Observation of redistribution for local conformational dynamics in cross-reactive antibody design

Abstract

Antibody engineering is often achieved through laborious mutagenesis and screening. However, the physicochemical basis of cross-reactivity-enhancing mutations remains unclear. We computationally redesigned the severe acute respiratory syndrome coronavirus (SARS-CoV)-1 neutralizing antibody m396 to recognize the SARS-CoV-2 receptor-binding domain (RBD) and characterized its biophysical properties. A first-generation variant carrying three light-chain substitutions (S30LW, S93LI and S94LF) acquired detectable SARS-CoV-2 RBD binding, while strengthening its affinity for the SARS-CoV RBD. A second-generation variant carrying two substitutions (T52HL and L54HW) further improved SARS-CoV-2 binding with a low micromolar affinity, predominantly driven by an approximately 200-fold increase in the association rate. Circular dichroism spectra indicated preserved global folding across the variants, whereas differential scanning calorimetry revealed stepwise decreases in lower-temperature unfolding transitions. Hydrogen-deuterium exchange mass spectrometry showed increased dynamics of CDR-L1 and localized rigidification near CDR-H2 in the second variant. These results suggest a biophysical model in which a small number of mutations reprogram cross-recognition by redistributing the local conformational dynamics.