The past, present, and future of antibody-based pandemic protection

From the Bloom Lab, Basic Sciences Division

Antibodies are the stars of our defense against viral infection. These little proteins play a critical surveillance role within our bodies, capable of recognizing viral invaders and calling in the immunological cavalry to fight them off. “Antibodies are central to the most important therapies developed to combat SARS-CoV-2”, says Dr. Tyler Starr, a postdoctoral fellow in the lab of Dr. Jesse Bloom in Fred Hutch’s Basic Sciences Division. “This includes the polyclonal antibodies that are elicited by vaccination, as well as monoclonal antibodies (and cocktails) that have been developed as drugs [to treat infections]”. But one of the antibody’s greatest strengths may also be its greatest weakness. These proteins are exquisitely precise in their abilities to recognize their viral targets, a quality that is crucial in ensuring that they do not mistakenly sic their immune allies on the wrong targets, potentially destroying friendly cells or even those of our own bodies. The downside to this quality is that even small changes to the structure of a virus can render it no longer recognizable. This weakness has been on display recently in the COVID-19 pandemic, as the rise of new genetic variants of the virus elicits fears that it may be evolving to evade the hard-won immunity generated by vaccines. So too, says Dr. Starr, “recent months have illustrated how tenuous these key therapeutics can be in light of ongoing viral evolution. For example, the first monoclonal antibodies against SARS-CoV-2 that received Emergency Use Authorization for treatment of COVID-19 were paused in their distribution mere months after their completion of Phase III clinical trials [due to decreased recognition of newly emerging variants of concern”. To combat this trend, he says, “we need strategies in the earliest stage of antibody development to prioritize antibodies that will be more robust to viral population evolution.”

For the past year, Drs. Starr and Bloom, along with graduate student Allie Greaney, have been seeking to get ahead of SARS-CoV-2 evolution and to improve vaccine design and antibody-based therapies. Their objective was to  examine how a multitude of changes to the sequence of the virus’s Receptor Binding Domain (RBD), the region most commonly targeted by antibodies, affect antibody binding (see past articles describing these studies here and here). In their latest effort, a collaborative project with Vir Biotechnology recently published in Nature, together with scientists in the Veesler lab at University of Washington and the Whelan lab at Washington University in St. Louis, the group describe their search for the holy grail of antibodies – one that offers high potency (strong protection against SARS-CoV-2 infection), low escapability (resistance to evolved viral evasion), and high breadth (the ability to recognize a suite of related viruses, called sarbecoviruses, that pose a risk of spurring the next major pandemic).

The authors began this study with a group of 12 antibodies developed by Vir Biotechnology that possessed varied potency against the SARS-CoV-2 RBD. They first examined the escapability of these antibodies using deep mutational scanning, a high-throughput approach in which they could test how each possible mutation in the RBD affected antibody binding. To further understand escape, they also performed an in vitro selection experiment in which they exposed RBD-containing virus to several of these antibodies and observed which mutations emerged to promote viral escape. To test breadth, they examined how well these antibodies bound to a diverse group of other sarbecoviruses. After this testing, two antibodies stood out for their exceptional breadth and resistance to escape: S2H97 and S2E12. To understand how they achieved these qualities, the authors used X-ray crystallography and cryoEM to visualize structures of these antibodies bound to the RBD. Interestingly, they found that these antibodies bind to different and unexpected parts of the protein: “S2H97 antibody targets a previously undescribed cryptic antigenic site, which we designated site V…[S2E12] binds the receptor-binding ridge [designated site Ia]”. The group posits that evolutionary constraints in these regions of the RBD likely led to the breadth observed in these antibodies, thus implicating these regions as potentially valuable epitopes for antibody design.

The wealth of insights gleaned from this study indicated not only which antibodies work best with regard to potency, escapability, and breadth, but also what general principles seem to impact these characteristics. In a perfect world, it would be easy to design an antibody with high potency and low escapability. But in reality, there are likely trade-offs that limit this potential. On the plus side, says Dr. Starr, “antibodies that have more breadth of binding over “long-term” virus evolution [aka high breadth against a variety of sarbecoviruses] also confer more breadth over short-term evolution of SARS-CoV-2 itself [aka low escapability]. The downside, though, was that increased breadth appears to come at the expense of potency and vice versa. Nevertheless, the authors were optimistic that their results “highlight the existence of antibodies that balance neutralization potency and breadth.” Ultimately, says Dr. Starr, these findings offer important insights into how best to approach antibody design. “Though classic methods for antibody development rely on the “potency” of an antibody toward SARS-CoV-2 alone to identify those for further development, we suggest that also weighting for cross-reactive breadth could help avoid this situation where antibodies are invested in and developed and quickly rendered ineffective by short-term viral evolution.” Finally, Dr. Starr was eager to point out the differences between improving therapeutic antibody design and the more challenging goal of improving vaccine design. “Developing monoclonal antibodies is more straightforward, since antibodies targeting rare epitopes can be isolated from patients and developed recombinantly. However, can we elicit these types of antibodies via vaccination? Many of these epitopes are largely “hidden” in the native viral context, but some vaccine platforms including those being developed by our collaborators can unmask these hidden epitopes, and therefore perhaps induce more broadly neutralizing vaccine responses that will be more robust to ongoing virus evolution.” Whatever challenges remain, it is clear that our rapidly growing understanding of antibody function presents great opportunities to protect against pandemic diseases that pose a threat now and in the future.

antibody binding map
Structure of the SARS-CoV-2 RBD highlighting the diversity of sites bound by the antibodies examined in this study. Image provided by Tyler Starr

This work was supported by the National Institutes of Health, the National Science Foundation, the Damon Runyon Cancer Research Foundation, the Gates Foundation, the Burroughs Wellcome Fund, the Wellcome Trust, Fast Grants, Bayer, the Molecular Sciences Software Institute, and the Howard Hughes Medical Institute.

Starr TN, Czudnochowski N, Liu Z, Zatta F, Park YJ, Addetia A, Pinto D, Beltramello M, Hernandez P, Greaney AJ, Marzi R, Glass WG, Zhang I, Dingens AS, Bowen JE, Tortorici MA, Walls AC, Wojcechowskyj JA, De Marco A, Rosen LE, Zhou J, Montiel-Ruiz M, Kaiser H, Dillen JR, Tucker H, Bassi J, Silacci-Fregni C, Housley MP, di Iulio J, Lombardo G, Agostini M, Sprugasci N, Culap K, Jaconi S, Meury M, Dellota E Jr, Abdelnabi R, Foo SC, Cameroni E, Stumpf S, Croll TI, Nix JC, Havenar-Daughton C, Piccoli L, Benigni F, Neyts J, Telenti A, Lempp FA, Pizzuto MS, Chodera JD, Hebner CM, Virgin HW, Whelan SPJ, Veesler D, Corti D, Bloom JD, Snell G. (2021) SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape. Nature 597(7874):97-102. doi: 10.1038/s41586-021-03807-6. Epub 2021 Jul 14. PMID: 34261126.