Kumar Ashutosh, Ito Akihiro, Takemoto Misao, Yoshida Minoru, Zhang Kam Y J
Zhang Initiative Research Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
J Chem Inf Model. 2014 Mar 24;54(3):870-80. doi: 10.1021/ci4007134. Epub 2014 Feb 19.
Small ubiquitin like modifier (SUMO) specific proteases (SENPs) are cysteine proteases that carry out the proteolytic processing of SUMO from its pro form as well as the deconjugation of SUMO from substrate proteins. SENPs are attractive targets for drug discovery due to their crucial role in the development of various diseases. However, the SENPs inhibitor discovery efforts were limited, and only a few inhibitors or activity based probes have been identified until now. Here, we report a new class of SENP2 inhibitors identified by a combination of structure based virtual screening and quantitative FRET based assay. Our virtual screening protocol initially involves the identification of small molecules that have similar shape and electrostatic properties with the conjugate of SUMO1 C-terminal residues and substrate lysine. Molecular docking was then used to prioritize these small molecules for a FRET based assay that quantifies their SENP2 endopeptidase activity. The initial round of virtual screening followed by FRET based assay has enabled the identification of eight compounds with >40% SENP2 inhibition at 30 μM compound concentration. Five of these compounds belong to two scaffolds containing a 1,2,5-oxadiazole core that represent a novel class of SENP2 inhibitors. To improve the inhibitory potency and explore the structure-activity relationship of these two 1,2,5-oxadiazole scaffolds, structurally related compounds were identified in another round of virtual screening. The biological assay results confirmed SENP2 inhibitory activity of these two scaffolds. The most potent compound of each scaffold showed an IC50 of 5.9 and 3.7 μM. Most of the compounds also inhibited closely related isoform SENP1, while no detectable inhibition on other proteases, such as papain and trypsin, was observed. Our study suggests that 1,2,5-oxadiazoles could be used as a starting point for the development of novel therapeutic agents against various diseases targeting SENPs.
小泛素样修饰物（SUMO）特异性蛋白酶（SENPs）是半胱氨酸蛋白酶，负责对SUMO前体形式进行蛋白水解加工，并将SUMO从底物蛋白上去共轭化。由于SENPs在多种疾病发展中起关键作用，因此是药物研发的有吸引力的靶点。然而，SENPs抑制剂的发现工作有限，到目前为止仅鉴定出少数抑制剂或基于活性的探针。在此，我们报告通过基于结构的虚拟筛选和基于定量FRET的测定相结合鉴定出的一类新型SENP2抑制剂。我们的虚拟筛选方案最初涉及鉴定与SUMO1 C末端残基和底物赖氨酸共轭物具有相似形状和静电性质的小分子。然后使用分子对接对这些小分子进行优先级排序，以进行基于FRET的测定，该测定可量化它们的SENP2内肽酶活性。第一轮虚拟筛选后进行基于FRET的测定，已鉴定出8种在30μM化合物浓度下对SENP2抑制率>40%的化合物。其中5种化合物属于两个含有1,2,5-恶二唑核心的支架，代表一类新型的SENP2抑制剂。为了提高抑制效力并探索这两个1,2,5-恶二唑支架的构效关系，在另一轮虚拟筛选中鉴定出结构相关的化合物。生物学测定结果证实了这两个支架的SENP2抑制活性。每个支架中最有效的化合物的IC50分别为5.9和3.7μM。大多数化合物还抑制密切相关的同工型SENP1，而未观察到对其他蛋白酶（如木瓜蛋白酶和胰蛋白酶）的可检测抑制。我们的研究表明，1,2,5-恶二唑可作为开发针对靶向SENPs的各种疾病的新型治疗剂的起点。
