School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, Guangdong, China.
Regenerative Bio Inc., Hangzhou 310059, Zhejiang, China.
Int J Biol Macromol. 2024 Mar;262(Pt 2):130131. doi: 10.1016/j.ijbiomac.2024.130131. Epub 2024 Feb 12.
Deleted in breast cancer 1 (DBC1) is a human nuclear protein that modulates the activities of various proteins involved in cell survival and cancer progression. Oxidized form of nicotinamide adenine dinucleotide (NAD) is suggested to bind to the Nudix homology domains (NHDs) of DBC1, thereby regulating DBC1-Poly (ADP-ribose) polymerase 1 (PARP1) interactions, resulting in the restoration of DNA repair. Using Nuclear Magnetic Resonance (NMR) and Isothermal Titration Calorimetry (ITC), we confirmed NAD and its precursor nicotinamide mononucleotide (NMN) both bind the NHD domain of DBC1 (DBC1). NAD likely interacts with DBC1 through hydrogen bonding, with a binding affinity (8.99 μM) nearly twice that of NMN (17.0 μM), and the key binding sites are primarily residues E363 and D372, in the agreement with Molecular Docking experiments. Molecular Dynamics (MD) simulation further demonstrated E363 and D372's anchoring role in the binding process. Additional mutagenesis experiments of E363 and D372 confirmed their critical involvement of ligand-protein interactions. These findings lead to a better understanding of how NAD and NMN regulate DBC1, thereby offering insights for the development of targeted therapies and drug research focused on DBC1-associated tumors.
乳腺癌缺失基因 1（DBC1）是一种人类核蛋白，可调节细胞存活和癌症进展过程中涉及的各种蛋白质的活性。烟酰胺腺嘌呤二核苷酸（NAD）的氧化形式被认为与 DBC1 的 Nudix 同源结构域（NHD）结合，从而调节 DBC1-多聚（ADP-核糖）聚合酶 1（PARP1）相互作用，导致 DNA 修复的恢复。我们使用核磁共振（NMR）和等温滴定量热法（ITC）证实 NAD 和其前体烟酰胺单核苷酸（NMN）都与 DBC1 的 NHD 结构域（DBC1）结合。NAD 可能通过氢键与 DBC1 相互作用，结合亲和力（8.99 μM）接近 NMN（17.0 μM）的两倍，关键结合位点主要是残基 E363 和 D372，与分子对接实验一致。分子动力学（MD）模拟进一步证明了 E363 和 D372 在结合过程中的锚定作用。E363 和 D372 的额外突变实验证实了它们在配体-蛋白相互作用中的关键作用。这些发现有助于更好地了解 NAD 和 NMN 如何调节 DBC1，从而为针对 DBC1 相关肿瘤的靶向治疗和药物研究提供了新的思路。
