Quaye Joanna Afokai, Gadda Giovanni
Department of Chemistry, Georgia State University, Atlanta, Georgia 30302-3965, United States.
Department of Biology, Georgia State University, Atlanta, Georgia 30302-3965, United States.
Biochemistry. 2025 Oct 7;64(19):4170-4180. doi: 10.1021/acs.biochem.5c00408. Epub 2025 Sep 8.
d-2-Hydroxyglutarate dehydrogenase (D2HGDH) has recently received considerable attention due to the involvement of d-2-hydroxyglutarate in various medical conditions. This enzyme has been reported to diverge in substrate scope depending on whether its source is prokaryotic or eukaryotic. The D2HGDH from , D2HGDH, is of particular interest due to its requirement for survival via the l-serine biosynthesis pathway and its potential use as a therapeutic target against the bacterium. The enzyme, which is active on d-2-hydroxyglutarate (D2HG) and d-malate, is a Zn- and FAD-dependent dehydrogenase that employs metal-triggered flavin reduction in its catalytic mechanism. While D2HGDH is the most extensively studied D2HGDH homologue, no studies have investigated the ligand-binding modalities in the enzyme, and─for that matter─any D2HGDH homologue. This study investigated the inhibition profiles of D2HGDH by various D2HG and d-malate analogues. The study demonstrates that stereochemistry and functional groups at the C2 position of ligands are key determinants of binding to D2HGDH. The enzyme recognizes d-isomeric ligands as substrates, with l-isomers acting as reversible inhibitors. Ligand binding requires bidentate coordination with the active site Zn cofactor, with longer chain ligands and polar ligands having lower and Δ values due to enhanced interactions with the highly polar active site. Hydrophobic and van der Waals interactions also contribute to ligand binding in D2HGDH. The study concludes that D2HGDH can be reversibly inhibited, providing a foundation for biochemical studies on D2HGDH inhibitors, with direct applications to D2HG biosensor development.
由于D-2-羟基戊二酸参与多种医学病症，D-2-羟基戊二酸脱氢酶（D2HGDH）最近受到了广泛关注。据报道，这种酶的底物范围因其来源是原核生物还是真核生物而有所不同。来自[具体来源未提及]的D2HGDH因其通过L-丝氨酸生物合成途径生存的需求以及作为针对该细菌的治疗靶点的潜在用途而特别受关注。该酶对D-2-羟基戊二酸（D2HG）和D-苹果酸具有活性，是一种依赖锌和黄素腺嘌呤二核苷酸（FAD）的脱氢酶，其催化机制采用金属触发的黄素还原。虽然D2HGDH是研究最广泛的D2HGDH同源物，但尚未有研究调查该酶中的配体结合模式，就此而言，也没有对任何D2HGDH同源物进行过此类研究。本研究调查了各种D2HG和D-苹果酸类似物对D2HGDH的抑制谱。研究表明，配体C2位置的立体化学和官能团是与D2HGDH结合的关键决定因素。该酶将D-异构体配体识别为底物，而L-异构体则作为可逆抑制剂。配体结合需要与活性位点的锌辅因子进行双齿配位，由于与高度极性的活性位点的相互作用增强，较长链配体和极性配体的[具体参数未提及]和Δ值较低。疏水相互作用和范德华相互作用也有助于D2HGDH中的配体结合。研究得出结论，D2HGDH可以被可逆抑制，这为D2HGDH抑制剂的生化研究提供了基础，并直接应用于D2HG生物传感器的开发。
