Structural and Molecular Dynamics of Mycobacterium tuberculosis Malic Enzyme, a Potential Anti-TB Drug Target.
Structural and Molecular Dynamics of Mycobacterium tuberculosis Malic Enzyme, a Potential Anti-TB Drug Target.
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DOI：
10.1021/acsinfecdis.0c00735
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发表时间：
2021-01-08
影响因子：
5.3
通讯作者：
Goulding CW
中科院分区：
文献类型：
--
作者：
Burley KH;Cuthbert BJ;Basu P;Newcombe J;Irimpan EM;Quechol R;Foik IP;Mobley DL;Beste DJV;Goulding CW
结核病（TB）是世界范围内最致命的细菌性传染病。众所周知，它很难治疗，需要数月的抗生素鸡尾酒疗法。结核病病原体结核分枝杆菌（Mtb）的致密蜡质外膜是阻止抗生素摄入的强大屏障。随后，参与维持Mtb细胞壁完整性的酶是有希望的药物靶标。最近，我们证明了Mtb缺乏苹果酸酶（MEZ）改变了细胞壁脂质组成，并减弱了巨噬细胞的摄取。这些结果表明MEZ通过以NAD（P）H的形式提供还原剂而有助于脂质生物合成。在这里，我们提出的X射线晶体结构的MEZ到3.6纳米。我们使用生物化学测定来证明MEZ在溶液中是二聚体的，并评估pH和变构调节剂对其动力学和热稳定性的影响。为了评估MEZ与其底物苹果酸和辅因子Mn 2+和NAD（P）+之间的相互作用，我们进行了一系列分子动力学（MD）模拟。首先，MD分析证实了我们的经验观察，MEZ是异常灵活的，即使加入底物和辅因子，仍然存在。其次，MD模拟揭示了二聚MEZ亚基在开放和闭合状态之间交替，并且MEZ可以以多种构象稳定地结合其NAD（P）+辅因子，包括无活性的紧凑NAD+形式。MEZ的结构和来自其动力学的见解可以一起用于设计靶向Mtb而不是人苹果酸酶同系物的MEZ抑制剂。这表明具有GER基序的真核大亚基苹果酸酶（ME）是四聚体，而具有非GER基序的原核ME是二聚体，包括Mtb。区别格尔和非格尔基序形成了潜在的紧密NAD+加合物的基础，该加合物可用于靶向Mtb而非人ME的基于结构的药物设计。
Tuberculosis (TB) is the most lethal bacterial infectious disease worldwide. It is notoriously difficult to treat, requiring a cocktail of antibiotics administered over many months. The dense, waxy outer membrane of the TB-causing agent, Mycobacterium tuberculosis (Mtb), acts as a formidable barrier against uptake of antibiotics. Subsequently, enzymes involved in maintaining the integrity of the Mtb cell wall are promising drug targets. Recently, we demonstrated that Mtb lacking malic enzyme (MEZ) has altered cell wall lipid composition and attenuated uptake by macrophages. These results suggest that MEZ contributes to lipid biosynthesis by providing reductants in the form of NAD(P)H. Here, we present the X-ray crystal structure of MEZ to 3.6 Å. We use biochemical assays to demonstrate MEZ is dimeric in solution and to evaluate the effects of pH and allosteric regulators on its kinetics and thermal stability. To assess the interactions between MEZ and its substrate malate and cofactors, Mn2+ and NAD(P)+, we ran a series of molecular dynamics (MD) simulations. First, the MD analysis corroborates our empirical observations that MEZ is unusually flexible, which persists even with the addition of substrate and cofactors. Second, the MD simulations reveal that dimeric MEZ subunits alternate between open and closed states, and that MEZ can stably bind its NAD(P)+ cofactor in multiple conformations, including an inactive, compact NAD+ form. Together the structure of MEZ and insights from its dynamics can be harnessed to inform the design of MEZ inhibitors that target Mtb and not human malic enzyme homologs. This shows that the eukaryotic large-subunit malic enzymes (MEs) which have the GER-motif are tetrameric and the prokaryotic MEs with a non-GER motif are dimeric including Mtb. The distinguishing GER and non-GER motif forms the basis for a potential compact NAD+ adduct that may be used for structure-based drug design that would target Mtb and not human ME.
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影响因子：
2.9
作者：
Coleman, DE;Rao, GSJ;Harris, BG
通讯作者：
Harris, BG
影响因子：
4.4
作者：
Costa MG;Benetti-Barbosa TG;Desdouits N;Blondel A;Bisch PM;Pascutti PG;Batista PR
通讯作者：
Batista PR
DOI：
10.1107/s0907444904019158
发表时间：
2004-12-01
影响因子：
2.2
作者：
Emsley, P;Cowtan, K
通讯作者：
Cowtan, K
DOI：
10.1107/s0907444901007120
发表时间：
2001-07-01
影响因子：
2.2
作者：
Guillot, B;Lecomte, C;Jelsch, C
通讯作者：
Jelsch, C
影响因子：
4.1
作者：
CHANG, GG;HUANG, TM;CHANG, TC
通讯作者：
CHANG, TC