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Kiang KMY, Tang W, Song Q, Liu J, Li N, Lam TL, Shum HC, Zhu Z, Leung GKK. Targeting unfolded protein response using albumin-encapsulated nanoparticles attenuates temozolomide resistance in glioblastoma. Br J Cancer 2023; 128:1955-1963. [PMID: 36927978 PMCID: PMC10147657 DOI: 10.1038/s41416-023-02225-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 02/26/2023] [Accepted: 03/01/2023] [Indexed: 03/18/2023] Open
Abstract
BACKGROUND Chemoresistant cancer cells frequently exhibit a state of chronically activated endoplasmic reticulum (ER) stress. Engaged with ER stress, the unfolded protein response (UPR) is an adaptive reaction initiated by the accumulation of misfolded proteins. Protein disulfide isomerase (PDI) is a molecular chaperone known to be highly expressed in glioblastomas with acquired resistance to temozolomide (TMZ). We investigate whether therapeutic targeting of PDI provides a rationale to overcome chemoresistance. METHODS The activity of PDI was suppressed in glioblastoma cells using a small molecule inhibitor CCF642. Either single or combination treatment with TMZ was used. We prepared nanoformulation of CCF642 loaded in albumin as a drug carrier for orthotopic tumour model. RESULTS Inhibition of PDI significantly enhances the cytotoxic effect of TMZ on glioblastoma cells. More importantly, inhibition of PDI is able to sensitise glioblastoma cells that are initially resistant to TMZ treatment. Nanoformulation of CCF642 is well-tolerated and effective in suppressing tumour growth. It activates cell death-triggering UPR beyond repair and induces ER perturbations through the downregulation of PERK signalling. Combination treatment of TMZ with CCF642 significantly reduces tumour growth compared with either modality alone. CONCLUSION Our study demonstrates modulation of ER stress by targeting PDI as a promising therapeutic rationale to overcome chemoresistance.
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Affiliation(s)
- Karrie Mei-Yee Kiang
- Department of Surgery, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong SAR, China
| | - Wanjun Tang
- Department of Surgery, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong SAR, China
| | - Qingchun Song
- Department of Mechanical Engineering, The University of Hong Kong, Hong Kong SAR, China
| | - Jiaxin Liu
- Department of Surgery, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong SAR, China
| | - Ning Li
- Department of Surgery, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong SAR, China
- Department of Neurosurgery, Zhongda Hospital, Southeast University, Nanjing, China
| | - Tsz-Lung Lam
- Department of Surgery, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong SAR, China
| | - Ho Cheung Shum
- Department of Mechanical Engineering, The University of Hong Kong, Hong Kong SAR, China
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Hnog SAR, China
| | - Zhiyuan Zhu
- Department of Surgery, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong SAR, China.
- Department of Functional Neurosurgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China.
| | - Gilberto Ka-Kit Leung
- Department of Surgery, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong SAR, China.
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Mouawad R, Neamati N. Inhibition of Protein Disulfide Isomerase (PDIA1) Leads to Proteasome-Mediated Degradation of Ubiquitin-like PHD and RING Finger Domain-Containing Protein 1 (UHRF1) and Increased Sensitivity of Glioblastoma Cells to Topoisomerase II Inhibitors. ACS Pharmacol Transl Sci 2022; 6:100-114. [PMID: 36654750 PMCID: PMC9841782 DOI: 10.1021/acsptsci.2c00186] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Indexed: 12/12/2022]
Abstract
Glioblastoma (GBM) is the most aggressive brain tumor, and the prognosis remains poor with current available treatments. PDIA1 is considered a promising therapeutic target in GBM. In this study, we demonstrate that targeting PDIA1 results in increased GBM cell death by topoisomerase II (Top-II) inhibitors resulting in proteasome-mediated degradation of the oncogenic protein UHRF1. Combination of the PDIA1 inhibitor, bepristat-2a, produces strong synergy with doxorubicin, etoposide, and mitoxantrone in GBM and other cancer cell lines. Our bioinformatics analysis of multiple datasets revealed downregulation of UHRF1, upon PDIA1 inhibition. In addition, PDIA1 inhibition results in proteasome-mediated degradation of UHRF1 protein. Interestingly, treatment of GBM cells with bepristat-2a results in increased apoptosis and resistance to ferroptosis. Our findings emphasize the importance of PDIA1 as a therapeutic target in GBM and present a promising new therapeutic approach using Top-II inhibitors for GBM treatment.
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3
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Wang R, Shang Y, Chen B, Xu F, Zhang J, Zhang Z, Zhao X, Wan X, Xu A, Wu L, Zhao G. Protein disulfide isomerase blocks the interaction of LC3II-PHB2 and promotes mTOR signaling to regulate autophagy and radio/chemo-sensitivity. Cell Death Dis 2022; 13:851. [PMID: 36202782 PMCID: PMC9537141 DOI: 10.1038/s41419-022-05302-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 09/22/2022] [Accepted: 09/26/2022] [Indexed: 11/08/2022]
Abstract
Protein disulfide isomerase (PDI) is an endoplasmic reticulum (ER) enzyme that mediates the formation of disulfide bonds, and is also a therapeutic target for cancer treatment. Our previous studies found that PDI mediates apoptotic signaling by inducing mitochondrial dysfunction. Considering that mitochondrial dysfunction is a major contributor to autophagy, how PDI regulates autophagy remains unclear. Here, we provide evidence that high expression of PDI in colorectal cancer tumors significantly increases the risk of metastasis and poor prognosis of cancer patients. PDI inhibits radio/chemo-induced cell death by regulating autophagy signaling. Mechanistically, the combination of PDI and GRP78 was enhanced after ER stress, which inhibits the degradation of AKT by GRP78, and eventually activates the mTOR pathway to inhibit autophagy initiation. In parallel, PDI can directly interact with the mitophagy receptor PHB2 in mitochondrial, then competitively blocks the binding of LC3II and PHB2 and inhibits the mitophagy signaling. Collectively, our results identify that PDI can reduce radio/chemo-sensitivity by regulating autophagy, which could be served as a potential target for radio/chemo-therapy.
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Affiliation(s)
- Ruru Wang
- grid.9227.e0000000119573309High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Chinese Academy of Sciences, Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031 China ,grid.59053.3a0000000121679639University of Science and Technology of China, Hefei, Anhui 230026 China
| | - Yajing Shang
- grid.9227.e0000000119573309High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Chinese Academy of Sciences, Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031 China ,grid.186775.a0000 0000 9490 772XAnhui Medical University, Hefei, Anhui 230032 China
| | - Bin Chen
- grid.9227.e0000000119573309High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Chinese Academy of Sciences, Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031 China ,grid.59053.3a0000000121679639University of Science and Technology of China, Hefei, Anhui 230026 China
| | - Feng Xu
- grid.9227.e0000000119573309High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Chinese Academy of Sciences, Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031 China ,grid.59053.3a0000000121679639University of Science and Technology of China, Hefei, Anhui 230026 China
| | - Jie Zhang
- grid.9227.e0000000119573309High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Chinese Academy of Sciences, Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031 China ,grid.59053.3a0000000121679639University of Science and Technology of China, Hefei, Anhui 230026 China
| | - Zhaoyang Zhang
- grid.9227.e0000000119573309High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Chinese Academy of Sciences, Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031 China ,grid.59053.3a0000000121679639University of Science and Technology of China, Hefei, Anhui 230026 China
| | - Xipeng Zhao
- grid.9227.e0000000119573309High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Chinese Academy of Sciences, Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031 China ,grid.252245.60000 0001 0085 4987Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601 China
| | - Xiangbo Wan
- grid.488525.6The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510275 China
| | - An Xu
- grid.9227.e0000000119573309High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Chinese Academy of Sciences, Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031 China
| | - Lijun Wu
- grid.9227.e0000000119573309High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Chinese Academy of Sciences, Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031 China ,grid.252245.60000 0001 0085 4987Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601 China
| | - Guoping Zhao
- grid.9227.e0000000119573309High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Chinese Academy of Sciences, Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031 China
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Roles of Protein Disulfide Isomerase in Breast Cancer. Cancers (Basel) 2022; 14:cancers14030745. [PMID: 35159012 PMCID: PMC8833603 DOI: 10.3390/cancers14030745] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/28/2022] [Accepted: 01/29/2022] [Indexed: 02/08/2023] Open
Abstract
Simple Summary Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer and has a poor prognosis and higher recurrence rate due to ineffective therapy. Even with newly approved therapeutics, only limited TNBC patients could have benefited from the regimens. Protein disulfide isomerase (PDI) has been of great interest as a potential therapeutic target for cancers due to its impacts on tumor progression, metastasis, and clinical outcomes. Here, we discuss the roles of PDI members in breast cancers such as TNBC and the PDI inhibitors studied in breast cancer research. Abstract Protein disulfide isomerase (PDI) is the endoplasmic reticulum (ER)’s most abundant and essential enzyme and serves as the primary catalyst for protein folding. Due to its apparent role in supporting the rapid proliferation of cancer cells, the selective blockade of PDI results in apoptosis through sustained activation of UPR pathways. The functions of PDI, especially in cancers, have been extensively studied over a decade, and recent research has explored the use of PDI inhibitors in the treatment of cancers but with focus areas of other cancers, such as brain or ovarian cancer. In this review, we discuss the roles of PDI members in breast cancer and PDI inhibitors used in breast cancer research. Additionally, a few PDI members may be suggested as potential molecular targets for highly metastatic breast cancers, such as TNBC, that require more attention in future research.
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Chamberlain N, Anathy V. Pathological consequences of the unfolded protein response and downstream protein disulphide isomerases in pulmonary viral infection and disease. J Biochem 2020; 167:173-184. [PMID: 31790139 PMCID: PMC6988748 DOI: 10.1093/jb/mvz101] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 11/08/2019] [Indexed: 12/15/2022] Open
Abstract
Protein folding within the endoplasmic reticulum (ER) exists in a delicate balance; perturbations of this balance can overload the folding capacity of the ER and disruptions of ER homoeostasis is implicated in numerous diseases. The unfolded protein response (UPR), a complex adaptive stress response, attempts to restore normal proteostasis, in part, through the up-regulation of various foldases and chaperone proteins including redox-active protein disulphide isomerases (PDIs). There are currently over 20 members of the PDI family each consisting of varying numbers of thioredoxin-like domains which, generally, assist in oxidative folding and disulphide bond rearrangement of peptides. While there is a large amount of redundancy in client proteins of the various PDIs, the size of the family would indicate more nuanced roles for the individual PDIs. However, the role of individual PDIs in disease pathogenesis remains uncertain. The following review briefly discusses recent findings of ER stress, the UPR and the role of individual PDIs in various respiratory disease states.
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Affiliation(s)
- Nicolas Chamberlain
- Department of Pathology and Laboratory Medicine, University of Vermont Larner College of Medicine, 149 Beaumont Ave, Burlington, VT 05405, USA
| | - Vikas Anathy
- Department of Pathology and Laboratory Medicine, University of Vermont Larner College of Medicine, 149 Beaumont Ave, Burlington, VT 05405, USA
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6
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Peng Z, Chen Y, Cao H, Zou H, Wan X, Zeng W, Liu Y, Hu J, Zhang N, Xia Z, Liu Z, Cheng Q. Protein disulfide isomerases are promising targets for predicting the survival and tumor progression in glioma patients. Aging (Albany NY) 2020; 12:2347-2372. [PMID: 32023222 PMCID: PMC7041756 DOI: 10.18632/aging.102748] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 01/07/2020] [Indexed: 12/24/2022]
Abstract
The present study focused on the expression patterns, prognostic values and potential mechanism of the PDI family in gliomas. Most PDI family members’ mRNA expressions were observed significantly different between gliomas classified by clinical features. Construction of the PDI signature, cluster and risk score models of glioma was done using GSVA, consensus clustering analysis, and LASSO Cox regression analysis respectively. High values of PDI signature/ risk score and cluster 1 in gliomas were associated with malignant clinicopathological characteristics and poor prognosis. Analysis of the distinctive genomic alterations in gliomas revealed that many cases having high PDI signature and risk score were associated with genomic aberrations of driver oncogenes. GSVA analysis showed that PDI family was involved in many signaling pathways in ERAD, apoptosis, and MHC class I among many more. Prognostic nomogram revealed that the risk score was a good prognosis indicator for gliomas. The qRT-PCR and immunohistochemistry confirmed that P4HB, PDIA4 and PDIA5 were overexpressed in gliomas. In summary, this research highlighted the clinical importance of PDI family in tumorigenesis and progression in gliomas.
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Affiliation(s)
- Zhigang Peng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan, P. R. China
| | - Yu Chen
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450001, Henan, P. R. China
| | - Hui Cao
- Department of Psychiatry, The Second People's Hospital of Hunan Province, The Affiliated Hospital of Hunan University of Chinese Medicine, Changsha 410007, Hunan, P. R. China
| | - Hecun Zou
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, P. R. China
| | - Xin Wan
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan, P. R. China
| | - Wenjing Zeng
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, P. R. China
| | - Yanling Liu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, P. R. China
| | - Jiaqing Hu
- Department of Emergency, The Second People's Hospital of Hunan Province, The Affiliated Hospital of Hunan University of Chinese Medicine, Changsha 410007, Hunan, P. R. China
| | - Nan Zhang
- School of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, Heilongjiang, P. R. China
| | - Zhiwei Xia
- Department of Neurology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, P. R. China
| | - Zhixiong Liu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan, P. R. China
| | - Quan Cheng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan, P. R. China.,Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, P. R. China.,Institute of Clinical Pharmacology, Central South University; Hunan Key Laboratory of Pharmacogenetics, Changsha 410078, Hunan, P. R. China
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7
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Li L, Liu J, Ding Y, Shi Z, Peng B, Yang N, Hong D, Zhang C, Yao C, Ge J, Huang W. Design, synthesis and evaluation of protein disulfide isomerase inhibitors with nitric oxide releasing activity. Bioorg Med Chem Lett 2020; 30:126898. [DOI: 10.1016/j.bmcl.2019.126898] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/27/2019] [Accepted: 12/07/2019] [Indexed: 01/27/2023]
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8
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Yuan K, Xie K, Lan T, Xu L, Chen X, Li X, Liao M, Li J, Huang J, Zeng Y, Wu H. TXNDC12 promotes EMT and metastasis of hepatocellular carcinoma cells via activation of β-catenin. Cell Death Differ 2019; 27:1355-1368. [PMID: 31570854 PMCID: PMC7206186 DOI: 10.1038/s41418-019-0421-7] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 07/23/2019] [Accepted: 09/04/2019] [Indexed: 02/05/2023] Open
Abstract
Metastasis is one of the main contributors to the poor prognosis of hepatocellular carcinoma (HCC). However, the underlying mechanism of HCC metastasis remains largely unknown. Here, we showed that TXNDC12, a thioredoxin-like protein, was upregulated in highly metastatic HCC cell lines as well as in portal vein tumor thrombus and lung metastasis tissues of HCC patients. We found that the enforced expression of TXNDC12 promoted metastasis both in vitro and in vivo. Subsequent mechanistic investigations revealed that TXNDC12 promoted metastasis through upregulation of the ZEB1-mediated epithelial-mesenchymal transition (EMT) process. We subsequently showed that TXNDC12 overexpression stimulated the nuclear translocation and activation of β-catenin, a positive transcriptional regulator of ZEB1. Accordingly, we found that TXNDC12 interacted with β-catenin and that the thioredoxin-like domain of TXNDC12 was essential for the interaction between TXNDC12 and β-catenin as well as for TXNDC12-mediated β-catenin activation. Moreover, high levels of TXNDC12 in clinical HCC tissues correlated with elevated nuclear β-catenin levels and predicted worse overall and disease-free survival. In summary, our study demonstrated that TXNDC12 could activate β-catenin via protein-protein interaction and promote ZEB1-mediated EMT and HCC metastasis.
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Affiliation(s)
- Kefei Yuan
- Department of Liver Surgery & Liver Transplantation, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China.,Laboratory of Liver Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Kunlin Xie
- Department of Liver Surgery & Liver Transplantation, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Tian Lan
- Department of Liver Surgery & Liver Transplantation, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Lin Xu
- Department of Liver Surgery & Liver Transplantation, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China.,Laboratory of Liver Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Xiangzheng Chen
- Department of Liver Surgery & Liver Transplantation, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China.,Laboratory of Liver Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Xuefeng Li
- Shenzhen Luohu People's Hospital, The Third Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong, China
| | - Mingheng Liao
- Department of Liver Surgery & Liver Transplantation, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Jiaxin Li
- Department of Liver Surgery & Liver Transplantation, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Jiwei Huang
- Department of Liver Surgery & Liver Transplantation, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Yong Zeng
- Department of Liver Surgery & Liver Transplantation, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China. .,Laboratory of Liver Surgery, West China Hospital, Sichuan University, Chengdu, China.
| | - Hong Wu
- Department of Liver Surgery & Liver Transplantation, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China. .,Laboratory of Liver Surgery, West China Hospital, Sichuan University, Chengdu, China.
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Yang S, Shergalis A, Lu D, Kyani A, Liu Z, Ljungman M, Neamati N. Design, Synthesis, and Biological Evaluation of Novel Allosteric Protein Disulfide Isomerase Inhibitors. J Med Chem 2019; 62:3447-3474. [PMID: 30759340 DOI: 10.1021/acs.jmedchem.8b01951] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protein disulfide isomerase (PDI) is responsible for nascent protein folding in the endoplasmic reticulum (ER) and is critical for glioblastoma survival. To improve the potency of lead PDI inhibitor BAP2 (( E)-3-(3-(4-hydroxyphenyl)-3-oxoprop-1-en-1-yl)benzonitrile), we designed and synthesized 67 analogues. We determined that PDI inhibition relied on the A ring hydroxyl group of the chalcone scaffold and cLogP increase in the sulfonamide chain improved potency. Docking studies revealed that BAP2 and analogues bind to His256 in the b' domain of PDI, and mutation of His256 to Ala abolishes BAP2 analogue activity. BAP2 and optimized analogue 59 have modest thiol reactivity; however, we propose that PDI inhibition by BAP2 analogues depends on the b' domain. Importantly, analogues inhibit glioblastoma cell growth, induce ER stress, increase expression of G2M checkpoint proteins, and reduce expression of DNA repair proteins. Cumulatively, our results support inhibition of PDI as a novel strategy to treat glioblastoma.
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Affiliation(s)
- Suhui Yang
- Department of Medicinal Chemistry, College of Pharmacy, Rogel Cancer Center , University of Michigan , North Campus Research Complex, 1600 Huron Parkway , Ann Arbor , Michigan 48109 , United States
| | - Andrea Shergalis
- Department of Medicinal Chemistry, College of Pharmacy, Rogel Cancer Center , University of Michigan , North Campus Research Complex, 1600 Huron Parkway , Ann Arbor , Michigan 48109 , United States
| | - Dan Lu
- Department of Medicinal Chemistry, College of Pharmacy, Rogel Cancer Center , University of Michigan , North Campus Research Complex, 1600 Huron Parkway , Ann Arbor , Michigan 48109 , United States
| | - Anahita Kyani
- Department of Medicinal Chemistry, College of Pharmacy, Rogel Cancer Center , University of Michigan , North Campus Research Complex, 1600 Huron Parkway , Ann Arbor , Michigan 48109 , United States
| | - Ziwei Liu
- Department of Medicinal Chemistry, College of Pharmacy, Rogel Cancer Center , University of Michigan , North Campus Research Complex, 1600 Huron Parkway , Ann Arbor , Michigan 48109 , United States
| | - Mats Ljungman
- Department of Radiation Oncology Rogel Cancer Center , University of Michigan Medical School and Rogel Cancer Center, School of Public Health , Ann Arbor , Michigan 48109 , United States
| | - Nouri Neamati
- Department of Medicinal Chemistry, College of Pharmacy, Rogel Cancer Center , University of Michigan , North Campus Research Complex, 1600 Huron Parkway , Ann Arbor , Michigan 48109 , United States
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Carroll WL, Evensen NA. Targeting a major hub of cell fate decisions - the mitochondrial-associated membrane. Haematologica 2019; 104:419-421. [PMID: 30819833 DOI: 10.3324/haematol.2018.208355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- William L Carroll
- Departments of Pediatrics and Pathology, Perlmutter Cancer Center, NYU-Langone Medical Center, New York, NY, USA
| | - Nikki A Evensen
- Departments of Pediatrics and Pathology, Perlmutter Cancer Center, NYU-Langone Medical Center, New York, NY, USA
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11
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Koczian F, Nagło O, Vomacka J, Vick B, Servatius P, Zisis T, Hettich B, Kazmaier U, Sieber SA, Jeremias I, Zahler S, Braig S. Targeting the endoplasmic reticulum-mitochondria interface sensitizes leukemia cells to cytostatics. Haematologica 2018; 104:546-555. [PMID: 30309851 PMCID: PMC6395311 DOI: 10.3324/haematol.2018.197368] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 10/04/2018] [Indexed: 12/20/2022] Open
Abstract
Combination chemotherapy has proven to be a favorable strategy to treat acute leukemia. However, the introduction of novel compounds remains challenging and is hindered by a lack of understanding of their mechanistic interactions with established drugs. In the present study, we demonstrate a highly increased response of various acute leukemia cell lines, drug-resistant cells and patient-derived xenograft cells by combining the recently introduced protein disulfide isomerase inhibitor PS89 with cytostatics. In leukemic cells, a proteomics-based target fishing approach revealed that PS89 affects a whole network of endoplasmic reticulum homeostasis proteins. We elucidate that the strong induction of apoptosis in combination with cytostatics is orchestrated by the PS89 target B-cell receptor-associated protein 31, which transduces apoptosis signals at the endoplasmic reticulum -mitochondria interface. Activation of caspase-8 and cleavage of B-cell receptor-associated protein 31 stimulate a pro-apoptotic crosstalk including release of calcium from the endoplasmic reticulum and an increase in the levels of reactive oxygen species resulting in amplification of mitochondrial apoptosis. The findings of this study promote PS89 as a novel chemosensitizing agent for the treatment of acute leukemia and uncovers that targeting the endoplasmic reticulum - mitochondrial network of cell death is a promising approach in combination therapy.
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Affiliation(s)
- Fabian Koczian
- Department of Pharmaceutical Biology, Ludwig Maximilian University of Munich
| | - Olga Nagło
- Department of Pharmaceutical Biology, Ludwig Maximilian University of Munich
| | - Jan Vomacka
- Department of Chemistry, Technical University of Munich, Garching
| | - Binje Vick
- Research Unit Gene Vectors, Helmholtz Zentrum München, German Center for Environmental Health, Munich
| | - Phil Servatius
- Institute of Organic Chemistry, Saarland University, Saarbrücken, Germany
| | - Themistoklis Zisis
- Department of Pharmaceutical Biology, Ludwig Maximilian University of Munich
| | - Britta Hettich
- Department of Pharmaceutical Biology, Ludwig Maximilian University of Munich
| | - Uli Kazmaier
- Institute of Organic Chemistry, Saarland University, Saarbrücken, Germany
| | - Stephan A Sieber
- Department of Chemistry, Technical University of Munich, Garching
| | - Irmela Jeremias
- Research Unit Gene Vectors, Helmholtz Zentrum München, German Center for Environmental Health, Munich
| | - Stefan Zahler
- Department of Pharmaceutical Biology, Ludwig Maximilian University of Munich
| | - Simone Braig
- Department of Pharmaceutical Biology, Ludwig Maximilian University of Munich
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12
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Cole KS, Grandjean JMD, Chen K, Witt CH, O'Day J, Shoulders MD, Wiseman RL, Weerapana E. Characterization of an A-Site Selective Protein Disulfide Isomerase A1 Inhibitor. Biochemistry 2018. [PMID: 29521097 DOI: 10.1021/acs.biochem.8b00178] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Protein disulfide isomerase A1 (PDIA1) is an endoplasmic reticulum (ER)-localized thiol-disulfide oxidoreductase that is an important folding catalyst for secretory pathway proteins. PDIA1 contains two active-site domains (a and a'), each containing a Cys-Gly-His-Cys (CGHC) active-site motif. The two active-site domains share 37% sequence identity and function independently to perform disulfide-bond reduction, oxidation, and isomerization. Numerous inhibitors for PDIA1 have been reported, yet the selectivity of these inhibitors toward the a and a' sites is poorly characterized. Here, we identify a potent and selective PDIA1 inhibitor, KSC-34, with 30-fold selectivity for the a site over the a' site. KSC-34 displays time-dependent inhibition of PDIA1 reductase activity in vitro with a kinact/ KI of 9.66 × 103 M-1 s-1 and is selective for PDIA1 over other members of the PDI family, and other cellular cysteine-containing proteins. We provide the first cellular characterization of an a-site selective PDIA1 inhibitor and demonstrate that KSC-34 has minimal sustained effects on the cellular unfolded protein response, indicating that a-site inhibition does not induce global protein folding-associated ER stress. KSC-34 treatment significantly decreases the rate of secretion of a destabilized, amyloidogenic antibody light chain, thereby minimizing pathogenic amyloidogenic extracellular proteins that rely on high PDIA1 activity for proper folding and secretion. Given the poor understanding of the contribution of each PDIA1 active site to the (patho)physiological functions of PDIA1, site selective inhibitors like KSC-34 provide useful tools for delineating the pathological role and therapeutic potential of PDIA1.
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Affiliation(s)
- Kyle S Cole
- Department of Chemistry , Boston College , Chestnut Hill , Massachusetts 02467 , United States
| | - Julia M D Grandjean
- Department of Molecular Medicine , The Scripps Research Institute , La Jolla , California 92037 , United States
| | - Kenny Chen
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Collin H Witt
- Department of Chemistry , Boston College , Chestnut Hill , Massachusetts 02467 , United States
| | - Johanna O'Day
- Department of Chemistry , Boston College , Chestnut Hill , Massachusetts 02467 , United States
| | - Matthew D Shoulders
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - R Luke Wiseman
- Department of Molecular Medicine , The Scripps Research Institute , La Jolla , California 92037 , United States
| | - Eranthie Weerapana
- Department of Chemistry , Boston College , Chestnut Hill , Massachusetts 02467 , United States
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13
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Kyani A, Tamura S, Yang S, Shergalis A, Samanta S, Kuang Y, Ljungman M, Neamati N. Discovery and Mechanistic Elucidation of a Class of Protein Disulfide Isomerase Inhibitors for the Treatment of Glioblastoma. ChemMedChem 2018; 13:164-177. [PMID: 29235250 DOI: 10.1002/cmdc.201700629] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 12/10/2017] [Indexed: 12/14/2022]
Abstract
Protein disulfide isomerase (PDI) is overexpressed in glioblastoma, the most aggressive form of brain cancer, and folds nascent proteins responsible for the progression and spread of the disease. Herein we describe a novel nanomolar PDI inhibitor, pyrimidotriazinedione 35G8, that is toxic in a panel of human glioblastoma cell lines. We performed a medium-throughput 20 000-compound screen of a diverse subset of 1 000 000 compounds to identify cytotoxic small molecules. Cytotoxic compounds were screened for PDI inhibition, and, from the screen, 35G8 emerged as the most cytotoxic inhibitor of PDI. Bromouridine labeling and sequencing (Bru-seq) of nascent RNA revealed that 35G8 induces nuclear factor-like 2 (Nrf2) antioxidant response, endoplasmic reticulum (ER) stress response, and autophagy. Specifically, 35G8 upregulated heme oxygenase 1 and solute carrier family 7 member 11 (SLC7A11) transcription and protein expression and repressed PDI target genes such as thioredoxin-interacting protein 1 (TXNIP) and early growth response 1 (EGR1). Interestingly, 35G8-induced cell death did not proceed via apoptosis or necrosis, but by a mixture of autophagy and ferroptosis. Cumulatively, our data demonstrate a mechanism for a novel PDI inhibitor as a chemical probe to validate PDI as a target for brain cancer.
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Affiliation(s)
- Anahita Kyani
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, North Campus Research Complex, 1600 Huron Parkway, Ann Arbor, MI, 48109, USA
| | - Shuzo Tamura
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, North Campus Research Complex, 1600 Huron Parkway, Ann Arbor, MI, 48109, USA
| | - Suhui Yang
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, North Campus Research Complex, 1600 Huron Parkway, Ann Arbor, MI, 48109, USA
| | - Andrea Shergalis
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, North Campus Research Complex, 1600 Huron Parkway, Ann Arbor, MI, 48109, USA
| | - Soma Samanta
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, North Campus Research Complex, 1600 Huron Parkway, Ann Arbor, MI, 48109, USA
| | - Yuting Kuang
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, North Campus Research Complex, 1600 Huron Parkway, Ann Arbor, MI, 48109, USA
| | - Mats Ljungman
- Departments of Radiation Oncology and Environmental Health Sciences, University of Michigan, North Campus Research Complex, 1600 Huron Parkway, Ann Arbor, MI, 48109, USA
| | - Nouri Neamati
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, North Campus Research Complex, 1600 Huron Parkway, Ann Arbor, MI, 48109, USA
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14
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Cunningham RM, DeRose VJ. Platinum Binds Proteins in the Endoplasmic Reticulum of S. cerevisiae and Induces Endoplasmic Reticulum Stress. ACS Chem Biol 2017; 12:2737-2745. [PMID: 28892625 DOI: 10.1021/acschembio.7b00553] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Pt(II)-based anticancer drugs are widely used in the treatment of a variety of cancers, but their clinical efficacy is hindered by undesirable side effects and resistance. While much research has focused on Pt(II) drug interactions with DNA, there is increasing interest in proteins as alternative targets and contributors to cytotoxic and resistance mechanisms. Here, we describe a chemical proteomic method for isolation and identification of cellular protein targets of platinum compounds using Pt(II) reagents that have been modified for participation in the 1,3 dipolar cycloaddition "click" reaction. Using this method to visualize and enrich for targets, we identified 152 proteins in Pt(II)-treated Saccharomyces cerevisiae. Of interest was the identification of multiple proteins involved in the endoplasmic reticulum (ER) stress response, which has been proposed to be an important cytoplasmic mediator of apoptosis in response to cisplatin treatment. Consistent with possible direct targeting of this pathway, the ER stress response was confirmed to be induced in Pt(II)-treated yeast along with in vitro Pt(II)-inhibition of one of the identified proteins, protein disulfide isomerase.
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Affiliation(s)
- Rachael M. Cunningham
- Department of Chemistry and
Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, United States
| | - Victoria J. DeRose
- Department of Chemistry and
Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, United States
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15
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Allimuthu D, Adams DJ. 2-Chloropropionamide As a Low-Reactivity Electrophile for Irreversible Small-Molecule Probe Identification. ACS Chem Biol 2017; 12:2124-2131. [PMID: 28613814 DOI: 10.1021/acschembio.7b00424] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Resurgent interest in covalent target engagement in drug discovery has demonstrated that small molecules containing weakly reactive electrophiles can be safe and effective therapies. Several recently FDA-approved drugs feature an acrylamide functionality to selectively engage cysteine side chains of kinases (Ibrutinib, Afatinib, and Neratinib). Additional electrophilic functionalities whose reactivity is compatible with highly selective target engagement and in vivo application could open new avenues in covalent small molecule discovery. Here, we report the synthesis and evaluation of a library of small molecules containing the 2-chloropropionamide functionality, which we demonstrate is less reactive than typical acrylamide electrophiles. Although many library members do not appear to label proteins in cells, we identified S-CW3554 as selectively labeling protein disulfide isomerase and inhibiting its enzymatic activity. Subsequent profiling of the library against five diverse cancer cell lines showed unique cytotoxicity for S-CW3554 in cells derived from multiple myeloma, a cancer recently reported to be sensitive to PDI inhibition. Our novel PDI inhibitor highlights the potential of 2-chloropropionamides as weak and stereochemically tunable electrophiles for covalent drug discovery.
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Affiliation(s)
- Dharmaraja Allimuthu
- Department of Genetics and
Genome Sciences and Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Drew J. Adams
- Department of Genetics and
Genome Sciences and Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, United States
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16
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Meier C, Steinhauer TN, Koczian F, Plitzko B, Jarolim K, Girreser U, Braig S, Marko D, Vollmar AM, Clement B. A Dual Topoisomerase Inhibitor of Intense Pro-Apoptotic and Antileukemic Nature for Cancer Treatment. ChemMedChem 2017; 12:347-352. [DOI: 10.1002/cmdc.201700026] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Indexed: 12/15/2022]
Affiliation(s)
- Christopher Meier
- Department of Pharmaceutical and Medicinal Chemistry; Pharmaceutical Institute of the Christian Albrechts University in Kiel; Gutenbergstraße 76 24118 Kiel Germany
| | - Tamara N. Steinhauer
- Department of Pharmaceutical and Medicinal Chemistry; Pharmaceutical Institute of the Christian Albrechts University in Kiel; Gutenbergstraße 76 24118 Kiel Germany
| | - Fabian Koczian
- Department of Pharmacy, Center for Drug Research; Pharmaceutical Biology; University of Munich; Butenandtstraße 5-13 81377 Munich Germany
| | - Birte Plitzko
- Department of Pharmaceutical and Medicinal Chemistry; Pharmaceutical Institute of the Christian Albrechts University in Kiel; Gutenbergstraße 76 24118 Kiel Germany
| | - Katharina Jarolim
- Department of Food Chemistry and Toxicology; University of Vienna; Währinger Straße 38 1090 Vienna Austria
| | - Ulrich Girreser
- Department of Pharmaceutical and Medicinal Chemistry; Pharmaceutical Institute of the Christian Albrechts University in Kiel; Gutenbergstraße 76 24118 Kiel Germany
| | - Simone Braig
- Department of Pharmacy, Center for Drug Research; Pharmaceutical Biology; University of Munich; Butenandtstraße 5-13 81377 Munich Germany
| | - Doris Marko
- Department of Food Chemistry and Toxicology; University of Vienna; Währinger Straße 38 1090 Vienna Austria
| | - Angelika M. Vollmar
- Department of Pharmacy, Center for Drug Research; Pharmaceutical Biology; University of Munich; Butenandtstraße 5-13 81377 Munich Germany
| | - Bernd Clement
- Department of Pharmaceutical and Medicinal Chemistry; Pharmaceutical Institute of the Christian Albrechts University in Kiel; Gutenbergstraße 76 24118 Kiel Germany
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17
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Kleiner P, Heydenreuter W, Stahl M, Korotkov VS, Sieber SA. Eine Gesamtproteom‐basierte Auflistung der Hintergrundbinder von Photovernetzern. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201605993] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Philipp Kleiner
- Center for Integrated Protein Science an der Fakultät für Chemie Technische Universität München Lichtenbergstraße 4 85747 Garching Deutschland
| | - Wolfgang Heydenreuter
- Center for Integrated Protein Science an der Fakultät für Chemie Technische Universität München Lichtenbergstraße 4 85747 Garching Deutschland
| | - Matthias Stahl
- Center for Integrated Protein Science an der Fakultät für Chemie Technische Universität München Lichtenbergstraße 4 85747 Garching Deutschland
| | - Vadim S. Korotkov
- Center for Integrated Protein Science an der Fakultät für Chemie Technische Universität München Lichtenbergstraße 4 85747 Garching Deutschland
| | - Stephan A. Sieber
- Center for Integrated Protein Science an der Fakultät für Chemie Technische Universität München Lichtenbergstraße 4 85747 Garching Deutschland
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18
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Kleiner P, Heydenreuter W, Stahl M, Korotkov VS, Sieber SA. A Whole Proteome Inventory of Background Photocrosslinker Binding. Angew Chem Int Ed Engl 2016; 56:1396-1401. [DOI: 10.1002/anie.201605993] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 09/15/2016] [Indexed: 11/07/2022]
Affiliation(s)
- Philipp Kleiner
- Center for Integrated Protein Science at the Department of Chemistry Technische Universität München Lichtenbergstrasse 4 85747 Garching Germany
| | - Wolfgang Heydenreuter
- Center for Integrated Protein Science at the Department of Chemistry Technische Universität München Lichtenbergstrasse 4 85747 Garching Germany
| | - Matthias Stahl
- Center for Integrated Protein Science at the Department of Chemistry Technische Universität München Lichtenbergstrasse 4 85747 Garching Germany
| | - Vadim S. Korotkov
- Center for Integrated Protein Science at the Department of Chemistry Technische Universität München Lichtenbergstrasse 4 85747 Garching Germany
| | - Stephan A. Sieber
- Center for Integrated Protein Science at the Department of Chemistry Technische Universität München Lichtenbergstrasse 4 85747 Garching Germany
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19
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Recent developments and applications of clickable photoprobes in medicinal chemistry and chemical biology. Future Med Chem 2015; 7:2143-71. [DOI: 10.4155/fmc.15.136] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Photoaffinity labeling is a well-known biochemical technique that has grown significantly since the turn of the century, principally due to its combination with bioorthogonal/click chemistry reactions. This review highlights new developments and applications of clickable photoprobes in medicinal chemistry and chemical biology. In particular, recent examples of clickable photoprobes for target identification, activity- or affinity-based protein profiling (ABPP or AfBPP), characterization of sterol– or lipid–protein interactions and characterization of ligand-binding sites are presented.
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20
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Zachmann M, Mathias G, Antes I. Parameterization of the Hamiltonian Dielectric Solvent (HADES) Reaction-Field Method for the Solvation Free Energies of Amino Acid Side-Chain Analogs. Chemphyschem 2015; 16:1739-49. [PMID: 25820235 DOI: 10.1002/cphc.201402861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 02/02/2015] [Indexed: 11/10/2022]
Abstract
Optimization of the Hamiltonian dielectric solvent (HADES) method for biomolecular simulations in a dielectric continuum is presented with the goal of calculating accurate absolute solvation free energies while retaining the model's accuracy in predicting conformational free-energy differences. The solvation free energies of neutral and polar amino acid side-chain analogs calculated by using HADES, which may optionally include nonpolar contributions, were optimized against experimental data to reach a chemical accuracy of about 0.5 kcal mol(-1). The new parameters were evaluated for charged side-chain analogs. The HADES results were compared with explicit-solvent, generalized Born, Poisson-Boltzmann, and QM-based methods. The potentials of mean force (PMFs) between pairs of side-chain analogs obtained by using HADES and explicit-solvent simulations were used to evaluate the effects of the improved parameters optimized for solvation free energies on intermolecular potentials.
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Affiliation(s)
- Martin Zachmann
- Theoretical Chemical Biology and Protein Modelling Group, Technische Universiät München (Germany)
| | - Gerald Mathias
- Lehrstuhl für Biomolekulare Optik, Ludwig-Maximilians Universität München (Germany).
| | - Iris Antes
- Theoretical Chemical Biology and Protein Modelling Group, Technische Universiät München (Germany).
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