Deamidation reaction network mapping of pharmacologic and related proteins: impact of solvation dielectric on the degradation energetics of asparagine dipeptides

Abstract

Monoclonal antibodies (mAbs) are one of the most lucrative pharmacologics currently on the market due to their diverse array of applications. However, the diversity of these therapeutics is often limited by the degradation mechanisms experienced both in the formulation process and on the shelf after production. Due to the size constraints of experimental approaches, molecular models are crucial for studying these degradation mechanisms. One such mechanism of interest is deamidation, also known as the transition from neutral residues to acidic residues. In this study, we mapped out the deamidation of Asn-X dipeptides into Asp-X dipeptides using density functional theory (DFT). Full network mapping enabled us to predict the selectivity of the deamidation reaction between three primary pathways, as well as one theoretical pathway, as a function of solvent dielectric (Fig. 1). To meet this goal, we studied a total of 115 dipeptide reactions per modeled dielectric (460 total reactions). Modeled at a neutral pH and using quantum chemical and statistical thermodynamic methods, we computed the following values: enthalpy of reaction (ΔH_RXN), entropy (ΔS_RXN), Gibbs free energy of reaction (ΔG_RXN), activation energy (E_A), and the Arrhenius pre-exponential factor (log(A)) for each dipeptide. Additionally, by using chemical reaction principles, we generated a database of computed rate coefficients for all possible N-terminus Asn-X deamidation reactions at a neutral pH, predicted the most likely deamidation reaction mechanism for each dipeptide reaction, and matched our results against quantitative and qualitative trends previously noted by experimental literature.