金诺芬衍生物的合成及抗肿瘤活性

设计合成了一类新型金诺芬衍生物, 采用核磁共振波谱(NMR)和高分辨质谱(HRMS)确认了其结构. 以目标化合物处理肿瘤细胞后, 采用四氮唑蓝盐(MTS)法检测细胞增殖情况, 用流式细胞仪检测细胞凋亡情况, 采用蛋白质免疫印迹(Western blot)法检测总的泛素化蛋白(Ub-Prs)、 K48 位链接多聚泛素化蛋白以及蛋白酶体外源性特异性底物(GFPu)的表达情况. 结果表明, 金诺芬衍生物可通过抑制蛋白酶体功能来发挥抗肿瘤效果.     

基于SVM方法分析蛋白酶体裂解位点的特异性

真核细胞中的泛素-蛋白酶体系统在抗原肽加工呈递途径中发挥着重要作用. 为了进一步研究蛋白酶体的酶切位点特异性, 采用支持向量机(support vector machine, SVM)方法建立了蛋白酶体的酶切位点预测模型. 在相同检验集下, 将本模型性能指标与其他预测模型方法比较, 结果是本模型性能指标优先, 预测准确度为83.1%. 由样本数据相应氨基酸对酶切位点形成的权重系数, 得出蛋白酶体酶切位点及其两侧区域氨基酸的裂解特异性, 反映了蛋白酶体裂解抗原蛋白的相互作用信息, 这表明蛋白酶体对抗原蛋白的酶切处理不是随机的, 而是有一定模式和选择性的.     

金属配合物作为蛋白酶体抑制剂的研究进展

蛋白酶体涉及机体的多种生理功能和许多疾病的发病机制.近年来的研究发现,金属配合物尤其是铜的配合物对肿瘤细胞中蛋白酶体活性有较强的抑制作用并能诱导肿瘤细胞凋亡.本文综述了金属配合物作为蛋白酶体抑制剂及肿瘤细胞凋亡诱导剂的研究进展.     

有机锡化合物与蛋白酶体β5亚基相互作用的分子模型

有机锡化合物能够抑制蛋白酶体的类糜蛋白酶活性(CT),导致细胞死亡,但是其与蛋白酶体的相互作用形式并不清楚.本文测定了丁基锡化合物和苯基锡化合物对蛋白酶体CT活性的IC50值,探讨了有机锡化合物对蛋白酶体CT活性的抑制作用形式.研究表明,对蛋白酶体CT活性,本文研究的一取代或二取代有机锡是弱的、可逆抑制剂,而三丁基锡、三苯基锡是强的、不可逆抑制剂.计算机分子对接分析表明,对于可逆抑制CT活性的有机锡化合物,其预测抑制常数与实测IC50值有良好的线性相关性.三丁基锡和三苯基锡上的Sn原子可能与β5亚基上的Thr1Oγ形成共价配位键,从而不可逆抑制CT活性.总之,本文建立的计算机分子对接模型很好地解释了有机锡化合物与蛋白酶体β5亚基的相互作用形式,这也将有助于了解类似金属化合物与蛋白酶体的相互作用机制.     

蛋白酶体对抗原蛋白酶切特异性的研究

在MHCI类分子结合的抗原表位加工呈递途径中,泛素-蛋白酶体系统对抗原蛋白的降解发挥着重要作用。为了进一步研究蛋白酶体的酶切特异性,采用偏最小二乘方法（partial least squares method,PLS）建立了蛋白酶体的酶切位点预测模型,预测准确度为82.8％;由样本数据相应氨基酸对酶切位点形成的权重系数,得出蛋白酶体酶切位点及其两侧区域氨基酸的裂解特异性,它反映了蛋白酶体对抗原蛋白酶切的相互作用信息,也表明蛋白酶体对抗原蛋白酶切处理不是随机的,而是有一定模式和选择性的。     

基于VHSE结构表征的蛋白酶体酶切位点预测及酶切特异性研究

泛素-蛋白酶体在真核生物的抗原呈递、细胞周期调控和转录因子激活等生理过程中发挥着极为重要的作用,其核心就是蛋白酶体对底物的选择性酶切作用,因此对选择性酶切位点的预测一直是计算生物学的一个重点研究内容.针对现有酶切位点预测方法的非线性和物理意义不明确等问题,借鉴定量构效关系研究方法,采用基于氨基酸物理化学性质的描述子——VHSE(Principal component score vector of hydrophobic,steric,and electronic properties)对收集的2650个MHC-I配体的源蛋白序列进行了结构表征,在此基础上利用支持向量机建立了蛋白酶体酶切位点的预测模型,其最优线性模型的灵敏度(Sensitivity)、特异性(Specificity)、接受者操作特征曲线下面积(area under receiver operatingcharacteristics curve,AUC)和马休斯相关系数(Matthews coefficient of correlation,MCC)分别为90.18%,69.63%,0.8797和0.6131.模型分析结果表明:影响酶切位点选择性的氨基酸性质由大到小依次为:疏水性、电性和立体特征;P9,P8,P4,P1,P3’,P4’和P5’位氨基酸对酶切位点的选择有重要影响,研究亦显示酶切位点上游P1位和下游P1’～P5’的"疏水势差"有利于蛋白酶体的切割作用.     

人红细胞20S蛋白酶体的蛋白质组学表征及不同来源20S蛋白酶体异质性的研究

通过整合差速离心和非变性聚丙烯酰胺凝胶电泳(native-PAGE)技术,建立了能有效分离20S蛋白酶体(20S core particle,CP)的方法.与传统纯化方法比较,此方法具有经济、快速的特点,并且能够对不同组织细胞来源的CP进行分离.利用本方法对人红细胞来源的CP亚基进行了2-DE分离和MALDI-TOF/TOF MS鉴定.结果显示,可鉴定出33个具有不同相对分子量和等电点的蛋白点,此数量远远多于CP亚基的14种.此外,利用非变性/变性十二烷基硫酸钠-聚丙烯酰胺凝胶电泳(native/SDS-PAGE)技术,比较了来源于酵母、小鼠肝脏、人红细胞、人胰腺癌细胞系SW1990和PANC-1的CP及其亚基在电泳行为方面的差异,进行了蛋白酶体异质性初探.     

环氧酮肽蛋白酶体抑制剂的构效关系及基于分子相似性的分子设计

针对56个环氧酮肽衍生物,分别采用比较分子场分析(comparative molecular field analysis,CoMFA)、比较分子相似性形状指数分析(comparative molecular similarity indices analysis,CoMSIA)、Topomer CoMFA、Holo-gram QSAR(HQSAR)以及基于一维和二维描述符的支持向量机(support vector machine,SVM)方法进行了细致的构效关系研究。研究显示:通过引入一维和二维描述符的SVM建模方法,避免了柔性分子在三维构效关系研究中的构象选择和叠合难题,亦可有效避免过拟合现象的发生。所建最优SVM模型的决定系数R2、均方根误差(RMS)、交互验证系数Q2和外部预测R2pred分别为0.681,0.436,0.572和0.641。分析结果显示:电性、拓扑特征、疏水性和分子体积是影响环氧酮肽蛋白酶体抑制活性的主要因素。在此基础上,以活性最高样本分子(CID:42638286的)为模板,基于相似性评价方法对其侧链进行设计,结合Lipinski"5规则"类药性筛选,共得到12个新颖目标分子,且预测活性均达到纳摩尔水平。     

微波辐射合成2-乙氧羰基甲硫基-4-取代苯基亚氨基-4H-1-萘酮类化合物

以对取代苯胺与2-乙氧羰基甲硫基-1,4-萘醌为底物,采用微波合成法合成了3个新型的蛋白酶体抑制剂的关键中间体——2-乙氧羰基甲硫基-4-苯基亚氨基-4H-1-萘酮类化合物(3a~3c),其结构经1H NMR和1D NOE表征。在最佳反应条件[THF为溶剂,TiCl4为催化剂,于60℃微波(240 W)反应15 min]下,2-乙氧羰基甲硫基-4-(4-硝基苯基)亚氨基-4H-1-萘酮(3a)的收率84.2%。     

Differential Expression of Molecular Chaperones in PC12 Cells Treated with PSI

<正>Parkinson's disease(PD) is a common neurodegenerative disorder whose primary pathology features are the degeneration of dopaminergic neurons in the substantia nigra pars compacta(SNc) and the presence of eosinophilic inclusions called Lewy body in the cytoplasm of the remained neurons.Growing evidence suggests that dysfunction of the ubiquitin-proteasome system(UPS) is involved in the etiopathogenesis of PD.In order to investigate the pathogenetic mechanism of ubiquitin-proteasome dysfunction in PD,2D-differential gel electrophoresis (2D-DIGE) and MALDI-TOF Pro MS were used to determine the proteins,which were differentially expressed,in PC12 cells that had undergone a synthetic proteasomal inhibitor PSI(10μmol/L) treatment for 24 h.Forty-six protein spots were differentially expressed in response to PSI administration,of which 34 were increased and 12 decreased. Six of these were identified as molecular charperones:endoplasmin precursor(GRP94),heat shock protein 105(HSP105),HSC-70-psl,glucose ruglated protein 75(GRP75),glucose ruglated protein 58(GRP58) and heat shock 27000 protein 1(HSP27).The results suggest that the molecular chaperones play an important role in the PD model induced by proteasomal inhibitor.     

Natural compounds with proteasome inhibitory activity for cancer prevention and treatment

The proteasome is a multicatalytic protease complex that degrades most endogenous proteins including misfolded or damaged proteins to ensure normal cellular function. The ubiquitin-proteasome degradation pathway plays an essential role in multiple cellular processes, including cell cycle progression, proliferation, apoptosis and angiogenesis. It has been shown that human cancer cells are more sensitive to proteasome inhibition than normal cells, indicating that a proteasome inhibitor could be used as a novel anticancer drug. Indeed, this idea has been supported by the encouraging results of the clinical trials using the proteasome inhibitor Bortezomib (Velcade, PS-341), a drug approved by the US Food and Drug Administration (FDA). Several natural compounds, including the microbial metabolite lactacystin, green tea polyphenols, and traditional medicinal triterpenes, have been shown to be potent proteasome inhibitors. These findings suggest the potential use of natural proteasome inhibitors as not only chemopreventive and chemotherapeutic agents, but also tumor sensitizers to conventional radiotherapy and chemotherapy. In this review, we will summarize the structures and biological activities of the proteasome and several natural compounds with proteasome inhibitory activity, and will discuss the potential use of these compounds for the prevention and treatment of human cancers.     

Proteasome inhibitors: from research tools to drug candidates

The 26S proteasome is a 2.4 MDa multifunctional ATP-dependent proteolytic complex, which degrades the majority of cellular polypeptides by an unusual enzyme mechanism. Several groups of proteasome inhibitors have been developed and are now widely used as research tools to study the role of the ubiquitin-proteasome pathway in various cellular processes, and two inhibitors are now in clinical trials for treatment of multiple cancers and stroke.     

Non-peptidic natural products as ubiquitin-proteasome inhibitors

Approval of bortezomib has validated ubiquitin-proteasome pathway as an important target for treatment of haematological malignancies. However, clinical shortcomings of bortezomib, a covalent peptide proteasome inhibitor, has prompted a paradigm shift in anti-proteasome drug discovery towards development of non-peptidic inhibitors and targeting of upstream ubiquitin system which has drawn traction for interdisciplinary forays. It is being widely recognized that natural products provide valuable leads in the discovery of potent, chemically diverse, non-peptidic inhibitors of 20S proteasome and of key enzymes involved in ubiquitination machinery. As a result, total synthesis of natural, non-peptidic inhibitors of ubiquitin-proteasome pathway has emerged as a critical interlink between organic synthesis, medicinal chemistry, biochemical profiling and drug discovery. An up-to-date account of contextual synthetic challenges, strategies and accomplishments as well as mapping of the chemical diversity space around the natural scaffolds has been captured in this review.     

Targeted Degradation of PD-L1 and Activation of the STING Pathway by Carbon-Dot-Based PROTACs for Cancer Immunotherapy

Proteolysis targeting chimeras (PROTACs) technology is an emerging approach to degrade disease-associated proteins. Here, we report carbon-dot (CD)-based PROTACs (CDTACs) that degrade membrane proteins via the ubiquitin-proteasome system. CDTACs can bind to programmed cell death ligand 1 (PD-L1), recruit cereblon (CRBN) to induce PD-L1 ubiquitination, and degrade them with proteasomes. Fasting-mimicking diet (FMD) is also used to enhance the cellular uptake and proteasome activity. More than 99 % or 90 % of PD-L1 in CT26 or B16-F10 tumor cells can be degraded by CDTACs, respectively. Furthermore, CDTACs can activate the stimulator of interferon genes (STING) pathway to trigger immune responses. Thus, CDTACs with FMD treatment effectively inhibit the growth of CT26 and B16-F10 tumors. Compared with small-molecule-based PROTACs, CDTACs offer several advantages, such as efficient membrane protein degradation, targeted tumor accumulation, immune system activation, and in vivo detection.     

The Molecular and Pathophysiological Functions of Members of the LNX/PDZRN E3 Ubiquitin Ligase Family

The ligand of Numb protein-X (LNX) family, also known as the PDZRN family, is composed of four discrete RING-type E3 ubiquitin ligases (LNX1, LNX2, LNX3, and LNX4), and LNX5 which may not act as an E3 ubiquitin ligase owing to the lack of the RING domain. As the name implies, LNX1 and LNX2 were initially studied for exerting E3 ubiquitin ligase activity on their substrate Numb protein, whose stability was negatively regulated by LNX1 and LNX2 via the ubiquitin-proteasome pathway. LNX proteins may have versatile molecular, cellular, and developmental functions, considering the fact that besides these proteins, none of the E3 ubiquitin ligases have multiple PDZ (PSD95, DLGA, ZO-1) domains, which are regarded as important protein-interacting modules. Thus far, various proteins have been isolated as LNX-interacting proteins. Evidence from studies performed over the last two decades have suggested that members of the LNX family play various pathophysiological roles primarily by modulating the function of substrate proteins involved in several different intracellular or intercellular signaling cascades. As the binding partners of RING-type E3s, a large number of substrates of LNX proteins undergo degradation through ubiquitin-proteasome system (UPS) dependent or lysosomal pathways, potentially altering key signaling pathways. In this review, we highlight recent and relevant findings on the molecular and cellular functions of the members of the LNX family and discuss the role of the erroneous regulation of these proteins in disease progression.     

The UFM1 Pathway Impacts HCMV US2-Mediated Degradation of HLA Class I

To prevent accumulation of misfolded proteins in the endoplasmic reticulum, chaperones perform quality control on newly translated proteins and redirect misfolded proteins to the cytosol for degradation by the ubiquitin-proteasome system. This pathway is called ER-associated protein degradation (ERAD). The human cytomegalovirus protein US2 induces accelerated ERAD of HLA class I molecules to prevent immune recognition of infected cells by CD8⁺ T cells. Using US2-mediated HLA-I degradation as a model for ERAD, we performed a genome-wide CRISPR/Cas9 library screen to identify novel cellular factors associated with ERAD. Besides the identification of known players such as TRC8, p97, and UBE2G2, the ubiquitin-fold modifier1 (UFM1) pathway was found to affect degradation of HLA-I. UFMylation is a post-translational modification resembling ubiquitination. Whereas we observe ubiquitination of HLA-I, no UFMylation was detected on HLA-I or several other proteins involved in degradation of HLA-I, suggesting that the UFM1 pathway impacts ERAD in a different manner than ubiquitin. Interference with the UFM1 pathway seems to specifically inhibit the ER-to-cytosol dislocation of HLA-I. In the absence of detectable UFMylation of HLA-I, UFM1 may contribute to US2-mediated HLA-I degradation by misdirecting protein sorting indirectly. Mass spectrometry analysis of US2-expressing cells showed that ribosomal proteins are a major class of proteins undergoing extensive UFMylation; the role of these changes in protein degradation may be indirect and remains to be established.     

Systematic quantification of the dynamics of newly synthesized proteins unveiling their degradation pathways in human cells

Proteins are continuously synthesized during cell growth and proliferation. At the same time, excessive and misfolded proteins have to be degraded, otherwise they are a burden to cells. Protein degradation is essential to maintain proteostasis in cells, and dysfunction of protein degradation systems results in numerous diseases such as cancer and neurodegenerative diseases. Despite the importance of protein degradation, the degradation pathways of many proteins remain to be explored. Here, we comprehensively investigated the degradation of newly synthesized proteins in human cells by integrating metabolic labeling, click chemistry, and multiplexed proteomics, and systematic and quantitative analysis of newly synthesized proteins first revealed the degradation pathways of many proteins. Bioinformatic analysis demonstrates that proteins degraded through two major pathways have distinct properties and functions. Proteins degraded through the ubiquitin-proteasome pathway contain more disordered structures, whereas those through the autophagy-lysosome pathway have significantly higher hydrophobicity. Systematic and quantitative investigation of the dynamics of newly synthesized proteins provides unprecedented and valuable information about protein degradation, which leads to a better understanding of protein properties and cellular activities.

Systematic quantification of the dynamics of newly synthesized proteins first reveals the degradation pathways of many proteins in human cells, and proteins degraded through each of the two major pathways have distinct properties and functions.     

An inhibitor of ubiquitin conjugation and aggresome formation

Proteasome inhibitors have revolutionized the treatment of multiple myeloma, and validated the therapeutic potential of the ubiquitin proteasome system (UPS). It is believed that in part, proteasome inhibitors elicit their therapeutic effect by inhibiting the degradation of misfolded proteins, which is proteotoxic and causes cell death. In spite of these successes, proteasome inhibitors are not effective against solid tumors, thus necessitating the need to explore alternative approaches. Furthermore, proteasome inhibitors lead to the formation of aggresomes that clear misfolded proteins via the autophagy–lysosome degradation pathway. Importantly, aggresome formation depends on the presence of polyubiquitin tags on misfolded proteins. We therefore hypothesized that inhibitors of ubiquitin conjugation should inhibit both degradation of misfolded proteins, and ubiquitin dependent aggresome formation, thus outlining the path forward toward more effective anticancer therapeutics. To explore the therapeutic potential of targeting the UPS to treat solid cancers, we have developed an inhibitor of ubiquitin conjugation (ABP A3) that targets ubiquitin and Nedd8 E1 enzymes, enzymes that are required to maintain the activity of the entire ubiquitin system. We have shown that ABP A3 inhibits conjugation of ubiquitin to intracellular proteins and prevents the formation of cytoprotective aggresomes in A549 lung cancer cells. Furthermore, ABP A3 induces activation of the unfolded protein response and apoptosis. Thus, similar to proteasome inhibitors MG132, bortezomib, and carfilzomib, ABP A3 can serve as a novel probe to explore the therapeutic potential of the UPS in solid and hematological malignancies.     

Current strategies for improving limitations of proteolysis targeting chimeras

Proteolysis targeting chimeras (PROTACs) are bifunctional degrader molecules via hijacking the ubiquitin-proteasome system (UPS) to specifically eliminate targeted proteins. PROTACs have gained momentum as a new modality of attractive technologies in the drug discovery landscape, since it allows to degrade disease-related proteins effectively. Although some PROTACs drugs reached the clinical research, they are still facing some bottlenecks and challenges that should not be neglected, such as poor oral bioavailability and potential toxic side effects. To overcome these limitations, herein, we provide an overview of recent strategies for improving the durability of PROTACs by enhancing cell permeability and reducing toxic side effects. Meanwhile, the impact of these strategies on improving oral bioavailability as well as their advantages and drawbacks will also be discussed. This review will give a useful reference toolbox for PROTACs design and further promote its clinical application.