The SARS-CoV-2 pandemic demonstrates how quickly we can find ourselves desperately needing new antivirals and therapeutics. But antivirals, typically small molecule drugs or antibodies, can be challenging to develop and deploy. Working in a highly collaborative manner, Cambridge-based biotechnology company Bicycle Therapeutics (an LMB spinout company founded by Sir Greg Winter) and a research team from LMB led by Leo James in the LMB’s PNAC Division, as well as other leading academic institutions, have developed a new class of antivirals that combine the advantages of both small molecules and antibodies whilst minimizing their disadvantages.

This new class of antiviral exploits molecules called Bicycles - short peptides wrapped around a small molecule scaffold to form a two looped “bi-cyclic” structure. As well as being highly potent, selective and stable, new Bicycles can be generated quickly in a manner analogous with how our bodies make new antibodies. To make an antiviral Bicycle against SARS-CoV-2, the team used a technology called ‘Phage Display’ (developed by Sir Greg Winter, for which he shared the 2018 Nobel Prize in Chemistry) to select molecules capable of binding the viral spike protein from a pool of billions of differently shaped molecules. The team responded to this urgent situation, identifying the first Bicycle binders within 4 weeks. Unlike antibodies, which tend to recognize only parts of a protein surface, Bicycles’ small size meant that molecules were found against almost every part of the spike protein.

Once the biology team at Bicycle had identified binders to the spike protein, the chemists then set to work and used multimerization, using individual Bicycles like building blocks where monomer Bicycles were chemically combined together. This generated high avidity compounds with higher affinity and much improved kinetic profiles when bound to the trivalent spike target. To test these Bicycles for antiviral activity, the LMB scientists quickly and safely developed multiple surrogate assays to screen for infectivity and antiviral activity. These assays allowed the joint team to determine how tightly the novel compounds bound to the spike protein. By coating it with these Bicycles, the viral protein was no longer able to adhere to cells and mediate infection. Furthermore, the team tracked the activity of Bicycles against the ever-evolving new emergent clinical strains of the virus. Here a new high containment facility that had been established during lockdown became crucial, allowing analysis of infectivity of clinical isolates in light of “real time” global epidemiology.

The joint team then took this building block strategy one step further, combining different Bicycles that targeted different parts of the spike protein. This generated antivirals that did not just prevent the virus from binding to cells but probably locked together, or stapled shut, parts of the spike machinery that normally have to rearrange to generate an infectious viral particle. By using this strategy, it was possible to quickly adapt and reconfigure the antiviral Bicycle design as new variants of concern (VoCs) emerged. Structural biology, conducted by additional collaborators at the University of Cambridge, was highly informative and allowed the teams to keep pace with a fast moving and constantly evolving virus by carefully matching Bicycles to target parts of the spike protein that were retained among various VoCs.

In a further extension of the collaboration, researchers at the University of Liverpool tested the most active Bicycles for their ability to prevent infection in animal models of Covid19. The team conclusively demonstrated that Bicycles cleared virus from infected mice and prevented a hyper-inflammatory response - a hallmark of Covid19 pathology. These results strongly suggested that anti-SARS-CoV-2 Bicycles have the potential to be developed into effective SARS-CoV-2 therapeutics.

The study demonstrates the power of collaboration in mounting a rapid and effective response to a new and unprecedented scientific challenge like SARS-CoV-2. It also highlights that Bicycles can be used as a molecular toolbox; when combined together like building blocks, they can have different antiviral mechanisms and maintain activity against diverse viral strains. This strategy could potentially be used to generate new antivirals against other viruses not just SARS-CoV-2, suggesting they could have a vital role in the global armamentarium of therapeutics to protect human health.