Force Spectroscopy and High Speed Atomic Force Microscopy in Viral Research

Recent waves of COVID-19 correlate with the emergence of the Delta and the Omicron variant. In this study, we combined high-speed atomic force microscopy with single molecule recognition force spectroscopy to investigate, at single molecule resolution, the interaction dynamics of trimeric Spike with its essential entry receptor ACE2. We report that Spike trimer undergoes rapid conformational changes on surfaces, resulting in arc-like movements of the three receptor binding domains (RBDs) that collectively screen a circular range of almost 360° degrees. Acting as a highly dynamic molecular caliper, it thereby forms up to three tight bonds through its RBDs with ACE2 expressed on the cell surface. The Spike of both Delta and Omicron (B.1.1.529) variant enhance and markedly prolong viral attachment to the host cell receptor ACE2, which likely not only increases the rate of viral uptake, but also enhances the resistance of the variants against host-cell detachment by shear forces such as airflow, mucus or blood flow. We uncovered distinct binding mechanisms and strategies employed by circulating SARS-CoV-2 variants to enhance infectivity and viral transmission.<br/>The capacity of lectins to block SARS-CoV-2 viral entry holds promise for pan-variant therapeutic interventions. Out of a lectin library, two lectins, Clec4g and CD209c, were identified to strongly bind to the Spike protein of SARS-CoV-2. Multiple bond formations lead to stable complex formation, in which the number of formed bonds enhanced the overall interaction strength and dynamic stability of the lectin/Spike complexes. We also determined the binding capacity of a molecularly engineered lectin cloned from banana, BanLec H84T, which was shown to display broad-spectrum antiviral activity against several RNA viruses. Our studies revealed that H84T-BanLec strongly interacts with the Spike protein of the original viral strain, Wuhan-1 and several variants of concern (Delta, Omicron), which makes it a promising clinical candidate for defeating viral infectivity and tramsmission.<br/> <br/>References<br/>Force-tuned avidity of spike variant-ACE2 interactions viewed on the single-molecule level, Nature Communications 13 (2022) 7926.<br/>Identification of lectin receptors for conserved SARS-CoV-2 glycosylation sites, The EMBO Journal (2021) e108375.<br/>A molecularly engineered, broad-spectrum anti-coronavirus Lectin Inhibits SARS-CoV-2 and MERS-CoV Infection In Vivo, Cell Reports Medicine, 3 (2022) 100774.