PubChem Tanimoto Similarity Library — NADD-Derived Focused Compound Set for MurA Virtual Screening

This dataset contains 2,751 compounds retrieved from the PubChem database via 2D structural similarity search using N-acetyl-dopamine dimer (NADD, CID: 10643865) as the query compound with a Tanimoto coefficient threshold of ≥0.85. The search was performed using the PubChem FastSimilarity2D API and targets structural analogs of NADD for virtual screening against MurA, the first committed enzyme in peptidoglycan biosynthesis of Paenibacillus larvae. The dataset was generated as part of a computational drug discovery study investigating honey bee sclerotization products as potential inhibitors of bacterial cell wall synthesis. NADD was identified as the lead compound through molecular docking (−9.525 kcal/mol) and MM-GBSA calculations (ΔG = −27.32 kcal/mol for the top library hit), with the focused library serving to validate the catecholamine/benzodioxin scaffold as a genuine pharmacophore for MurA inhibition.本数据集包含2751个化合物，均通过以N-乙酰多巴胺二聚体（N-acetyl-dopamine dimer, NADD，CID: 10643865）作为查询化合物，基于Tanimoto系数（Tanimoto coefficient）阈值≥0.85的二维结构相似性搜索，从PubChem数据库中检索得到。本次搜索使用PubChem FastSimilarity2D API完成，目标为获取NADD的结构类似物，用于针对MurA的虚拟筛选——MurA是幼虫芽孢杆菌（Paenibacillus larvae）肽聚糖生物合成途径中的首个关键酶。 本数据集是一项计算药物发现研究的产物，该研究旨在探索蜜蜂鞣化产物作为细菌细胞壁合成潜在抑制剂的潜力。研究通过分子对接（结合能为-9.525 kcal/mol）与MM-GBSA计算（顶级化合物库命中物的自由能变化ΔG = -27.32 kcal/mol），将NADD鉴定为先导化合物；本次构建的聚焦化合物库用于验证儿茶酚胺/苯并二噁英骨架（catecholamine/benzodioxin scaffold）可作为MurA抑制的真实药效团（pharmacophore）。