POLR3A

研究背景由与E3泛素连接酶配体连接蛋白质靶向配体形成的蛋白水解靶向嵌合体（PROTAC）的靶向蛋白质降解已成为一种通过蛋白酶体介导的降解致病蛋白质的强大治疗方式。虽然有超过600个E3连接酶，但是大多数PROTAC只利用了Cullin-RING E3泛素连接酶的底物受体——cereblon和VHL。近年来，还发现了许多其他针对其他E3连接酶的募集蛋白，包括cIAP、MDM2、DCAF16、DCAF11、RNF114、RNF4、FEM1B、KEAP1和DCAF1。并不是所有的E3连接酶都对癌细胞活力至关重要，因此，癌细胞中可能会出现耐药机制，从而损害E3连接酶募集并使PROTAC无效。开发针对泛素-蛋白酶体机制核心成分的募集剂，例如针对对细胞活力至关重要的CUL1-CUL7 E3连接酶中的Cullin-RING E3连接酶复合接头蛋白（如DDB1、SKP1 或ELOB/ELOC）的募集剂，可以避免PROTAC可能产生的潜在未来耐药机制。加州大学伯克利分校Nomura课题组研究了CUL1-RING E3连接酶接头蛋白SKP1是否可以被募集用于PROTAC介导的新底物降解。研究内容该课题组在基于凝胶的基于活性的蛋白质分析（ABPP）中筛选了1284个半胱氨酸反应性共价配体，筛选了针对人SKP1-FBXO7-CUL1-RBX1复合物（图1）。该筛选产生的性能最良好的化合物是EN884（图2）。EN884显示了SKP1-FBXO7-CUL1-RBX1复合物中人SKP1蛋白的半胱氨酸反应性探针的剂量反应置换（图3）。   图1.半胱氨酸反应性共价配体库筛选结果（针对SKP1-FBXO7-CUL1-RBX1复合物）图2.EN884结构图3.EN884与半胱氨酸探针反应该课题组对与 EN884 一起孵育的SKP1-FBXO7-CUL1-RBX1复合物进行了串联质谱（MS/MS）分析，以确定修饰位点（图4），发现了一个被修饰的位点——SKP1上的C160（图5），该位点由于特定的F-Box结构域，表现出独特的构象。因此，该课题组假设EN884可能会利用SKP1和CUL1底物受体之间的集体界面并结合。图4.串联质谱分析图5.结合位点位置 接下来，该课题组合成了两个基于EN884的炔烃功能化探针SJH1-37-m、SJH1-37-p（图6）。基于凝胶的ABPP评估这些探针与SKP1复合物的结合，与对位相比，间位结合能力更佳（图7）。    图6.探针结构图7.探针结合能力值得注意的是，由于C160位置特殊，EN884和SJH1-37m不与单体SKP1结合（图8）。这表明，CUL1复合物的其余部分，或至少是底物受体，是配体与SKP1结合所必需的。图8.探针与单体SKP1结合       该课题组进一步证明，SJH1-37m通过SKP1的下拉在细胞中结合SKP1，而不是不相关的蛋白质，如GAPDH（图9）。   图9.SJH1-37m探针的SKP1下拉接下来，该课题组进行了基于质谱的ABPP，以使用先前建立的同位素脱硫生物素-ABPP（isoDTB-ABPP）鉴定HEK293T细胞中EN884参与SKP1的半胱氨酸。该课题组发现EN884在SKP1上与C160有7%的最小参与（图10）。这种最小参与与已应用在PROTAC（包括DCAF16、DCAF11和RNF114）中的其他共价E3连接酶募集剂观察到的最小参与一致。图10.HEK293T细胞中EN884的isoDTB-ABPP分析为了证明共价SKP1配体可用于PROTAC应用，该课题组合成了四种不同的PROTAC，通过C2、C4、C5或PEG3连接子将EN884的衍生物与BET家族抑制剂JQ1连接起来，分别生成SJH1-51A、SJH1-51B、SJH1-51C和SJH1-51D（图11）。所有四种PROTAC都降解了HEK293T细胞中BRD4的短亚型（图12），其中使用C4烷基接头的SJH1-51B观察到的降解最强。   图11.四种PROTAC结构图12.四种PROTAC降解效果并且，基于串联质量标记（TMT）的MDA-MB-231细胞中SJH1-51B的定量蛋白质组学分析显示BRD4中等选择性降解，其中16种蛋白质的水平显着降低>50%（图13）。   图13.SJH1-51B的定量蛋白质组学与蛋白酶体介导的降解一致，SJH1-51B介导的BRD4降解通过用蛋白酶体抑制剂硼替佐米预处理而减弱（图14）。它还显示出对活性Cullin RING E3连接酶所需的NEDD化的依赖性，NEDD化抑制剂MLN4924可减弱BRD4的降解（图15）。最重要的是，该课题组证明SKP1敲低完全减弱了SJH1-51B在HEK293T细胞中对BRD4的降解（图16）。图14.硼替佐米预处理结果图15.MLN4924预处理结果图16.SKP1敲低细胞结果BRD4是一种相对容易被PROTAC降解的蛋白质。因此，该课题组接下来测试了共价SKP1募集剂是否可用于降解另一种新底物蛋白——雄激素受体（AR）。该课题组合成了4种AR PROTAC，将共价SKP1募集剂与来自ARV-110的Arvinas AR PROTAC靶向配体连接起来，没有连接子或C4、C6或C7烷基连接子，分别产生SJH1-63、SJH1-62C、SJH1-62D和SJH1-62B（图17）。该课题组观察到所有4种PROTAC的AR降解，其中带有C7烷基接头的SJH1-62B在LNCaP前列腺癌细胞中显示出最有效和最强大的AR降解（图17）。 图17.四种AR PROTAC结构与降解效果该课题组进一步证明，SJH1-62B介导的AR降解在蛋白酶体抑制剂预处理后减弱（图18）。定量蛋白质组学分析还表明，AR与其他11种蛋白质的选择性降解在5000多种定量蛋白质中也显著降低（图19）。图18.SJH1-62B的硼替佐米预处理结果图19.SJH1-62B的定量蛋白质组学研究总结 该课题组发现了一种SKP1募集物，它共价靶向位于SKP1和CUL1 F-box底物受体界面的SKP1的固有无序C160。这一观察结果为发现仅在含有IDR的蛋白质与其相互作用的蛋白质形成复合物时出现的可连接位点提供了概念证明。他们进一步证明，这种共价SKP1配体可用于PROTAC应用，以降解细胞中的新底物，如BRD4和AR。鉴于SKP1的重要性，SKP1的共价募集可能潜在地克服在癌症治疗中利用非本质E3连接酶的PROTAC的耐药性机制。虽然该课题组证明了在PROTAC中使用Cullin RING E3连接酶衔接蛋白的概念，但SKP1配体仍处于早期阶段，需要进行重大的药物化学优化，以提高效力、选择性和类药物特性。   该课题组的研究结果还强调了使用共价化学蛋白质组学方法来识别泛素-蛋白酶体系统中蛋白质的补充物的实用性，该系统可用于靶向蛋白质降解应用。作者：潘相奕校审：周金明编辑：郑一榕时间：2024年3月29日参考文献Exploiting the Cullin E3 Ligase Adaptor Protein SKP1 for Targeted Protein Degradation ACS Chemical Biology 2024 19 (2), 442-450. DOI: 10.1021/acschembio.3c00642    声明：发表/转载本文仅仅是出于传播信息的需要，并不意味着代表本公众号观点或证实其内容的真实性。据此内容作出的任何判断，后果自负。若有侵权，告知必删！长按关注本公众号   粉丝群/投稿/授权/广告等请联系公众号助手 觉得本文好看，请点这里↓

BOSTON--(BUSINESS WIRE)-- Clinicians at Variantyx, a leader in high complexity hereditary disease testing, recently completed analysis of their 2,500th patient genome. The milestone highlights the growing need for whole genome sequencing (WGS)-based tests in patient genetic diagnostics. Variantyx’s Genomic Unity® tests pair the patient’s complete DNA sequence with proprietary data analysis algorithms and phenotype-driven filters to uniquely identify and definitively report on all major types of genetic variation within a single assay. Including genome-wide small sequence changes, structural variants, mitochondrial variants and tandem repeat expansions. Review of the cases identified many examples of positive test results using Variantyx testing after multiple rounds of failed exome and other NGS tests. A 26 year old with symptoms of ataxia who had received at least 12 prior genetic tests including chromosomal microarray (CMA), targeted gene testing and exome sequencing and was found to have two pathogenic variants in the POLR3A gene associated with progressive spastic ataxia, including a non-exonic SNV and a >16kb deletion. Both variant types were not identifiable with prior testing because of the limitations of standard next generation sequencing assays. A 44 year old with symptoms of dystonia and Parkinsonism who had received at least 4 prior genetic tests including exome sequencing and was found to have two pathogenic repeat expansions in the ATXN8OS gene associated with spinocerebellar ataxia 8. A 5 year old with seizures and symptoms of developmental delay who had received prior exome testing and was found to have a de novo, pathogenic 2 exon deletion in the KIAA2022 gene associated with X-linked intellectual disability 98. A 17 year old with symptoms of neuropathy who had received at least three prior comprehensive gene panel tests and was found to have two pathogenic variants in the FXN gene associated with Friedreich’s ataxia, including an SNV and a repeat expansion. A newborn with symptoms of skeletal dysplasia who had received prenatal NIPT, CMA, and panel testing as well as postnatal CMA and panel testing was found to have two pathogenic splice variants in the SBDS gene associated with Shwachman-Diamond syndrome. “Providing diagnoses for patients using the most comprehensive testing available is a milestone like no other and puts Variantyx at the leading edge of genomic technology. Not only are we identifying results for patients at the end of long diagnostic odysseys of years and sometimes decades, but we are also seeing the real impact of genomes being a first line test in diagnosing patients early and during a time where treatments may still be effective,” said Christine Stanley, PhD, FACMG, Chief Director of Clinical Genomics at Variantyx. “Our team of MDs, PhDs and Genetic Counselors are honored and humbled to lead the way in using genomes to not only identify single nucleotide variants, but, by using our sophisticated software, to also identify challenging variant types like copy number variants, short tandem repeats, Alu insertions, inversions, single exon deletions and mosaic aneuploidy. By overcoming the limitations of all other platforms used today, we’re providing much needed answers to patients and their families.” About Variantyx Variantyx is a CLIA/CAP laboratory providing Genomic Unity®, a whole genome sequencing (WGS)-based testing program for diagnosis of rare inherited and neurological disorders. Its single method approach to comprehensive genetic testing identifies multiple variant types within a single patient sample to provide a unified clinical report. For more information, please visit .