Antibiotic resistance is a major threat to global public health. β-lactamases, which catalyze breakdown of β-lactam antibiotics, are a principal cause. Metallo β-lactamases (MBLs) represent a particular challenge because they hydrolyze almost all β-lactams and to date no MBL inhibitor has been approved for clinical use. Molecular simulations can aid drug discovery, for example, predicting inhibitor complexes, but empirical molecular mechanics (MM) methods often perform poorly for metalloproteins. Here we present a multiscale approach to model thiol inhibitor binding to IMP-1, a clinically important MBL containing two catalytic zinc ions, and predict the binding mode of a 2-mercaptomethyl thiazolidine (MMTZ) inhibitor. Inhibitors were first docked into the IMP-1 active site, testing different docking programs and scoring functions on multiple crystal structures. Complexes were then subjected to molecular dynamics (MD) simulations and subsequently refined through QM/MM optimization with a density functional theory (DFT) method, B3LYP/6-31G(d), increasing the accuracy of the method with successive steps. This workflow was tested on two IMP-1:MMTZ complexes, for which it reproduced crystallographically observed binding, and applied to predict the binding mode of a third MMTZ inhibitor for which a complex structure was crystallographically intractable. We also tested a 12-6-4 nonbonded interaction model in MD simulations and optimization with a SCC-DFTB QM/MM approach. The results show the limitations of empirical models for treating these systems and indicate the need for higher level calculations, for example, DFT/MM, for reliable structural predictions. This study demonstrates a reliable computational pipeline that can be applied to inhibitor design for MBLs and other zinc-metalloenzyme systems.

中文翻译：

---

预测金属β-内酰胺酶抑制剂结合模式的多尺度方法

抗生素耐药性是全球公共卫生的主要威胁。催化 β-内酰胺类抗生素分解的 β-内酰胺酶是主要原因。金属 β-内酰胺酶 (MBL) 代表了一个特殊的挑战，因为它们水解几乎所有的 β-内酰胺，并且迄今为止还没有 MBL 抑制剂被批准用于临床。分子模拟可以帮助药物发现，例如，预测抑制剂复合物，但经验分子力学 (MM) 方法通常对金属蛋白表现不佳。在这里，我们提出了一种多尺度方法来模拟硫醇抑制剂与 IMP-1 的结合，IMP-1 是一种临床上重要的 MBL，含有两个催化锌离子，并预测 2-巯基甲基噻唑烷 (MMTZ) 抑制剂的结合模式。抑制剂首先对接到 IMP-1 活性位点，在多个晶体结构上测试不同的对接程序和评分功能。然后对复合物进行分子动力学 (MD) 模拟，随后使用密度泛函理论 (DFT) 方法 B3LYP/6-31G(d) 通过 QM/MM 优化进行精炼，通过连续步骤提高方法的准确性。该工作流程在两个 IMP-1:MMTZ 复合物上进行了测试，它再现了晶体学观察到的结合，并应用于预测复杂结构在晶体学上难以处理的第三种 MMTZ 抑制剂的结合模式。我们还使用 SCC-DFTB QM/MM 方法在 MD 模拟和优化中测试了 12-6-4 非键合相互作用模型。结果显示了处理这些系统的经验模型的局限性，并表明需要更高级别的计算，例如 DFT/MM，用于可靠的结构预测。本研究展示了一个可靠的计算管道，可应用于 MBL 和其他锌金属酶系统的抑制剂设计。