NDM-1 Aryl Bisphosphonate Inhibitor Discovery: Structure-Based Virtual Screening, Molecular Dynamics, and Bonded-Zinc Validation Datasets

This dataset supports the study entitled “Structure-based virtual screening and molecular dynamics identify an aryl bisphosphonate as a candidate inhibitor of New Delhi metallo-β-lactamase 1” (Yeşil & Yeşil, 2026). It provides all data and scripts necessary to reproduce the computational workflow and figures reported in the manuscript. The dataset comprises a structure-based virtual screening pipeline targeting NDM-1 (PDB ID: 5ZGE) applied to 20,546 ADMET-filtered compounds derived from DrugBank v5.1 and COCONUT v2.0, GAFF2/AM1-BCC parameterisation files for the candidate inhibitor DB04204, and molecular dynamics simulations including three independent 1 μs trajectories generated using Li/Merz 12–6 non-bonded zinc parameters with the AMBER ff19SB force field and TIP3P water model, as well as three independent 500 ns trajectories generated using the CADM bonded-zinc approach (gen_seed = 200, 137, 271) to assess parameterisation robustness. The dataset further includes re-docking validation against taniborbactam (PDB ID: 6RMF) and L-captopril (PDB ID: 4EXS), together with all analysis scripts and per-figure CSV files used to generate the reported results. Trajectories are provided as solvent-stripped GROMACS .xtc files (50 ps stride) to reduce storage requirements, with full system reconstruction enabled via the accompanying topology and coordinate files. All simulations and analyses were performed using GROMACS 2024.5, AmberTools 23, RDKit 2024.03, gnina 1.3, and MDAnalysis 2.10. The dataset is released under the Creative Commons Attribution 4.0 International (CC BY 4.0) license.本数据集支撑题为《基于结构的虚拟筛选与分子动力学研究发现芳基双膦酸酯作为新德里金属β-内酰胺酶1候选抑制剂》（Yeşil & Yeşil, 2026）的研究工作，提供了复现该论文中报道的计算流程与所有图表所需的全部数据与脚本。本数据集包含针对NDM-1（PDB ID：5ZGE）的基于结构的虚拟筛选流程，该流程针对从DrugBank v5.1与COCONUT v2.0数据库中筛选得到的20546个经过ADMET（吸收、分布、代谢、排泄、毒性）过滤的化合物；候选抑制剂DB04204的GAFF2/AM1-BCC参数化文件；以及两类分子动力学模拟轨迹：其一为使用Li/Merz 12–6非键合锌参数、AMBER ff19SB力场与TIP3P水模型构建的3条独立的1 μs轨迹，其二为采用CADM键合锌方法（生成种子gen_seed=200、137、271）构建的3条独立的500 ns轨迹，用于评估参数化方案的鲁棒性。本数据集还包含针对他尼硼巴坦（taniborbactam，PDB ID：6RMF）与L-卡托普利（L-captopril，PDB ID：4EXS）的重新对接验证数据，以及用于生成报道结果的全部分析脚本与分图CSV文件。为降低存储需求，轨迹以剥离溶剂的GROMACS .xtc文件（步长50 ps）形式提供，可通过配套的拓扑与坐标文件完整重建模拟体系。所有模拟与分析工作均使用GROMACS 2024.5、AmberTools 23、RDKit 2024.03、gnina 1.3与MDAnalysis 2.10完成。本数据集采用知识共享署名4.0国际（CC BY 4.0）协议发布。