Oxime-phosphorus-distances calculations.

The ability of the cyclodextrin-oxime construct 6-OxP-CD to bind and degrade the nerve agents Cyclosarin (GF), Soman (GD) and S-[2-[Di(propan-2-yl)amino]ethyl] O-ethyl methylphosphonothioate (VX) has been studied using 31P-nuclear magnetic resonance (NMR) under physiological conditions. While 6-OxP-CD was found to degrade GF instantaneously under these conditions, it was found to form an inclusion complex with GD and significantly improve its degradation (t1/2 ~ 2 hrs) relative over background (t1/2 ~ 22 hrs). Consequently, effective formation of the 6-OxP-CD:GD inclusion complex results in the immediate neutralization of GD and thus preventing it from inhibiting its biological target. In contrast, NMR experiments did not find evidence for an inclusion complex between 6-OxP-CD and VX, and the agent’s degradation profile was identical to that of background degradation (t1/2 ~ 24 hrs). As a complement to this experimental work, molecular dynamics (MD) simulations coupled with Molecular Mechanics-Generalized Born Surface Area (MM-GBSA) calculations have been applied to the study of inclusion complexes between 6-OxP-CD and the three nerve agents. These studies provide data that informs the understanding of the different degradative interactions exhibited by 6-OxP-CD with each nerve agent as it is introduced in the CD cavity in two different orientations (up and down). For its complex with GF, it was found that the oxime in 6-OxP-CD lies in very close proximity (PGF⋯OOxime ~ 4–5 Å) to the phosphorus center of GF in the ‘downGF’ orientation for most of the simulation accurately describing the ability of 6-OxP-CD to degrade this nerve agent rapidly and efficiently. Further computational studies involving the center of masses (COMs) for both components (GF and 6-OxP-CD) also provided some insight on the nature of this inclusion complex. Distances between the COMs (ΔCOM) lie closer in space in the ‘downGF’ orientation than in the ‘upGF’ orientation; a correlation that seems to hold true not only for GF but also for its congener, GD. In the case of GD, calculations for the ‘downGD’ orientation showed that the oxime functional group in 6-OxP-CD although lying in close proximity (PGD⋯OOxime ~ 4–5 Å) to the phosphorus center of the nerve agent for most of the simulation, adopts another stable conformation that increase this distance to ~ 12–14 Å, thus explaining the ability of 6-OxP-CD to bind and degrade GD but with less efficiency as observed experimentally (t1/2 ~ 4 hr. vs. immediate). Lastly, studies on the VX:6-OxP-CD system demonstrated that VX does not form a stable inclusion complex with the oxime-bearing cyclodextrin and as such does not interact in a way that is conducive to an accelerated degradation scenario. Collectively, these studies serve as a basic platform from which the development of new cyclodextrin scaffolds based on 6-OxP-CD can be designed in the development of medical countermeasures against these highly toxic chemical warfare agents.本研究在生理条件下采用磷-31核磁共振（31P-nuclear magnetic resonance, NMR）波谱法，探究了环糊精-肟缀合物6-OxP-CD结合并降解神经毒剂环沙林（Cyclosarin, GF）、索曼（Soman, GD）以及S-[二(丙-2-基)氨基]乙基 O-乙基甲基硫代膦酸酯（VX）的能力。实验发现，6-OxP-CD可在该条件下瞬时降解GF；其与GD可形成包合物，相较于本底降解（半衰期约22小时），可显著加速GD的降解（半衰期约2小时）。因此，6-OxP-CD与GD成功形成包合物后，可立即中和GD，阻断其对生物靶点的抑制作用。与之相反，核磁共振实验未发现6-OxP-CD与VX形成包合物的证据，该毒剂的降解曲线与本底降解完全一致（半衰期约24小时）。作为本实验研究的补充，本研究结合分子动力学（molecular dynamics, MD）模拟与分子力学-广义玻恩表面积（Molecular Mechanics-Generalized Born Surface Area, MM-GBSA）计算，对6-OxP-CD与三种神经毒剂形成的包合物展开了研究。上述研究阐明了6-OxP-CD与每种神经毒剂的不同降解相互作用机制——当毒剂以「正向」与「反向」两种取向进入环糊精空腔时的相互作用差异。针对6-OxP-CD与GF的复合物，模拟结果显示，在「反向GF（downGF）」取向中，6-OxP-CD上的肟基团与GF的磷中心始终保持极近的距离（P_GF⋯O_肟 ≈ 4–5 Å），这准确解释了6-OxP-CD可快速高效降解该神经毒剂的实验现象。进一步针对两组分（GF与6-OxP-CD）的质心（center of masses, COMs）展开的计算研究，也为该包合物的本质提供了新的见解。两组分的质心间距（ΔCOM）在「反向GF」取向中较「正向GF（upGF）」取向更短；这一相关性不仅适用于GF，对其同系物GD同样成立。对于GD体系，「反向GD（downGD）」取向的计算结果显示，尽管在多数模拟时长内，6-OxP-CD的肟基团与GD的磷中心仍保持较近距离（P_GD⋯O_肟 ≈ 4–5 Å），但该体系同时存在另一种稳定构象，此时两者间距增至约12–14 Å，这解释了实验中观察到的：6-OxP-CD可结合并降解GD，但降解效率低于GF（半衰期约2小时vs瞬时降解）。针对VX:6-OxP-CD体系的研究则证实，VX无法与该含肟环糊精形成稳定包合物，因此二者不会发生可加速降解的相互作用。综上，本研究为基于6-OxP-CD的新型环糊精骨架开发提供了基础平台，助力针对这类高毒性化学战剂的医学防护手段研发。