P01-13

Predicting Lysine Reactivity: Insights from Constant-pH MD Simulations and Experimental Correlation

Osamu ICHIHARA *

Schrödinger KK
( * E-mail: osamu.ichihara@schrodinger.com )

The selective functionalization of lysine residues in proteins is a key strategy in the development of bioconjugates. However, the reactivity of lysine residues varies significantly depending on their local environment, influencing the success of such modifications. In this study, we focus on RNase A as a model system, utilizing Schrödinger’s constant-pH molecular dynamics (MD) simulation tool implemented in the Desmond program to predict the pKa values of lysine residues and correlate these with experimentally determined reactivity data from Xi Chen et al. (Bioconjugation Chemistry 2012, 23, 500-508).

Our results reveal a strong correlation between the predicted pKa values and the reactivity of lysines in RNase A, with some discussion extending to Lysozyme C and Somatostatin. This correlation underscores the potential of constant-pH MD simulations as a predictive tool for identifying reactive lysine sites, which could streamline the design of site-selective functionalization strategies. While this study primarily focuses on RNase A, the insights gained suggest potential applications in Antibody-Drug Conjugates (ADCs), where precise conjugation is critical. Although still an emerging possibility, this approach could contribute to more efficient and targeted ADC development. Our findings highlight the value of integrating computational predictions with experimental data to advance protein engineering, bioconjugation strategies, and potentially, ADC design.