Degradation of Novichok nerve agent A234 by phosphotriesterase: insight into the pH-regulated mechanism from QM/MM and MM MD simulations

Abstract

The pK_a value represents a fundamental physicochemical parameter, which dictates molecular speciation and reactivity in biological systems. A234 [Novichok family nerve agent, EtO-P(O)(F)-NC(Me)-N(Et)₂] exhibits extreme toxicity but poorly characterized biodegradation. Phosphotriesterase (PTE), well-known for hydrolyzing organophosphates effectively, shows potential for A234 detoxification. By using density functional theory (DFT) calculations, we determined the pK_a value of protonated S_p-enantiomer A234-H⁺ [EtO-P(O)(F)-N(H)C(Me)-N(Et)₂]⁺ as 8.65, suggesting that it is a dominant form of S_p-enantiomer A234 under neutral and acidic conditions. Further QM/MM calculations and molecular dynamics (MD) simulations reveal stark pH-dependent mechanisms for the enzymatic degradation of S_p-A234 and S_p-A234-H⁺. At pH = 7.0, the low-energy hydrolytic reaction of A234-H⁺ is initiated by the nucleophilic attack of the bridging OH⁻, leading to the bidentate coordination degraded product with an energy barrier of 14.0 kcal mol⁻¹. The subsequent bidentate-to-monodentate coordination conversion, coupled with proton transfer, as the rate-limiting step for the entire enzymatic degradation, yields the electroneutral degraded product with an energy barrier of 17.8 kcal mol⁻¹. Under alkaline environments (pH = 9.0), the deprotonated A234 binds to the active site tightly but is hydrolytically inert, resisting PTE catalysis. The present results establish protonation state as the critical switch controlling PTE's catalytic efficiency against A234, resolving the mechanistic basis of pH-dependent nerve agent degradation.