Singh Rahul, Purohit Rituraj
Structural Bioinformatics Lab, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, Himachal Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
Structural Bioinformatics Lab, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, Himachal Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
Biochem Biophys Res Commun. 2025 Apr 5;756:151575. doi: 10.1016/j.bbrc.2025.151575. Epub 2025 Mar 6.
Mycobacterium tuberculosis (MTB), the pathogen responsible for tuberculosis (TB), remains a significant global health concern, especially with the growing prevalence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains. This study focuses on understanding the molecular basis of pyrazinamide (PZA) resistance, particularly mutations in the pyrazinamidase (Pzase) enzyme, including D8G, H71R, K96T, and S104R. We used computational methods to explore the effects of bioactive compounds on these PZA-resistant mutations. The structures of wild-type (WT) Pzase and its mutant variants were prepared, and molecular docking simulations were carried out using the CDOCKER protocol to assess potential binding interactions. To evaluate the stability of these interactions, we performed 0.5 μs molecular dynamics (MD) simulations followed by MM-PBSA analysis to calculate the binding free energies. Our results showed that garcinone D and neodiospyrin had stronger binding affinities than the reference molecule, pyrazinoic acid (POA), across both WT and mutant forms of Pzase. These compounds demonstrated lower Root Mean Square Deviation (RMSD) and radius of gyration (Rg) values, suggesting more stable binding interactions. Further validation through steered molecular dynamics (SMD) simulations indicated that garcinone D and neodiospyrin required significantly higher pulling forces to dissociate from the binding site compared to POA. Additionally, umbrella sampling simulations revealed more negative binding free energies for these two compounds, reinforcing their strong interaction with Pzase. These findings position garcinone D and neodiospyrin as promising candidates for the development of new treatments for MDR-TB and XDR-TB, offering a potential strategy to combat drug-resistant TB. This study provides valuable insights into the binding mechanisms and stability of these compounds, advancing the search for novel anti-TB therapies.
结核分枝杆菌（MTB）是导致结核病（TB）的病原体，仍然是全球重大的健康问题，尤其是随着耐多药（MDR）和广泛耐药（XDR）菌株的日益流行。本研究聚焦于理解吡嗪酰胺（PZA）耐药性的分子基础，特别是吡嗪酰胺酶（Pzase）中的突变，包括D8G、H71R、K96T和S104R。我们使用计算方法来探究生物活性化合物对这些PZA耐药突变的影响。制备了野生型（WT）Pzase及其突变变体的结构，并使用CDOCKER协议进行分子对接模拟，以评估潜在的结合相互作用。为了评估这些相互作用的稳定性，我们进行了0.5微秒的分子动力学（MD）模拟，随后进行MM-PBSA分析以计算结合自由能。我们的结果表明，藤黄双黄酮D和新柿叶素在Pzase的野生型和突变型形式中均比参考分子吡嗪酸（POA）具有更强的结合亲和力。这些化合物表现出更低的均方根偏差（RMSD）和回转半径（Rg）值，表明结合相互作用更稳定。通过引导分子动力学（SMD）模拟的进一步验证表明，与POA相比，藤黄双黄酮D和新柿叶素从结合位点解离需要显著更高的拉力。此外，伞形采样模拟显示这两种化合物的结合自由能更负，进一步证明了它们与Pzase的强相互作用。这些发现使藤黄双黄酮D和新柿叶素成为耐多药结核病和广泛耐药结核病新治疗方法开发的有希望的候选药物，为对抗耐药结核病提供了一种潜在策略。本研究为这些化合物的结合机制和稳定性提供了有价值的见解，推动了新型抗结核疗法的探索。
