Nanobody-decorated IgMs target viral epitopes and block mutation escape

Scientists led by a team at the Icahn School of Medicine at Mount Sinai have developed an antibody-based platform they call adaptive multi-epitope targeting with increased avidity (AMETA) to address a key challenge in treating rapidly evolving viruses such as SARS-CoV-2, which is the viral ability to mutate and evade existing vaccines and treatments.

AMETA was designed as a modular, multivalent platform that uses engineered nanobodies (Nbs) to simultaneously target multiple stable regions of a virus that are less likely to mutate. The technology conjugates potent bispecific nanobodies with a human immunoglobulin M (IgM) scaffold. The researchers suggest that this multi-targeting strategy, coupled with a significant increase in binding strength, provides a more durable and resilient defense against evolving viruses.

In their newly published article in celllead author Yi Shi, PhD, and colleagues outlined preclinical testing in mice that demonstrated the effectiveness of the AMETA constructs against sarbecoviruses, including the latest Omicron variants of SARS-CoV-2. “AMETA's flexible design allows for rapid adaptation to a variety of pathogens, providing an agile and dynamic solution to emerging infections,” said Shi, associate professor of pharmacological sciences at Icahn Mount Sinai. “Our results represent a major advance in overcoming mutational escape in viruses and antibiotic-resistant microbes.”

In their report titled “Adaptive multi-epitope targeting and avidity-enhanced nanobody platform for ultrapotent, durable antiviral therapy,” the researchers commented, “Overall, these results highlight AMETA as a modular, effective, and durable strategy against challenging pathogens.”

Pathogens such as viruses and bacteria often exhibit high genetic diversity and share the ability to develop escape mutations that undermine the effectiveness of host immunity and therapeutics, the authors noted. Since the start of the COVID-19 pandemic, SARS-CoV-2 has mutated rapidly, making many vaccines and treatments less effective. “Escape from the mutation in SARS-CoV-2 represents an ongoing challenge as current vaccines and treatments struggle to keep up with the rapid evolution of the virus,” Shi added. “Most therapeutic antibodies target a single viral site and lose effectiveness within a year as new variants emerge.” As the authors further noted, “Developing durable countermeasures requires targeting multiple neutralizing and, ideally, evolutionarily conserved epitopes.”

Nanobodies have emerged as a promising solution for antiviral therapy, the team continued. “Affinity-matured Nbs can specifically bind a variety of neutralizing epitopes, including conserved and cryptic sites, employing diverse mechanisms to prevent viral infections.”

Using the AMETA platform, special nanobodies are attached to a scaffold made of human IgM, part of the immune system's natural defenses that help fight infections. This allows for the simultaneous imaging of more than 20 nanobodies, significantly increasing the ability to bind to the virus by targeting multiple stable regions on its surface, the researchers noted. As a result, AMETA is far more effective against advanced variants, offering up to a million times greater potency compared to traditional antibodies that focus on a single target.

“Our AMETA system combines the strong avidity of the IgM scaffold with the high specificity and exceptional biotechnological potential of Nbs,” the researchers explained. “The miniature size and small footprint of Nbs enable avidity binding of AMETA constructs to a broad range of pathogenic epitopes, including small corners, crevices and conserved sites.”

Both laboratory tests and experiments in mice showed that AMETA constructs are highly effective against a range of SARS-CoV-2 variants, including the heavily mutated Omicron sublineages and even the closely related SARS-CoV-2 virus, the researchers said . “By leveraging multi-epitope SARS-CoV-2 nanobodies and structure-guided design, AMETA constructs exponentially increase antiviral efficacy, exceeding that of monomeric nanobodies by more than a million-fold,” the team explained. “Using murine infection models, we have demonstrated robust in vivo efficacy of a representative AMETA construct for both prophylactic and therapeutic applications… These constructs demonstrate highly potent, broad, and durable activity against pathogenic sarbecoviruses, including Omicron sublineages, with robust preclinical results.”

Working with researchers at the University of Oxford and Case Western Reserve University, the team used advanced imaging techniques such as cryo-electron microscopy and cryotomography to show that AMETA constructs neutralize the virus through several unexpected mechanisms. “Through cryo-ET analysis, we discovered a variety of antiviral mechanisms of AMETA that go beyond the classical mechanism of neutralization through competition with binding to the receptor,” they wrote. These include clumping virus particles together, binding to key regions of the spike protein, and disrupting the spike structure in ways not seen with other antiviral treatments, thereby preventing the virus from infecting cells.

“Our goal with AMETA is to create a long-lasting platform that overcomes the rapidly evolving properties of viral pathogens,” noted Adolfo Garcia-Sastre, PhD, co-senior author of the study, Irene and Dr. Arthur M. Fishberg Professor of Medicine and Director of the Global Health and Emerging Pathogens Institute at Icahn Mount Sinai. “This platform is not only a solution to COVID-19, but could also serve as a framework for combating other rapidly mutating human microbes, such as HIV, and protecting against future emerging viruses, including influenza viruses with pandemic potential.”

The authors commented: “Our results expand the scope of therapeutic strategies against infectious diseases and drug-resistant systems and pave the way for innovative approaches to combat a variety of pathogens.”

Shi added: “AMETA's flexible design enables rapid adaptation to combat a wide range of pathogens, providing an agile and dynamic solution to emerging infections.” Our findings represent a major advance in overcoming mutational escape in viruses and antibiotic-resistant microbes .”

With its modular design, AMETA also enables the rapid and cost-effective production of new nanobody constructs, making it an ideal candidate for dealing with future pandemics, the researchers say. “AMETA’s modularity enables rapid, cost-effective production and adaptation to evolving pathogens,” they explained. Shi and Garcia-Sastre's teams are currently preparing for further preclinical and potential clinical studies to evaluate the therapeutic potential of AMETA in various diseases.