By Ian Haydon, MS

Scientists in the Department of Biochemistry are pursuing several research projects related to COVID-19, including the development of vaccines, treatments, and new technologies for diagnosing infection and detecting immunity.

PROVIDING A BLUEPRINT FOR VACCINES AND THERAPEUTICS

SARS-CoV-2 emerged in late 2019 and has resulted in the ongoing COVID-19 pandemic which has caused more than 25 million infections, over 844,000 deaths, and paralyzed the global economy. The spike glycoprotein of the novel coronavirus promotes entry into cells through attachment to host receptors and fusion of the viral and host membranes to initiate infection. Due to its key roles in pathogenesis and prominent location at the viral surface, the spike is also the main target of neutralizing antibodies upon infection and the focus of vaccine and therapeutic design. 

A few weeks after the first novel coronavirus isolate was sequenced, the Veesler lab showed that this new virus uses angiotensin-converting enzyme 2 (ACE2) to enter target cells and that its receptor-binding domain efficiently interacts with ACE2, correlating with the efficient spread of SARS-CoV-2 among humans. As reported in Cell, the Veesler lab determined cryoEM structures of the SARS-CoV-2 spike ectodomain trimer in multiple conformations, corresponding to distinct stages of viral entry, that provided a blueprint for the design of vaccines and inhibitors of viral entry used by thousands of research labs worldwide over the past six months. Finally, this work provided proof-of-principle that cross-neutralization of SARS-CoV-2, SARS-CoV and related viruses was possible and fostered subsequent efforts to identify cross-reactive therapeutics against these coronaviruses. This work was led by Alexandra “Lexi” Walls, and Young-Jun Park, two research scientists in the Veesler lab.

DEVELOPING CANDIDATE ANTIBODY TREATMENTS

A few months after the identification of the newly emerged coronavirus, the Veesler lab worked in collaboration with Vir Biotechnology, Inc to isolate and characterize multiple monoclonal antibodies targeting the SARS-CoV-2 spike glycoprotein from the memory B cells of a SARS survivor infected in 2003. As reported in Nature, a monoclonal antibody, named S309, was found to potently neutralize SARS-CoV-2 and SARS-CoV through recognition of a conserved epitope within the spike receptor-binding domain. Antibody cocktails including S309 along with other antibodies targeting distinct receptor-binding epitopes were shown to synergistically enhance SARS-CoV-2 neutralization and may prove especially useful to limit the emergence of viral neutralization-escape mutants. These results paved the way for using S309 and S309-containing antibody cocktails for prophylaxis in individuals at high risk of exposure or as a post-exposure therapy to limit or treat severe disease and provide immediate protection in humans. The potent S309 monoclonal neutralizing antibody entered an accelerated manufacturing path earlier this year and clinical trials are initiating this week in the US. This work was led by Young-Jun Park and Alexandra “Lexi” Walls in the Veesler lab as well as Dora Pinto and Martina Beltramello at Vir Biotechnology.

More recently, the Veesler lab also published a collaborative report in Science on the isolation and characterization of two ultrapotent SARS-CoV-2 neutralizing antibodies (S2E12 and S2M11) that protect hamsters against SARS-CoV-2 challenge. Cryo-electron microscopy structures show that these antibodies competitively prevent viral attachment via ACE2 and that S2M11 also locks the spike in a closed conformation. Cocktails including S2M11, S2E12 or the previously identified S309 antibody broadly neutralize circulating SARS-CoV-2 variants and activate effector functions. These results pave the way to implement antibody cocktails for prophylaxis or therapy, circumventing or limiting the emergence of viral escape mutants.

CONTROLLING THE VIRAL SPIKE WITH PROTEIN ENGINEERING 

Matthew McCallum, a postdoctoral fellow in the Veesler lab, designed a stabilized version of the SARS-CoV-2 spike that locks the protein in a closed or inactive conformation. This method is broadly applicable to all coronavirus spikes tested. This disulfide stabilized SARS-CoV-2 spike can be used as a diagnostic laboratory tool and will be tested as a vaccine candidate.

COLLABORATIVE VACCINE DESIGN

Efforts are underway to create potent vaccines against the virus that causes COVD-19. Using a proprietary vaccine nanoparticle platform, the King and Veesler labs have worked together to fast-tracked several vaccine candidates through design, production, characterization, animal testing, and early process development. Initial results have been published as a preprint.

Extensive mouse immunization studies have been completed. The current best vaccine candidates, even at a six-fold lower dose, are approximately ten times more potent at eliciting neutralizing antibodies than the SARS-CoV-2 spike glycoprotein, which is what most current vaccine candidates are based on. Importantly, mice immunized with a leading nanoparticle vaccine candidate were completely protected from viral challenge using a mouse-adapted virus.

Efforts to date have primarily focused on the genetic fusion of the SARS-CoV-2 Spike glycoprotein to a self-assembling two-component icosahedral nanoparticle system. The group has succeeded in producing milligram quantities of purified vaccine nanoparticles displaying different densities of the antigenic component. In collaboration with the Bill and Melinda Gates Foundation, the IPD Core Labs have completed technology and material transfer of a lead vaccine candidate to a commercial partner abroad, and also to Icosavax, a local IPD spinout. Both companies are seeking additional funding (e.g. from CEPI) for further vaccine development, including human clinical trials.

DESIGN OF ANTIVIRAL PROTEINS

In a new report published in Science, a team of IPD researchers led by Baker Lab postdoctoral scholar Longxing Cao have designed on the computer antiviral proteins that prevent SARS-CoV-2 from infecting human cells. The current best minibinders, which were characterized in collaboration with the Veesler lab, can neutralize live virus with activities rivaling the most potent antibodies identified to date. These drug candidates are being advanced into preclinical testing. Such molecules might ultimately be useful either as prophylactic (before infection) or therapeutic (after infection) treatments. 

The intrinsic stability, ease of manufacturing, and relative low immunogenicity (based on previous data for designed anti-flu peptides) of minibinder proteins may offer significant advantages over traditional antibody treatments, especially for global distribution and use in low-income geographies. Minibinders combine the specificity of antibodies with the high stability and manufacturability of small-molecule antiviral drugs.

DEVELOPMENT OF RAPID DIAGNOSTICS

IPD researchers are also developing technology to detect coronavirus particles or COVID-19 antibodies in body fluid samples. The goal is to arrive at a simple device that can be used at home to detect coronavirus in a nasal swab or COVID-19 antibodies in a finger-prick blood sample.

To create sensors capable of detecting viral particles directly, a team of IPD researchers led by Baker lab graduate student Alfredo Quijano Rubio have designed a molecular sensor with an outstanding dynamic range (1700%), a low limit of detection, and minimal background noise. This sensor, which emits light when mixed with a solution that contains coronavirus proteins, can operate properly in the presence of 50% serum. The team created sensitive sensors that emit light when mixed with COVID-19 antibodies. A preprint describing the development of these sensors has been published. This technology is currently being optimized to enable wide-spread and inexpensive detection of COVID-19 immunity. 

CROWDSOURCING COVID-19 TREATMENTS

To engage the public in the race for a COVID-19 cure, the computer game Foldit is now being used to crowdsource the design of coronavirus drugs. To date, over 20,000 new players have tried their hands at drug discovery. The most promising drug candidates designed by Foldit gamers are being manufactured and tested at the Institute for Protein Design. To learn more, visit the Foldit on YouTube.