Department of Chemistry, Faculty of Science, Damietta University, Damietta, Egypt.
Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, N9B 3P4, Canada.
J Mol Graph Model. 2022 Sep;115:108224. doi: 10.1016/j.jmgm.2022.108224. Epub 2022 May 23.
β-Hydroxynorvaline (βHNV) is unnatural amino acid structurally identical to the threonine amino acid with branched ethyl group instead of threonine's methyl. It is a known competitive inhibitor that readily bind to Threonyl-tRNA synthetase's (ThrRS) catalytic site and blocks its function. In this work, we utilized a combination of Molecular Dynamics simulation (MD) and Quantum Mechanics/Molecular Mechanics (QM/MM) methodologies to provide mechanistic insights into its inhibition reaction for ThrRS. Due to the presence of Zn(II) with its Lewis acidity character, only the ionized form of βHNV gives an enzymatically feasible energy barrier. Furthermore, in consistence with the homochirality behavior of this active site, we observed only one conformation of βHNV that could be acylated in the active site of ThrRS. Considering these new findings together with the recent search for new antibacterial agents, our findings should guide pharmaceutical scientists with further knowledge regarding the chemical nature of this drug. Moreover, benchmarking analysis of the utilized DFT functional has also been performed to identify the impact of various DFT functionals on representing the geometry and kinetics of our system. Notably, our Zn(II) containing chemical models are found to be responsive to the %HF contribution included together with the dispersion correction. Importantly, the BP86(0%HF)-D3 functional is found to display the greatest impact on the rate-limiting step kinetically. The crucial role played by Zn(II) is further enriched when its mutation with the chemically similar Cd(II) led to dramatic difference via obtaining less feasible reaction mechanism from thermodynamic and kinetic perspectives.
β-羟基正缬氨酸（βHNV）是一种结构上与苏氨酸相同的非天然氨基酸，但其支链乙基取代了苏氨酸的甲基。它是一种已知的竞争性抑制剂，能够轻易地与苏氨酰-tRNA 合成酶（ThrRS）的催化位点结合并阻断其功能。在这项工作中，我们结合使用分子动力学模拟（MD）和量子力学/分子力学（QM/MM）方法，为 ThrRS 的抑制反应提供了机制上的见解。由于存在具有路易斯酸性的 Zn(II)，只有βHNV 的离子化形式才能给出具有酶促可行性的能量势垒。此外，与该活性位点的手性一致性一致，我们仅观察到一种可以在 ThrRS 的活性位点中酰化的βHNV 构象。考虑到这些新发现以及最近对新型抗菌剂的研究，我们的发现应该为药物化学家提供关于该药物化学性质的进一步知识。此外，还对所使用的 DFT 功能进行了基准分析，以确定各种 DFT 功能在代表我们系统的几何形状和动力学方面的影响。值得注意的是，我们含有 Zn(II)的化学模型对包含的 %HF 贡献以及弥散校正具有响应性。重要的是，BP86(0%HF)-D3 功能对速率限制步骤的动力学影响最大。当其与化学相似的 Cd(II)发生突变时，Zn(II)的关键作用进一步得到了丰富，从热力学和动力学的角度来看，该突变导致反应机制变得不太可行。
