A Comprehensive Understanding of Enzymatic Degradation of the G-Type Nerve Agent by Phosphotriesterase: Revised Role of Water Molecules and Rate-Limiting Product Release

Abstract

Nerve agents are highly toxic organophosphorus compounds, and the wild-type phosphotriesterase (PTE) enzyme is capable of hydrolyzing these organophosphates but with a low catalytic efficiency. Here the whole enzymatic detoxification process of the G-type nerve agent sarin by the PTE enzyme, including the substrate delivery, the chemical reaction, and the product release, has been explored by extensive QM/MM MD and MM MD simulations. The plausible mechanisms for the chemical and nonchemical steps, the roles of water molecules, and the key residues have been discussed. The enzymatic P–F cleavage of sarin is a two-step exothermic process with the free-energy span of 12.3 kcal/mol, and it should be facile in the whole enzymatic catalysis. On the contrary, the initial degraded product is tightly bound to the binuclear zinc center, and its dissociation experiences multiple chemical steps with the free-energy barriers of 21.0 kcal/mol for the recombination process and 18.3 kcal/mol for the release of the product phosphoester from the active site. Notably, the solvation of hydrophilic products in the bulk water is generally exothermic, which provides the driving force for the release of products from the active site. The side-chain residues Leu271 and Phe132 in the transportation channel function as the entrance gate in PTE and play an important gate-switching role to manipulate the substrate access to the active site and the product release. These mechanistic details for the enzymatic degradation of sarin by PTE provide significant clues to improve its activity toward the nerve agents.

Mechanical Bond Approach to Introducing Self-Adaptive Active Sites in Covalent Organic Frameworks for Zinc-Catalyzed Organophosphorus Degradation

“…In order to elucidate the exceptional activity of Crown-COF-Zn, long-term molecular dynamics simulations were conducted. A key feature of the active site in naturally occurring organophosphorus hydrolase is a self-adaptive binuclear zinc center, where two zinc ions become close through the coordination of the nascent OH – , with a distance of ∼3.4 Å. − Once the reaction occurs, the bridging OH – ion is substituted by a phosphate group of POM substrates into the form of the Zn­(II)··O–P = O·Zn­(II) intermediate state, and the Zn α –Zn β distance increases to ∼4.0 Å. As the hydrolysis proceeds further, the dissociated Zn α –Zn β centers release the degraded phosphate from the active site and restore their original state for the next cycle.…”

“… 4 − 6 In its active domain, a responsive structural transformation for two zinc fragments is observed within 3.3–4.6 Å of the distance, which corresponds to the important transition-state barrier crossing and the product-releasing steps. 7 − 9 Due to these conformational dynamics, OPHs hydrolyze OP compounds at rates several orders of magnitude higher than artificial catalysts. However, the poor stability under harsh environments (including high temperatures, heavy metal ions, and acids/bases) makes their industrial utilization unfeasible.…”

“…Organophosphate (OP) compounds, one of the most toxic agents, are illegally but widely used in chemical warfare, destroy the neurotransmitter acetylcholine, and damage the nervous system. , Frequent military events have led to an urgent requirement for the rapid degradation of these banned chemical weapons . Naturally occurring organophosphorus hydrolase (OPH) exhibits an outstanding ability to hydrolyze various organophosphate esters. − In its active domain, a responsive structural transformation for two zinc fragments is observed within 3.3–4.6 Å of the distance, which corresponds to the important transition-state barrier crossing and the product-releasing steps. − Due to these conformational dynamics, OPHs hydrolyze OP compounds at rates several orders of magnitude higher than artificial catalysts. However, the poor stability under harsh environments (including high temperatures, heavy metal ions, and acids/bases) makes their industrial utilization unfeasible. − Recently, a remarkable example was explored to construct a biomimetic covalent organic framework (COF) catalyst with porphyrin active sites, which involves the design and development of catalysts that resemble the structure and functionality of natural enzymes. − The feasible synthesis of COFs allows for the modulation of pore size, network topology, and chemical functionality, thus endowing COFs with huge potentials for biocomposite performance.…”

Building a Porous Molecular Machine That Replicates Natural Enzymes

“… 2 Central to their design philosophy is replicating the active domain of OPH, which involves two zinc fragments within a 3.3–4.6 Å distance, corresponding to the transition-state barrier crossing and the product-release steps, as depicted in Figure 1 . 3 These next-generation artificial enzymes are affectionately called nanozymes. 4 …”

“…(B) Coordination of the binuclear zinc center. Reprinted with permission from ref ( 3 ). Copyright 2019.…”