulates through the body of rhesus macaques. A team led by Jacob Martin and Darrell Irvine at MIT found that after three days, it became concentrated in lymph node tissues, which is where B cells learn how to fight infection. This may account in part for the observed enhanced immunity.

“Simply injecting an antigen is not necessarily enough to confer a protective immune response. Our goal was to create new protein-based vaccines that mimic the repetitive and spiky shape of a virus because this can drive a more protective immune response. What we found in this study was that the nanoparticle vaccines are also retained better in lymph nodes than antigen alone.” said Ueda.

Relevance for COVID-19

The team chose to focus on HIV, RSV, and influenza because those viruses all contain surface proteins with similar shapes — trimers. The virus that causes COVID-19 also contains a trimeric surface protein. Efforts are now underway at UW Medicine and at the National Institutes of Health Vaccine Research Center to develop nanoparticle vaccines against COVID-19 using this new strategy.

“We have found that the two-component nanoparticles we’ve been designing can be used to improve the potency of antigens from a number of important pathogens, including SARS-CoV-2. We’re convinced that they are a robust and versatile platform for designing nanoparticle vaccines.”

Neil King, head of vaccine design at the IPD.

This collaborative research was led by UW Medicine, Scripps Research, and the Koch Institute for Integrative Cancer Research at MIT. It also included researchers from Cornell University,  Emory University, University of Amsterdam, University of Southampton, the Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, the Lawrence Berkeley Laboratory, and the National Institute of Allergy and Infectious Diseases at the National Institutes of Health.

This work was supported by the Bill and Melinda Gates Foundation and the Collaboration for AIDS Vaccine Discovery; the National Institute of Allergy and Infectious Diseases Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, Center for HIV/AIDS Vaccine Development; and by the National Science Foundation; and by The Audacious Project; and by the Howard Hughes Medical Institute. This work was also supported by the European Union’s Horizon 2020 research and innovation program. This work was partially funded by IAVI with the generous support of USAID, Ministry of Foreign Affairs of the Netherlands, and the Bill & Melinda Gates Foundation.

With an emergency meeting, RosettaCommons aims to accelerate COVID-19 research

On the day the number of confirmed global COVID-19 infections crossed one million, a team of over three hundred scientists from around the world kicked off a virtual conference aimed at stopping the virus.

The event was an emergency meeting of member labs from the RosettaCommons, a consortium of over 90 laboratories who together develop and apply Rosetta, a powerful molecular modeling suite. Using this software, scientists have previously created experimental vaccines, candidate antiviral drugs and helped solve the structures of important infectious disease proteins, enabling further drug development. 

As of early April, dozens of RosettaCommons labs had begun research on COVID-19. 

This community of computational biochemists normally gathers in person each summer and winter to share updates and spark new collaborations. Given the urgency of the pandemic, however, an emergency meeting was called by Jeffrey Gray, a RosettaCommons member and professor of chemical and biomolecular engineering at Johns Hopkins. 

“I think our community has much to offer,” said Gray. “We have powerful tools that have led to new technologies and a strong tradition of collaboration. Our work is needed now.”

Computer-generated vaccines

Vaccine design was a major focus of the two-day event. Multiple researchers presented their preliminary efforts to create custom vaccines against SARS-CoV-2, the virus that causes COVID-19. Rosetta’s proven ability to enable the atomically accurate design of custom immunogens [1,2] makes it a powerful tool in the race for an effective vaccine.

Neil King, assistant professor of biochemistry at the University of Washington and member of the Institute for Protein Design (IPD), shared his lab’s efforts to design and test multiple subunit and nanoparticle vaccines. This research, which is among the only work still being done in person at the IPD, is largely supported by the Bill & Melinda Gates Foundation. 

Tim Whitehead, associate professor of chemical and biological engineering at CU Boulder, is using Rosetta to stabilize proteins from SARS-CoV-2, including the spike protein, in hopes of improving their immunogenicity. 

Researchers from Scripps Research and the Wistar Institute also presented their unique efforts to create novel vaccines by design, including strategies for presentation of specific and broadly neutralizing epitopes [3]. 

Designer antivirals

The spike protein from SARS-CoV-2 is “a beast,” noted Eva-Maria Strauch, assistant professor of pharmaceutical and biomedical sciences at the University of Georgia, Athens. Her lab is applying  Rosetta to try to create proteins that could block the coronavirus spike. If successful, these molecules would constitute a new class of antivirals. 

“Each [virus] has its own secrets,” said Strauch, whose initial round of experimental coronavirus antivirals will be tested in the lab soon. Strauch has been researching countermeasures for infectious disease proteins for years, but she said with COVID-19, her academic niche “became pretty real.”

Similar efforts are being persuaded in David Baker’s lab at the IPD. Graduate students Brian Coventry and Buwei Huang presented a new method for designing binders in high throughput. IPD scientist Brian Koepnick also shared how the computer game Foldit is challenging players to come up with their own antiviral designs. Ninety-nine of the most promising solutions from Foldit players will soon be tested for activity in Seattle. 

The Fleichman lab at the Weizmann Institute of Science in Israel is working to automate the design of certain antivirals. Graduate student Jonathan Weinstein shared an update on their efforts to automatically design anti-coronavirus nanobodies. These natural proteins resemble antibodies, but are much smaller, potentially making them easier and cheaper to produce. 

The role of machine learning 

Several labs are applying techniques from machine learning to enhance their research. 

In the Baker lab, graduate student Nao Hiranuma is developing deep learning models that make filtering binders designs two to three times more successful. Coming up with millions of putative binders on the computer is now relatively easy, said Coventry. “Filtering has been the name of the game.” The team aims to test only the most promising candidates, then to use data from high-throughput experiments to guide further rounds of design.

In the Meiler Lab at Vanderbilt University, machine learning techniques are being used to guide the design of SARS-CoV-2 protease inhibitors. Graduate student Benjamin Brown presented an “in-progress algorithm” that he has readapted due to the urgent need to stop COVID-19. 

The power of teamwork

Even in extraordinary times, the RosettaCommons pulls together. Preliminary data and research efforts were shared openly during the conference. Members are also creating lists of resources — reagents, genes and computational methods — to help coordinate global efforts.

The RosettaCommons maintains its commitment to continue communicating and supporting member labs, including a long-standing effort to be inclusive of all people in our work. During the conference, live closed-captioning was donated by Verbit.ai.

5 questions about designing coronavirus vaccines from our Reddit AMA

Researchers from our vaccine design team recently participated in a Reddit ‘Ask Me Anything’ about our SARS-CoV-2 vaccine research. Reddit users asked over a hundred questions by the time the live event ended — we are sorry we could not address them all. 

We were lucky to be joined by Lexi Walls, a postdoctoral scholar in the UW Veesler lab, who recently helped lead an effort to determine the structure of the SARS-CoV-2 spike protein by cyro-electron microscopy. “It was so wonderful to see such a broad audience pour in so many well-thought out questions about our research,” said Erin Yang, a Baker lab graduate student who helped organize the event.

Here is our pick for the top five vaccine-related questions from our Reddit AMA:

If a vaccine was created, and proven to work, how long would it take for it to be mass produced and for it to reach the general public?

The projections of 1 year to 18 months to have an FDA approved vaccine are probably accurate — if some of the vaccine candidates that [are] either in development or about to start clinical trials as of today do in fact provide protection (which we don’t know yet) and everything goes well.

Vaccines, like all medicines, have to be very safe. The safety bar for vaccines is very high as they are administered to large numbers of people. Much of the time that will be required to get a vaccine out will be devoted to ensuring that vaccine candidates are very safe, as well as effective.

— Lauren Carter

Is there a chance we’ll ever develop one day the technology to create and manufacture vaccines for new diseases, quickly enough to tackle their extremely damaging first wave (so essentially have a vaccine ready within 2, 3 months of a disease being discovered)?

Potentially. There will always be a need for safety trials, but new vaccine platforms that are modular (like ours) — once they have been proven in clinical trials — could be developed quickly for new indications. As an example, annual flu vaccines are manufactured relatively rapidly, but there is room for further improvement.  — Lauren Carter

One long-term goal (which will not be ready for this pandemic) would be to create vaccines that could provide universal coverage against any family of viruses that has a high chance of causing a pandemic. For example, one could imagine having a single vaccine that protects against all possible coronaviruses, another vaccine that protects all possible flu viruses, etc. Based on what we know about how the immune system responds to flu, a universal flu vaccine does look possible as there are pieces of flu that are conserved between all flu viruses that infect humans. Coronaviruses are less studied in this regard. Hopefully greater study of them in the coming years will show that such a vaccine could be possible.

— Dan Ellis

What are we seeing in the human antibodies from recovered patients and how does that influence a potential vaccine? Are there other proteins we can target aside from the spike protein? 

There are a variety of proteins present in coronaviruses, but the spike protein is the major vaccine and antibody target because it is present on the outside of virus and is the major protein that our immune systems target during natural infection. The spike protein is also the workhorse of viral entry — the spike protein’s role is to bind to host cells and fuse viral and host membranes to allow for infection. The spike is therefore the first target the immune system sees and acts against. This also means that if we can target antibodies to it, we could prevent viral entry into host cells completely and block infection (which is the ultimate goal!). The most promising target on the spike protein is called the receptor binding domain, the goal being to block the interaction with host (our) receptor. If this interaction is blocked, then the virus cannot enter cells and no infection can occur.

As for what we are seeing from human antibodies from infected patients… this is a pre-print (not yet peer-reviewed- a way to publicly post results early to allow for sharing of knowledge as fast as possible, but submitted to a scientific journal to go through that process) on just that topic!

 — Lexi Walls

What makes creating a vaccine so hard? I genuinely want to understand the work and tech that goes behind creating something that kills a virus.

This is a really complex question, and we’ll only be able to provide a partial answer. If you are curious about how vaccines and drugs are developed, here are a few other resources: https://www.sciencedirect.com/topics/medicine-and-dentistry/vaccine-development

At a very basic level, making vaccines is hard because we don’t fully understand how the immune system perceives pathogens and most effectively marshals its forces (T cells, B cells, etc.) to eliminate pathogens. We know some things, like antibodies and T cells are important. So the job of vaccinologists is to make a thing that stimulates the immune system — which we do not fully understand — in just the right way. You want to raise the right flags for the immune system to see in order to identify the threat, but you don’t want to overwhelm the system or alert it to the wrong thing.

Another challenge in making vaccines is that they must be exceedingly safe. Vaccines are administered to large numbers of healthy people, so they must do no harm. Making a thing that provokes a potent, protective immune response but that is totally safe requires a lot of knowledge, skill, and operational excellence.

Finally, viruses and bacteria are experts at evading the immune system — they have developed lots of tricks to subvert or suppress immune responses. So you have to know enough about the bug (the virus or bacterium or whatever) to teach the immune system how to eliminate it, despite the tricks the bug tries to play.

— Neil King

How many vaccine candidates are there currently? Where are the trials being conducted?

A few different vaccine candidates from other groups have entered the earliest stage of clinical testing, and many others are racing to get there. A handful of patients have been injected in Seattle as part of one mRNA vaccine trial (Phase 1).

This is an incredible moment for science — all hands are on deck, moving quickly but safely.

— Erin Yang

 

Volunteers rally to Rosetta@Home to stop COVID-19

Planetariums, businesses and more are now donating idle computing power to help advance biomedical research. Image: Frost Science

As schools, museums, offices and stores shutter to slow the spread of the new coronavirus, millions of people are now finding themselves stuck at home. Fortunately, even in these trying times, there are are small steps that anyone can be take to help combat COVID-19.

One option is to donate to biomedical research — but doing so doesn’t necessarily require opening your wallet.

Rosetta@Home is a distributed computing project that relies on a network of volunteer computers. The goal of the project is to learn more about important biomolecules, including the proteins that comprise the new coronavirus. In doing so, scientists may discover how to create medicines and vaccines to stop it. Rosetta@Home operates on the Berkeley Open Infrastructure for Network Computing, or BOINC, which has existed since 2002. BOINC is open-source and funded primarily by the National Science Foundation.

In recent days, Rosetta@Home has seen a surge of new volunteers who are generously donating the use of their idle desktop, laptop and smartphone processors. The number of active users has doubled, and four of the project’s ten best compute days have occurred just in the last week. This giving is powering research on the new coronavirus at the UW Institute for Protein Design and at other universities.

New volunteers stepping up

To keep the public safe from the new coronavirus, the Phillip and Patricia Frost Museum of Science in Miami, Floria has had to temporarily close. The museum is home to a state-of-the-art planetarium, powered by the Frost Planetarium’s Dell PowerEdge 7910 servers, consisting of 168 processors. The Frost Museum just announced that it is generously donating its computer downtime to the Rosetta@Home project.

 

Image: Frost Science

“As a leading scientific institution, we wanted to find a way to repurpose the powerful computing technology we had idle with our closure. We are now actively supporting groundbreaking research that will help us solve some of the world’s biggest challenges, such as COVID-19. Now more than ever, we need to work together and keep science and high quality research at the forefront of our thinking. We encourage others to join our Frost Science BOINC team and help make a difference, right from their homes” said Frank Steslow, Frost Science President & CEO.

Modus Create, a multi-national consulting firm, has also announced that it is donating all spare computer parts at its headquarters in Reston, Virginia to both Rosetta@Home and Folding@Home, a similar project. “Humanity’s ingenuity is often best demonstrated at times of crisis,” they write. Like many volunteers, Modus has also created a team on BOINC to organize their giving.  Over 11,000 such teams have been formed, including many from universities, business and other institutions.

It is easy to join Rosetta@Home

Joining Rosetta@Home is simple. First, download the BOINC app on a compatible device (Windows, Mac, Linux or Android). Then, select Rosetta@Home as your preferred project. That’s it! Rosetta@Home is not for profit, operated by academics and will not collect any of your personal information. Follow the project on Twitter for updates: @RosettaAtHome

With Rosetta@Home running on your devices, you can contribute to science even as you sleep.

Play Foldit to help stop coronavirus (VIDEO)

You don’t have to be a scientist to do science! By playing the computer game Foldit, you can help discover new antiviral drugs that might stop the novel coronavirus. The most promising solutions will be manufactured and tested at the University of Washington Institute for Protein Design in Seattle.

Foldit is run by academic research scientists. It is free to play and not-for-profit. To get started, download Foldit on your computer and create a username.

We recommend that new players start with the Foldit Intro Puzzles.
After some practice, move on to the Science Puzzles and try out the Beginner: Coronavirus puzzle.
We also have an advanced coronavirus puzzle where you can try to design an antiviral protein from scratch!

To meet other players, check out the Foldit Discord channels.

Note: Foldit is an interactive computer game and not a distributed computing project. If you would like to donate spare computer time to science, please check out the Rosetta@Home project on BOINC.

To support laboratory testing, please consider making a donation to the Institute for Protein Design at the UW School of Medicine.

Follow Foldit on Twitter.

Rosetta’s role in fighting coronavirus

We are happy to report that the Rosetta molecular modeling suite was recently used to accurately predict the atomic-scale structure of an important coronavirus protein weeks before it could be measured in the lab. Knowledge gained from studying this viral protein is now being used to guide the design of novel vaccines and antiviral drugs.

On January 30, the World Health Organization declared the ongoing coronavirus outbreak (COVID-19, caused by the virus SARS-CoV-2) a public health emergency of international concern. Scientists around the world are racing to learn more about this deadly virus which has already spread to more than 30 countries.

The best predicted structure of the spike protein (blue) closely matches the structure later solved by Cryo-EM (tan).

Importantly, structural biologists are quickly gaining insights into what the proteins that make up this virus look like and how they function.

One viral protein in particular — the spike protein — allows SARS-CoV-2 to fuse its membrane with those on human cells, leading to infection. Researchers at UT Austin this week used cryo-electron microscopy to create the first 3D atomic-scale map of the SARS-CoV-2 spike protein in its prefusion state. Like other viral spike proteins, this spear-like molecule is thought to take on two distinct conformations: one before it infects cells, and a different, ‘post-fusion’ state after. Other groups are also applying similar techniques in their laboratories to learn even more about this critically important protein.

Coronavirus spike proteins — like the proteins found in your body — ‘fold up’ in order to function.

Robetta, our online Rosetta-based protein structure prediction server that is free to use for academics, was able to accurately predict the results of this folding process. In early February, it calculated 3D atomic-scale models of the SARS-CoV-2 spike protein in its prefusion state that closely match those later discovered in the lab.

To download these models, click here.

Designing therapeutics

With this knowledge in hand, researchers at the Institute for Protein Design are now working to create new proteins to neutralize coronavirus. If successful, these antiviral proteins would stick to the SARS-CoV-2 spike protein and thereby prevent viral particles from infecting healthy cells.

A de novo miniprotein binder (pink) designed to bind to the SARS-CoV-2 spike protein.

These new drug candidates — a type of molecule we call ‘mini-protein binders’ — seek to combine the specificity of antibodies with the high stability and manufacturability of small molecule drugs. Mini-protein binders are custom-designed on the computer to adhere only to specific targets, such as specific grooves on the SARS-CoV-2 spike protein.

In 2017 we first reported our high-throughput mini-protein binder design strategy. Together with colleagues we designed and tested over 22,000 mini-proteins that target influenza and botulinum neurotoxin B, along with over 6,000 control sequences to probe contributions to folding and binding, and identified 2,618 high-affinity binders. 

The de novo designed mini-protein binders produced in that study exhibited much greater stability at elevated temperatures and better neutralization in animal models than comparable antibodies and natural protein derivatives. Probably as a result of their small size and very high stability, they also elicited little immune response. The best of the flu-targeting designs provide prophylactic (before infection) and therapeutic (after infection) protection against influenza infection in mouse models with a potency rivaling or surpassing that of antibodies.

Our researchers are now designing on the computer tens of thousands of anti-coronavirus mini-protein binders. In the coming weeks we hope to produce these mini-proteins in the lab and measure their ability to bind to spike protein. Following this, much more laboratory testing would still be needed to evaluate the safety and efficacy of these experimental coronavirus drugs.

Designing coronavirus vaccines

Technology developed in the King Lab at the Institute for Protein Design is also being applied to try to create an effective vaccine against SARS-CoV-2.

This experimental SARS-CoV-2 vaccine was made by fusing multiple copies of the coronavirus spike protein (red) to the outside of a designed protein nanoparticle (orange and gray).

Our colleagues in the Veesler Lab in UW Biochemistry and at the Vaccine Research Center at the National Institutes of Health have fused coronavirus spike proteins to the outside of Rosetta-designed protein nanoparticles to form self-assembling vaccine candidates. Some of these are currently being evaluated in mice. This work builds off our recent efforts to create respiratory vaccines by design

“We are working with our collaborators at UW, the NIH, and the Bill & Melinda Gates Foundation to help create a safe and effective vaccine for not only SARS-CoV-2 but other coronaviruses as well,” said Neil King, who leads the IPD’s vaccine design efforts.

“This outbreak has illustrated that it’s all hands on deck, and all of us together against the bugs, in the fight against infectious disease. The good news is that the community has developed robust methods for antigen design and display over the last several years that are allowing the rapid generation of vaccine candidates that will likely be highly immunogenic.”