A combined computational-experimental approach to define the structural origin of antibody recognition of sialyl-Tn, a tumor-associated carbohydrate antigen.

Anti-carbohydrate monoclonal antibodies (mAbs) hold great promise as cancer therapeutics and diagnostics. However, their specificity can be mixed, and detailed characterization is problematic, because antibody-glycan complexes are challenging to crystallize. Here, we developed a generalizable approach employing high-throughput techniques for characterizing the structure and specificity of such mAbs, and applied it to the mAb TKH2 developed against the tumor-associated carbohydrate antigen sialyl-Tn (STn). The mAb specificity was defined by apparent KD values determined by quantitative glycan microarray screening. Key residues in the antibody combining site were identified by site-directed mutagenesis, and the glycan-antigen contact surface was defined using saturation transfer difference NMR (STD-NMR). These features were then employed as metrics for selecting the optimal 3D-model of the antibody-glycan complex, out of thousands plausible options generated by automated docking and molecular dynamics simulation. STn-specificity was further validated by computationally screening of the selected antibody 3D-model against the human sialyl-Tn-glycome. This computational-experimental approach would allow rational design of potent antibodies targeting carbohydrates

Eliminating Monitor Overuse (EMO) Type III Effectiveness-Deimplementation Cluster-Randomized Trial: Statistical Analysis Plan

Background: Deimplementing overused health interventions is essential to maximizing quality and value while minimizing harm, waste, and inefficiencies. Three national guidelines discourage continuous pulse oximetry (SpO2) monitoring in children who are not receiving supplemental oxygen, but the guideline-discordant practice remains prevalent, making it a prime target for deimplementation. This paper details the statistical analysis plan for the Eliminating Monitor Overuse (EMO) SpO2 trial, which compares the effect of two competing deimplementation strategies (unlearning only vs. unlearning plus substitution) on the sustainment of deimplementation of SpO2 monitoring in children with bronchiolitis who are in room air. Methods: The EMO Trial is a hybrid type 3 effectiveness-deimplementation trial with a longitudinal cluster-randomized design, conducted in Pediatric Research in Inpatient Settings Network hospitals. The primary outcome is deimplementation sustainment, analyzed as a longitudinal difference-in-differences comparison between study arms. This analysis will use generalized hierarchical mixed-effects models for longitudinal clustering outcomes. Secondary outcomes include the length of hospital stay and oxygen supplementation duration, modeled using linear mixed-effects regressions. Using the well-established counterfactual approach, we will also perform a mediation analysis of hospital-level mechanistic measures on the association between the deimplementation strategy and the sustainment outcome. Discussion: We anticipate that the EMO Trial will advance the science of deimplementation by providing new insights into the processes, mechanisms, and likelihood of sustained practice change using rigorously designed deimplementation strategies. This pre-specified statistical analysis plan will mitigate reporting bias and support data-driven approaches

Bfmp: a method for discretizing and visualizing pyranose conformations

We report a new classification method for pyranose ring conformations called Best-fit, Four-Membered Plane (BFMP), which describes pyranose ring conformations based on reference planes defined by four atoms. The method is able to characterize all asymmetrical and symmetrical shapes of a pyran ring, is readily automated, easy to interpret, and maps trivially to IUPAC definitions. It also provides a qualitative measurement of the distortion of the ring. Example applications include the analysis of data from crystal structures and molecular dynamics simulations

Specificity of furanoside-protein recognition through antibody engineering and molecular modeling

Recognition of furanosides (five-membered ring sugars) by proteins plays important roles in host-pathogen interactions. In comparison to their six-membered ring counterparts (pyranosides), detailed studies of the molecular motifs involved in the recognition of furanosides by proteins are scarce. Here the first in-depth molecular characterization of a furanoside-protein interaction system, between an antibody (CS-35) and cell wall polysaccharides of mycobacteria, including the organism responsible for tuberculosis is reported. The approach was centered on the generation of the single chain variable fragment of CS-35 and a rational library of its mutants. Investigating the interaction from various aspects revealed the structural motifs that govern the interaction, as well as the relative contribution of molecular forces involved in the recognition. The specificity of the recognition was shown to originate mainly from multiple CH- interactions and, to a lesser degree, hydrogen bonds formed in critical distances and geometries

Specificity of furanoside-protein recognition through antibody engineering and molecular modeling

Recognition of furanosides (five-membered ring sugars) by proteins plays important roles in host-pathogen interactions. In comparison to their six-membered ring counterparts (pyranosides), detailed studies of the molecular motifs involved in the recognition of furanosides by proteins are scarce. Here the first in-depth molecular characterization of a furanoside-protein interaction system, between an antibody (CS-35) and cell wall polysaccharides of mycobacteria, including the organism responsible for tuberculosis is reported. The approach was centered on the generation of the single chain variable fragment of CS-35 and a rational library of its mutants. Investigating the interaction from various aspects revealed the structural motifs that govern the interaction, as well as the relative contribution of molecular forces involved in the recognition. The specificity of the recognition was shown to originate mainly from multiple CH- interactions and, to a lesser degree, hydrogen bonds formed in critical distances and geometries

BFMP: A Method for Discretizing and Visualizing Pyranose Conformations

We report a new classification method for pyranose ring conformations called Best-fit, Four-Membered Plane (BFMP), which describes pyranose ring conformations based on reference planes defined by four atoms. The method is able to characterize all asymmetrical and symmetrical shapes of a pyran ring, is readily automated, easy to interpret, and maps trivially to IUPAC definitions. It also provides a qualitative measurement of the distortion of the ring. Example applications include the analysis of data from crystal structures and molecular dynamics simulations