MVsim is a toolset for quantifying and designing multivalent interactions

Assembly of adaptive engineering aptamers for Escherichia coli and their application in all-in-one rapid detection

Multivalent engineering aptamers (multi-Apts) adaptive and specific to whole Escherichia coli (E. coli: CMCC 44102) cells based on hybridization chain reaction (HCR) were constructed for the first time. The dissociation constant (Kd) value for these multi-Apts was 48 nM, demonstrating a higher affinity than that of monovalent aptamers (mono-Apts) (Kd = 102 nM). Furthermore, the reaction equilibrium of multi-Apts was achieved within 20 min, with a reaction rate twice that of mono-Apts. To validate the exceptional performance of these multi-Apts, they were employed as recognition elements in conjunction with gold nanoparticles (AuNPs) colorimetric assays for the all-in-one rapid detection of E. coli. This method exhibited a linear detection range from 1 × 102 to 1 × 10⁷ CFU mL⁻1, achieving a limit of detection (LOD) as low as 19 CFU mL⁻1. The recovery of this method in tap water and milk were 85.7% to 101% and 81.8% to 98.2%, respectively. The results indicated that this method not only provided a wide detection range but also exhibited high sensitivity and accuracy. Additionally, this study demonstrated that multi-Apts possessed greater application potential in the detection of macromolecular substances such as bacteria. In short, this work provided a novel approach for rapid and all-in-one detection of E. coli in food.

The molecular reach of antibodies crucially underpins their viral neutralisation capacity

Key functions of antibodies, such as viral neutralisation, depend on high-affinity binding. However, viral neutralisation poorly correlates with antigen affinity for reasons that have been unclear. Here, we use a new mechanistic model of bivalent binding to study  >45 patient-isolated IgG1 antibodies interacting with SARS-CoV-2 RBD surfaces. The model provides the standard monovalent affinity/kinetics and new bivalent parameters, including the molecular reach: the maximum antigen separation enabling bivalent binding. We find large variations in these parameters across antibodies, including reach variations (22-46 nm) that exceed the physical antibody size (~15 nm). By using antigens of different physical sizes, we show that these large molecular reaches are the result of both the antibody and antigen sizes. Although viral neutralisation correlates poorly with affinity, a striking correlation is observed with molecular reach. Indeed, the molecular reach explains differences in neutralisation for antibodies binding with the same affinity to the same RBD-epitope. Thus, antibodies within an isotype class binding the same antigen can display differences in molecular reach, substantially modulating their binding and functional properties.

Designing Multivalent and Multispecific Biologics

In the era of precision medicine, multivalent and multispecific therapeutics present a promising approach for targeted disease intervention. These therapeutics are designed to interact with multiple targets simultaneously, promising enhanced efficacy, reduced side effects, and resilience against drug resistance. We dissect the principles guiding the design of multivalent biologics, highlighting challenges and strategies that must be considered to maximize therapeutic effect. Engineerable elements in multivalent and multispecific biologic design-domain affinities, valency, and spatial presentation-must be considered in the context of the molecular targets as well as the balance of important properties such as target avidity and specificity. We illuminate recent applications of these principles in designing protein and cell therapies and identify exciting future directions in this field, underscored by advances in biomolecular and cellular engineering and computational approaches. Expected final online publication date for the Annual Review of Chemical and Biomolecular Engineering , Volume 15 is June 2024. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Facile Display of Homomultivalent Proteins for In Vitro Selections

Low-affinity protein binders are emerging as valuable domains for therapeutic applications because of their higher specificity when presented in multivalent ligands that increase the overall strength and selectivity of receptor binding. De novo discovery of low-affinity binders would be enhanced by the large library sizes attainable with in vitro selection systems, but these platforms generally maximize recovery of high-affinity monovalent binders. Here, we present a facile technology that uses rolling circle amplification to create homomultivalent libraries. We show proof of principle of this approach in ribosome display with off-rate selections of a bivalent ligand against monovalent and bivalent targets, thereby demonstrating high enrichment (up to 166-fold) against a low-affinity target that is bivalent but not monovalent. This approach to homomultivalent library construction can be applied to any binder tolerant of N- and C-terminal fusions and provides a platform for performing in vitro display selections with controlled protein valency and orientation.