Can hydroxylamine be a more potent nucleophile for the reactivation of tabun-inhibited AChE than prototype oxime drugs? An answer derived from quantum chemical and steered molecular dynamics studies

Abstract

Organophosphorus nerve agents are highly toxic compounds which strongly inhibit acetylcholinesterase (AChE) in the blood and in the central nervous system (CNS). Tabun is one of the highly toxic organophosphorus (OP) compounds and is resistant to many oxime drugs formulated for the reactivation of AChE. The reactivation mechanism of tabun-conjugated AChE with various drugs has been examined with density functional theory and ab initio quantum chemical calculations. The presence of a lone-pair located on the amidic group resists the nucleophilic attack at the phosphorus center of the tabun-conjugated AChE. We have shown that the newly designed drug candidate N-(pyridin-2-yl)hydroxylamine, at the MP2/6-31+G*//M05-2X/6-31G* level in the aqueous phase with the polarizable continuum solvation model (PCM), is more effective in reactivating the tabun-conjugated AChE than typical oxime drugs. The rate determining activation barrier with N-(pyridin-2-yl)hydroxylamine was found to be ∼1.7 kcal mol(-1), which is 7.2 kcal mol(-1) lower than the charged oxime trimedoxime (one of the most efficient reactivators in tabun poisonings). The greater nucleophilicity index (ω(-)) and higher CHelpG charge of pyridinylhydroxylamine compared to TMB4 support this observation. Furthermore, we have also examined the reactivation process of tabun-inhibited AChE with some other bis-quaternary oxime drug candidates such as methoxime (MMB4) and obidoxime. The docking analysis suggests that charged bis-quaternary pyridinium oximes have greater binding affinity inside the active-site gorge of AChE compared to the neutral pyridinylhydroxylamine. The peripheral ligand attached to the neutral pyridinylhydroxylamine enhanced the binding with the aromatic residues in the active-site gorge of AChE through effective π-π interactions. Steered molecular dynamics (SMD) simulations have also been performed with the charged oxime (TMB4) and the neutral hydroxylamine. From protein-drug interaction parameters (rupture force profiles, hydrogen bonds, hydrophobic interactions), geometry and the orientation of the drug candidates, the hydroxylamine is suggested to orchestrate the reactivation process better than TMB4. Furthermore, the calculated log P values show the effective penetration of the neutral drug candidate through the blood-brain barrier. The toxicity measurements and the IC50 values (a measure of the intrinsic affinity toward AChE) suggest that the pyridinylhydroxylamine compound could have similar toxic behavior compared to the prototype oxime antidotes used for reactivation purposes. The newly designed pyridinylhydroxylamine drug candidate can be an effective antidote both kinetically and structurally to reactivate the tabun-inhibited enzyme.

On the Influence of the Protonation States of Active Site Residues on AChE Reactivation: A QM/MM Approach

“…The Ganguly group assessed various reactivators by QM analysis, and showed that uncharged ones are kinetically more efficient . Later, they demonstrate that the rate‐limiting step is different for charged pyridinium oximes and non‐charged pyridine oximes: both species proceed through an addition–elimination mechanism; for charged species, the rate‐determining step is elimination, whereas it is addition for uncharged species . It was also demonstrated by semi‐empirical QM/MM that the peripheral‐site moiety of the active site is helpful to bind the reactivator and to stabilize the key transition state .…”

Identification of organophosphate modifications by high‐resolution mass spectrometry

“…The AChE's ser-OH group loses its hydrogen and, via nucleophilic reaction, forms a bond with OP. 24,25 We observed that the most reactive modification site, Y411 is a nucleophile, as shown in Figure 4b. The electro F I G U R E 1 Human albumin from PDB (1BJ5) was visualized and labeled with sites that were observed to be modified by OP or OP-like molecules using UCSF Chimera…”

Probing the Role of Imidazopyridine and Imidazophosphorine Scaffolds To Design Novel Proton Pump Inhibitor for H+,K+-ATPase: A DFT Study

“…We have further carried out steered molecular dynamics (SMD) simulations to examine the role of the active site amino acid residue in stabilizing the drug molecules. It is reported that the SMD simulation technique is suitable for the study of time-dependent unbinding of the ligand molecule from the active site of the protein. − The time-dependent unbinding of the inhibitor molecule from the active site of the protein in SMD simulation has been performed with the application of an external harmonic pulling force on the inhibitor molecule in the z direction, which is considered as a favorable exit route from the active site. , We have considered 2YN9 Protein Data Bank (PDB) ID for the molecular dynamics simulation with tenatoprazole and inhibitor-5 as a representative case . The maximum ligand unbinding force required for unbinding of tenatoprazole is found to be 344.2 kJ/(mol nm), while that for inhibitor-5 is 360.6 kJ/(mol nm).…”