Uncloaking the invisible killer and developing an antidote to SARS-CoV-2

Ligandal harnesses the use of genetic medicine through peptides, as part of nanomedicine and drug delivery technologies, and since the COVID-19 pandemic began, has shifted focus to delivering a peptide-based cure to the COVID-19 pandemic (SARS-CoV-2 coronavirus). Andre Watson, CEO and Founder of Ligandal, discusses their approach:

The COVID-19 pandemic has accelerated the development of our first product and allowed us to focus on just the peptide delivery portion of our platform without gene editing or gene delivery. Let me focus my attention on what we are trying to do right now in response to the COVID-19 pandemic, starting with why peptides are an essential part of the solution to SARS-CoV-2.

In the present instance, we have sought to recreate a peptide portion of the SARS-CoV-2 spike protein, which famously binds to the ACE2 receptor on cells and triggers an immune response. If a peptide could be synthesized to bind to the ACE2 receptor, it would theoretically block infection by giving the virus nowhere to engage. Furthermore, such an ‘antidote’ would double as an immune stimulant, generating neutralizing antibodies against the spike peptide. Lacking any of the other genetic machinery of the virus, the peptide would not trigger infection but would serve this dual function of blocking binding and promoting antibody maturation. No one had previously demonstrated the feasibility of such an approach.

Importantly, humans do not build long-term neutralizing antibody-mediated immunity to coronaviruses, though T cells are found to be cross-reactive to SARS-CoV-2 for a number of years and the innate immune system also plays an important role in viral clearance. You can think of antibodies, which are created by B cells, as being the invisible army of proteins running through your blood, tagging invaders for destruction by the rest of your system. On the other hand, T cells do not release these ‘tags’ into your blood, and instead rely on the T-cell receptor to bind to and eliminate pathogens. In a sense, you can think of an individual T cell as having to find an infected cell (though it sometimes also has the ability to bind to viruses directly, but this process is much less efficient) and destroying the infected cell before it bursts and releases more viruses.

SARS-CoV-2 infected cells have a similar mechanism to some other viruses, such as herpesviruses, in preventing the expression of a protein called MHC-1, which normally presents little pieces of chewed up virus on the cell surface for killer (CD8+) T cells to bind to and destroy. Shutting off this system effectively provides the virus with an immune cloaking capacity. Furthermore, as shown in our recent preprint (‘Peptide antidotes to SARS-CoV-2 (COVID-19)’), the ACE2 viral entry receptor also exists in soluble form and is capable of binding to circulating virus and preventing antibodies from binding to the virus. Innate immune cells are capable of killing cells that have no MHC-1 tags, as well as viruses directly; however, the innate immune response is not sufficient across the majority of the population and does not ‘learn’ how to become more efficacious at clearing a pathogen the same way as the adaptive (T cell and B cell) immune system does. Numerous studies, including a recent one by Dr Marta Galanti and Professor Jeff Shaman of Columbia University, demonstrate that immunity to the four endemic coronaviruses typically only lasts for a matter of months, and a double-digit percentage of recovered individuals have undetectable neutralizing antibodies as little as 39 days following symptom onset.

Without the sort of long-term immune response elicited by, say, an influenza vaccine, we speculated that a conventional vaccine against SARS-CoV-2 would only be partially effective in some people, and only for some of the time. There is little reason that a vaccine based on a virus that has limited immune memory would act differently than its viral counterpart. This means that conventional vaccine technologies are unlikely to give us the complete solution we need to end this pandemic, and that antidotes and immune-stimulating agents are necessary to offset the global crisis.

Unlike the other four endemic coronaviruses, SARS-CoV-2 has a relatively high infection fatality rate and leaves a wide range of complications in its wake. It is not a virus we can have circulating the population if we want to have our social and economic model that is based on free association and widespread trade. In our opinion, a partially effective response would not be good enough to return the world to a pre-pandemic model. The virus needs to be eradicated through vaccination or neutralized through a highly effective treatment. In theory, a peptide would be capable of doing both. But how does it work?

The Ligandal peptide, now called SARS-BLOCK™, was based on sections of the spike protein, with added features that would enable it to elicit a powerful and targeted immune response. This means that not only would it inhibit infection, but it would also help the body clear the virus more effectively. As such, it is initially being developed as a treatment, and its utility as a vaccine will then be explored.

Once we had completed modelling, we set to work synthesizing SARS-BLOCK™. Working in collaboration with Professor Robert Stroud’s lab at the University of California San Francisco, we tested SARS-BLOCK™ against the spike protein and pseudotyped virus exhibiting the SARS-CoV-2 spike protein, in ACE2-expressing cells. SARS-BLOCK™ inhibited infection at a rate of over 95% and also demonstrated affinity to neutralizing antibodies. In short, this suggests it will perform the dual therapeutic and immune-stimulating functions described above.

SARS-BLOCK™ attains single-micromolar binding affinities for ACE2 and a neutralizing antibody against the SARS-CoV-2 receptor binding domain (RBD) and demonstrates significant reduction of infection in nanomolar doses. In plain English, it sticks to the right places and works at tiny concentrations.

As part of the experiments, which we conducted in collaboration with the Stroud Lab at UCSF, we also demonstrated that soluble ACE2 abrogates binding of RBD to neutralizing antibodies, which we posit is an essential immune-evasive mechanism of the virus. Effectively, the virus can hide from the immune system by binding with soluble ACE2, which can carry it around the body (Figure 1 with ACE2 shown in red and SARS-CoV-2 spike protein shown in cyan and green in “closed” and “open” states, respectively; PDB IDs 6VXX and 6VYB, respectively). SARS-BLOCK™ was designed with this phenomenon in mind and is designed to ‘uncloak’ the viral ACE2 coating mechanism, while also binding to neutralizing antibodies with the intention of stimulating a specific neutralizing antibody response.

Our lab results so far suggest that SARS-BLOCK™ is highly effective and performs as we expected. We now feel positive that this synthetic peptide can become an effective combination treatment and vaccine to COVID-19. So, what’s next?

We are now on an accelerated pathway to demonstrate the safety and efficacy for mass distribution. As the first step in that process we have partnered with the National Institute of Allergy and Infectious Diseases (NIAID) and National Institutes of Health to conduct further trials with live virus. We are seeing positive data with greater than 90% inhibition of viral infection with live virus. If SARS-BLOCK™ continues to prove effective, it will radically reshape our response to this virus, and synergize with existing vaccines to improve the specificity of immune responses to both vaccines and infections.

Significantly, the potential of this technology goes far beyond COVID-19. In meeting the challenge of creating small, targeted, highly effective synthetic peptide sequences, we actually have the potential to solve many other viral, rare genetic and oncological diseases using our patented technologies. We have extensive experience in using peptides for gene delivery and CRISPR-based gene editing, so fast-tracking this initial COVID-19 application will subsequently result in many more drugs being developed for diverse diseases using our platform technologies. Ultimately, solving the problem of SARS-CoV-2 will hopefully be a first step towards a much brighter future for human health.