Laboratorio de Biología Molecular y Virología, Centro de Investigación Biomédica de Oriente, Instituto Mexicano del Seguro Social, Metepec, Atlixco, PUEBLA, México.
Instrumentación Analítica y Biosensores, Centro de Investigación en Biotecnología Aplicada (CIBA), Instituto Politécnico Nacional, Tepetitla de Lardizábal, Tlaxcala, México.
PeerJ. 2022 Aug 4;10:e13650. doi: 10.7717/peerj.13650. eCollection 2022.
Dengue and Zika are two major vector-borne diseases. Dengue causes up to 25,000 deaths and nearly a 100 million cases worldwide per year, while the incidence of Zika has increased in recent years. Although Zika has been associated to fetal microcephaly and Guillain-Barré syndrome both it and dengue have common clinical symptoms such as severe headache, retroocular pain, muscle and join pain, nausea, vomiting, and rash. Currently, vaccines have been designed and antivirals have been identified for these diseases but there still need for more options for treatment. Our group previously obtained some fractions from medicinal plants that blocked dengue virus (DENV) infection . In the present work, we explored the possible targets by molecular docking a group of molecules contained in the plant fractions against DENV and Zika virus (ZIKV) NS3-helicase (NS3-hel) and NS3-protease (NS3-pro) structures. Finally, the best ligands were evaluated by molecular dynamic simulations.
To establish if these molecules could act as wide spectrum inhibitors, we used structures from four DENV serotypes and from ZIKV. ADFR 1.2 rc1 software was used for docking analysis; subsequently molecular dynamics analysis was carried out using AMBER20.
Docking suggested that 3,5-dicaffeoylquinic acid (DCA01), quercetin 3-rutinoside (QNR05) and quercetin 3,7-diglucoside (QND10) can tightly bind to both NS3-hel and NS3-pro. However, after a molecular dynamics analysis, tight binding was not maintained for NS3-hel. In contrast, NS3-pro from two dengue serotypes, DENV3 and DENV4, retained both QNR05 and QND10 which converged near the catalytic site. After the molecular dynamics analysis, both ligands presented a stable trajectory over time, in contrast to DCA01. These findings allowed us to work on the design of a molecule called MOD10, using the QND10 skeleton to improve the interaction in the active site of the NS3-pro domain, which was verified through molecular dynamics simulation, turning out to be better than QNR05 and QND10, both in interaction and in the trajectory.
Our results suggests that NS3-hel RNA empty binding site is not a good target for drug design as the binding site located through docking is too big. However, our results indicate that QNR05 and QND10 could block NS3-pro activity in DENV and ZIKV. In the interaction with these molecules, the sub-pocket-2 remained unoccupied in NS3-pro, leaving opportunity for improvement and drug design using the quercetin scaffold. The analysis of the NS3-pro in complex with MOD10 show a molecule that exerts contact with sub-pockets S1, S1', S2 and S3, increasing its affinity and apparent stability on NS3-pro.
登革热和寨卡热是两种主要的虫媒病毒病。登革热每年在全球导致多达 2.5 万人死亡和近 1 亿例病例，而寨卡热的发病率近年来有所增加。尽管寨卡热与胎儿小头畸形和格林-巴利综合征有关，但它和登革热都有严重头痛、眼后疼痛、肌肉和关节疼痛、恶心、呕吐和皮疹等共同的临床症状。目前，已经针对这些疾病设计了疫苗和抗病毒药物，但仍需要更多的治疗选择。我们的研究小组之前从药用植物中获得了一些能够阻止登革热病毒（DENV）感染的化合物。在本工作中，我们通过分子对接，将植物部分中的一组分子对接 DENV 和寨卡病毒（ZIKV）NS3-解旋酶（NS3-helicase，NS3-hel）和 NS3-蛋白酶（NS3-protease，NS3-pro）结构，探索了可能的靶点。最后，通过分子动力学模拟对最佳配体进行了评估。
为了确定这些分子是否可以作为广谱抑制剂，我们使用了来自四种 DENV 血清型和 ZIKV 的结构。使用 ADFR 1.2 rc1 软件进行对接分析；随后使用 AMBER20 进行分子动力学分析。
对接结果表明，3,5-二咖啡酰奎宁酸（DCA01）、槲皮素 3-鼠李糖苷（QNR05）和槲皮素 3,7-二葡萄糖苷（QND10）可以紧密结合 NS3-hel 和 NS3-pro。然而，经过分子动力学分析，NS3-hel 的紧密结合并未得到维持。相比之下，来自两种登革热血清型 DENV3 和 DENV4 的 NS3-pro 保留了 QNR05 和 QND10，它们在催化部位附近聚集。经过分子动力学分析，与 DCA01 相比，这两种配体在时间上都呈现出稳定的轨迹。
我们的结果表明，NS3-hel RNA 空结合位点不是药物设计的理想靶点，因为通过对接定位的结合位点太大。然而，我们的结果表明，QNR05 和 QND10 可能会阻止 DENV 和 ZIKV 中的 NS3-pro 活性。在与这些分子的相互作用中，NS3-pro 的亚口袋-2 仍然未被占据，为使用槲皮素支架进行药物设计和改进提供了机会。分析与 MOD10 复合的 NS3-pro 显示出一种与亚口袋 S1、S1'、S2 和 S3 相互作用的分子，增加了其与 NS3-pro 的亲和力和表观稳定性。
