Rational design of neutralising antibodies resilient to virus escape

The current outbreak of a previously unknown betacoronavirus, SARS-CoV-2, started in 2019 in the city of Wuhan, China. Within a few weeks it reached pandemic proportions. As of today, virtually every country was involved and the virus caused over 160 million infections, claiming millions of lives. SARS-CoV-2 is the third coronavirus to cause outbreaks in less than twenty years. However, unlike the previous two, SARS-CoV-2 will likely continue to circulate and cause disease. Thus, there is urgent need to discover and develop effective preventive measures and treatments. Passive immunotherapy with recombinant monoclonal antibodies (mABs) that bind to the SARS-CoV-2 spike (S) protein on the virus surface, has proven highly effective in preventing progression to severe disease if administered early to individuals with COVID-19. In fact, a single injection of mABs provides immediate protection, making mABs an ideal complement to vaccination in high-risk populations and individuals that fail to respond, or respond only poorly to vaccines. The early success of first-generation mABs against SARS-CoV-2 has prompted regulatory agencies to provide emergency use authorization (EUA). However, the emergence of SARS-CoV-2 variants, that bear amino acid changes in the S, threatens to reduce the effectiveness of these first-generation mABs. Therefore, innovative strategies are needed to anticipate the dangers posed by new SARS-CoV-2 variants, which are expected to emerge. The overall goal of this proposal is to design, produce and evaluate a novel kind of antibody, an antibody that is resilient to virus escape, and to rapidly develop it towards clinical testing in patients infected by SARS-CoV-2. The entry of SARS-CoV-2 into human cells depends on the receptor binding domain (RBD) of the virus S protein engaging its primary cellular receptor, human angiotensin-converting enzyme 2 (ACE2). Consequently, antibodies that bind to the RBD are able to potently prevent infection and disease. The RBD is however also one of the most mutable regions of S, and several virus variants of concern (VoC) with amino-acids substitutions in the RBD have emerged. Importantly, these substitutions, while reducing the affinity of existing antibodies to S, do not reduce, and in many cases increase, the affinity of the virus for its receptor. Taking advantage of this fact, we will design and evaluate new molecules that combine the soluble portion of ACE2 with carefully selected human mABs, generating chimeric AntiBodies REsiLIEnt to Virus Escape (AB-RELIEVEs). These antibodies will have the advantage that escape mutations reducing the affinity of the AB-RELIEVEs will also decrease the affinity of the virus for its receptor, thus reducing its fitness. Conversely, mutations increasing the affinity to ACE2 will automatically improve AB-RELIEVEs' binding.To achieve this goal, we will:(1) use computer modelling to design chimeric antibodies (AB-RELIEVEs) starting from available atomistic structures of complexes of ACE2, S protein and various antibodies; and (2) perform isolation of novel antibodies binding to specific portions of the S protein, at optimal distances from the ACE2 binding domain on the RBD; (3) recombinantly produce, biochemically characterize and evaluate AB-RELIEVE for neutralization of SARS-CoV-2 in vitro and in vivo.