Abstract

Toxoplasma gondii is an opportunistic obligate parasite, ubiquitous around the globe with seropositivity rates that range from 10% to 90% and infection by the parasite of pregnant women causes pre-natal death of the foetus in most cases and severe neurodegenerative syndromes in some. No vaccine is currently available, and since drug-resistance is common among T. gondii strains, discovering lead compounds for drug design using diverse tactics is necessary. In this study, the sole constituent isoform of an enzymatic 3-oxoacyl-[acyl-carrier-protein] reduction step in an apicoplast-located fatty acid biosynthesis pathway was chosen as a possible drug target. FASII is prokaryotic therefore, targeting it would pose fewer side-effects to human hosts. After a homology 3D modelling of TgFabG, a high-throughput virtual screening of 9867 compounds, the elimination of ligands was carried out by a flexible ligand molecular docking and 200 ns molecular dynamics simulations, with additional DCCM and PC plot analyses. Molecular Dynamics and related post-MD analyses of the top 3 TgFabG binders selected for optimal free binding energies, showed that L2 maintained strong H-bonds with TgFabG and facilitated structural reorientation expected of FabGs, namely an expansion of the Rossmann Fold and a flexible lid capping. The most flexible TgFabG sites were the α7 helix (the flexible lid region) and the β4-α4 and β5-α6 loops. For TgFabG-L2, the movements of these regions toward the active site enabled greater ligand stability. Thus, L2 ("Skimmine"; PubChem ID: 320361), was ultimately selected as the optimal candidate for the discovery of lead compounds for rational drug design.

Communicated by Ramaswamy H. Sarma

摘要

刚地弓形虫是一种机会性专性寄生虫，在全球范围内普遍存在，血清阳性率从 10% 到 90% 不等，孕妇的寄生虫感染在大多数情况下会导致胎儿在产前死亡，在某些情况下会导致严重的神经退行性综合征。目前没有可用的疫苗，因为耐药性在弓形虫中很常见菌株，有必要使用多种策略发现用于药物设计的先导化合物。在这项研究中，选择位于 apicoplast 的脂肪酸生物合成途径中的酶促 3-氧代酰基-[酰基-载体-蛋白质] 还原步骤的唯一成分异构体作为可能的药物靶点。FASII 是原核生物，因此，以它为目标将对人类宿主造成较少的副作用。在对 TgFabG 进行同源 3D 建模（对 9867 种化合物进行高通量虚拟筛选）后，通过灵活的配体分子对接和 200 ns 分子动力学模拟以及额外的 DCCM 和 PC 图分析来消除配体。为获得最佳自由结合能而选择的前 3 种 TgFabG 结合剂的分子动力学和相关的 MD 后分析，表明 L2 与 TgFabG 保持强氢键并促进 FabG 预期的结构重新定向，即罗斯曼折叠的扩展和灵活的盖帽。最灵活的 TgFabG 位点是 α7 螺旋（柔性盖区域）和 β4-α4 和 β5-α6 环。对于 TgFabG-L2，这些区域向活性位点的移动能够提高配体稳定性。因此，L2（“Skimmine”；PubChem ID：320361）最终被选为发现用于合理药物设计的先导化合物的最佳候选者。

由 Ramaswamy H. Sarma 传达