Purificação Aline D, Benz Laila S, Lima Silva Wemenes J, Emery Flavio S, Andrade Carolina Horta, Weiss Manfred S, Nonato Maria Cristina
Center for the Research and Advancement in Fragments and Molecular Targets (CRAFT), School of Pharmaceutical Sciences at Ribeirao Preto, University of São Paulo, Ribeirão Preto 14040-903, São Paulo, Brazil.
Protein Crystallography Laboratory, Department of Biomolecular Sciences, School of Pharmaceutical Sciences at Ribeirao Preto, University of São Paulo, Ribeirão Preto 14040-903, São Paulo, Brazil.
ACS Omega. 2025 Jul 3;10(27):29087-29097. doi: 10.1021/acsomega.5c01536. eCollection 2025 Jul 15.
Dihydroorotate dehydrogenase (DHODH) is a key enzyme in the pyrimidine biosynthesis pathway, playing a critical role in cellular processes and offering therapeutic potential for antiviral, antineoplastic, and autoimmune treatments. Human DHODH (DHODH) utilizes ubiquinone as a second substrate, positioning its quinone-binding site as a promising target for inhibitor development. Lapachol, a natural naphthoquinone, has gained prominence as a valuable natural product for the discovery of novel therapeutic agents, thanks to its wide range of biological activities. In this study, we present the first crystal structure of DHODH in complex with lapachol, providing valuable insights into the interactions between this natural product and the enzyme. The structure reveals key binding interactions that mediate lapachol's affinity for DHODH and validates previously proposed computational models. Complementary molecular dynamics simulations further highlight the stability of the complex and the importance of water-mediated interactions in ligand binding. These findings enhance our understanding of how naphthoquinone derivatives, such as lapachol, interact with class 2 DHODHs, offering a foundation for the design of optimized inhibitors for therapeutic applications. By integration of structural and computational data, this study contributes to the rational design of novel DHODH inhibitors, paving the way for future exploration of lapachol and its derivatives in drug discovery.
二氢乳清酸脱氢酶（DHODH）是嘧啶生物合成途径中的关键酶，在细胞过程中起关键作用，并为抗病毒、抗肿瘤和自身免疫治疗提供治疗潜力。人二氢乳清酸脱氢酶（DHODH）利用泛醌作为第二底物，将其醌结合位点定位为抑制剂开发的有前景的靶点。拉帕醇是一种天然萘醌，由于其广泛的生物活性，作为发现新型治疗药物的有价值的天然产物而备受关注。在本研究中，我们展示了DHODH与拉帕醇复合物的首个晶体结构，为这种天然产物与该酶之间的相互作用提供了有价值的见解。该结构揭示了介导拉帕醇对DHODH亲和力的关键结合相互作用，并验证了先前提出的计算模型。互补的分子动力学模拟进一步突出了复合物的稳定性以及水介导的相互作用在配体结合中的重要性。这些发现增强了我们对萘醌衍生物（如拉帕醇）如何与2类DHODHs相互作用的理解，为设计用于治疗应用的优化抑制剂提供了基础。通过整合结构和计算数据，本研究有助于合理设计新型DHODH抑制剂，为未来在药物发现中探索拉帕醇及其衍生物铺平道路。
