In silico and In vitro Antibody Affinity Quantification: SARS-CoV-2 SD2 Major Disulfide Loop (SD2MDL) B-cell Epitope Analysis (initially presented at the 25th University of the Philippines Manila Science and Technology Week)

This research presents a comprehensive antibody affinity quantification study focusing on the SARS-CoV-2 Spike protein (S protein), specifically the SD2 Major Disulfide Loop (SD2MDL). Using the HAPTIC algorithm for in silico prediction and indirect ELISA for in vitro validation, we characterize the binding kinetics of antipeptide antibodies (ApAbs).Key Technical Highlights:Computational Modeling: HAPTIC-predicted affinity of 3.54 nM for the S621 peptide analog.Experimental Validation: ELISA-measured affinity of 1.14 nM, demonstrating high correlation between theoretical and wet-lab data.Clinical Diagnostics: Performance evaluation across 1,222 clinical samples and 221 controls, yielding 90% sensitivity and 71.79% accuracy.Structural Biology: Analysis of the immunogen sequence within the spike protein trimer and its conservation across variants (Alpha, Beta, Gamma, Delta, Epsilon, and Omicron BA.2.86).This study provides critical data for diagnostic assay development, vaccine immunogen design, and serological surveillance of COVID-19 variants.