1
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Batra S, Vaquer-Alicea JI, Valdez C, Taylor SP, Manon VA, Vega AR, Kashmer OM, Kolay S, Lemoff A, Cairns NJ, White CL, Diamond MI. VCP regulates early tau seed amplification via specific cofactors. RESEARCH SQUARE 2024:rs.3.rs-4307848. [PMID: 38826306 PMCID: PMC11142303 DOI: 10.21203/rs.3.rs-4307848/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Background Neurodegenerative tauopathies may progress based on seeding by pathological tau assemblies, whereby an aggregate is released from one cell, gains entry to an adjacent or connected cell, and serves as a specific template for its own replication in the cytoplasm. In vitro seeding reactions typically take days, yet seeding into the complex cytoplasmic milieu happens within hours, implicating a machinery with unknown players that controls this process in the acute phase. Methods We used proximity labeling to identify factors that control seed amplification within 5h of seed exposure. We fused split-APEX2 to the C-terminus of tau repeat domain (RD) to reconstitute peroxidase activity 5h after seeded intracellular tau aggregation. Valosin containing protein (VCP/p97) was the top hit. VCP harbors dominant mutations that underlie two neurodegenerative diseases, multisystem proteinopathy and vacuolar tauopathy, but its mechanistic role is unclear. We used immortalized cells and human neurons to study the effects of VCP on tau seeding. We exposed cells to fibrils or brain homogenates in cell culture media and measured effects on uptake and induction of intracellular tau aggregation following various genetic and chemical manipulations of VCP. Results VCP knockdown reduced tau seeding. Chemical inhibitors had opposing effects on aggregation in HEK293T tau biosensor cells and human neurons alike: ML-240 increased seeding efficiency, whereas NMS-873 decreased it. The inhibitors were effective only when administered within 8h of seed exposure, indicating a role for VCP early in seed processing. We screened 30 VCP co-factors in HEK293T biosensor cells by genetic knockout or knockdown. Reduction of ATXN3, NSFL1C, UBE4B, NGLY1, and OTUB1 decreased tau seeding, as did NPLOC4, which also uniquely increased soluble tau levels. By contrast, reduction of FAF2 increased tau seeding. Conclusions Divergent effects on tau seeding of chemical inhibitors and cofactor reduction indicate that VCP regulates this process. This is consistent with a dedicated cytoplasmic processing complex based on VCP that directs seeds acutely towards degradation vs. amplification.
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Affiliation(s)
- Sushobhna Batra
- UT Southwestern: The University of Texas Southwestern Medical Center
| | | | - Clarissa Valdez
- UT Southwestern: The University of Texas Southwestern Medical Center
| | - Skyler P Taylor
- UT Southwestern: The University of Texas Southwestern Medical Center
| | - Victor A Manon
- UT Southwestern: The University of Texas Southwestern Medical Center
| | - Anthony R Vega
- UT Southwestern: The University of Texas Southwestern Medical Center
| | - Omar M Kashmer
- UT Southwestern: The University of Texas Southwestern Medical Center
| | - Sourav Kolay
- UT Southwestern: The University of Texas Southwestern Medical Center
| | - Andrew Lemoff
- UT Southwestern: The University of Texas Southwestern Medical Center
| | - Nigel J Cairns
- University of Exeter Faculty of Health and Life Sciences
| | - Charles L White
- UT Southwestern: The University of Texas Southwestern Medical Center
| | - Marc I Diamond
- UT Southwestern: The University of Texas Southwestern Medical Center
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2
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de Oliveira C, Leswing K, Feng S, Kanters R, Abel R, Bhat S. FEP Protocol Builder: Optimization of Free Energy Perturbation Protocols Using Active Learning. J Chem Inf Model 2023; 63:5592-5603. [PMID: 37594480 DOI: 10.1021/acs.jcim.3c00681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
Significant improvements have been made in the past decade to methods that rapidly and accurately predict binding affinity through free energy perturbation (FEP) calculations. This has been driven by recent advances in small-molecule force fields and sampling algorithms combined with the availability of low-cost parallel computing. Predictive accuracies of ∼1 kcal mol-1 have been regularly achieved, which are sufficient to drive potency optimization in modern drug discovery campaigns. Despite the robustness of these FEP approaches across multiple target classes, there are invariably target systems that do not display expected performance with default FEP settings. Traditionally, these systems required labor-intensive manual protocol development to arrive at parameter settings that produce a predictive FEP model. Due to the (a) relatively large parameter space to be explored, (b) significant compute requirements, and (c) limited understanding of how combinations of parameters can affect FEP performance, manual FEP protocol optimization can take weeks to months to complete, and often does not involve rigorous train-test set splits, resulting in potential overfitting. These manual FEP protocol development timelines do not coincide with tight drug discovery project timelines, essentially preventing the use of FEP calculations for these target systems. Here, we describe an automated workflow termed FEP Protocol Builder (FEP-PB) to rapidly generate accurate FEP protocols for systems that do not perform well with default settings. FEP-PB uses an active-learning workflow to iteratively search the protocol parameter space to develop accurate FEP protocols. To validate this approach, we applied it to pharmaceutically relevant systems where default FEP settings could not produce predictive models. We demonstrate that FEP-PB can rapidly generate accurate FEP protocols for the previously challenging MCL1 system with limited human intervention. We also apply FEP-PB in a real-world drug discovery setting to generate an accurate FEP protocol for the p97 system. FEP-PB is able to generate a more accurate protocol than the expert user, rapidly validating p97 as amenable to free energy calculations. Additionally, through the active-learning workflow, we are able to gain insight into which parameters are most important for a given system. These results suggest that FEP-PB is a robust tool that can aid in rapidly developing accurate FEP protocols and increasing the number of targets that are amenable to the technology.
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Affiliation(s)
- César de Oliveira
- Schrodinger, Inc., 9868 Scranton Road, Suite 3200, San Diego, California 92121, United States
| | - Karl Leswing
- Schrodinger, Inc., 1540 Broadway, 24th Floor, New York, New York 10036, United States
| | - Shulu Feng
- Schrodinger, Inc., 1540 Broadway, 24th Floor, New York, New York 10036, United States
| | - René Kanters
- Schrodinger, Inc., 1540 Broadway, 24th Floor, New York, New York 10036, United States
| | - Robert Abel
- Schrodinger, Inc., 1540 Broadway, 24th Floor, New York, New York 10036, United States
| | - Sathesh Bhat
- Schrodinger, Inc., 1540 Broadway, 24th Floor, New York, New York 10036, United States
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Shakya A, Liu P, Godek J, McKee NW, Dodson M, Anandhan A, Ooi A, Garcia JGN, Costa M, Chapman E, Zhang DD. The NRF2-p97-NRF2 negative feedback loop. Redox Biol 2023; 65:102839. [PMID: 37573837 PMCID: PMC10428046 DOI: 10.1016/j.redox.2023.102839] [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: 05/19/2023] [Revised: 07/15/2023] [Accepted: 08/04/2023] [Indexed: 08/15/2023] Open
Abstract
p97 is a ubiquitin-targeted ATP-dependent segregase that regulates proteostasis, in addition to a variety of other cellular functions. Previously, we demonstrated that p97 negatively regulates NRF2 by extracting ubiquitylated NRF2 from the KEAP1-CUL3-RBX1 E3 ubiquitin ligase complex, facilitating proteasomal destruction. In the current study, we identified p97 as an NRF2-target gene that contains a functional ARE, indicating the presence of an NRF2-p97-NRF2 negative feedback loop that maintains redox homeostasis. Using CRISPR/Cas9 genome editing, we generated endogenous p97 ARE-mutated BEAS-2B cell lines. These p97 ARE-mutated cell lines exhibit altered expression of p97 and NRF2, as well as a compromised response to NRF2 inducers. Importantly, we also found a positive correlation between NRF2 activation and p97 expression in human cancer patients. Finally, using chronic arsenic-transformed cell lines, we demonstrated a synergistic effect of NRF2 and p97 inhibition in killing cancer cells with high NRF2 and p97 expression. Our study suggests dual upregulation of NRF2 and p97 occurs in certain types of cancers, suggesting that inhibition of both NRF2 and p97 could be a promising treatment strategy for stratified cancer patients.
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Affiliation(s)
- Aryatara Shakya
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ, 85721, USA
| | - Pengfei Liu
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ, 85721, USA; National & Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China; International Joint Research Center on Cell Stress and Disease Diagnosis and Therapy, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Jack Godek
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ, 85721, USA
| | - Nicholas W McKee
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ, 85721, USA
| | - Matthew Dodson
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ, 85721, USA
| | - Annadurai Anandhan
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ, 85721, USA
| | - Aikseng Ooi
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ, 85721, USA
| | - Joe G N Garcia
- The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, FL, 33458, USA
| | - Max Costa
- Departments of Environmental Medicine, and Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, 10010, USA
| | - Eli Chapman
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ, 85721, USA.
| | - Donna D Zhang
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ, 85721, USA.
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Batra S, Vaquer-Alicea J, Manon VA, Kashmer OM, Lemoff A, Cairns NJ, White CL, Diamond MI. VCP increases or decreases tau seeding using specific cofactors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.30.555637. [PMID: 37693404 PMCID: PMC10491269 DOI: 10.1101/2023.08.30.555637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Background Neurodegenerative tauopathies may progress based on seeding by pathological tau assemblies, whereby an aggregate is released from one cell, gains entry to an adjacent or connected cell, and serves as a specific template for its own replication in the cytoplasm. In vitro seeding reactions typically take days, yet seeding into the complex cytoplasmic milieu can happen within hours. A cellular machinery might regulate this process, but potential players are unknown. Methods We used proximity labeling to identify factors that control seed amplification. We fused split-APEX2 to the C-terminus of tau repeat domain (RD) to reconstitute peroxidase activity upon seeded intracellular tau aggregation. We identified valosin containing protein (VCP/p97) 5h after seeding. Mutations in VCP underlie two neurodegenerative diseases, multisystem proteinopathy and vacuolar tauopathy, but its mechanistic role is unclear. We utilized tau biosensors, a cellular model for tau aggregation, to study the effects of VCP on tau seeding. Results VCP knockdown reduced tau seeding. However, distinct chemical inhibitors of VCP and the proteasome had opposing effects on aggregation, but only when given <8h of seed exposure. ML-240 increased seeding efficiency ~40x, whereas NMS-873 decreased seeding efficiency by 50%, and MG132 increased seeding ~10x. We screened VCP co-factors in HEK293 biosensor cells by genetic knockout or knockdown. Reduction of ATXN3, NSFL1C, UBE4B, NGLY1, and OTUB1 decreased tau seeding, as did NPLOC4, which also uniquely increased soluble tau levels. Reduction of FAF2 and UBXN6 increased tau seeding. Conclusions VCP uses distinct cofactors to determine seed replication efficiency, consistent with a dedicated cytoplasmic processing complex that directs seeds towards dissolution vs. amplification.
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Affiliation(s)
- Sushobhna Batra
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX
| | - Jaime Vaquer-Alicea
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX
| | - Victor A Manon
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX
| | - Omar M Kashmer
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX
| | - Andrew Lemoff
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX
| | - Nigel J Cairns
- Department of Clinical and Biological Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Charles L White
- Department of Pathology, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX
| | - Marc I Diamond
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX
- Department of Neurology, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX
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5
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Wei R, Cao Y, Wu H, Liu X, Jiang M, Luo X, Deng Z, Wang Z, Ke M, Zhu Y, Chen S, Gu C, Yang Y. Inhibition of VCP modulates NF-κB signaling pathway to suppress multiple myeloma cell proliferation and osteoclast differentiation. Aging (Albany NY) 2023; 15:8220-8236. [PMID: 37606987 PMCID: PMC10497005 DOI: 10.18632/aging.204965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 07/20/2023] [Indexed: 08/23/2023]
Abstract
Multiple myeloma (MM) is the second most common hematological malignancy, in which the dysfunction of the ubiquitin-proteasome pathway is associated with the pathogenesis. The valosin containing protein (VCP)/p97, a member of the AAA+ ATPase family, possesses multiple functions to regulate the protein quality control including ubiquitin-proteasome system and molecular chaperone. VCP is involved in the occurrence and development of various tumors while still elusive in MM. VCP inhibitors have gradually shown great potential for cancer treatment. This study aims to identify if VCP is a therapeutic target in MM and confirm the effect of a novel inhibitor of VCP (VCP20) on MM. We found that VCP was elevated in MM patients and correlated with shorter survival in clinical TT2 cohort. Silencing VCP using siRNA resulted in decreased MM cell proliferation via NF-κB signaling pathway. VCP20 evidently inhibited MM cell proliferation and osteoclast differentiation. Moreover, exosomes containing VCP derived from MM cells partially alleviated the inhibitory effect of VCP20 on cell proliferation and osteoclast differentiation. Mechanism study revealed that VCP20 inactivated the NF-κB signaling pathway by inhibiting ubiquitination degradation of IκBα. Furthermore, VCP20 suppressed MM cell proliferation, prolonged the survival of MM model mice and improved bone destruction in vivo. Collectively, our findings suggest that VCP is a novel target in MM progression. Targeting VCP with VCP20 suppresses malignancy progression of MM via inhibition of NF-κB signaling pathway.
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Affiliation(s)
- Rongfang Wei
- School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yuhao Cao
- School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Hongjie Wu
- School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Xin Liu
- School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Mingmei Jiang
- School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Xian Luo
- School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Zhendong Deng
- School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Ze Wang
- School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Mengying Ke
- School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yongqiang Zhu
- College of Life Science, Nanjing Normal University, Nanjing, China
| | - Siqing Chen
- Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Chunyan Gu
- School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Ye Yang
- School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
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Bai Y, Yu G, Zhou HM, Amarasinghe O, Zhou Y, Zhu P, Li Q, Zhang L, Nguele Meke F, Miao Y, Chapman E, Tao WA, Zhang ZY. PTP4A2 promotes lysophagy by dephosphorylation of VCP/p97 at Tyr805. Autophagy 2023; 19:1562-1581. [PMID: 36300783 PMCID: PMC10240998 DOI: 10.1080/15548627.2022.2140558] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 10/21/2022] [Accepted: 10/21/2022] [Indexed: 11/02/2022] Open
Abstract
Overexpression of PTP4A phosphatases are associated with advanced cancers, but their biological functions are far from fully understood due to limited knowledge about their physiological substrates. VCP is implicated in lysophagy via collaboration with specific cofactors in the ELDR complex. However, how the ELDR complex assembly is regulated has not been determined. Moreover, the functional significance of the penultimate and conserved Tyr805 phosphorylation in VCP has not been established. Here, we use an unbiased substrate trapping and mass spectrometry approach and identify VCP/p97 as a bona fide substrate of PTP4A2. Biochemical studies show that PTP4A2 dephosphorylates VCP at Tyr805, enabling the association of VCP with its C-terminal cofactors UBXN6/UBXD1 and PLAA, which are components of the ELDR complex responsible for lysophagy, the autophagic clearance of damaged lysosomes. Functionally, PTP4A2 is required for cellular homeostasis by promoting lysophagy through facilitating ELDR-mediated K48-linked ubiquitin conjugate removal and autophagosome formation on the damaged lysosomes. Deletion of Ptp4a2 in vivo compromises the recovery of glycerol-injection induced acute kidney injury due to impaired lysophagy and sustained lysosomal damage. Taken together, our data establish PTP4A2 as a critical regulator of VCP and uncover an important role for PTP4A2 in maintaining lysosomal homeostasis through dephosphorylation of VCP at Tyr805. Our study suggests that PTP4A2 targeting could be a potential therapeutic approach to treat cancers and other degenerative diseases by modulating lysosomal homeostasis and macroautophagy/autophagy.Abbreviations: AAA+: ATPases associated with diverse cellular activities; AKI: acute kidney injury; CBB: Coomassie Brilliant Blue; CRISPR: clustered regularly interspaced short palindromic repeats; ELDR: endo-lysosomal damage response; GFP: green fluorescent protein; GST: glutathione S-transferase; IHC: immunohistochemistry; IP: immunoprecipitation; LAMP1: lysosomal-associated membrane protein 1; LC-MS: liquid chromatography-mass spectrometry; LGALS3/Gal3: galectin 3; LLOMe: L-leucyl-L-leucine methyl ester; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MEF: mouse embryonic fibroblast; PLAA: phospholipase A2, activating protein; PTP4A2: protein tyrosine phosphatase 4a2; PUB: NGLY1/PNGase/UBA- or UBX-containing protein; PUL: PLAP, Ufd3, and Lub1; TFEB: transcription factor EB; UBXN6/UBXD1: UBX domain protein 6; UPS: ubiquitin-proteasome system; VCP/p97: valosin containing protein; VCPIP1: valosin containing protein interacting protein 1; YOD1: YOD1 deubiquitinase.
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Affiliation(s)
- Yunpeng Bai
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, USA
| | - Guimei Yu
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, USA
| | - Hong-Ming Zhou
- Department of Dermatology, Indiana University School of Medicine, Indianapolis, IN, USA
| | | | - Yuan Zhou
- Department of Biochemistry, Purdue University, West Lafayette, USA
| | - Peipei Zhu
- Department of Chemistry, Purdue University, West Lafayette, USA
| | - Qinglin Li
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, USA
| | - Lujuan Zhang
- Department of Speech, Language, and Hearing Sciences, Purdue University, West Lafayette, IN, USA
| | - Frederick Nguele Meke
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, USA
| | - Yiming Miao
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, USA
| | - Eli Chapman
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, A, USA
| | - W. Andy Tao
- Department of Chemistry, Purdue University, West Lafayette, USA
- Department of Biochemistry, Purdue University, West Lafayette, USA
- Center for Cancer Research
| | - Zhong-Yin Zhang
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, USA
- Department of Chemistry, Purdue University, West Lafayette, USA
- Center for Cancer Research
- Institute for Drug Discovery, Purdue University, West Lafayette, IN, USA
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Valimehr S, Sethi A, Shukla M, Bhattacharyya S, Kazemi M, Rouiller I. Molecular Mechanisms Driving and Regulating the AAA+ ATPase VCP/p97, an Important Therapeutic Target for Treating Cancer, Neurological and Infectious Diseases. Biomolecules 2023; 13:biom13050737. [PMID: 37238606 DOI: 10.3390/biom13050737] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/15/2023] [Accepted: 04/13/2023] [Indexed: 05/28/2023] Open
Abstract
p97/VCP, a highly conserved type II ATPase associated with diverse cellular activities (AAA+ ATPase), is an important therapeutic target in the treatment of neurodegenerative diseases and cancer. p97 performs a variety of functions in the cell and facilitates virus replication. It is a mechanochemical enzyme that generates mechanical force from ATP-binding and hydrolysis to perform several functions, including unfolding of protein substrates. Several dozens of cofactors/adaptors interact with p97 and define the multifunctionality of p97. This review presents the current understanding of the molecular mechanism of p97 during the ATPase cycle and its regulation by cofactors and small-molecule inhibitors. We compare detailed structural information obtained in different nucleotide states in the presence and absence of substrates and inhibitors. We also review how pathogenic gain-of-function mutations modify the conformational changes of p97 during the ATPase cycle. Overall, the review highlights how the mechanistic knowledge of p97 helps in designing pathway-specific modulators and inhibitors.
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Affiliation(s)
- Sepideh Valimehr
- Department of Biochemistry & Pharmacology, The University of Melbourne, Melbourne, VIC 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
- Bio21 Ian Holmes Imaging Centre, Department of Biochemistry & Pharmacology, The University of Melbourne, Melbourne, VIC 3010, Australia
- ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Ashish Sethi
- Department of Biochemistry & Pharmacology, The University of Melbourne, Melbourne, VIC 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
- Australian Nuclear Science Technology Organisation, The Australian Synchrotron, 800 Blackburn Rd, Clayton, VIC 3168, Australia
| | - Manjari Shukla
- Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur, Jodhpur 342030, Rajasthan, India
| | - Sudipta Bhattacharyya
- Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur, Jodhpur 342030, Rajasthan, India
| | - Mohsen Kazemi
- Department of Biochemistry & Pharmacology, The University of Melbourne, Melbourne, VIC 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
- ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Isabelle Rouiller
- Department of Biochemistry & Pharmacology, The University of Melbourne, Melbourne, VIC 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
- ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, The University of Melbourne, Melbourne, VIC 3010, Australia
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8
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Columbres RCA, Chin Y, Pratti S, Quinn C, Gonzalez-Cuyar LF, Weiss M, Quintero-Rivera F, Kimonis V. Novel Variants in the VCP Gene Causing Multisystem Proteinopathy 1. Genes (Basel) 2023; 14:genes14030676. [PMID: 36980948 PMCID: PMC10048343 DOI: 10.3390/genes14030676] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 02/28/2023] [Accepted: 03/02/2023] [Indexed: 03/30/2023] Open
Abstract
Valosin-containing protein (VCP) gene mutations have been associated with a rare autosomal dominant, adult-onset progressive disease known as multisystem proteinopathy 1 (MSP1), or inclusion body myopathy (IBM), Paget's disease of bone (PDB), frontotemporal dementia (FTD), (IBMPFD), and amyotrophic lateral sclerosis (ALS). We report the clinical and genetic analysis findings in five patients, three from the same family, with novel VCP gene variants: NM_007126.5 c.1106T>C (p.I369T), c.478G>A (p.A160T), and c.760A>T (p.I254F), associated with cardinal MSP1 manifestations including myopathy, PDB, and FTD. Our report adds to the spectrum of heterozygous pathogenic variants found in the VCP gene and the high degree of clinical heterogeneity. This case series prompts increased awareness and early consideration of MSP1 in the differential diagnosis of myopathies and/or PDB, dementia, or ALS to improve the diagnosis and early management of clinical symptoms.
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Affiliation(s)
- Rod Carlo Agram Columbres
- Division of Genetics and Genomic Medicine, Department of Pediatrics, University of California, Irvine, CA 92697, USA
- College of Osteopathic Medicine, William Carey University, Hattiesburg, MS 39401, USA
| | - Yue Chin
- College of Osteopathic Medicine, William Carey University, Hattiesburg, MS 39401, USA
| | - Sanjana Pratti
- College of Osteopathic Medicine, William Carey University, Hattiesburg, MS 39401, USA
| | - Colin Quinn
- Department of Neurology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Luis F Gonzalez-Cuyar
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98104, USA
| | - Michael Weiss
- Department of Neurology, University of Washington, Seattle, WA 98195, USA
| | - Fabiola Quintero-Rivera
- Division of Genetics and Genomic Medicine, Department of Pediatrics, University of California, Irvine, CA 92697, USA
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA 92697, USA
| | - Virginia Kimonis
- Division of Genetics and Genomic Medicine, Department of Pediatrics, University of California, Irvine, CA 92697, USA
- Department of Neurology, University of California, Irvine, CA 92697, USA
- Department of Pathology, University of California, Irvine, CA 92697, USA
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9
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Kilgas S, Ramadan K. Inhibitors of the ATPase p97/VCP: From basic research to clinical applications. Cell Chem Biol 2023; 30:3-21. [PMID: 36640759 DOI: 10.1016/j.chembiol.2022.12.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 11/13/2022] [Accepted: 12/21/2022] [Indexed: 01/15/2023]
Abstract
Protein homeostasis deficiencies underlie various cancers and neurodegenerative diseases. The ubiquitin-proteasome system (UPS) and autophagy are responsible for most of the protein degradation in mammalian cells and, therefore, represent attractive targets for cancer therapy and that of neurodegenerative diseases. The ATPase p97, also known as VCP, is a central component of the UPS that extracts and disassembles its substrates from various cellular locations and also regulates different steps in autophagy. Several UPS- and autophagy-targeting drugs are in clinical trials. In this review, we focus on the development of various p97 inhibitors, including the ATPase inhibitors CB-5083 and CB-5339, which reached clinical trials by demonstrating effective anti-tumor activity across various tumor models, providing an effective alternative to targeting protein degradation for cancer therapy. Here, we provide an overview of how different p97 inhibitors have evolved over time both as basic research tools and effective UPS-targeting cancer therapies in the clinic.
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Affiliation(s)
- Susan Kilgas
- Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK.
| | - Kristijan Ramadan
- Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK.
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10
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Fragment screening using biolayer interferometry reveals ligands targeting the SHP-motif binding site of the AAA+ ATPase p97. Commun Chem 2022; 5:169. [PMID: 36697690 PMCID: PMC9814400 DOI: 10.1038/s42004-022-00782-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 11/17/2022] [Indexed: 12/12/2022] Open
Abstract
Biosensor techniques have become increasingly important for fragment-based drug discovery during the last years. The AAA+ ATPase p97 is an essential protein with key roles in protein homeostasis and a possible target for cancer chemotherapy. Currently available p97 inhibitors address its ATPase activity and globally impair p97-mediated processes. In contrast, inhibition of cofactor binding to the N-domain by a protein-protein-interaction inhibitor would enable the selective targeting of specific p97 functions. Here, we describe a biolayer interferometry-based fragment screen targeting the N-domain of p97 and demonstrate that a region known as SHP-motif binding site can be targeted with small molecules. Guided by molecular dynamics simulations, the binding sites of selected screening hits were postulated and experimentally validated using protein- and ligand-based NMR techniques, as well as X-ray crystallography, ultimately resulting in the first structure of a small molecule in complex with the N-domain of p97. The identified fragments provide insights into how this region could be targeted and present first chemical starting points for the development of a protein-protein interaction inhibitor preventing the binding of selected cofactors to p97.
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11
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Mitochondrial proteotoxicity: implications and ubiquitin-dependent quality control mechanisms. Cell Mol Life Sci 2022; 79:574. [DOI: 10.1007/s00018-022-04604-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 06/04/2022] [Accepted: 10/17/2022] [Indexed: 11/27/2022]
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12
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Wang F, Li S, Rosencrans WM, Cheng KW, Stott GM, Mroczkowski B, Chou TF. Sulforaphane is Synergistic with CB-5083 and Inhibits Colony Formation of CB-5083-Resistant HCT116 Cells. ChemMedChem 2022; 17:e202200030. [PMID: 35451199 DOI: 10.1002/cmdc.202200030] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 04/04/2022] [Indexed: 11/09/2022]
Abstract
Human p97 is a potential drug target in oncology. Mutation-driven drug resistance is an obstacle to the long-term efficacy of targeted therapy. We found that the ATPase activity for one of the CB-5083-resistant p97 mutants was reduced, which also attenuated the degradation of K48 ubiquitinated proteins in cells. To understand how p97 mutant cells with significantly reduced ATPase activity can still grow, we discovered reduced levels of CHOP and NF-κB activation in the p97 mutant cells and these cellular changes can potentially protect HCT116 cells from death due to lowered p97 activity. In addition, the NF-kB inhibitor Sulforaphane reduces proliferation of CB-5083 resistant cells and acts synergistically with CB-5083 to block proliferation of the parental HCT116 cells. The combination of Sulforaphane and CB-5083 may be a useful treatment strategy to combat CB-5083 resistance.
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Affiliation(s)
- Feng Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Shan Li
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - William M Rosencrans
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Kai-Wen Cheng
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Gordon M Stott
- NExT Program Support, Applied/Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Barbara Mroczkowski
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Tsui-Fen Chou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.,Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
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13
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Song A, Wen AQ, Wen YE, Dzieciatkowska M, Kellems RE, Juneja HS, D'Alessandro A, Xia Y. p97 dysfunction underlies a loss of quality control of damaged membrane proteins and promotes oxidative stress and sickling in sickle cell disease. FASEB J 2022; 36:e22246. [PMID: 35405035 DOI: 10.1096/fj.202101500rr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 02/19/2022] [Accepted: 02/23/2022] [Indexed: 11/11/2022]
Abstract
Sickling is the central pathogenic process of sickle cell disease (SCD), one of the most prevalent inherited hemolytic disorders. Having no easy access to antioxidants in the cytosol, elevated levels of reactive oxygen species (ROS) residing at the plasma membrane in sickle red blood cells (sRBCs) easily oxidize membrane proteins and thus contribute to sickling. Although the ubiquitin-proteasome system (UPS) is essential to rapidly clear ROS-damaged membrane proteins and maintain cellular homeostasis, the function and regulatory mechanism of the UPS for their clearance in sRBCs remains unidentified. Elevated levels of polyubiquitinated membrane-associated proteins in human sRBCs are reported here. High throughput and untargeted proteomic analyses of membrane proteins immunoprecipitated by ubiquitin antibodies detected elevated levels of ubiquitination of a series of proteins including cytoskeletal proteins, transporters, ROS-related proteins, and UPS machinery components in sRBCs. Polyubiquitination of membrane-associated catalase was increased in sRBCs, associated with decreased catalase activity and elevated ROS. Surprisingly, shuttling of p97 (ATP-dependent valosin-containing chaperone protein), a key component of the UPS to shuttle polyubiquitinated proteins from the membrane to cytosol for proteasomal degradation, was significantly impaired, resulting in significant accumulation of p97 along with polyubiquitinated proteins in the membrane of human sRBCs. Functionally, inhibition of p97 directly promoted accumulation of polyubiquitinated membrane-associated proteins, excessive ROS levels, and sickling in response to hypoxia. Overall, we revealed that p97 dysfunction underlies impaired UPS and contributes to oxidative stress in sRBCs.
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Affiliation(s)
- Anren Song
- Department of Biochemistry and Molecular Biology, the University of Texas McGovern Medical School, Houston, Texas, USA
| | - Alexander Q Wen
- Department of Biochemistry and Molecular Biology, the University of Texas McGovern Medical School, Houston, Texas, USA.,University of California at San Diego, La Jolla, California, USA
| | - Y Edward Wen
- Department of Biochemistry and Molecular Biology, the University of Texas McGovern Medical School, Houston, Texas, USA.,University of Texas Southwestern Medical School, Dallas, Texas, USA
| | - Monika Dzieciatkowska
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Rodney E Kellems
- Department of Biochemistry and Molecular Biology, the University of Texas McGovern Medical School, Houston, Texas, USA.,Graduate Program in Biochemistry and Cell Biology, University of Texas MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, Texas, USA
| | - Harinder S Juneja
- Department of Internal Medicine, Divison of Hematology, the University of Texas McGovern Medical School, Houston, Texas, USA
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Yang Xia
- Department of Biochemistry and Molecular Biology, the University of Texas McGovern Medical School, Houston, Texas, USA.,Graduate Program in Biochemistry and Cell Biology, University of Texas MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, Texas, USA
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14
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Scarian E, Fiamingo G, Diamanti L, Palmieri I, Gagliardi S, Pansarasa O. The Role of VCP Mutations in the Spectrum of Amyotrophic Lateral Sclerosis-Frontotemporal Dementia. Front Neurol 2022; 13:841394. [PMID: 35273561 PMCID: PMC8902152 DOI: 10.3389/fneur.2022.841394] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 01/28/2022] [Indexed: 01/02/2023] Open
Abstract
Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal Dementia (FTD) are two neurological diseases which, respectively, and primarily affect motor neurons and frontotemporal lobes. Although they can lead to different signs and symptoms, it is now evident that these two pathologies form a continuum and that hallmarks of both diseases can be present within the same person in the so-called ALS-FTD spectrum. Many studies have focused on the genetic overlap of these pathologies and it is now clear that different genes, such as C9orf72, TARDBP, SQSTM1, FUS, and p97/VCP can be mutated in both the diseases. VCP was one of the first genes associated with both FTD and ALS representing an early example of gene overlapping. VCP belongs to the type II AAA (ATPases Associated with diverse cellular activities) family and is involved in ubiquitinated proteins degradation, autophagy, lysosomal clearance and mitochondrial quality control. Since its numerous roles, mutations in this gene lead to different pathological features, first and foremost TDP-43 mislocalization. This review aims to outline recent findings on VCP roles and on how its mutations are linked to the neuropathology of ALS and FTD.
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Affiliation(s)
- Eveljn Scarian
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy.,Cellular Models and Neuroepigenetics Unit, IRCCS Mondino Foundation, Pavia, Italy
| | - Giuseppe Fiamingo
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
| | - Luca Diamanti
- Neuroncology Unit, IRCCS Mondino Foundation, Pavia, Italy
| | - Ilaria Palmieri
- Department of Molecular Medicine, University of Pavia, Pavia, Italy.,Neurogenetics Research Center, IRCCS Mondino Foundation, Pavia, Italy
| | - Stella Gagliardi
- Molecular Biology and Transcriptomics Unit, IRCCS Mondino Foundation, Pavia, Italy
| | - Orietta Pansarasa
- Cellular Models and Neuroepigenetics Unit, IRCCS Mondino Foundation, Pavia, Italy
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15
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An Integrated In Silico, In Vitro and Tumor Tissues Study Identified Selenoprotein S (SELENOS) and Valosin-Containing Protein (VCP/p97) as Novel Potential Associated Prognostic Biomarkers in Triple Negative Breast Cancer. Cancers (Basel) 2022; 14:cancers14030646. [PMID: 35158912 PMCID: PMC8833666 DOI: 10.3390/cancers14030646] [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: 01/05/2022] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 02/01/2023] Open
Abstract
Simple Summary Triple negative breast cancer (TNBC) represents a clinical challenge because its early relapse, poor overall survival and lack of effective treatments. Altered levels selenoproteins have been correlated with development and progression of some cancers, however, no consistent data are available about their involvement in TNBC. Here we analyzed the expression profile of all twenty-five human selenoproteins in TNBC cells and tissues by a systematic approach, integrating in silico and wet lab approaches. We showed that the expression profiles of five selenoproteins are specifically dysregulated in TNBC. Most importantly, by a bioinformatics analysis, we selected selenoprotein S and its interacting protein valosin-containing protein (VCP/p97) as inter-related with the others and whose coordinated over-expression is associated with poor prognosis in TNBC. Overall, we highlighted two mechanistically related novel proteins whose correlated expression could be exploited for a better definition of prognosis as well as suggested as novel therapeutic target in TNBC. Abstract Background. Triple negative breast cancer (TNBC) is a heterogeneous group of tumors with early relapse, poor overall survival, and lack of effective treatments. Hence, new prognostic biomarkers and therapeutic targets are needed. Methods. The expression profile of all twenty-five human selenoproteins was analyzed in TNBC by a systematic approach.In silicoanalysis was performed on publicly available mRNA expression datasets (Cancer Cell Line Encyclopedia, CCLE and Library of Integrated Network-based Cellular Signatures, LINCS). Reverse transcription quantitative PCR analysis evaluated selenoprotein mRNA expression in TNBC versus non-TNBC and normal breast cells, and in TNBC tissues versus normal counterparts. Immunohistochemistry was employed to study selenoproteins in TNBC tissues. STRING and Cytoscape tools were used for functional and network analysis. Results.GPX1, GPX4, SELENOS, TXNRD1 and TXNRD3 were specifically overexpressed in TNBC cells, tissues and CCLE/LINCS datasets. Network analysis demonstrated that SELENOS-binding valosin-containing protein (VCP/p97) played a critical hub role in the TNBCselenoproteins sub-network, being directly associated with SELENOS expression. The combined overexpression of SELENOS and VCP/p97 correlated with advanced stages and poor prognosis in TNBC tissues and the TCGA dataset. Conclusion. Combined evaluation of SELENOS and VCP/p97 might represent a novel potential prognostic signature and a therapeutic target to be exploited in TNBC.
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16
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Pharmacological targeting of endoplasmic reticulum stress in disease. Nat Rev Drug Discov 2021; 21:115-140. [PMID: 34702991 DOI: 10.1038/s41573-021-00320-3] [Citation(s) in RCA: 183] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2021] [Indexed: 02/08/2023]
Abstract
The accumulation of misfolded proteins in the endoplasmic reticulum (ER) leads to ER stress, resulting in activation of the unfolded protein response (UPR) that aims to restore protein homeostasis. However, the UPR also plays an important pathological role in many diseases, including metabolic disorders, cancer and neurological disorders. Over the last decade, significant effort has been invested in targeting signalling proteins involved in the UPR and an array of drug-like molecules is now available. However, these molecules have limitations, the understanding of which is crucial for their development into therapies. Here, we critically review the existing ER stress and UPR-directed drug-like molecules, highlighting both their value and their limitations.
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17
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Li XJ, Zhang YY, Fu YH, Zhang H, Li HX, Li QF, Li HL, Tan RK, Jiang CX, Jiang W, Li ZX, Luo C, Lu BX, Dang YJ. Gossypol, a novel modulator of VCP, induces autophagic degradation of mutant huntingtin by promoting the formation of VCP/p97-LC3-mHTT complex. Acta Pharmacol Sin 2021; 42:1556-1566. [PMID: 33495516 PMCID: PMC8463700 DOI: 10.1038/s41401-020-00605-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 12/23/2020] [Indexed: 02/02/2023] Open
Abstract
Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder caused by toxic aggregates of mutant huntingtin protein (mHTT) in the brain. Decreasing mHTT is a potential strategy for therapeutic purpose of HD. Valosin-containing protein (VCP/p97) is a crucial regulator of proteostasis, which regulates the degradation of damaged protein through proteasome and autophagy pathway. Since VCP has been implicated in pathogenesis of HD as well as other neurodegenerative diseases, small molecules that specifically regulate the activity of VCP may be of therapeutic benefits for HD patients. In this study we established a high-throughput screening biochemical assay for VCP ATPase activity measurement and identified gossypol, a clinical approved drug in China, as a novel modulator of VCP. Gossypol acetate dose-dependently inhibited the enzymatic activity of VCP in vitro with IC50 of 6.53±0.6 μM. We further demonstrated that gossypol directly bound to the interface between the N and D1 domains of VCP. Gossypol acetate treatment not only lowered mHTT levels and rescued HD-relevant phenotypes in HD patient iPS-derived Q47 striatal neurons and HD knock-in mouse striatal cells, but also improved motor function deficits in both Drosophila and mouse HD models. Taken together, gossypol acetate acted through a gain-of-function way to induce the formation of VCP-LC3-mHTT ternary complex, triggering autophagic degradation of mHTT. This study reveals a new strategy for treatment of HD and raises the possibility that an existing drug can be repurposed as a new treatment of neurodegenerative diseases.
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Affiliation(s)
- Xiao-jing Li
- grid.8547.e0000 0001 0125 2443Key Laboratory of Metabolism and Molecular Medicine, the Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032 China
| | - Yuan-yuan Zhang
- grid.9227.e0000000119573309Drug Discovery and Design Center, The Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203 China
| | - Yu-hua Fu
- grid.8547.e0000 0001 0125 2443Neurology Department at Huashan Hospital, State Key Laboratory of Medical Neurobiology, School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Hao Zhang
- grid.9227.e0000000119573309Drug Discovery and Design Center, The Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203 China
| | - He-xuan Li
- grid.8547.e0000 0001 0125 2443Neurology Department at Huashan Hospital, State Key Laboratory of Medical Neurobiology, School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Quan-fu Li
- grid.8547.e0000 0001 0125 2443Key Laboratory of Metabolism and Molecular Medicine, the Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032 China
| | - Hai-ling Li
- grid.8547.e0000 0001 0125 2443Key Laboratory of Metabolism and Molecular Medicine, the Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032 China
| | - Ren-ke Tan
- grid.8547.e0000 0001 0125 2443Key Laboratory of Metabolism and Molecular Medicine, the Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032 China
| | - Chen-xiao Jiang
- grid.8547.e0000 0001 0125 2443Key Laboratory of Metabolism and Molecular Medicine, the Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032 China
| | - Wei Jiang
- grid.8547.e0000 0001 0125 2443Key Laboratory of Metabolism and Molecular Medicine, the Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032 China
| | - Zeng-xia Li
- grid.8547.e0000 0001 0125 2443Key Laboratory of Metabolism and Molecular Medicine, the Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032 China
| | - Cheng Luo
- grid.9227.e0000000119573309Drug Discovery and Design Center, The Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203 China
| | - Bo-xun Lu
- grid.8547.e0000 0001 0125 2443Neurology Department at Huashan Hospital, State Key Laboratory of Medical Neurobiology, School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Yong-jun Dang
- grid.8547.e0000 0001 0125 2443Key Laboratory of Metabolism and Molecular Medicine, the Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032 China
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18
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Valosin-Containing Protein (VCP)/p97: A Prognostic Biomarker and Therapeutic Target in Cancer. Int J Mol Sci 2021; 22:ijms221810177. [PMID: 34576340 PMCID: PMC8469696 DOI: 10.3390/ijms221810177] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/17/2021] [Accepted: 09/18/2021] [Indexed: 01/02/2023] Open
Abstract
Valosin-containing protein (VCP)/p97, a member of the AAA+ ATPase family, is a molecular chaperone recruited to the endoplasmic reticulum (ER) membrane by binding to membrane adapters (nuclear protein localization protein 4 (NPL4), p47 and ubiquitin regulatory X (UBX) domain-containing protein 1 (UBXD1)), where it is involved in ER-associated protein degradation (ERAD). However, VCP/p97 interacts with many cofactors to participate in different cellular processes that are critical for cancer cell survival and aggressiveness. Indeed, VCP/p97 is reported to be overexpressed in many cancer types and is considered a potential cancer biomarker and therapeutic target. This review summarizes the role of VCP/p97 in different cancers and the advances in the discovery of small-molecule inhibitors with therapeutic potential, focusing on the challenges associated with cancer-related VCP mutations in the mechanisms of resistance to inhibitors.
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19
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Conserved L464 in p97 D1-D2 linker is critical for p97 cofactor regulated ATPase activity. Biochem J 2021; 478:3185-3204. [PMID: 34405853 DOI: 10.1042/bcj20210288] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 08/10/2021] [Accepted: 08/18/2021] [Indexed: 11/17/2022]
Abstract
p97 protein is a highly conserved, abundant, functionally diverse, structurally dynamic homohexameric AAA enzyme-containing N, D1, and D2 domains. A truncated p97 protein containing the N and D1 domains and the D1-D2 linker (ND1L) exhibits 79% of wild-type (WT) ATPase activity whereas the ND1 domain alone without the linker only has 2% of WT activity. To investigate the relationship between the D1-D2 linker and the D1 domain, we produced p97 ND1L mutants and demonstrated that this 22-residue linker region is essential for D1 ATPase activity. The conserved amino acid leucine 464 (L464) is critical for regulating D1 and D2 ATPase activity by p97 cofactors p37, p47, and Npl4-Ufd1 (NU). Changing leucine to alanine, proline, or glutamate increased the maximum rate of ATP turnover (kcat) of p47-regulated ATPase activities for these mutants, but not for WT. p37 and p47 increased the kcat of the proline substituted linker, suggesting that they induced linker conformations facilitating ATP hydrolysis. NU inhibited D1 ATPase activities of WT and mutant ND1L proteins, but activated D2 ATPase activity of full-length p97. To further understand the mutant mechanism, we used single-particle cryo-EM to visualize the full-length p97L464P and revealed the conformational change of the D1-D2 linker, resulting in a movement of the helix-turn-helix motif (543-569). Taken together with the biochemical and structural results we conclude that the linker helps maintain D1 in a competent conformation and relays the communication to/from the N-domain to the D1 and D2 ATPase domains, which are ∼50 Å away.
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20
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Endoplasmic Reticulum-Associated Degradation Controls Virus Protein Homeostasis, Which Is Required for Flavivirus Propagation. J Virol 2021; 95:e0223420. [PMID: 33980593 DOI: 10.1128/jvi.02234-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Many positive-stranded RNA viruses encode polyproteins from which viral proteins are generated by processing the polyproteins. This system produces an equal amount of each viral protein, though the required amounts for each protein are not the same. In this study, we found the extra membrane-anchored nonstructural (NS) proteins of Japanese encephalitis virus and dengue virus are rapidly and selectively degraded by the endoplasmic reticulum-associated degradation (ERAD) pathway. Our gene targeting study revealed that ERAD involving Derlin2 and SEL1L, but not Derlin1, is required for the viral genome replication. Derlin2 is predominantly localized in the convoluted membrane (CM) of the viral replication organelle, and viral NS proteins are degraded in the CM. Hence, these results suggest that viral protein homeostasis is regulated by Derlin2-mediated ERAD in the CM, and this process is critical for the propagation of these viruses. IMPORTANCE The results of this study reveal the cellular ERAD system controls the amount of each viral protein in virus-infected cells and that this "viral protein homeostasis" is critical for viral propagation. Furthermore, we clarified that the "convoluted membrane (CM)," which was previously considered a structure with unknown function, serves as a kind of waste dump where viral protein degradation occurs. We also found that the Derlin2/SEL1L/HRD1-specific pathway is involved in this process, whereas the Derlin1-mediated pathway is not. This novel ERAD-mediated fine-tuning system for the stoichiometries of polyprotein-derived viral proteins may represent a common feature among polyprotein-encoding viruses.
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21
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Prattes M, Grishkovskaya I, Hodirnau VV, Rössler I, Klein I, Hetzmannseder C, Zisser G, Gruber CC, Gruber K, Haselbach D, Bergler H. Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine. Nat Commun 2021; 12:3483. [PMID: 34108481 PMCID: PMC8190095 DOI: 10.1038/s41467-021-23854-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/20/2021] [Indexed: 02/01/2023] Open
Abstract
The hexameric AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis and initiates cytoplasmic maturation of the large ribosomal subunit by releasing the shuttling maturation factor Rlp24. Drg1 monomers contain two AAA-domains (D1 and D2) that act in a concerted manner. Rlp24 release is inhibited by the drug diazaborine which blocks ATP hydrolysis in D2. The mode of inhibition was unknown. Here we show the first cryo-EM structure of Drg1 revealing the inhibitory mechanism. Diazaborine forms a covalent bond to the 2'-OH of the nucleotide in D2, explaining its specificity for this site. As a consequence, the D2 domain is locked in a rigid, inactive state, stalling the whole Drg1 hexamer. Resistance mechanisms identified include abolished drug binding and altered positioning of the nucleotide. Our results suggest nucleotide-modifying compounds as potential novel inhibitors for AAA-ATPases.
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Affiliation(s)
- Michael Prattes
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Irina Grishkovskaya
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, Austria
| | | | - Ingrid Rössler
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Isabella Klein
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | | | - Gertrude Zisser
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | | | - Karl Gruber
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
- Field of Excellence BioHealth - University of Graz, Graz, Austria
| | - David Haselbach
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, Austria.
| | - Helmut Bergler
- Institute of Molecular Biosciences, University of Graz, Graz, Austria.
- BioTechMed-Graz, Graz, Austria.
- Field of Excellence BioHealth - University of Graz, Graz, Austria.
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22
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Analysis of Zika virus capsid-Aedes aegypti mosquito interactome reveals pro-viral host factors critical for establishing infection. Nat Commun 2021; 12:2766. [PMID: 33986255 PMCID: PMC8119459 DOI: 10.1038/s41467-021-22966-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 04/06/2021] [Indexed: 02/06/2023] Open
Abstract
The escalating global prevalence of arboviral diseases emphasizes the need to improve our understanding of their biology. Research in this area has been hindered by the lack of molecular tools for studying virus-mosquito interactions. Here, we develop an Aedes aegypti cell line which stably expresses Zika virus (ZIKV) capsid proteins in order to study virus-vector protein-protein interactions through quantitative label-free proteomics. We identify 157 interactors and show that eight have potentially pro-viral activity during ZIKV infection in mosquito cells. Notably, silencing of transitional endoplasmic reticulum protein TER94 prevents ZIKV capsid degradation and significantly reduces viral replication. Similar results are observed if the TER94 ortholog (VCP) functioning is blocked with inhibitors in human cells. In addition, we show that an E3 ubiquitin-protein ligase, UBR5, mediates the interaction between TER94 and ZIKV capsid. Our study demonstrates a pro-viral function for TER94/VCP during ZIKV infection that is conserved between human and mosquito cells.
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Valosin-containing protein/p97 plays critical roles in the Japanese encephalitis virus life cycle. J Virol 2021; 95:JVI.02336-20. [PMID: 33731458 PMCID: PMC8139707 DOI: 10.1128/jvi.02336-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Host factors provide critical support for every aspect of the virus life cycle. We recently identified the valosin-containing protein (VCP)/p97, an abundant cellular ATPase with diverse cellular functions, as a host factor important for Japanese encephalitis virus (JEV) replication. In cultured cells, using siRNA-mediated protein depletion and pharmacological inhibitors, we show that VCP is crucial for replication of three flaviviruses: JEV, Dengue, and West Nile viruses. An FDA-approved VCP inhibitor, CB-5083, extended survival of mice in the animal model of JEV infection. While VCP depletion did not inhibit JEV attachment on cells, it delayed capsid degradation, potentially through the entrapment of the endocytosed virus in clathrin-coated vesicles (CCVs). Early during infection, VCP-depleted cells showed an increased colocalization of JEV capsid with clathrin, and also higher viral RNA levels in purified CCVs. We show that VCP interacts with the JEV nonstructural protein NS5 and is an essential component of the virus replication complex. The depletion of the major VCP cofactor UFD-1 also significantly inhibited JEV replication. Mechanistically, thus, VCP affected two crucial steps of the JEV life cycle - nucleocapsid release and RNA replication. Our study establishes VCP as a common host factor with a broad antiviral potential against flaviviruses.ImportanceJEV is the leading cause of viral encephalitis epidemics in South-east Asia, affecting majorly children with high morbidity and mortality. Identification of host factors is thus essential for the rational design of anti-virals that are urgently need as therapeutics. Here we have identified the VCP protein as one such host-factor. This protein is highly abundant in cells and engages in diverse functions and cellular pathways by its ability to interact with different co-factors. Using siRNA mediated protein knockdown, we show that this protein is essential for release of the viral RNA into the cell so that it can initiate replication. The protein plays a second crucial role for the formation of the JEV replication complex. FDA-approved drugs targeting VCP show enhanced mouse survival in JE model of disease, suggesting that this could be a druggable target for flavivirus infections.
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Higgins R, Kabbaj MH, Sherwin D, Howell LA, Hatcher A, Tomko RJ, Wang Y. The Cdc48 Complex Alleviates the Cytotoxicity of Misfolded Proteins by Regulating Ubiquitin Homeostasis. Cell Rep 2021; 32:107898. [PMID: 32668237 DOI: 10.1016/j.celrep.2020.107898] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 05/04/2020] [Accepted: 06/22/2020] [Indexed: 10/23/2022] Open
Abstract
The accumulation of misfolded proteins is associated with multiple neurodegenerative disorders, but it remains poorly defined how this accumulation causes cytotoxicity. Here, we demonstrate that the Cdc48/p97 segregase machinery drives the clearance of ubiquitinated model misfolded protein Huntingtin (Htt103QP) and limits its aggregation. Nuclear ubiquitin ligase San1 acts upstream of Cdc48 to ubiquitinate Htt103QP. Unexpectedly, deletion of SAN1 and/or its cytosolic counterpart UBR1 rescues the toxicity associated with Cdc48 deficiency, suggesting that ubiquitin depletion, rather than compromised proteolysis of misfolded proteins, causes the growth defect in cells with Cdc48 deficiency. Indeed, Cdc48 deficiency leads to elevated protein ubiquitination levels and decreased free ubiquitin, which depends on San1/Ubr1. Furthermore, enhancing free ubiquitin levels rescues the toxicity in various Cdc48 pathway mutants and restores normal turnover of a known Cdc48-independent substrate. Our work highlights a previously unappreciated function for Cdc48 in ensuring the regeneration of monoubiquitin that is critical for normal cellular function.
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Affiliation(s)
- Ryan Higgins
- Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL 32306, USA
| | - Marie-Helene Kabbaj
- Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL 32306, USA
| | - Delaney Sherwin
- Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL 32306, USA
| | - Lauren A Howell
- Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL 32306, USA
| | - Alexa Hatcher
- College of Nursing, Florida State University, 600 West College Avenue, Tallahassee, FL 32306, USA
| | - Robert J Tomko
- Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL 32306, USA
| | - Yanchang Wang
- Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL 32306, USA.
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Wang Y, Soto-Acosta R, Ding R, Chen L, Geraghty RJ. Anti-HCMV activity by an irreversible p97 inhibitor LC-1310. Med Chem Res 2021; 30:440-448. [PMID: 33456290 PMCID: PMC7794631 DOI: 10.1007/s00044-020-02679-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 12/02/2020] [Indexed: 11/25/2022]
Abstract
The AAA+ (ATPase associated with various cellular activities) protein p97, also called valosin-containing protein, is a hexameric ring ATPase and uses ATP hydrolysis to unfold or extract proteins from biological complexes. Many cellular processes are affected by p97 including ER-associated degradation, DNA damage response, cell signaling (NF-κB), cell cycle progression, autophagy, and others. Not surprisingly, with its role in many fundamental cellular processes, p97 function is important for the replication of many viruses. We tested irreversible p97-targeting compounds for their ability to inhibit the replication of multiple viruses compared to the known p97 inhibitors NMS-873 and CB-5083. Our results indicate that overall cellular toxicity for p97 compounds provides a challenge for antivirals targeting p97. However, we identified one compound with sub-micromolar activity against human cytomegalovirus and improved cell viability to provide evidence for the potential of irreversible p97 inhibitors as antivirals. ![]()
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Affiliation(s)
- Yan Wang
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455 USA
- Present Address: Translational Medicine R&D Center, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 China
| | - Ruben Soto-Acosta
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455 USA
| | - Rui Ding
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455 USA
| | - Liqiang Chen
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455 USA
| | - Robert J. Geraghty
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455 USA
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Pan M, Zheng Q, Yu Y, Ai H, Xie Y, Zeng X, Wang C, Liu L, Zhao M. Seesaw conformations of Npl4 in the human p97 complex and the inhibitory mechanism of a disulfiram derivative. Nat Commun 2021; 12:121. [PMID: 33402676 PMCID: PMC7785736 DOI: 10.1038/s41467-020-20359-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 11/25/2020] [Indexed: 01/29/2023] Open
Abstract
p97, also known as valosin-containing protein (VCP) or Cdc48, plays a central role in cellular protein homeostasis. Human p97 mutations are associated with several neurodegenerative diseases. Targeting p97 and its cofactors is a strategy for cancer drug development. Despite significant structural insights into the fungal homolog Cdc48, little is known about how human p97 interacts with its cofactors. Recently, the anti-alcohol abuse drug disulfiram was found to target cancer through Npl4, a cofactor of p97, but the molecular mechanism remains elusive. Here, using single-particle cryo-electron microscopy (cryo-EM), we uncovered three Npl4 conformational states in complex with human p97 before ATP hydrolysis. The motion of Npl4 results from its zinc finger motifs interacting with the N domain of p97, which is essential for the unfolding activity of p97. In vitro and cell-based assays showed that the disulfiram derivative bis-(diethyldithiocarbamate)-copper (CuET) can bypass the copper transporter system and inhibit the function of p97 in the cytoplasm by releasing cupric ions under oxidative conditions, which disrupt the zinc finger motifs of Npl4, locking the essential conformational switch of the complex.
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Affiliation(s)
- Man Pan
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Qingyun Zheng
- Tsinghua-Peking Center for Life Sciences, Department of Chemistry, Tsinghua University, 100084, Beijing, China
| | - Yuanyuan Yu
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Huasong Ai
- Tsinghua-Peking Center for Life Sciences, Department of Chemistry, Tsinghua University, 100084, Beijing, China
| | - Yuan Xie
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Xin Zeng
- Peking-Tsinghua Center for Life Sciences, College of Chemistry and Molecular Engineering, Peking University, 100871, Beijing, China
| | - Chu Wang
- Peking-Tsinghua Center for Life Sciences, College of Chemistry and Molecular Engineering, Peking University, 100871, Beijing, China
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences, Department of Chemistry, Tsinghua University, 100084, Beijing, China.
| | - Minglei Zhao
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA.
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27
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Glaza P, Ranaweera CB, Shiva S, Roy A, Geisbrecht BV, Schoenen FJ, Zolkiewski M. Repurposing p97 inhibitors for chemical modulation of the bacterial ClpB-DnaK bichaperone system. J Biol Chem 2021; 296:100079. [PMID: 33187983 PMCID: PMC7948422 DOI: 10.1074/jbc.ra120.015413] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 10/31/2020] [Accepted: 11/13/2020] [Indexed: 01/18/2023] Open
Abstract
The ClpB-DnaK bichaperone system reactivates aggregated cellular proteins and is essential for survival of bacteria, fungi, protozoa, and plants under stress. AAA+ ATPase ClpB is a promising target for the development of antimicrobials because a loss of its activity is detrimental for survival of many pathogens and no apparent ClpB orthologs are found in metazoans. We investigated ClpB activity in the presence of several compounds that were previously described as inhibitor leads for the human AAA+ ATPase p97, an antitumor target. We discovered that N2,N4-dibenzylquinazoline-2,4-diamine (DBeQ), the least potent among the tested p97 inhibitors, binds to ClpB with a Kd∼60 μM and inhibits the casein-activated, but not the basal, ATPase activity of ClpB with an IC50∼5 μM. The remaining p97 ligands, which displayed a higher affinity toward p97, did not affect the ClpB ATPase. DBeQ also interacted with DnaK with a Kd∼100 μM and did not affect the DnaK ATPase but inhibited the DnaK chaperone activity in vitro. DBeQ inhibited the reactivation of aggregated proteins by the ClpB-DnaK bichaperone system in vitro with an IC50∼5 μM and suppressed the growth of cultured Escherichia coli. The DBeQ-induced loss of E. coli proliferation was exacerbated by heat shock but was nearly eliminated in a ClpB-deficient E. coli strain, which demonstrates a significant selectivity of DBeQ toward ClpB in cells. Our results provide chemical validation of ClpB as a target for developing novel antimicrobials. We identified DBeQ as a promising lead compound for structural optimization aimed at selective targeting of ClpB and/or DnaK.
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Affiliation(s)
- Przemyslaw Glaza
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, USA
| | - Chathurange B Ranaweera
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, USA
| | - Sunitha Shiva
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, USA
| | - Anuradha Roy
- High Throughput Screening Laboratory, University of Kansas, Lawrence, Kansas, USA; Lead Development and Optimization Shared Resource, University of Kansas Cancer Center, Kansas City, Kansas, USA
| | - Brian V Geisbrecht
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, USA
| | - Frank J Schoenen
- Lead Development and Optimization Shared Resource, University of Kansas Cancer Center, Kansas City, Kansas, USA; Higuchi Biosciences Center, University of Kansas, Lawrence, Kansas, USA
| | - Michal Zolkiewski
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, USA.
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Cayli S, Sahin C, Sanci TO, Nakkas H. Inhibition of p97/VCP function leads to defective autophagosome maturation, cell cycle arrest and apoptosis in mouse Sertoli cells. Theriogenology 2020; 158:196-206. [PMID: 32966945 DOI: 10.1016/j.theriogenology.2020.09.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 09/07/2020] [Accepted: 09/14/2020] [Indexed: 12/16/2022]
Abstract
p97/valosin-containing protein (VCP) is expressed in many cells and plays critical functions in a broad range of diverse cellular processes. Because it is expressed in the mouse testes, predominantly in Sertoli cells, and is known to play a critical role in autophagy and apoptosis in different cell types, we set out to investigate its function in autophagosome maturation, apoptosis and cell cycle arrest in a mouse Sertoli cell line. To study the mechanism of p97/VCP action, p97/VCP siRNA and a specific p97/VCP inhibitor, N2,N4-dibenzylquinazoline-2,4-diamine (DBeQ), were used in the mouse 15P1 Sertoli cell line. Loss of p97/VCP activity due to DBeQ exposure and silencing of p97/VCP (siVCP) expression results in autophagosome (LC3 and p62) accumulation in the cytoplasm of Sertoli cells. The coexpression of autophagosomal and lysosomal markers (LAMP1 and LAMP2) was reduced in cells in which p97/VCP expression had been inactivated. To better understand in which step of autophagy p97/VCP functions, the interaction between autophagosomal and autolysosomal markers was studied by coimmunoprecipitation and colocalization experiments. The interaction between autophagosomal markers and lysosomal markers decreased in siVCP-expressing and DBeQ-exposed cells. Moreover, the expression of siVCP and DBeQ exposure caused cytoplasmic vacuolation, induced caspase 3-7-mediated cell death and decreased cell cycle progression in mouse Sertoli cells. Taken together, the results show that p97/VCP is essential for autophagosome maturation and cell survival in mouse Sertoli cells. When these functions are prevented, impaired autophagy and apoptosis may have a detrimental effect on germ cells and cause male infertility.
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Affiliation(s)
- Sevil Cayli
- Ankara Yıldırım Beyazıt University, Medical Faculty, Dept. of Histology and Embryology, Ankara, Turkey.
| | - Cansu Sahin
- Ankara Yıldırım Beyazıt University, Medical Faculty, Dept. of Histology and Embryology, Ankara, Turkey
| | - Tuba Ozdemir Sanci
- Ankara Yıldırım Beyazıt University, Medical Faculty, Dept. of Histology and Embryology, Ankara, Turkey
| | - Hilal Nakkas
- Ankara Yıldırım Beyazıt University, Medical Faculty, Dept. of Histology and Embryology, Ankara, Turkey
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29
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Ramanathan HN, Zhang S, Douam F, Mar KB, Chang J, Yang PL, Schoggins JW, Ploss A, Lindenbach BD. A Sensitive Yellow Fever Virus Entry Reporter Identifies Valosin-Containing Protein (VCP/p97) as an Essential Host Factor for Flavivirus Uncoating. mBio 2020; 11:e00467-20. [PMID: 32291299 PMCID: PMC7157815 DOI: 10.1128/mbio.00467-20] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 03/16/2020] [Indexed: 01/17/2023] Open
Abstract
While the basic mechanisms of flavivirus entry and fusion are understood, little is known about the postfusion events that precede RNA replication, such as nucleocapsid disassembly. We describe here a sensitive, conditionally replication-defective yellow fever virus (YFV) entry reporter, YFVΔSK/Nluc, to quantitively monitor the translation of incoming, virus particle-delivered genomes. We validated that YFVΔSK/Nluc gene expression can be neutralized by YFV-specific antisera and requires known flavivirus entry pathways and cellular factors, including clathrin- and dynamin-mediated endocytosis, endosomal acidification, YFV E glycoprotein-mediated fusion, and cellular LY6E and RPLP1 expression. The initial round of YFV translation was shown to require cellular ubiquitylation, consistent with recent findings that dengue virus capsid protein must be ubiquitylated in order for nucleocapsid uncoating to occur. Importantly, translation of incoming YFV genomes also required valosin-containing protein (VCP)/p97, a cellular ATPase that unfolds and extracts ubiquitylated client proteins from large complexes. RNA transfection and washout experiments showed that VCP/p97 functions at a postfusion, pretranslation step in YFV entry. Finally, VCP/p97 activity was required by other flaviviruses in mammalian cells and by YFV in mosquito cells. Together, these data support a critical role for VCP/p97 in the disassembly of incoming flavivirus nucleocapsids during a postfusion step in virus entry.IMPORTANCE Flaviviruses are an important group of RNA viruses that cause significant human disease. The mechanisms by which flavivirus nucleocapsids are disassembled during virus entry remain unclear. Here, we used a yellow fever virus entry reporter, which expresses a sensitive reporter enzyme but does not replicate, to show that nucleocapsid disassembly requires the cellular protein-disaggregating enzyme valosin-containing protein, also known as p97.
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Affiliation(s)
- Harish N Ramanathan
- Department of Microbial Pathogenesis, Yale University, New Haven, Connecticut, USA
| | - Shuo Zhang
- Department of Microbial Pathogenesis, Yale University, New Haven, Connecticut, USA
| | - Florian Douam
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Katrina B Mar
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Jinhong Chang
- Department of Experimental Therapeutics, The Baruch S. Blumberg Institute, Doylestown, Pennsylvania, USA
| | - Priscilla L Yang
- Department of Microbiology and the Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - John W Schoggins
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Alexander Ploss
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Brett D Lindenbach
- Department of Microbial Pathogenesis, Yale University, New Haven, Connecticut, USA
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Hassannia B, Logie E, Vandenabeele P, Vanden Berghe T, Vanden Berghe W. Withaferin A: From ayurvedic folk medicine to preclinical anti-cancer drug. Biochem Pharmacol 2020; 173:113602. [DOI: 10.1016/j.bcp.2019.08.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 08/05/2019] [Indexed: 12/26/2022]
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31
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Pharmacophore modeling, atom-based 3D-QSAR and molecular docking studies on N-benzylpyrimidin-4-amine derivatives as VCP/p97 inhibitors. Med Chem Res 2020. [DOI: 10.1007/s00044-020-02517-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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32
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Abstract
p97 belongs to the functional diverse superfamily of AAA+ (ATPases Associated with diverse cellular Activities) ATPases and is characterized by an N-terminal regulatory domain and two stacked hexameric ATPase domains forming a central protein conducting channel. p97 is highly versatile and has key functions in maintaining protein homeostasis including protein quality control mechanisms like the ubiquitin proteasome system (UPS) and autophagy to disassemble polyubiquitylated proteins from chromatin, membranes, macromolecular protein complexes and aggregates which are either degraded by the proteasome or recycled. p97 can use energy derived from ATP hydrolysis to catalyze substrate unfolding and threading through its central channel. The function of p97 in a large variety of different cellular contexts is reflected by its simultaneous association with different cofactors, which are involved in substrate recognition and processing, thus leading to the formation of transient multi-protein complexes. Dysregulation in protein homeostasis and proteotoxic stress are often involved in the development of cancer and neurological diseases and targeting the UPS including p97 in cancer is a well-established pharmacological strategy. In this chapter we will describe structural and functional aspects of the p97 interactome in regulating diverse cellular processes and will discuss the role of p97 in targeted cancer therapy.
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Figuerola-Conchas A, Saarbach J, Daguer JP, Cieren A, Barluenga S, Winssinger N, Gotta M. Small-Molecule Modulators of the ATPase VCP/p97 Affect Specific p97 Cellular Functions. ACS Chem Biol 2020; 15:243-253. [PMID: 31790201 DOI: 10.1021/acschembio.9b00832] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
VCP/p97 belongs to the AAA+ ATPase family and has an essential role in several cellular processes ranging from cell division to protein homeostasis. Compounds targeting p97 inhibit the main ATPase domain and cause cell death. Here, using PNA-encoded chemical libraries, we have identified two small molecules that target the regulatory domain of p97, comprising the N-terminal and the D1 ATPase domains, and do not cause cell death. One molecule, NW1028, inhibits the degradation of a p97-dependent reporter, whereas the other, NW1030, increases it. ATPase assays show that NW1028 and NW1030 do not affect the main catalytic domain of p97. Mapping of the binding site using a photoaffinity conjugate points to a cleft at the interface of the N-terminal and the D1 ATPase domains. We have therefore discovered two new compounds that bind to the regulatory domain of p97 and modulate specific p97 cellular functions. Using these compounds, we have revealed a role for p97 in the regulation of mitotic spindle orientation in HeLa cells.
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Affiliation(s)
- Ainoa Figuerola-Conchas
- Department of Cell Physiology and Metabolism, University of Geneva, 1211 Geneva 4, Switzerland
- National Centre of Competence in Research (NCCR) in Chemical Biology, University of Geneva, Geneva, Switzerland
| | - Jacques Saarbach
- Department of Cell Physiology and Metabolism, University of Geneva, 1211 Geneva 4, Switzerland
- National Centre of Competence in Research (NCCR) in Chemical Biology, University of Geneva, Geneva, Switzerland
| | - Jean-Pierre Daguer
- National Centre of Competence in Research (NCCR) in Chemical Biology, University of Geneva, Geneva, Switzerland
- Department of Organic Chemistry, University of Geneva, 1211 Geneva 4, Switzerland
| | - Adeline Cieren
- Department of Cell Physiology and Metabolism, University of Geneva, 1211 Geneva 4, Switzerland
- National Centre of Competence in Research (NCCR) in Chemical Biology, University of Geneva, Geneva, Switzerland
| | - Sofia Barluenga
- National Centre of Competence in Research (NCCR) in Chemical Biology, University of Geneva, Geneva, Switzerland
- Department of Organic Chemistry, University of Geneva, 1211 Geneva 4, Switzerland
| | - Nicolas Winssinger
- National Centre of Competence in Research (NCCR) in Chemical Biology, University of Geneva, Geneva, Switzerland
- Department of Organic Chemistry, University of Geneva, 1211 Geneva 4, Switzerland
| | - Monica Gotta
- Department of Cell Physiology and Metabolism, University of Geneva, 1211 Geneva 4, Switzerland
- National Centre of Competence in Research (NCCR) in Chemical Biology, University of Geneva, Geneva, Switzerland
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Abstract
Endoplasmic reticulum-associated degradation (ERAD) is an essential process that removes misfolded proteins from the ER, preventing cellular dysfunction and disease. While most of the key components of ERAD are known, their specific localization remains a mystery. This study uses in situ cryo-electron tomography to directly visualize the ERAD machinery within the native cellular environment. Proteasomes and Cdc48, the complexes that extract and degrade ER proteins, cluster together in non–membrane-bound cytosolic microcompartments that contact ribosome-free patches on the ER membrane. This discrete molecular organization may facilitate efficient ERAD. Structural analysis reveals that proteasomes directly engage ER-localized substrates, providing evidence for a noncanonical “direct ERAD” pathway. In addition, live-cell fluorescence microscopy suggests that these ER-associated proteasome clusters form by liquid–liquid phase separation. To promote the biochemical reactions of life, cells can compartmentalize molecular interaction partners together within separated non–membrane-bound regions. It is unknown whether this strategy is used to facilitate protein degradation at specific locations within the cell. Leveraging in situ cryo-electron tomography to image the native molecular landscape of the unicellular alga Chlamydomonas reinhardtii, we discovered that the cytosolic protein degradation machinery is concentrated within ∼200-nm foci that contact specialized patches of endoplasmic reticulum (ER) membrane away from the ER–Golgi interface. These non–membrane-bound microcompartments exclude ribosomes and consist of a core of densely clustered 26S proteasomes surrounded by a loose cloud of Cdc48. Active proteasomes in the microcompartments directly engage with putative substrate at the ER membrane, a function canonically assigned to Cdc48. Live-cell fluorescence microscopy revealed that the proteasome clusters are dynamic, with frequent assembly and fusion events. We propose that the microcompartments perform ER-associated degradation, colocalizing the degradation machinery at specific ER hot spots to enable efficient protein quality control.
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35
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Zhang H, Read C, Nguyen CC, Siddiquey MNA, Shang C, Hall CM, von Einem J, Kamil JP. The Human Cytomegalovirus Nonstructural Glycoprotein UL148 Reorganizes the Endoplasmic Reticulum. mBio 2019; 10:e02110-19. [PMID: 31822584 PMCID: PMC6904874 DOI: 10.1128/mbio.02110-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 10/29/2019] [Indexed: 12/17/2022] Open
Abstract
Human cytomegalovirus (HCMV) encodes an endoplasmic reticulum (ER)-resident glycoprotein, UL148, which activates the unfolded protein response (UPR) but is fully dispensable for viral replication in cultured cells. Hence, its previously ascribed roles in immune evasion and modulation of viral cell tropism are hypothesized to cause ER stress. Here, we show that UL148 is necessary and sufficient to drive the formation of prominent ER-derived structures that on average occupy 5% of the infected cell cytoplasm. The structures are sites where UL148 coalesces with cellular proteins involved in ER quality control, such as HRD1 and EDEM1. Electron microscopy revealed that cells infected with wild-type but not UL148-null HCMV show prominent accumulations of densely packed ruffled ER membranes which connect to distended cisternae of smooth and partially rough ER. During ectopic expression of UL148-green fluorescent protein (GFP) fusion protein, punctate signals traffic to accumulate at conspicuous structures. The structures exhibit poor recovery of fluorescence after photobleaching, which suggests that their contents are poorly mobile and do not efficiently exchange with the rest of the ER. Small-molecule blockade of the integrated stress response (ISR) prevents the formation of puncta, leading to a uniform reticular fluorescent signal. Accordingly, ISR inhibition during HCMV infection abolishes the coalescence of UL148 and HRD1 into discrete structures, which argues that UL148 requires the ISR to cause ER reorganization. Given that UL148 stabilizes immature forms of a receptor binding subunit for a viral envelope glycoprotein complex important for HCMV infectivity, our results imply that stress-dependent ER remodeling contributes to viral cell tropism.IMPORTANCE Perturbations to endoplasmic reticulum (ER) morphology occur during infection with various intracellular pathogens and in certain genetic disorders. We identify that a human cytomegalovirus (HCMV) gene product, UL148, profoundly reorganizes the ER during infection and is sufficient to do so when expressed on its own. Our results reveal that UL148-dependent reorganization of the ER is a prominent feature of HCMV-infected cells. Moreover, we find that this example of virally induced organelle remodeling requires the integrated stress response (ISR), a stress adaptation pathway that contributes to a number of disease states. Since ER reorganization accompanies roles of UL148 in modulation of HCMV cell tropism and in evasion of antiviral immune responses, our results may have implications for understanding the mechanisms involved. Furthermore, our findings provide a basis to utilize UL148 as a tool to investigate organelle responses to stress and to identify novel drugs targeting the ISR.
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Affiliation(s)
- Hongbo Zhang
- Department of Microbiology and Immunology, LSU Health Sciences Center, Shreveport, Louisiana, USA
| | - Clarissa Read
- Institute of Virology, Ulm University Medical Center, Ulm, Germany
- Central Facility for Electron Microscopy, Ulm University, Ulm, Germany
| | - Christopher C Nguyen
- Department of Microbiology and Immunology, LSU Health Sciences Center, Shreveport, Louisiana, USA
| | - Mohammed N A Siddiquey
- Department of Microbiology and Immunology, LSU Health Sciences Center, Shreveport, Louisiana, USA
| | - Chaowei Shang
- Research Core Facility, LSU Health Sciences Center, Shreveport, Louisiana, USA
| | - Cameron M Hall
- Department of Microbiology and Immunology, LSU Health Sciences Center, Shreveport, Louisiana, USA
| | - Jens von Einem
- Institute of Virology, Ulm University Medical Center, Ulm, Germany
| | - Jeremy P Kamil
- Department of Microbiology and Immunology, LSU Health Sciences Center, Shreveport, Louisiana, USA
- Center for Molecular and Tumor Virology, LSU Health Sciences Center, Shreveport, Louisiana, USA
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36
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McHugh A, Fernandes K, Chinner N, Ibrahim AFM, Garg AK, Boag G, Hepburn LA, Proby CM, Leigh IM, Saville MK. The Identification of Potential Therapeutic Targets for Cutaneous Squamous Cell Carcinoma. J Invest Dermatol 2019; 140:1154-1165.e5. [PMID: 31705877 PMCID: PMC7254059 DOI: 10.1016/j.jid.2019.09.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 08/27/2019] [Accepted: 09/23/2019] [Indexed: 02/06/2023]
Abstract
We performed a small interfering RNA screen to identify targets for cutaneous squamous cell carcinoma (cSCC) therapy in the ubiquitin/ubiquitin-like system. We provide evidence for selective anti-cSCC activity of knockdown of the E3 ubiquitin ligase MARCH4, the ATPase p97/VCP, the deubiquitinating enzyme USP8, the cullin-RING ligase (CRL) 4 substrate receptor CDT2/DTL, and components of the anaphase-promoting complex/cyclosome (APC/C). Specifically attenuating CRL4CDT2 by CDT2 knockdown can be more potent in killing cSCC cells than targeting CRLs or CRL4s in general by RBX1 or DDB1 depletion. Suppression of the APC/C or forced APC/C activation by targeting its repressor EMI1 are both potential therapeutic approaches. We observed that cSCC cells can be selectively killed by small-molecule inhibitors of USP8 (DUBs-IN-3/compound 22c) and the NEDD8 E1 activating enzyme/CRLs (MLN4924/pevonedistat). A substantial proportion of cSCC cell lines are very highly MLN4924-sensitive. Pathways that respond to defects in proteostasis are involved in the anti-cSCC activity of p97 suppression. Targeting USP8 can reduce the expression of growth factor receptors that participate in cSCC development. EMI1 and CDT2 depletion can selectively cause DNA re-replication and DNA damage in cSCC cells.
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Affiliation(s)
- Angela McHugh
- Division of Cancer Research, School of Medicine, University of Dundee, Dundee, United Kingdom
| | - Kenneth Fernandes
- Division of Cancer Research, School of Medicine, University of Dundee, Dundee, United Kingdom
| | - Nerime Chinner
- Division of Cancer Research, School of Medicine, University of Dundee, Dundee, United Kingdom
| | - Adel F M Ibrahim
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Amit K Garg
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Garry Boag
- Division of Cancer Research, School of Medicine, University of Dundee, Dundee, United Kingdom
| | - Lydia A Hepburn
- Division of Cancer Research, School of Medicine, University of Dundee, Dundee, United Kingdom
| | - Charlotte M Proby
- Division of Cancer Research, School of Medicine, University of Dundee, Dundee, United Kingdom; Division of Molecular and Clinical Medicine, School of Medicine, University of Dundee, Dundee, United Kingdom
| | - Irene M Leigh
- Division of Cancer Research, School of Medicine, University of Dundee, Dundee, United Kingdom; Institute of Dentistry, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Mark K Saville
- Division of Cancer Research, School of Medicine, University of Dundee, Dundee, United Kingdom.
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37
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Fletcher A, Read ML, Thornton CEM, Larner DP, Poole VL, Brookes K, Nieto HR, Alshahrani M, Thompson RJ, Lavery GG, Landa I, Fagin JA, Campbell MJ, Boelaert K, Turnell AS, Smith VE, McCabe CJ. Targeting Novel Sodium Iodide Symporter Interactors ADP-Ribosylation Factor 4 and Valosin-Containing Protein Enhances Radioiodine Uptake. Cancer Res 2019; 80:102-115. [PMID: 31672844 DOI: 10.1158/0008-5472.can-19-1957] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 09/17/2019] [Accepted: 10/25/2019] [Indexed: 12/31/2022]
Abstract
The sodium iodide symporter (NIS) is required for iodide uptake, which facilitates thyroid hormone biosynthesis. NIS has been exploited for over 75 years in ablative radioiodine (RAI) treatment of thyroid cancer, where its ability to transport radioisotopes depends on its localization to the plasma membrane. The advent of NIS-based in vivo imaging and theranostic strategies in other malignancies and disease modalities has recently increased the clinical importance of NIS. However, NIS trafficking remains ill-defined. Here, we used tandem mass spectrometry followed by coimmunoprecipitation and proximity ligation assays to identify and validate two key nodes-ADP-ribosylation factor 4 (ARF4) and valosin-containing protein (VCP)-controlling NIS trafficking. Using cell-surface biotinylation assays and highly inclined and laminated optical sheet microscopy, we demonstrated that ARF4 enhanced NIS vesicular trafficking from the Golgi to the plasma membrane, whereas VCP-a principal component of endoplasmic reticulum (ER)-associated degradation-governed NIS proteolysis. Gene expression analysis indicated VCP expression was particularly induced in aggressive thyroid cancers and in patients who had poorer outcomes following RAI treatment. Two repurposed FDA-approved VCP inhibitors abrogated VCP-mediated repression of NIS function, resulting in significantly increased NIS at the cell-surface and markedly increased RAI uptake in mouse and human thyroid models. Collectively, these discoveries delineate NIS trafficking and highlight the new possibility of systemically enhancing RAI therapy in patients using FDA-approved drugs. SIGNIFICANCE: These findings show that ARF4 and VCP are involved in NIS trafficking to the plasma membrane and highlight the possible therapeutic role of VCP inhibitors in enhancing radioiodine effectiveness in radioiodine-refractory thyroid cancer.
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Affiliation(s)
- Alice Fletcher
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom
| | - Martin L Read
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom
| | - Caitlin E M Thornton
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom
| | - Dean P Larner
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom
| | - Vikki L Poole
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom
| | - Katie Brookes
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom
| | - Hannah R Nieto
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom
| | - Mohammed Alshahrani
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom
| | - Rebecca J Thompson
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom
| | - Gareth G Lavery
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom
| | - Iñigo Landa
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - James A Fagin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Moray J Campbell
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, Ohio
| | - Kristien Boelaert
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom
| | - Andrew S Turnell
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Vicki E Smith
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom
| | - Christopher J McCabe
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom.
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38
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Huryn DM, Kornfilt DJP, Wipf P. p97: An Emerging Target for Cancer, Neurodegenerative Diseases, and Viral Infections. J Med Chem 2019; 63:1892-1907. [PMID: 31550150 DOI: 10.1021/acs.jmedchem.9b01318] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The AAA+ ATPase, p97, also referred to as VCP, plays an essential role in cellular homeostasis by regulating endoplasmic reticulum-associated degradation (ERAD), mitochondrial-associated degradation (MAD), chromatin-associated degradation, autophagy, and endosomal trafficking. Mutations in p97 have been linked to a number of neurodegenerative diseases, and overexpression of wild type p97 is observed in numerous cancers. Furthermore, p97 activity has been shown to be essential for the replication of certain viruses, including poliovirus, herpes simplex virus (HSV), cytomegalovirus (CMV), and influenza. Taken together, these observations highlight the potential for targeting p97 as a therapeutic approach in neurodegeneration, cancer, and certain infectious diseases. This Perspective reviews recent advances in the discovery of small molecule inhibitors of p97, their optimization and characterization, and therapeutic potential.
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Morozov AV, Karpov VL. Proteasomes and Several Aspects of Their Heterogeneity Relevant to Cancer. Front Oncol 2019; 9:761. [PMID: 31456945 PMCID: PMC6700291 DOI: 10.3389/fonc.2019.00761] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 07/29/2019] [Indexed: 01/19/2023] Open
Abstract
The life of every organism is dependent on the fine-tuned mechanisms of protein synthesis and breakdown. The degradation of most intracellular proteins is performed by the ubiquitin proteasome system (UPS). Proteasomes are central elements of the UPS and represent large multisubunit protein complexes directly responsible for the protein degradation. Accumulating data indicate that there is an intriguing diversity of cellular proteasomes. Different proteasome forms, containing different subunits and attached regulators have been described. In addition, proteasomes specific for a particular tissue were identified. Cancer cells are highly dependent on the proper functioning of the UPS in general, and proteasomes in particular. At the same time, the information regarding the role of different proteasome forms in cancer is limited. This review describes the functional and structural heterogeneity of proteasomes, their association with cancer as well as several established and novel proteasome-directed therapeutic strategies.
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Affiliation(s)
- Alexey V. Morozov
- Laboratory of Regulation of Intracellular Proteolysis, W.A. Engelhardt Institute of Molecular Biology RAS, Moscow, Russia
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40
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Rycenga HB, Wolfe KB, Yeh ES, Long DT. Uncoupling of p97 ATPase activity has a dominant negative effect on protein extraction. Sci Rep 2019; 9:10329. [PMID: 31316150 PMCID: PMC6637110 DOI: 10.1038/s41598-019-46949-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 07/04/2019] [Indexed: 12/13/2022] Open
Abstract
p97 is a highly abundant, homohexameric AAA+ ATPase that performs a variety of essential cellular functions. Characterized as a ubiquitin-selective chaperone, p97 recognizes proteins conjugated to K48-linked polyubiquitin chains and promotes their removal from chromatin and other molecular complexes. Changes in p97 expression or activity are associated with the development of cancer and several related neurodegenerative disorders. Although pathogenic p97 mutations cluster in and around p97’s ATPase domains, mutant proteins display normal or elevated ATPase activity. Here, we show that one of the most common p97 mutations (R155C) retains ATPase activity, but is functionally defective. p97-R155C can be recruited to ubiquitinated substrates on chromatin, but is unable to promote substrate removal. As a result, p97-R155C acts as a dominant negative, blocking protein extraction by a similar mechanism to that observed when p97’s ATPase activity is inhibited or inactivated. However, unlike ATPase-deficient proteins, p97-R155C consumes excess ATP, which can hinder high-energy processes. Together, our results shed new insight into how pathogenic mutations in p97 alter its cellular function, with implications for understanding the etiology and treatment of p97-associated diseases.
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Affiliation(s)
- Halley B Rycenga
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Kelly B Wolfe
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Elizabeth S Yeh
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - David T Long
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, 29425, USA.
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41
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Brünnert D, Kraus M, Stühmer T, Kirner S, Heiden R, Goyal P, Driessen C, Bargou RC, Chatterjee M. Novel cell line models to study mechanisms and overcoming strategies of proteasome inhibitor resistance in multiple myeloma. Biochim Biophys Acta Mol Basis Dis 2019; 1865:1666-1676. [PMID: 30954557 DOI: 10.1016/j.bbadis.2019.04.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 12/20/2018] [Accepted: 01/06/2019] [Indexed: 12/13/2022]
Abstract
Experimental data on resistance mechanisms of multiple myeloma (MM) to ixazomib (IXA), a second-generation proteasome inhibitor (PI), are currently lacking. We generated MM cell lines with a 10-fold higher resistance to IXA as their sensitive counterparts, and observed cross-resistance towards the PIs carfilzomib (CFZ) and bortezomib (BTZ). Analyses of the IXA-binding proteasome subunits PSMB5 and PSMB1 show increased PSMB5 expression and activity in all IXA-resistant MM cells, and upregulated PSMB1 expression in IXA-resistant AMO1 cells. In addition, sequence analysis of PSMB5 revealed a p.Thr21Ala mutation in IXA-resistant MM1.S cells, and a p.Ala50Val mutation in IXA-resistant L363 cells, whereas IXA-resistant AMO1 cells lack PSMB5 mutations. IXA-resistant cells retain their sensitivity to therapeutic agents that mediate cytotoxic effects via induction of proteotoxic stress. Induction of ER stress and apoptosis by the p97 inhibitor CB-5083 was strongly enhanced in combination with the PI3Kα inhibitor BYL-719 or the HDAC inhibitor panobinostat suggesting potential therapeutic strategies to circumvent IXA resistance in MM. Taken together, our newly established IXA-resistant cell lines provide first insights into resistance mechanisms and overcoming treatment strategies, and represent suitable models to further study IXA resistance in MM.
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Affiliation(s)
- Daniela Brünnert
- University Hospital of Würzburg, Comprehensive Cancer Center Mainfranken, Translational Oncology, Würzburg, Germany.
| | - Marianne Kraus
- Kantonsspital St. Gallen, Clinic for Oncology/Hematology, St. Gallen, Switzerland
| | - Thorsten Stühmer
- University Hospital of Würzburg, Comprehensive Cancer Center Mainfranken, Translational Oncology, Würzburg, Germany
| | - Stefanie Kirner
- University Hospital of Würzburg, Comprehensive Cancer Center Mainfranken, Translational Oncology, Würzburg, Germany
| | - Robin Heiden
- University Hospital of Würzburg, Comprehensive Cancer Center Mainfranken, Translational Oncology, Würzburg, Germany
| | - Pankaj Goyal
- Central University of Rajasthan, Department of Biotechnology, School of Life Sciences, Bandar Sindri, Kishangarh, India
| | - Christoph Driessen
- Kantonsspital St. Gallen, Clinic for Oncology/Hematology, St. Gallen, Switzerland
| | - Ralf C Bargou
- University Hospital of Würzburg, Comprehensive Cancer Center Mainfranken, Translational Oncology, Würzburg, Germany
| | - Manik Chatterjee
- University Hospital of Würzburg, Comprehensive Cancer Center Mainfranken, Translational Oncology, Würzburg, Germany
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42
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Using chemical inhibitors to probe AAA protein conformational dynamics and cellular functions. Curr Opin Chem Biol 2019; 50:45-54. [PMID: 30913482 DOI: 10.1016/j.cbpa.2019.02.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 02/18/2019] [Accepted: 02/19/2019] [Indexed: 01/24/2023]
Abstract
The AAA proteins are a family of enzymes that play key roles in diverse dynamic cellular processes, ranging from proteostasis to directional intracellular transport. Dysregulation of AAA proteins has been linked to several diseases, including cancer, suggesting a possible therapeutic role for inhibitors of these enzymes. In the past decade, new chemical probes have been developed for AAA proteins including p97, dynein, midasin, and ClpC1. In this review, we discuss how these compounds have been used to study the cellular functions and conformational dynamics of AAA proteins. We discuss future directions for inhibitor development and early efforts to utilize AAA protein inhibitors in the clinical setting.
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43
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Ding R, Zhang T, Wilson DJ, Xie J, Williams J, Xu Y, Ye Y, Chen L. Discovery of Irreversible p97 Inhibitors. J Med Chem 2019; 62:2814-2829. [PMID: 30830772 DOI: 10.1021/acs.jmedchem.9b00144] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Inhibitors of human p97 (also known as valosin-containing protein) have been actively pursued because of their potential therapeutic applications in cancer and other diseases. However, covalent and irreversible p97 inhibitors have not been well explored. Herein, we report our design, synthesis, and biological evaluation of covalent and irreversible inhibitors of p97. Among an amide and a reverse amide series we synthesized, we have identified a p97 inhibitor whose functional irreversibility has been established both in vitro and in cells. Also importantly, mass spectrometry reveals three potential cysteine residues labeled by this compound, and mutagenesis together with computer modeling suggests Cys522 as a major site, which when modified, could compromise the function of p97. Taken together, this new inhibitor may provide a template for designing more potent p97 inhibitors with covalent and irreversible characteristics.
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Affiliation(s)
- Rui Ding
- Center for Drug Design, College of Pharmacy , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Ting Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Daniel J Wilson
- Center for Drug Design, College of Pharmacy , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Jiashu Xie
- Center for Drug Design, College of Pharmacy , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Jessica Williams
- Center for Drug Design, College of Pharmacy , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Yue Xu
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Yihong Ye
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Liqiang Chen
- Center for Drug Design, College of Pharmacy , University of Minnesota , Minneapolis , Minnesota 55455 , United States
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44
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Suvarna K, Honda K, Muroi M, Kondoh Y, Osada H, Watanabe N. A small-molecule ligand of valosin-containing protein/p97 inhibits cancer cell-accelerated fibroblast migration. J Biol Chem 2019; 294:2988-2996. [PMID: 30610116 DOI: 10.1074/jbc.ra118.004741] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 12/21/2018] [Indexed: 12/21/2022] Open
Abstract
Carcinoma-associated fibroblasts are fibroblasts activated by surrounding cancer cells. Carcinoma-associated fibroblasts exhibit enhanced cell migration, which plays an important role in cancer metastasis. Previously, we demonstrated enhanced migration of NIH3T3 fibroblasts when they were cultured in the presence of MCF7 breast cancer cells. Human fibroblasts displayed a similar phenomenon even when they were co-cultured with cancer cells other than MCF7 cells. In this study, we screened ∼16,000 compounds from the RIKEN Natural Products Depository chemical library for inhibitors of enhanced NIH3T3 cell migration in the presence of MCF7. We identified NPD8733 as an inhibitor of cancer cell-enhanced fibroblast migration. This inhibition was observed not only in a wound-healing co-culture assay but also in a Transwell migration assay. Using NPD8733 and a structurally similar but inactive derivative, NPD8126, on immobilized beads, we found that NPD8733, but not NPD8126, specifically binds to valosin-containing protein (VCP)/p97, a member of the ATPase-associated with diverse cellular activities (AAA+) protein family. Using VCP truncation variants, we found that NPD8733 binds to the D1 domain of VCP. Because VCP's D1 domain is important for its function, we concluded that NPD8733 may act on VCP by binding to this domain. siRNA-mediated silencing of VCP in NIH3T3 fibroblasts, but not in MCF7 cells, reduced the migration of the co-cultured NIH3T3 fibroblasts. These results indicate that MCF7 activates the migration of NIH3T3 cells through VCP and that NPD8733 binds VCP and thereby inhibits its activity.
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Affiliation(s)
- Kruthi Suvarna
- From the Bio-Active Compounds Discovery Research Unit.,the Tokyo Medical Dental University, Yushima, Tokyo 113-8510, Japan
| | - Kaori Honda
- From the Bio-Active Compounds Discovery Research Unit.,Chemical Biology Research Group, and
| | | | | | - Hiroyuki Osada
- Chemical Biology Research Group, and.,RIKEN-Max Planck Joint Research Division, RIKEN Center for Sustainable Resource Science, Saitama 351-0198, Japan and
| | - Nobumoto Watanabe
- From the Bio-Active Compounds Discovery Research Unit, .,the Tokyo Medical Dental University, Yushima, Tokyo 113-8510, Japan.,RIKEN-Max Planck Joint Research Division, RIKEN Center for Sustainable Resource Science, Saitama 351-0198, Japan and
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45
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Fraga H, Rodriguez B, Bardera A, Cid C, Akopian T, Kandror O, Park A, Colmenarejo G, Lelievre J, Goldberg A. Development of high throughput screening methods for inhibitors of ClpC1P1P2 from Mycobacteria tuberculosis. Anal Biochem 2018; 567:30-37. [PMID: 30543804 DOI: 10.1016/j.ab.2018.12.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 12/03/2018] [Indexed: 01/10/2023]
Abstract
Tuberculosis affects about 100 million people worldwide and causes nearly 2 million deaths annually. It has been estimated that one third of all humans is infected with latent Mycobacterium tuberculosis (Mtb). Moreover, Mtb has become increasingly resistant to available antibiotics. Consequently, it is important to identify and characterize new therapeutic targets in Mtb and to synthesize selective inhibitors. ClpP1, ClpP2 and their associated regulatory ATPases, ClpX and ClpC1 are required for the growth of Mtb and for its virulence during murine infection and are highly attractive drug targets, especially since they are not present in the cytosol of mammalian cells, and they differ markedly from the mitochondrial ClpP complex. The importance of these proteins in Mtb is emphasized by the existence of several natural antibiotics targeting this system. In order to find new inhibitors of ClpC1P1P2 system, we developed an assay based on the ATP-dependent degradation of a fluorescent protein substrate. The hits obtained were further characterized with a set of secondary assays to identify precise targets within a complex. A large library of compounds was screened and led to the identification of a ClpC1 ATPase inhibitor demonstrating that this approach can be used in future searches for anti-TB agents.
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Affiliation(s)
- Hugo Fraga
- Diseases of the Developing World, Global Health R&D, GlaxoSmithKline, Severo Ochoa 2, 28760, Tres Cantos, Spain; Department Cell Biology, Harvard Medical School, USA; Institut de Biologie Structurale, Grenoble, France; Departamento de Bioquímica, Faculdade de Medicina da Universidade do Porto, Portugal.
| | - Beatriz Rodriguez
- Diseases of the Developing World, Global Health R&D, GlaxoSmithKline, Severo Ochoa 2, 28760, Tres Cantos, Spain
| | - Ana Bardera
- Diseases of the Developing World, Global Health R&D, GlaxoSmithKline, Severo Ochoa 2, 28760, Tres Cantos, Spain
| | - Concha Cid
- Diseases of the Developing World, Global Health R&D, GlaxoSmithKline, Severo Ochoa 2, 28760, Tres Cantos, Spain
| | - Tatos Akopian
- School of Public Health, Harvard Medical School, USA
| | - Olga Kandror
- School of Public Health, Harvard Medical School, USA
| | - Annie Park
- School of Public Health, Harvard Medical School, USA
| | - Gonzalo Colmenarejo
- Diseases of the Developing World, Global Health R&D, GlaxoSmithKline, Severo Ochoa 2, 28760, Tres Cantos, Spain; Biostatisics and Bioinformatics Unit, IMDEA Food Institute, Madrid, Spain
| | - Joel Lelievre
- Diseases of the Developing World, Global Health R&D, GlaxoSmithKline, Severo Ochoa 2, 28760, Tres Cantos, Spain
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LaPorte MG, Burnett JC, Colombo R, Bulfer SL, Alverez C, Chou TF, Neitz RJ, Green N, Moore WJ, Yue Z, Li S, Arkin MR, Wipf P, Huryn DM. Optimization of Phenyl Indole Inhibitors of the AAA+ ATPase p97. ACS Med Chem Lett 2018; 9:1075-1081. [PMID: 30429948 PMCID: PMC6231190 DOI: 10.1021/acsmedchemlett.8b00372] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 09/18/2018] [Indexed: 12/30/2022] Open
Abstract
![]()
Optimization
of the side-chain of a phenyl indole scaffold identified
from a high-throughput screening campaign for inhibitors of the AAA+
ATPase p97 is reported. The addition of an N-alkyl
piperazine led to high potency of this series in a biochemical assay,
activity in cell-based assays, and excellent pharmaceutical properties.
Molecular modeling based on a subsequently obtained cryo-EM structure
of p97 in complex with a phenyl indole was used to rationalize the
potency of these allosteric inhibitors.
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Affiliation(s)
- Matthew G. LaPorte
- University of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - James C. Burnett
- University of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Computational Drug Development Group, Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland 20892, United States
| | - Raffaele Colombo
- University of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Stacie L. Bulfer
- Department of Pharmaceutical Chemistry, Small Molecule Discovery Center, University of California, San Francisco, California 94158, United States
| | - Celeste Alverez
- University of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Tsui-Fen Chou
- Division of Medical Genetics, Department of Pediatrics, Harbor−UCLA Medical Center and Los Angeles Biomedical Research Institute, Torrance, California 90502, United States
| | - R. Jeffrey Neitz
- Department of Pharmaceutical Chemistry, Small Molecule Discovery Center, University of California, San Francisco, California 94158, United States
| | - Neal Green
- Leidos Biomedical Research, Inc., Frederick, Maryland 21702, United States
| | - William J. Moore
- Leidos Biomedical Research, Inc., Frederick, Maryland 21702, United States
| | - Zhizhou Yue
- University of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Shan Li
- Division of Medical Genetics, Department of Pediatrics, Harbor−UCLA Medical Center and Los Angeles Biomedical Research Institute, Torrance, California 90502, United States
| | - Michelle R. Arkin
- Department of Pharmaceutical Chemistry, Small Molecule Discovery Center, University of California, San Francisco, California 94158, United States
| | - Peter Wipf
- University of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Donna M. Huryn
- University of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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47
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Wei Y, Toth JI, Blanco GA, Bobkov AA, Petroski MD. Adapted ATPase domain communication overcomes the cytotoxicity of p97 inhibitors. J Biol Chem 2018; 293:20169-20180. [PMID: 30381397 DOI: 10.1074/jbc.ra118.004301] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 10/10/2018] [Indexed: 12/15/2022] Open
Abstract
The AAA+ ATPase p97 regulates ubiquitin-dependent protein homeostasis and has been pursued as a cancer drug target. The ATP-competitive inhibitor CB-5083 and allosteric inhibitor NMS-873 are the most advanced p97 inhibitors described to date. Previous studies have reported that their cytotoxicity can be readily overcome and involves single p97 mutations in the linker between the D1 and D2 ATPase domains and within D2. We report here that the proline 472 to leucine (P472L) mutation, in the D1-D2 linker and identified in CB-5083-resistant cells, desensitizes p97 to both inhibitor classes. This mutation does not disrupt the distinct D2-binding sites of the inhibitors. Instead, P472L changes ATPase domain communication within the p97 hexamer. P472L enhances cooperative D2 ATP binding and hydrolysis. This mechanism alters the function of the D1-D2 linker in the control of D2 activity involving the ATP-bound state of D1. Although increased D2 activity is sufficient to desensitize the P472L mutant to NMS-873, the mutant's desensitization to CB-5083 also requires D1 ATPase domain function. Our study highlights the remarkable adaptability of p97 ATPase domain communication that enables escape from mechanistically distinct classes of cytotoxic p97 inhibitors.
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Affiliation(s)
- Yang Wei
- From the NCI-designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037
| | - Julia I Toth
- From the NCI-designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037
| | - Gabrielle A Blanco
- From the NCI-designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037
| | - Andrey A Bobkov
- From the NCI-designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037
| | - Matthew D Petroski
- From the NCI-designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037.
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48
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p62-Dependent Phase Separation of Patient-Derived KEAP1 Mutations and NRF2. Mol Cell Biol 2018; 38:MCB.00644-17. [PMID: 30126895 DOI: 10.1128/mcb.00644-17] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Accepted: 08/08/2018] [Indexed: 12/19/2022] Open
Abstract
Cancer-derived loss-of-function mutations in the KEAP1 tumor suppressor gene stabilize the NRF2 transcription factor, resulting in a prosurvival gene expression program that alters cellular metabolism and neutralizes oxidative stress. In a recent genotype-phenotype study, we classified 40% of KEAP1 mutations as ANCHOR mutants. By immunoprecipitation, these mutants bind more NRF2 than wild-type KEAP1 and ubiquitylate NRF2, but they are incapable of promoting NRF2 degradation. BioID-based protein interaction studies confirmed increased abundance of NRF2 within the KEAP1 ANCHOR mutant complexes, with no other statistically significant changes to the complexes. Discrete molecular dynamic simulation modeling and limited proteolysis suggest that the ANCHOR mutations stabilize residues in KEAP1 that contact NRF2. The modeling supports an intramolecular salt bridge between the R470C ANCHOR mutation and E493; mutation of the E493 residue confirmed the model, resulting in the ANCHOR phenotype. In live cells, the KEAP1 R320Q and R470C ANCHOR mutants colocalize with NRF2, p62/SQSTM1, and polyubiquitin in structured spherical droplets that rapidly fuse and dissolve. Transmission electron microscopy coupled with confocal fluorescent imaging revealed membraneless phase-separated biomolecular condensates. We present a model wherein ANCHOR mutations form p62-dependent biomolecular condensates that may represent a transitional state between impaired proteasomal degradation and autophagy.
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49
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Guedes Aguiar B, Padmanabhan PK, Dumas C, Papadopoulou B. Valosin-containing protein VCP/p97 is essential for the intracellular development of Leishmania and its survival under heat stress. Cell Microbiol 2018; 20:e12867. [PMID: 29895095 DOI: 10.1111/cmi.12867] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 05/14/2018] [Accepted: 06/05/2018] [Indexed: 12/15/2022]
Abstract
Valosin-containing protein (VCP)/p97/Cdc48 is one of the best-characterised type II cytosolic AAA+ ATPases most known for their role in ubiquitin-dependent protein quality control. Here, we provide functional insights into the role of the Leishmania VCP/p97 homologue (LiVCP) in the parasite intracellular development. We demonstrate that although LiVCP is an essential gene, Leishmania infantum promastigotes can grow with less VCP. In contrast, growth of axenic and intracellular amastigotes is dramatically affected upon decreased LiVCP levels in heterozygous and temperature sensitive (ts) LiVCP mutants or the expression of dominant negative mutants known to specifically target the second conserved VCP ATPase domain, a major contributor of the VCP overall ATPase activity. Interestingly, these VCP mutants are also unable to survive heat stress, and a ts VCP mutant is defective in amastigote growth. Consistent with LiVCP's essential function in amastigotes, LiVCP messenger ribonucleic acid undergoes 3'Untranslated Region (UTR)-mediated developmental regulation, resulting in higher VCP expression in amastigotes. Furthermore, we show that parasite mutant lines expressing lower VCP levels or dominant negative VCP forms exhibit high accumulation of polyubiquitinated proteins and increased sensitivity to proteotoxic stress, supporting the ubiquitin-selective chaperone function of LiVCP. Together, these results emphasise the crucial role LiVCP plays under heat stress and during the parasite intracellular development.
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Affiliation(s)
- Bruno Guedes Aguiar
- Research Center in Infectious Diseases, CHU de Quebec Research Center-University Laval, Quebec, Canada.,Department of Microbiology-Infectious Disease and Immunology, Faculty of Medicine, University Laval, Quebec, Canada.,Department of Community Medicine, Federal University of Piauí, Teresina, Brazil
| | - Prasad K Padmanabhan
- Research Center in Infectious Diseases, CHU de Quebec Research Center-University Laval, Quebec, Canada.,Department of Microbiology-Infectious Disease and Immunology, Faculty of Medicine, University Laval, Quebec, Canada
| | - Carole Dumas
- Research Center in Infectious Diseases, CHU de Quebec Research Center-University Laval, Quebec, Canada.,Department of Microbiology-Infectious Disease and Immunology, Faculty of Medicine, University Laval, Quebec, Canada
| | - Barbara Papadopoulou
- Research Center in Infectious Diseases, CHU de Quebec Research Center-University Laval, Quebec, Canada.,Department of Microbiology-Infectious Disease and Immunology, Faculty of Medicine, University Laval, Quebec, Canada
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50
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Pöhler R, Krahn JH, van den Boom J, Dobrynin G, Kaschani F, Eggenweiler HM, Zenke FT, Kaiser M, Meyer H. A Non-Competitive Inhibitor of VCP/p97 and VPS4 Reveals Conserved Allosteric Circuits in Type I and II AAA ATPases. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201711429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Robert Pöhler
- Molecular Biology I, Centre for Medical Biotechnology; University of Duisburg-Essen; 45117 Essen Germany
| | - Jan H. Krahn
- Chemical Biology, Centre for Medical Biotechnology; University of Duisburg-Essen; 45117 Essen Germany
| | - Johannes van den Boom
- Molecular Biology I, Centre for Medical Biotechnology; University of Duisburg-Essen; 45117 Essen Germany
| | - Grzegorz Dobrynin
- Molecular Biology I, Centre for Medical Biotechnology; University of Duisburg-Essen; 45117 Essen Germany
| | - Farnusch Kaschani
- Chemical Biology, Centre for Medical Biotechnology; University of Duisburg-Essen; 45117 Essen Germany
| | - Hans-Michael Eggenweiler
- Medicinal Chemistry DA and Translational Innovation Platform Oncology, Global R&D, Healthcare; Merck KGaA; Frankfurter Str. 250 64293 Darmstadt Germany
| | - Frank T. Zenke
- Medicinal Chemistry DA and Translational Innovation Platform Oncology, Global R&D, Healthcare; Merck KGaA; Frankfurter Str. 250 64293 Darmstadt Germany
| | - Markus Kaiser
- Chemical Biology, Centre for Medical Biotechnology; University of Duisburg-Essen; 45117 Essen Germany
| | - Hemmo Meyer
- Molecular Biology I, Centre for Medical Biotechnology; University of Duisburg-Essen; 45117 Essen Germany
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