Zhao Xue Zhi, Wang Wenjie, Suazo Kiall F, Al Mahmud Md Rasel, Agama Keli, Lountos George T, Andresson Thorkell, Pommier Yves, Burke Terrence R
Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA.
Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
Sci Rep. 2025 Jul 21;15(1):26510. doi: 10.1038/s41598-025-12503-8.
Tyrosyl-DNA phosphodiesterase 1 (TDP1) is an important therapeutic target. We recently reported several crystal structures of TDP1 with small molecules bound within the catalytic pocket. These molecules bind by forming hydrogen bonds with residues of the catalytic HKN motifs. Guided by these interactions, in our current work, we used the MolSoft ICM Pro suite of software to perform a virtual screen of the publicly available DrugBank 5.0 (3449 structures) for the ability to bind to the TDP1 catalytic pocket. Among compounds identified as giving good binding scores were several β-lactams. The β-lactam pharmacophore serves as a key component in a range of antibiotics. We subjected a subset of the β-lactam hits to gel-based TDP1 fluorescence catalytic assays and established that certain members showed micromolar TDP1 inhibition. In follow-up, we evaluated a commercially available library of 90 β-lactam antibiotics. This led to our identification of additional β-lactams having micromolar TDP1 inhibitory potencies. In particular, cephalosporin C showed single-digit micromolar TDP1 IC values. Since β-lactams can form covalent bonds with serine residues in target penicillin-binding proteins (PBPs), we performed docking studies with cephalosporin C, which showed that it bound within the catalytic pocket and extended into the DNA substrate binding channel. Importantly, the modeling indicated that both noncovalent and covalent binding modes were theoretically possible. Surface plasmon resonance analysis demonstrated its non-covalent binding mode. Thus, β-lactams may serve as a new and potentially useful platform to design TDP1-binding ligands that interact with the catalytic pocket and extend into the DNA substrate binding channel.
酪氨酰 - DNA磷酸二酯酶1（TDP1）是一个重要的治疗靶点。我们最近报道了TDP1的几个晶体结构，其催化口袋内结合有小分子。这些分子通过与催化HKN基序的残基形成氢键而结合。在这些相互作用的指导下，在我们目前的工作中，我们使用MolSoft ICM Pro软件套件对公开可用的DrugBank 5.0（3449个结构）进行虚拟筛选，以评估其与TDP1催化口袋的结合能力。在被鉴定为具有良好结合分数的化合物中，有几种β-内酰胺类药物。β-内酰胺药效基团是一系列抗生素的关键成分。我们对一部分β-内酰胺类命中化合物进行了基于凝胶的TDP1荧光催化测定，并确定某些成员表现出微摩尔级别的TDP1抑制作用。接下来，我们评估了一个包含90种β-内酰胺类抗生素的商业文库。这使我们鉴定出了其他具有微摩尔级TDP1抑制效力的β-内酰胺类药物。特别是，头孢菌素C显示出个位数微摩尔的TDP1 IC值。由于β-内酰胺类药物可以与靶标青霉素结合蛋白（PBPs）中的丝氨酸残基形成共价键，我们对头孢菌素C进行了对接研究，结果表明它结合在催化口袋内并延伸到DNA底物结合通道。重要的是，模型表明非共价和共价结合模式在理论上都是可能的。表面等离子体共振分析证明了其非共价结合模式。因此，β-内酰胺类药物可能成为一个新的且潜在有用的平台，用于设计与催化口袋相互作用并延伸到DNA底物结合通道的TDP1结合配体。
