PO.CH03.01 · 化学
抑制苹果酸酶作为利用癌症代谢重编程的策略：一种基于结构的方法
Malic enzyme inhibition as a strategy to exploit metabolic reprogramming in cancer: A structure-based approach
作者与单位 Authors & Affiliations
摘要 Abstract
中文摘要
背景：癌症仍是一项全球健康挑战，迫切需要能够改善临床结局和患者生活质量的治疗方法。肿瘤细胞通常会重编程代谢以维持增殖和存活，尤其是通过增加对谷氨酰胺的依赖以及上调线粒体苹果酸酶2（ME2），后者产生丙酮酸和NAD(P)H。ME2在胰腺癌、黑色素瘤和肺癌中过表达，使其成为一个引人注目但仍未被充分探索的治疗靶点。
方法：表达重组人ME1、ME2和ME3，并在有无抑制剂存在的条件下对其进行动力学表征。我们解析了三种同工型与一种强效苹果酸酶抑制剂结合的完整X射线晶体结构，揭示了配体和金属的配位方式。这些结构指导了对一个精选文库（多达1400万个类药和片段分子）的虚拟筛选，以鉴定新型苹果酸酶抑制剂。生化命中化合物被推进至细胞实验以评估疗效；先导化合物NPD-389和FLA在黑色素瘤和三阴性乳腺癌细胞系中检测了抗增殖活性。
结果：动力学分析显示各ME同工型之间存在不同的活性和抑制模式。X射线晶体学观察到强效、非同工型选择性抑制剂NPD-389以金属配位模式结合，并捕获到一种意外的苹果酸酶构象。针对该构象的基于结构的虚拟筛选鉴定出多个具有生化抑制活性的新型骨架。其中一个骨架FLA表现出独特的选择性特征，被发现结合于ME2一个先前隐蔽的口袋中，该口袋在配体结合时发生重排，并邻近NAD+辅因子和苹果酸结合位点。在一组黑色素瘤和三阴性乳腺癌细胞系中，NPD-389和FLA在大多数模型中降低了增殖，支持其作为进一步开发的化学先导物的潜力。
结论：这些结果确立了线粒体苹果酸酶，尤其是ME2/ME3，作为可成药的癌症治疗靶点。对NPD-389金属结合模式以及FLA隐蔽/变构结合口袋的结构阐明，为效力和同工型选择性的合理优化提供了坚实基础。选择性ME抑制剂——无论是同工型特异性的还是线粒体靶向的——有望作为检查点抑制剂或化疗的辅助手段，实现更有效的、以代谢为导向的癌症治疗。
参考文献：1.Heon, J., Slayton, M., Krinkel, B., 等，苹果酸酶2、从头丝氨酸合成与苹果酸-天冬氨酸穿梭之间的相互作用驱动三阴性乳腺癌的代谢适应。Cancer & Metabolism，2025。
查看英文原文 English abstract
Background: Cancer remains a global health challenge and urgently requires therapies that improve clinical outcomes and patient quality of life. Tumor cells commonly reprogram metabolism to sustain proliferation and survival, notably by increasing glutamine dependence and upregulating mitochondrial malic enzyme 2 (ME2), which produces pyruvate and NAD(P)H. ME2 is overexpressed in pancreatic, melanoma, and lung cancers, making it a compelling therapeutic target that remains underexplored.
Methods: Recombinant human ME1, ME2, and ME3 were expressed and kinetically characterized in the presence and absence of inhibitors. We solved a complete set of X-ray crystal structures for the three isoforms with a potent malic enzyme inhibitor bound, revealing ligand and metal coordination. These structures guided virtual screening of a curated library of up to 14 million drug-like and fragment molecules to identify novel malic enzyme inhibitors. Biochemical hits were advanced to cellular assays to evaluate efficacy; lead compounds NPD-389 and FLA were tested for antiproliferative activity in melanoma and triple-negative breast cancer cell lines.
Results: Kinetic analyses show distinct activity and inhibition patterns across ME isoforms. X-ray crystallography visualized the potent, isoform-nonselective inhibitor NPD-389 bound in a metal-coordinating mode and captured an unexpected malic enzyme conformation. Structure-based virtual screening against this conformation identified multiple novel scaffolds with biochemical inhibitory activity. One scaffold, FLA, exhibited a unique selectivity profile and was found bound to ME2 in a previously cryptic pocket that rearranges upon ligand engagement and sits adjacent to the NAD + cofactor and malate-binding site. In a panel of melanoma and triple-negative breast cancer cell lines, NPD-389 and FLA reduced proliferation in most models, supporting their potential as chemical leads for further development.
Conclusions: These results establish mitochondrial malic enzymes, particularly ME2/ME3, as tractable targets for cancer therapy. Structural elucidation of NPD-389's metal-binding mode and of FLA's cryptic/allosteric binding pocket provides a robust foundation for rational optimization of potency and isoform selectivity. Selective ME inhibitors-either isoform-specific or mitochondrially targeted-have potential as adjuncts to checkpoint inhibitors or chemotherapy, enabling more effective, metabolism-directed cancer treatment.
References: 1.Heon, J., Slayton, M., Krinkel, B., et al., Interplay Between Malic Enzyme 2, de novo Serine Synthesis, and the Malate-Aspartate Shuttle Drives Metabolic Adaptation in Triple-Negative Breast Cancer. Cancer & Metabolism , 2025.
利益披露 Disclosure
B. A. Krinkel, None..
Y. Yosaatmadja, None.