Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa.
Protein J. 2020 Apr;39(2):106-117. doi: 10.1007/s10930-020-09885-1.
Therapeutic targeting of folate biosynthetic pathway has recently been explored as a viable strategy in the treatment of tuberculosis. The bioactive metabolite substrate of Para-amino salicyclic acid (PAS-M) reportedly dual-targets dihydrofolate reductase (DHFR) and flavin-dependent thymidylate synthase (FDTS), two essential enzymes in folate biosynthetic pathway. However, the molecular mechanisms and structural dynamics of this dual inhibitory activity of the PAS-M remain elusive. Molecular dynamics simulations revealed that binding of PAS-M towards DHFR is characterized by a recurrence of strong conventional hydrogen bond interactions between a peculiar DHFR binding site residue (Asp27) and the 2-amino-decahydropteridin-4-ol group of PAS-M. Similarly, the binding of PAS-M towards FDTS also involved consistent strong conventional hydrogen bond interactions between some specific residues (Tyr101, Arg172, Thr4, Gln103, Arg87 and Gln106) and, the 2-amino-decahydropteridin-4-ol group, thus establishing the cruciality of the group. Structural dynamics of the bound complexes of both enzymes revealed that, upon binding, PAS-M is anchored at the entrance of hydrophobic pockets by strong hydrogen bond interactions while the rest of the structure gains access to deeper hydrophobic residues to engage in favorable interactions. Further analysis of atomistic changes of both enzymes showed increased C-α atom deviations as well as an increase C-α atoms radius of gyration consistent with structural disorientations. These conformational changes possibly interfered with the biological functions of the enzymes and hence their inhibition as experimentally reported. Structural Insights provided could open up a novel paradigm of structure-based design of multi-targeting inhibitors of biological targets in the folate biosynthetic pathway toward tuberculosis therapy.
最近，人们探索靶向叶酸生物合成途径作为治疗结核病的一种可行策略。据报道，对氨基水杨酸（PAS-M）的生物活性代谢物底物双重靶向二氢叶酸还原酶（DHFR）和黄素依赖性胸苷酸合成酶（FDTS），这两种都是叶酸生物合成途径中的必需酶。然而，PAS-M 的这种双重抑制活性的分子机制和结构动力学仍然难以捉摸。分子动力学模拟表明，PAS-M 与 DHFR 的结合特征是在 PAS-M 的特殊 DHFR 结合位点残基（天冬氨酸 27）和 2-氨基-十氢喋呤-4-醇基团之间存在反复的强常规氢键相互作用。同样，PAS-M 与 FDTS 的结合也涉及一些特定残基（酪氨酸 101、精氨酸 172、苏氨酸 4、谷氨酰胺 103、精氨酸 87 和谷氨酰胺 106）和 2-氨基-十氢喋呤-4-醇基团之间的一致强常规氢键相互作用，从而确立了该基团的重要性。两种酶的结合复合物的结构动力学表明，结合后，PAS-M 通过强氢键相互作用被锚定在疏水性口袋的入口处，而其余结构则进入更深的疏水性残基以进行有利的相互作用。对两种酶的原子变化的进一步分析表明，C-α 原子的偏差增加以及 C-α 原子的回转半径增加，与结构的定向变化一致。这些构象变化可能干扰了酶的生物学功能，因此正如实验报道的那样，它们被抑制。提供的结构见解可能为基于结构的设计开辟一个新的范例，用于设计针对叶酸生物合成途径中的生物靶标作为结核病治疗的多靶向抑制剂。
