PDF(Pubmed)
Abstract：
Inflammation is a protective stress response triggered by external stimuli, with 5-lipoxygenase (5LOX) playing a pivotal role as a potent mediator of the leukotriene (Lts) inflammatory pathway. Nordihydroguaiaretic acid (NDGA) functions as a natural orthosteric inhibitor of 5LOX, while 3-acetyl-11-keto-β-boswellic acid (AKBA) acts as a natural allosteric inhibitor targeting 5LOX. However, the precise mechanisms of inhibition have remained unclear. In this study, Gaussian accelerated molecular dynamics (GaMD) simulation was employed to elucidate the inhibitory mechanisms of NDGA and AKBA on 5LOX. It was found that the orthosteric inhibitor NDGA was tightly bound in the protein\'s active pocket, occupying the active site and inhibiting the catalytic activity of the 5LOX enzyme through competitive inhibition. The binding of the allosteric inhibitor AKBA induced significant changes at the distal active site, leading to a conformational shift of residues 168-173 from a loop to an α-helix and significant negative correlated motions between residues 285-290 and 375-400, reducing the distance between these segments. In the simulation, the volume of the active cavity in the stable conformation of the protein was reduced, hindering the substrate\'s entry into the active cavity and, thereby, inhibiting protein activity through allosteric effects. Ultimately, Markov state models (MSM) were used to identify and classify the metastable states of proteins, revealing the transition times between different conformational states. In summary, this study provides theoretical insights into the inhibition mechanisms of 5LOX by AKBA and NDGA, offering new perspectives for the development of novel inhibitors specifically targeting 5LOX, with potential implications for anti-inflammatory drug development.
摘要：
炎症是由外界刺激引发的保护性应激反应,5-脂氧合酶（5LOX）作为白三烯（Lts）炎症途径的有效介质发挥关键作用。去甲二氢愈创木酸（NDGA）作为5LOX的天然正构抑制剂，而3-乙酰基-11-酮-β-乳香酸（AKBA）作为靶向5LOX的天然变构抑制剂。然而,抑制的确切机制尚不清楚.在这项研究中,采用高斯加速分子动力学（GaMD）模拟来阐明NDGA和AKBA对5LOX的抑制机制。发现正构抑制剂NDGA紧密结合在蛋白质的活性口袋中，占据活性位点并通过竞争性抑制抑制5LOX酶的催化活性。变构抑制剂AKBA的结合诱导了远端活性位点的显著变化，导致残基168-173从环到α-螺旋的构象移位以及残基285-290和375-400之间的显着负相关运动，从而减少了这些片段之间的距离。在模拟中,蛋白质稳定构象的活性腔体积减少，阻碍衬底进入有源腔，因此，通过变构效应抑制蛋白质活性。最终,马尔可夫状态模型(MSM)用于识别和分类蛋白质的亚稳态，揭示了不同构象状态之间的过渡时间。总之,本研究为AKBA和NDGA对5LOX的抑制机制提供了理论见解，为开发专门针对5LOX的新型抑制剂提供了新的视角，对抗炎药物的开发有潜在的影响。
