Mechanism of Ligand Discrimination by the NMT1 Riboswitch
Mechanism of Ligand Discrimination by the NMT1 Riboswitch
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DOI：
10.1021/acs.jcim.3c00835
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发表时间：
2023-07
影响因子：
5.6
通讯作者：
Amit Kumar;Harish Vashisth
中科院分区：
文献类型：
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作者：
Amit Kumar;Harish Vashisth
核糖开关是信使核糖核酸（mRNA）中保守的功能结构域，几乎只存在于细菌中。它们通过特异性结合小分子来调控氨基酸以及诸如辅酶、核碱基及其衍生物等必需代谢物的生物合成和运输。由于它们能够精确区分不同的同源分子，并且在细菌中普遍存在，核糖开关已成为潜在的抗菌药物靶点，可能提供具有新型作用机制的急需的抗生素。在这项工作中，我们报道了一种被称为NMT1核糖开关的RNA基序对嘌呤降解过程中产生的四种氧化产物（黄嘌呤（XAN）、氮杂鸟嘌呤（AZA）、尿酸（UAC）和次黄嘌呤（HPA））的识别机制。具体而言，我们通过计算核糖开关配体结合口袋中关键核碱基突变时的自由能变化，研究了核糖开关与氧化代谢物之间的物理相互作用。我们发现静电相互作用对该核糖开关区分配体至关重要。突变的相对结合自由能进一步表明，一些突变还可以增强配体（AZA、UAC和HPA）的结合亲和力。这些机制细节在设计针对核糖开关的新型化合物时也可能具有相关性。
Riboswitches are conserved functional domains in mRNA that almost exclusively exist in bacteria. They regulate the biosynthesis and transport of amino acids and essential metabolites such as coenzymes, nucleobases, and their derivatives by specifically binding small molecules. Due to their ability to precisely discriminate between different cognate molecules as well as their common existence in bacteria, riboswitches have become potential antibacterial drug targets that could deliver urgently needed antibiotics with novel mechanisms of action. In this work, we report the recognition mechanisms of four oxidization products (XAN, AZA, UAC, and HPA) generated during purine degradation by an RNA motif termed the NMT1 riboswitch. Specifically, we investigated the physical interactions between the riboswitch and the oxidized metabolites by computing the changes in the free energy on mutating key nucleobases in the ligand binding pocket of the riboswitch. We discovered that the electrostatic interactions are central to ligand discrimination by this riboswitch. The relative binding free energies of the mutations further indicated that some of the mutations can also strengthen the binding affinities of the ligands (AZA, UAC, and HPA). These mechanistic details are also potentially relevant in the design of novel compounds targeting riboswitches.