1
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Bhattacharjee A, Bachovchin DA. DPP8/9 are not Required to Cleave Most Proline-Containing Peptides. Isr J Chem 2023; 63:e202200117. [PMID: 37982048 PMCID: PMC10655806 DOI: 10.1002/ijch.202200117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Indexed: 02/16/2023]
Abstract
Small molecule inhibitors of the intracellular serine peptidases DPP8 and DPP9 (DPP8/9) activate the NLRP1 and CARD8 inflammasomes, but the key DPP8/9 substrates have not yet been identified. DPP8/9 cleave after proline to remove N-terminal dipeptides from peptides or proteins, and studies using pseudo-peptide reporter substrates have suggested that these enzymes may play key roles in the catabolism of many proline-containing peptides generated by the proteasome. Here, we evaluated the degradation of a wide array of actual peptides in cell lysates, and discovered that DPP8/9 are not in fact involved in the processing of the vast majority of proline-containing peptides. Overall, these results indicate that DPP8/9 have a much more limited substrate scope than previously thought, and likely specifically cleave some critically important, but as yet unknown, intracellular peptide or protein that regulates inflammasome activation.
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Affiliation(s)
- Abir Bhattacharjee
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, 10065, USA
| | - Daniel A Bachovchin
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, 10065, USA
- Pharmacology Program of the Weill Cornell, Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, New York, 10065, USA
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, 10065, USA
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2
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Cravatt BF. Activity-based protein profiling - finding general solutions to specific problems. Isr J Chem 2023; 63:e202300029. [PMID: 37206575 PMCID: PMC10191372 DOI: 10.1002/ijch.202300029] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Indexed: 03/06/2023]
Abstract
In this retrospective/perspective, I will share thoughts on developing and applying the activity-based protein profiling (ABPP) technology, an endeavor that has consumed much of our lab's attention over our 25+ year existence. Before doing so, I first wish to thank the colleagues who so kindly contributed to this Special Issue. I am appreciative and humbled that they were willing to share their innovative and impactful science in this format.
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Affiliation(s)
- Benjamin F Cravatt
- The Department of Chemistry, The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla, CA 92037
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3
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Racioppo B, Qiu N, Adibekian A. Serine Hydrolase Activity‐Based Probes for use in Chemical Proteomics. Isr J Chem 2023. [DOI: 10.1002/ijch.202300016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Affiliation(s)
- Brittney Racioppo
- Department of Chemistry University of Illinois Chicago Chicago Illinois 60607 United States
- Skaggs Doctoral Program in the Chemical and Biological Sciences, Scripps Research La Jolla California 92037 United States
| | - Nan Qiu
- Department of Chemistry University of Illinois Chicago Chicago Illinois 60607 United States
- Skaggs Doctoral Program in the Chemical and Biological Sciences, Scripps Research La Jolla California 92037 United States
| | - Alexander Adibekian
- Department of Chemistry University of Illinois Chicago Chicago Illinois 60607 United States
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4
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A deeply conserved protease, acylamino acid-releasing enzyme (AARE), acts in ageing in Physcomitrella and Arabidopsis. Commun Biol 2023; 6:61. [PMID: 36650210 PMCID: PMC9845386 DOI: 10.1038/s42003-023-04428-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 01/05/2023] [Indexed: 01/18/2023] Open
Abstract
Reactive oxygen species (ROS) are constant by-products of aerobic life. In excess, ROS lead to cytotoxic protein aggregates, which are a hallmark of ageing in animals and linked to age-related pathologies in humans. Acylamino acid-releasing enzymes (AARE) are bifunctional serine proteases, acting on oxidized proteins. AARE are found in all domains of life, albeit under different names, such as acylpeptide hydrolase (APEH/ACPH), acylaminoacyl peptidase (AAP), or oxidized protein hydrolase (OPH). In humans, AARE malfunction is associated with age-related pathologies, while their function in plants is less clear. Here, we provide a detailed analysis of AARE genes in the plant lineage and an in-depth analysis of AARE localization and function in the moss Physcomitrella and the angiosperm Arabidopsis. AARE loss-of-function mutants have not been described for any organism so far. We generated and analysed such mutants and describe a connection between AARE function, aggregation of oxidized proteins and plant ageing, including accelerated developmental progression and reduced life span. Our findings complement similar findings in animals and humans, and suggest a unified concept of ageing may exist in different life forms.
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5
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Volpe MR, Velilla JA, Daniel-Ivad M, Yao JJ, Stornetta A, Villalta PW, Huang HC, Bachovchin DA, Balbo S, Gaudet R, Balskus EP. A small molecule inhibitor prevents gut bacterial genotoxin production. Nat Chem Biol 2023; 19:159-167. [PMID: 36253549 PMCID: PMC9889270 DOI: 10.1038/s41589-022-01147-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 08/19/2022] [Indexed: 02/04/2023]
Abstract
The human gut bacterial genotoxin colibactin is a possible key driver of colorectal cancer (CRC) development. Understanding colibactin's biological effects remains difficult owing to the instability of the proposed active species and the complexity of the gut microbiota. Here, we report small molecule boronic acid inhibitors of colibactin biosynthesis. Designed to mimic the biosynthetic precursor precolibactin, these compounds potently inhibit the colibactin-activating peptidase ClbP. Using biochemical assays and crystallography, we show that they engage the ClbP binding pocket, forming a covalent bond with the catalytic serine. These inhibitors reproduce the phenotypes observed in a clbP deletion mutant and block the genotoxic effects of colibactin on eukaryotic cells. The availability of ClbP inhibitors will allow precise, temporal control over colibactin production, enabling further study of its contributions to CRC. Finally, application of our inhibitors to related peptidase-encoding pathways highlights the power of chemical tools to probe natural product biosynthesis.
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Affiliation(s)
- Matthew R. Volpe
- grid.38142.3c000000041936754XDepartment of Chemistry and Chemical Biology, Harvard University, Cambridge, MA USA
| | - José A. Velilla
- grid.38142.3c000000041936754XDepartment of Molecular and Cellular Biology, Harvard University, Cambridge, MA USA
| | - Martin Daniel-Ivad
- grid.38142.3c000000041936754XDepartment of Chemistry and Chemical Biology, Harvard University, Cambridge, MA USA
| | - Jenny J. Yao
- grid.38142.3c000000041936754XDepartment of Chemistry and Chemical Biology, Harvard University, Cambridge, MA USA
| | - Alessia Stornetta
- grid.17635.360000000419368657Masonic Cancer Center, University of Minnesota, Minneapolis, MN USA
| | - Peter W. Villalta
- grid.17635.360000000419368657Masonic Cancer Center, University of Minnesota, Minneapolis, MN USA ,grid.17635.360000000419368657Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN USA
| | - Hsin-Che Huang
- grid.51462.340000 0001 2171 9952Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Daniel A. Bachovchin
- grid.51462.340000 0001 2171 9952Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Silvia Balbo
- grid.17635.360000000419368657Masonic Cancer Center, University of Minnesota, Minneapolis, MN USA ,grid.17635.360000000419368657Division of Environmental Health Sciences, School of Public Health, University of Minnesota, Minneapolis, MN USA
| | - Rachelle Gaudet
- grid.38142.3c000000041936754XDepartment of Molecular and Cellular Biology, Harvard University, Cambridge, MA USA
| | - Emily P. Balskus
- grid.38142.3c000000041936754XDepartment of Chemistry and Chemical Biology, Harvard University, Cambridge, MA USA ,grid.38142.3c000000041936754XHoward Hughes Medical Institute, Harvard University, Cambridge, MA USA
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6
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Abstract
The biggest challenge to immune control of HIV infection is the rapid within-host viral evolution, which allows selection of viral variants that escape from T cell and antibody recognition. Thus, it is impossible to clear HIV infection without targeting "immutable" components of the virus. Unlike the adaptive immune system that recognizes cognate epitopes, the CARD8 inflammasome senses the essential enzymatic activity of the HIV-1 protease, which is immutable for the virus. Hence, all subtypes of HIV clinical isolates can be recognized by CARD8. In HIV-infected cells, the viral protease is expressed as a subunit of the viral Gag-Pol polyprotein and remains functionally inactive prior to viral budding. A class of anti-HIV drugs, the non-nucleoside reverse transcriptase inhibitors (NNRTIs), can promote Gag-pol dimerization and subsequent premature intracellular activation of the viral protease. NNRTI treatment triggers CARD8 inflammasome activation, which leads to pyroptosis of HIV-infected CD4+ T cells and macrophages. Targeting the CARD8 inflammasome can be a potent and broadly effective strategy for HIV eradication.
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Affiliation(s)
- Kolin M Clark
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, Saint Louis, MO, United States
| | - Priya Pal
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, Saint Louis, MO, United States
| | - Josh G Kim
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, Saint Louis, MO, United States
| | - Qiankun Wang
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, Saint Louis, MO, United States
| | - Liang Shan
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, Saint Louis, MO, United States; Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, MO, United States.
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7
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Faria SS, Fernando AJ, de Lima VCC, Rossi AG, de Carvalho JMA, Magalhães KG. Induction of pyroptotic cell death as a potential tool for cancer treatment. J Inflamm (Lond) 2022; 19:19. [PMID: 36376979 PMCID: PMC9664674 DOI: 10.1186/s12950-022-00316-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/14/2022] [Indexed: 11/16/2022] Open
Abstract
Cancer is a complex pathological disease and the existing strategies for introducing chemotherapeutic agents have restricted potential due to a lack of cancer cell targeting specificity, cytotoxicity, bioavailability, and induction of multi-drug resistance. As a prospective strategy in tackling cancer, regulating the inflammatory pyroptosis cell death pathway has been shown to successfully inhibit the proliferation and metastasis of various cancer cell types. Activation of inflammasomes such as the NLRP3 results in pyroptosis through cleavage of gasdermins, which forms pores in the cell membranes, inducing membrane breakage, cell rupture, and death. Furthermore, pyroptotic cells release pro-inflammatory cytokines such as IL-1β and IL-18 along with various DAMPs that prime an auxiliary anti-tumor immune response. Thus, regulation of pyroptosis in cancer cells is a way to enhance their immunogenicity. However, immune escape involving myeloid-derived suppressor cells has limited the efficacy of most pyroptosis-based immunotherapy strategies. In this review, we comprehensively summarize the cellular and molecular mechanisms involved in the inflammasome-mediated pyroptosis pathways in cancer cells, exploring how it could modulate the tumor microenvironment and be beneficial in anti-cancer treatments. We discuss various existing therapeutic strategies against cancer, including immunotherapy, oncolytic virus therapy, and nanoparticle-based therapies that could be guided to trigger and regulate pyroptosis cell death in cancer cells, and reduce tumor growth and spread. These pyroptosis-based cancer therapies may open up fresh avenues for targeted cancer therapy approaches in the future and their translation into the clinic.
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Affiliation(s)
- Sara Socorro Faria
- Laboratory of Immunology and Inflammation, Department of Cell Biology, University of Brasilia, DF Brasilia, Brazil
| | - Anuruddika Jayawanthi Fernando
- Edinburgh BioQuarter, University of Edinburgh Centre for Inflammation Research, Queen’s Medical Research. Institute, University of Edinburgh, Edinburgh, UK
| | | | - Adriano Giorgio Rossi
- Laboratory of Immunology and Inflammation, Department of Cell Biology, University of Brasilia, DF Brasilia, Brazil
| | | | - Kelly Grace Magalhães
- Laboratory of Immunology and Inflammation, Department of Cell Biology, University of Brasilia, DF Brasilia, Brazil
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8
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Mi L, Min X, Chai Y, Zhang J, Chen X. NLRP1 Inflammasomes: A Potential Target for the Treatment of Several Types of Brain Injury. Front Immunol 2022; 13:863774. [PMID: 35707533 PMCID: PMC9189285 DOI: 10.3389/fimmu.2022.863774] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/28/2022] [Indexed: 12/28/2022] Open
Abstract
NOD-like receptor (NLR) family pyrin domain-containing 1 (NLRP1) is a member of the NLR family. The NLRP1 inflammasome consists of the NLRP1 protein, the adaptor protein apoptosis-associated speck-like protein containing a CARD domain, and the effector molecule pro-caspase-1. When stimulated, the inflammasome initiates the cleavage of pro-caspase-1 and converts it into its active form, caspase-1; then, caspase-1 facilitates the cleavage of the proinflammatory cytokines interleukin-1β and interleukin-18 into their active and secreted forms. In addition, caspase-1 also mediates the cleavage of gasdermin D, which leads to pyroptosis, an inflammatory form of cell death. Pathological events that damage the brain and result in neuropathological conditions can generally be described as brain injury. Neuroinflammation, especially that driven by NLRP1, plays a considerable role in the pathophysiology of brain injury, such as early brain injury (EBI) of subarachnoid hemorrhage, ischemic brain injury during stroke, and traumatic brain injury (TBI). In this article, a thorough overview of NLRP1 is presented, including its structure, mechanism of activation, and role in neuroinflammation. We also present recent studies on NLRP1 as a target for the treatment of EBI, ischemic brain injury, TBI, and other types of brain injury, thus highlighting the perspective of NLRP1 as an effective mediator of catastrophic brain injury.
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Affiliation(s)
- Liang Mi
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China
- Tianjin Neurological Institute, Key Laboratory of Posttrauma Neurorepair and Regeneration in Central Nervous System, Ministry of Education, Tianjin Key Laboratory of Injuries, Variations and Regeneration of Nervous System, Tianjin, China
| | - Xiaobin Min
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China
- Baodi Clinical College, Tianjin Medical University, Tianjin, China
| | - Yan Chai
- Tianjin Neurological Institute, Key Laboratory of Posttrauma Neurorepair and Regeneration in Central Nervous System, Ministry of Education, Tianjin Key Laboratory of Injuries, Variations and Regeneration of Nervous System, Tianjin, China
| | - Jianning Zhang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China
- Tianjin Neurological Institute, Key Laboratory of Posttrauma Neurorepair and Regeneration in Central Nervous System, Ministry of Education, Tianjin Key Laboratory of Injuries, Variations and Regeneration of Nervous System, Tianjin, China
| | - Xin Chen
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China
- Tianjin Neurological Institute, Key Laboratory of Posttrauma Neurorepair and Regeneration in Central Nervous System, Ministry of Education, Tianjin Key Laboratory of Injuries, Variations and Regeneration of Nervous System, Tianjin, China
- *Correspondence: Xin Chen,
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9
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Wang H, Xie M, Rizzi G, Li X, Tan K, Fussenegger M. Identification of Sclareol As a Natural Neuroprotective Ca v 1.3-Antagonist Using Synthetic Parkinson-Mimetic Gene Circuits and Computer-Aided Drug Discovery. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2102855. [PMID: 35040584 PMCID: PMC8895113 DOI: 10.1002/advs.202102855] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 11/30/2021] [Indexed: 05/14/2023]
Abstract
Parkinson's disease (PD) results from selective loss of substantia nigra dopaminergic (SNc DA) neurons, and is primarily caused by excessive activity-related Ca2+ oscillations. Although L-type voltage-gated calcium channel blockers (CCBs) selectively inhibiting Cav 1.3 are considered promising candidates for PD treatment, drug discovery is hampered by the lack of high-throughput screening technologies permitting isoform-specific assessment of Cav-antagonistic activities. Here, a synthetic-biology-inspired drug-discovery platform enables identification of PD-relevant drug candidates. By deflecting Cav-dependent activation of nuclear factor of activated T-cells (NFAT)-signaling to repression of reporter gene translation, they engineered a cell-based assay where reporter gene expression is activated by putative CCBs. By using this platform in combination with in silico virtual screening and a trained deep-learning neural network, sclareol is identified from a essential oils library as a structurally distinctive compound that can be used for PD pharmacotherapy. In vitro studies, biochemical assays and whole-cell patch-clamp recordings confirmed that sclareol inhibits Cav 1.3 more strongly than Cav 1.2 and decreases firing responses of SNc DA neurons. In a mouse model of PD, sclareol treatment reduced DA neuronal loss and protected striatal network dynamics as well as motor performance. Thus, sclareol appears to be a promising drug candidate for neuroprotection in PD patients.
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Affiliation(s)
- Hui Wang
- Department of Biosystems Science and EngineeringETH ZurichMattenstrasse 26Basel4058Switzerland
- Present address:
Lonza AGLonzastrasseVisp3930Switzerland
| | - Mingqi Xie
- Department of Biosystems Science and EngineeringETH ZurichMattenstrasse 26Basel4058Switzerland
- Present address:
Key Laboratory of Growth Regulation and Translational Research of Zhejiang ProvinceSchool of Life SciencesWestlake UniversityShilongshan Road 18HangzhouP. R. China
| | - Giorgio Rizzi
- BiozentrumUniversity of BaselKlingelbergstrasse 50/70Basel4056Switzerland
- Present address:
Inscopix IncEmbarcadero WayPalo AltoCA94303USA
| | - Xin Li
- Department of Biosystems Science and EngineeringETH ZurichMattenstrasse 26Basel4058Switzerland
- Present address:
Key Laboratory of Growth Regulation and Translational Research of Zhejiang ProvinceSchool of Life SciencesWestlake UniversityShilongshan Road 18HangzhouP. R. China
| | - Kelly Tan
- BiozentrumUniversity of BaselKlingelbergstrasse 50/70Basel4056Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and EngineeringETH ZurichMattenstrasse 26Basel4058Switzerland
- University of BaselFaculty of ScienceMattenstrasse 26BaselCH‐4058Switzerland
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10
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Zhang M, Zhang L, Guo R, Xiao C, Yin J, Zhang S, Yang M. Structural basis for the catalytic activity of filamentous human serine beta-lactamase-like protein LACTB. Structure 2022; 30:685-696.e5. [PMID: 35247327 DOI: 10.1016/j.str.2022.02.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 11/16/2021] [Accepted: 02/07/2022] [Indexed: 01/10/2023]
Abstract
Serine beta-lactamase-like protein (LACTB) is a mammalian mitochondrial serine protease that can specifically hydrolyze peptide bonds adjacent to aspartic acid residues and is structurally related to prokaryotic penicillin-binding proteins. Here, we determined the cryoelectron microscopy structures of human LACTB (hLACTB) filaments from wild-type protein, a middle region deletion mutant, and in complex with the inhibitor Z-AAD-CMK at 3.0-, 3.1-, and 2.8-Å resolution, respectively. Structural analysis and activity assays revealed that three interfaces are required for the assembly of hLACTB filaments and that the formation of higher order helical structures facilitates its cleavage activity. Further structural and enzymatic analyses of middle region deletion constructs indicated that, while this region is necessary for substrate hydrolysis, it is not required for filament formation. Moreover, the inhibitor-bound structure showed that hLACTB may cleave peptide bonds adjacent to aspartic acid residues. These findings provide the structural basis underlying hLACTB catalytic activity.
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Affiliation(s)
- Minghui Zhang
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Laixing Zhang
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Runyu Guo
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Chun Xiao
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jian Yin
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Sensen Zhang
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Maojun Yang
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Cryo-EM Facility Center, Southern University of Science & Technology, Shenzhen 518055, Guangdong, China.
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11
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Jung Y, Noda N, Takaya J, Abo M, Toh K, Tajiri K, Cui C, Zhou L, Sato SI, Uesugi M. Discovery of Non-Cysteine-Targeting Covalent Inhibitors by Activity-Based Proteomic Screening with a Cysteine-Reactive Probe. ACS Chem Biol 2022; 17:340-347. [PMID: 35076225 DOI: 10.1021/acschembio.1c00824] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Covalent inhibitors of enzymes are increasingly appreciated as pharmaceutical seeds, yet discovering non-cysteine-targeting inhibitors remains challenging. Herein, we report an intriguing experience during our activity-based proteomic screening of 1601 reactive small molecules, in which we monitored the ability of library molecules to compete with a cysteine-reactive iodoacetamide probe. One epoxide molecule, F8, exhibited unexpected enhancement of the probe reactivity for glyceraldehyde-3-phosphate dehydrogenase (GAPDH), a rate-limiting glycolysis enzyme. In-depth mechanistic analysis suggests that F8 forms a covalent adduct with an aspartic acid in the active site to displace NAD+, a cofactor of the enzyme, with concomitant enhancement of the probe reaction with the catalytic cysteine. The mechanistic underpinning permitted the identification of an optimized aspartate-reactive GAPDH inhibitor. Our findings exemplify that activity-based proteomic screening with a cysteine-reactive probe can be used for discovering covalent inhibitors that react with non-cysteine residues.
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Affiliation(s)
- Yejin Jung
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
- Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Naotaka Noda
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
- Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Junichiro Takaya
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
- Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Masahiro Abo
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Kohei Toh
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Ken Tajiri
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Changyi Cui
- School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Lu Zhou
- School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Shin-ichi Sato
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Motonari Uesugi
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
- School of Pharmacy, Fudan University, Shanghai 201203, China
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Uji, Kyoto 611-0011, Japan
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12
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Liu HF, Xie YK, Zhong BY, Zhang JH, Song CX, Liu YW, Yang Y, Xie BH. Dipeptidyl peptidase-8 induces Sorafenib resistance via binding with c-Rel to mediate NF-κB signaling in hepatocellular carcinoma. Cell Biol Int 2021; 46:213-221. [PMID: 34719075 DOI: 10.1002/cbin.11719] [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: 05/17/2021] [Revised: 10/25/2021] [Accepted: 10/25/2021] [Indexed: 12/24/2022]
Abstract
Sorafenib is the important first standard drug for patients with advanced hepatocellular carcinoma (HCC). A major obstacle to successful treatment is Sorafenib resistance. However, the mechanism of Sorafenib resistance is unclear. The present study aimed to determine the involvement of dipeptidyl peptidase-8 (DPP8) in Sorafenib resistance. DPP8 expression was detected using quantitative real-time PCR (qPCR) and western blotting. The effect of DPP8 on Sorafenib resistance was examined using terminal deoxynulceotidyl transferase nick-end-labeling (TUNEL), colony formation, flow cytometry, luciferase reporter, immunofluorescence, and immunoprecipitation (IP) assays. We found that DPP8 mRNA and protein levels were dramatically upregulated in HCC. Gene set enrichment analysis (GSEA) illustrated that DPP8 might be involved in apoptosis regulation. Downregulation of DPP8 substantially promoted the sensitivity of HCC cells to Sorafenib. Further analysis showed that DPP8 might regulate nuclear factor kappa B (NF-κB) signaling, which was confirmed using a luciferase reporter assay. Downregulation of DPP8 decreased the expression levels of downstream genes of the NF-κB pathway. IP showed that DPP8 can interact with NF-κB subunit c-Rel, an important protein of NF-κB signaling. Finally, a drug combination of Sorafenib and Val-boroPro induced higher mortality of HCC cells than Sorafenib alone in DPP8-upregulated cells. Our findings indicated that using the inhibitor Val-boroPro might be a promising method to enhance Sorafenib sensitivity in advanced HCC. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Hong-Fu Liu
- Medical College, Soochow University, Suzhou, P.R., China.,Department of General Surgery, the First Affiliated Hospital of Gannan Medical University, Ganzhou, P.R., China
| | - Yuan-Kang Xie
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of Gannan Medical University, Ganzhou, P.R., China
| | - Bai-Yin Zhong
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of Gannan Medical University, Ganzhou, P.R., China
| | - Jian-Hong Zhang
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of Gannan Medical University, Ganzhou, P.R., China
| | - Cai-Xin Song
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of Gannan Medical University, Ganzhou, P.R., China
| | - Yu-Wen Liu
- Gannan Medical University, Ganzhou, P.R., China
| | - Yan Yang
- Gannan Medical University, Ganzhou, P.R., China
| | - Bin-Hui Xie
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of Gannan Medical University, Ganzhou, P.R., China
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13
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Varela-Calviño R, Rodríguez-Quiroga M, Dias Carvalho P, Martins F, Serra-Roma A, Vázquez-Iglesias L, Páez de la Cadena M, Velho S, Cordero OJ. The mechanism of sitagliptin inhibition of colorectal cancer cell lines' metastatic functionalities. IUBMB Life 2021; 73:761-773. [PMID: 33615655 DOI: 10.1002/iub.2454] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 01/29/2021] [Accepted: 01/29/2021] [Indexed: 12/14/2022]
Abstract
The cell membrane glycoprotein CD26 with peptidase activity (DPP4) and/or its soluble CD26/DPP4 counterpart expression and/or activity are altered in several cancers. Its role in metastasis development was recently highlighted by the discovery of CD26+ cancer stem cell subsets and the fact that clinical DPP4 inhibitors showed antimetastatic effects in animal models. Also, diabetic patients treated with the DPP4 inhibitor sitagliptin showed greater overall survival after colorectal or lung cancer surgery than patients under other diabetic therapies. However, the mechanism of action of these inhibitors in this context is unclear. We studied the role of CD26 and its DPP4 enzymatic activity in malignant cell features such as cell-to-cell homotypic aggregation, cancer cell motility, and invasion in a panel of human colorectal cancer (CRC) cell lines, avoiding models that include the physiological role of DPP4 in chemotaxis. Present results indicate that CD26 participates in the induction of cell invasion, motility, and aggregation of CD26-positive CRC cell lines. Moreover, only invasion and motility assays, which are collagen matrix-dependent, showed a decrease upon treatment with the DPP4 inhibitor sitagliptin. Sitagliptin showed opposite effects to those of transforming growth factor-β1 on epithelial-to-mesenchymal transition and cell cycle, but this result does not explain its CD26/DPP4-dependent effect. These results contribute to the elucidation of the molecular mechanisms behind sitagliptin inhibition of metastatic traits. At the same time, this role of sitagliptin may help to define areas of medicine where DPP4 inhibitors might be introduced. However, they also suggest that additional tools against CD26 as a target might be used or developed for metastasis prevention in addition to gliptins.
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Affiliation(s)
- Rubén Varela-Calviño
- Department of Biochemistry and Molecular Biology, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Marta Rodríguez-Quiroga
- Institute of Research in Health and Innovation, Universidade do Porto, Porto, Portugal.,IPATIMUP (Institute of Molecular Pathology and Immunology), University of Porto, Porto, Portugal.,Department of Biochemistry, Immunology and Genetics, University of Vigo, Vigo, Spain
| | - Patrícia Dias Carvalho
- Institute of Research in Health and Innovation, Universidade do Porto, Porto, Portugal.,IPATIMUP (Institute of Molecular Pathology and Immunology), University of Porto, Porto, Portugal
| | - Flavia Martins
- Institute of Research in Health and Innovation, Universidade do Porto, Porto, Portugal.,IPATIMUP (Institute of Molecular Pathology and Immunology), University of Porto, Porto, Portugal
| | - André Serra-Roma
- Institute of Research in Health and Innovation, Universidade do Porto, Porto, Portugal.,IPATIMUP (Institute of Molecular Pathology and Immunology), University of Porto, Porto, Portugal
| | | | | | - Sérgia Velho
- Institute of Research in Health and Innovation, Universidade do Porto, Porto, Portugal.,IPATIMUP (Institute of Molecular Pathology and Immunology), University of Porto, Porto, Portugal
| | - Oscar J Cordero
- Department of Biochemistry and Molecular Biology, University of Santiago de Compostela, Santiago de Compostela, Spain
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14
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Wu Y, Shi T, Wang J, He R. Talabostat Alleviates Obesity and Associated Metabolic Dysfunction via Suppression of Macrophage-Driven Adipose Inflammation. Obesity (Silver Spring) 2021; 29:327-336. [PMID: 33342076 DOI: 10.1002/oby.23058] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 08/30/2020] [Accepted: 09/21/2020] [Indexed: 01/10/2023]
Abstract
OBJECTIVE Adipose tissue macrophages (ATMs) play critical roles in obesity-associated inflammation that contributes to metabolic dysfunction. Talabostat (TB) exerts some therapeutic effects on tumors and obesity. However, it remains unknown whether the metabolic benefits of TB on obesity is dependent on ATM-mediated adipose inflammation. METHODS Male C57BL/6J mice were fed a normal chow diet (NCD) or a high-fat diet for 12 weeks, and mice were orally administered TB daily at a low dose (0.5 mg/kg). RESULTS Administration of TB to mice fed a high-fat diet significantly improved adiposity and obesity-associated metabolic dysfunction, including glucose intolerance and insulin resistance, hyperlipidemia and hepatic steatosis, which were accompanied by increased whole-body energy expenditure. RNA sequencing analysis revealed extensive alterations in the transcriptome profiles associated with lipid metabolism and immune responses in adipose tissue of obese mice. Notably, TB treatment led to a significant reduction in ATM accumulation and a shift of the activation state of ATMs from the proinflammatory M1-like to the anti-inflammatory M2-like phenotype. Moreover, depletion of ATMs significantly abolished the TB-induced metabolic benefits. CONCLUSIONS Our study demonstrates that TB at a low dose could increase energy expenditure and control ATM-mediated adipose inflammation in obese mice, thereby alleviating obesity and its associated metabolic dysfunction.
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Affiliation(s)
- Yunyun Wu
- Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Tiancong Shi
- Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Jiqiu Wang
- Shanghai National Clinical Research Center for Metabolic Diseases, Department of Endocrinology and Metabolism, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Rui He
- Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai, China
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China
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15
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Geng L, Lam KSL, Xu A. The therapeutic potential of FGF21 in metabolic diseases: from bench to clinic. Nat Rev Endocrinol 2020; 16:654-667. [PMID: 32764725 DOI: 10.1038/s41574-020-0386-0] [Citation(s) in RCA: 262] [Impact Index Per Article: 65.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/26/2020] [Indexed: 01/10/2023]
Abstract
Fibroblast growth factor 21 (FGF21) is a stress-inducible hormone that has important roles in regulating energy balance and glucose and lipid homeostasis through a heterodimeric receptor complex comprising FGF receptor 1 (FGFR1) and β-klotho. Administration of FGF21 to rodents or non-human primates causes considerable pharmacological benefits on a cluster of obesity-related metabolic complications, including a reduction in fat mass and alleviation of hyperglycaemia, insulin resistance, dyslipidaemia, cardiovascular disorders and non-alcoholic steatohepatitis (NASH). However, native FGF21 is unsuitable for clinical use owing to poor pharmacokinetic and biophysical properties. A large number of long-acting FGF21 analogues and agonistic monoclonal antibodies for the FGFR1-β-klotho receptor complexes have been developed. Several FGF21 analogues and mimetics have progressed to early phases of clinical trials in patients with obesity, type 2 diabetes mellitus and NASH. In these trials, the primary end points of glycaemic control have not been met, whereas substantial improvements were observed in dyslipidaemia, hepatic fat fractions and serum markers of liver fibrosis in patients with NASH. The complexity and divergence in pharmacology and pathophysiology of FGF21, interspecies variations in FGF21 biology, the possible existence of obesity-related FGF21 resistance and endogenous FGF21 inactivation enzymes represent major obstacles to clinical implementation of FGF21-based pharmacotherapies for metabolic diseases.
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Affiliation(s)
- Leiluo Geng
- State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong, Hong Kong, China
- Department of Medicine, The University of Hong Kong, Hong Kong, China
| | - Karen S L Lam
- State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong, Hong Kong, China
- Department of Medicine, The University of Hong Kong, Hong Kong, China
| | - Aimin Xu
- State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong, Hong Kong, China.
- Department of Medicine, The University of Hong Kong, Hong Kong, China.
- Department of Pharmacology and Pharmacy, The University of Hong Kong, Hong Kong, China.
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16
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Direct Antiviral Treatments for Hepatitis C Virus Have Off-Target Effects of Oncologic Relevance in Hepatocellular Carcinoma. Cancers (Basel) 2020; 12:cancers12092674. [PMID: 32961688 PMCID: PMC7565876 DOI: 10.3390/cancers12092674] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 09/14/2020] [Accepted: 09/15/2020] [Indexed: 12/25/2022] Open
Abstract
Simple Summary Hepatitis C virus (HCV) eradication by direct-acting antiviral agents (DAAs) reduces de novo hepatocellular carcinoma incidence in cirrhosis; however, contrasting evidence on higher incidence of hepatocellular carcinoma (HCC) was reported in patients previously treated for HCC. Here, we showed that sofosbuvir and daclatasvir can modulate cell proliferation, invasion capability and gene expression in HCC-derived cell lines, suggesting that off-target effects of these drugs might be responsible for both the increase and reduction of cell proliferation and migration capability. Off-target gene modulation, mainly affecting mitochondrial functions, ribosomal genes and histones, was consistent with matched phenotypic changes and might account either for pro-oncogenic or tumor-suppressive functions of DAAs, that seemed to be dictated by the molecular background. Abstract Background and Aims: HCV eradication by direct-acting antiviral agents (DAAs) reduces de novo hepatocellular carcinoma (HCC) incidence in cirrhosis; however, contrasting evidence about beneficial or detrimental effects still exists in patients who have already developed HCC. Methods: we investigated whether sofosbuvir and daclatasvir modulate cell proliferation, invasion capability and gene expression (RNA-seq) in HCC-derived cell lines, hypothesizing possible off-target effects of these drugs. Results observed in HCC cell lines were validated in non-HCC cancer-derived cell lines and a preliminary series of human HCC tissues by qPCR and IHC. Results: DAAs can affect HCC cell proliferation and migration capability by either increasing or reducing them, showing transcriptomic changes consistent with some unexpected drug-associated effects. Off-target gene modulation, mainly affecting ribosomal genes, mitochondrial functions and histones, points to epigenetics and proliferation as relevant events, consistent with matched phenotypic changes. A preliminary validation of in vitro findings was performed in a restricted cohort of HCC patients previously treated with DAAs, with immunohistochemical correlations suggesting DAA-treated HCCs to be more aggressive in terms of migration and epidermal-to-mesenchymal transition. Conclusions: Our findings suggested the possible occurrence of off-target effects ultimately modulating cell proliferation and/or migration and potentially justified previous findings showing some instances of particularly aggressive HCC recurrence as well as reduced incidence of recurrence of HCC following treatment with DAAs.
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17
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Tholen M, Yim JJ, Groborz K, Yoo E, Martin BA, Berg NS, Drag M, Bogyo M. Design of Optical‐Imaging Probes by Screening of Diverse Substrate Libraries Directly in Disease‐Tissue Extracts. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006719] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Martina Tholen
- Department of Pathology Stanford University School of Medicine 300 Pasteur Drive Stanford CA 94305 USA
| | - Joshua J. Yim
- Department of Pathology Stanford University School of Medicine 300 Pasteur Drive Stanford CA 94305 USA
- Department of Chemical and System Biology Stanford University School of Medicine 300 Pasteur Drive Stanford CA 94305 USA
| | - Katarzyna Groborz
- Department of Chemical Biology and Bioimaging Faculty of Chemistry Wrocław University of Science and Technology Wrocław Poland
| | - Euna Yoo
- Department of Pathology Stanford University School of Medicine 300 Pasteur Drive Stanford CA 94305 USA
- Current address: Chemical Biology Laboratory, Center for Cancer Research National Cancer Institute Frederick MD 20850 USA
| | - Brock A. Martin
- Department of Pathology Stanford University School of Medicine 300 Pasteur Drive Stanford CA 94305 USA
| | - Nynke S. Berg
- Department of Otolaryngology-Head and Neck Surgery Stanford University School of Medicine 900 Blake Wilbur Drive Stanford CA 94305 USA
| | - Marcin Drag
- Department of Chemical Biology and Bioimaging Faculty of Chemistry Wrocław University of Science and Technology Wrocław Poland
| | - Matthew Bogyo
- Department of Pathology Stanford University School of Medicine 300 Pasteur Drive Stanford CA 94305 USA
- Department of Chemical and System Biology Stanford University School of Medicine 300 Pasteur Drive Stanford CA 94305 USA
- Microbiology and Immunology Stanford University School of Medicine 300 Pasteur Drive Stanford CA 94305 USA
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18
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Tholen M, Yim JJ, Groborz K, Yoo E, Martin BA, van den Berg NS, Drag M, Bogyo M. Design of Optical-Imaging Probes by Screening of Diverse Substrate Libraries Directly in Disease-Tissue Extracts. Angew Chem Int Ed Engl 2020; 59:19143-19152. [PMID: 32589815 DOI: 10.1002/anie.202006719] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 06/25/2020] [Indexed: 12/13/2022]
Abstract
Fluorescently quenched probes that are specifically activated in the cancer microenvironment have great potential application for diagnosis, early detection, and surgical guidance. These probes are often designed to target specific enzymes associated with diseases by direct optimization using single purified enzymes. However, this can result in painstaking chemistry efforts to produce a probe with suboptimal performance when applied in vivo. We describe here an alternate, unbiased activity-profiling approach in which whole tissue extracts are used to directly identify optimal peptide sequences for probe design. Screening of tumor extracts with a hybrid combinatorial substrate library (HyCoSuL) identified a combination of natural and non-natural amino-acid residues that was used to generate highly efficient tumor-specific probes. This new strategy simplifies and enhances the process of probe optimization without any a priori knowledge of enzyme targets and has the potential to be applied to diverse disease states using clinical or animal-model tissue samples.
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Affiliation(s)
- Martina Tholen
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305, USA
| | - Joshua J Yim
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305, USA.,Department of Chemical and System Biology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305, USA
| | - Katarzyna Groborz
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Euna Yoo
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305, USA.,Current address: Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 20850, USA
| | - Brock A Martin
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305, USA
| | - Nynke S van den Berg
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, 900 Blake Wilbur Drive, Stanford, CA, 94305, USA
| | - Marcin Drag
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305, USA.,Department of Chemical and System Biology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305, USA.,Microbiology and Immunology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305, USA
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19
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Taabazuing CY, Griswold AR, Bachovchin DA. The NLRP1 and CARD8 inflammasomes. Immunol Rev 2020; 297:13-25. [PMID: 32558991 PMCID: PMC7483925 DOI: 10.1111/imr.12884] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/06/2020] [Accepted: 05/14/2020] [Indexed: 12/28/2022]
Abstract
Inflammasomes are multiprotein complexes that activate inflammatory cytokines and induce pyroptosis in response to intracellular danger-associated signals. NLRP1 and CARD8 are related germline-encoded pattern recognition receptors that form inflammasomes, but their activation mechanisms and biological purposes have not yet been fully established. Both NLRP1 and CARD8 undergo post-translational autoproteolysis to generate two non-covalently associated polypeptide chains. NLRP1 and CARD8 activators induce the proteasome-mediated destruction of the N-terminal fragment, liberating the C-terminal fragment to form an inflammasome. Here, we review the danger-associated stimuli that have been reported to activate NLRP1 and/or CARD8, including anthrax lethal toxin, Toxoplasma gondii, Shigella flexneri and the small molecule DPP8/9 inhibitor Val-boroPro, focusing on recent mechanistic insights and highlighting unresolved questions. In addition, we discuss the recently identified disease-associated mutations in NLRP1 and CARD8, the potential role that DPP9's protein structure plays in inflammasome regulation, and the emerging link between NLRP1 and metabolism. Finally, we summarize all of this latest research and consider the possible biological purposes of these enigmatic inflammasomes.
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Affiliation(s)
| | - Andrew R Griswold
- Weill Cornell, Rockefeller, Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY, USA.,Pharmacology Program of the Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel A Bachovchin
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Pharmacology Program of the Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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20
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Kim JT, Terrell SM, Li VL, Wei W, Fischer CR, Long JZ. Cooperative enzymatic control of N-acyl amino acids by PM20D1 and FAAH. eLife 2020; 9:55211. [PMID: 32271712 PMCID: PMC7145423 DOI: 10.7554/elife.55211] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 03/21/2020] [Indexed: 12/28/2022] Open
Abstract
The N-acyl amino acids are a family of bioactive lipids with pleiotropic physiologic functions, including in energy homeostasis. Their endogenous levels are regulated by an extracellular mammalian N-acyl amino acid synthase/hydrolase called PM20D1 (peptidase M20 domain containing 1). Using an activity-guided biochemical approach, we report the molecular identification of fatty acid amide hydrolase (FAAH) as a second intracellular N-acyl amino acid synthase/hydrolase. In vitro, FAAH exhibits a more restricted substrate scope compared to PM20D1. In mice, genetic ablation or selective pharmacological inhibition of FAAH bidirectionally dysregulates intracellular, but not circulating, N-acyl amino acids. Dual blockade of both PM20D1 and FAAH reveals a dramatic and non-additive biochemical engagement of these two enzymatic pathways. These data establish FAAH as a second intracellular pathway for N-acyl amino acid metabolism and underscore enzymatic division of labor as an enabling strategy for the regulation of a structurally diverse bioactive lipid family.
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Affiliation(s)
- Joon T Kim
- Department of Pathology, Stanford University School of Medicine, Stanford, United States.,Stanford ChEM-H, Stanford University, Stanford, United States
| | - Stephanie M Terrell
- Department of Pathology, Stanford University School of Medicine, Stanford, United States.,Stanford ChEM-H, Stanford University, Stanford, United States
| | - Veronica L Li
- Department of Pathology, Stanford University School of Medicine, Stanford, United States.,Stanford ChEM-H, Stanford University, Stanford, United States
| | - Wei Wei
- Department of Pathology, Stanford University School of Medicine, Stanford, United States.,Stanford ChEM-H, Stanford University, Stanford, United States.,Department of Biology, Stanford University, Stanford, United States
| | - Curt R Fischer
- Stanford ChEM-H, Stanford University, Stanford, United States
| | - Jonathan Z Long
- Department of Pathology, Stanford University School of Medicine, Stanford, United States.,Stanford ChEM-H, Stanford University, Stanford, United States
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21
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Shenoy VM, Thompson BR, Shi J, Zhu HJ, Smith DE, Amidon GL. Chemoproteomic Identification of Serine Hydrolase RBBP9 as a Valacyclovir-Activating Enzyme. Mol Pharm 2020; 17:1706-1714. [DOI: 10.1021/acs.molpharmaceut.0c00131] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Vikram M. Shenoy
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109-1065, United States
| | - Brian R. Thompson
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109-1065, United States
| | - Jian Shi
- Department of Clinical Pharmacy, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109-1065, United States
| | - Hao-Jie Zhu
- Department of Clinical Pharmacy, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109-1065, United States
| | - David E. Smith
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109-1065, United States
| | - Gordon L. Amidon
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109-1065, United States
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22
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Bun JS, Slack MD, Schemenauer DE, Johnson RJ. Comparative analysis of the human serine hydrolase OVCA2 to the model serine hydrolase homolog FSH1 from S. cerevisiae. PLoS One 2020; 15:e0230166. [PMID: 32182256 PMCID: PMC7077851 DOI: 10.1371/journal.pone.0230166] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 02/20/2020] [Indexed: 11/22/2022] Open
Abstract
Over 100 metabolic serine hydrolases are present in humans with confirmed functions in metabolism, immune response, and neurotransmission. Among potentially clinically-relevant but uncharacterized human serine hydrolases is OVCA2, a serine hydrolase that has been linked with a variety of cancer-related processes. Herein, we developed a heterologous expression system for OVCA2 and determined the comprehensive substrate specificity of OVCA2 against two ester substrate libraries. Based on this analysis, OVCA2 was confirmed as a serine hydrolase with a strong preference for long-chain alkyl ester substrates (>10-carbons) and high selectivity against a variety of short, branched, and substituted esters. Substitutional analysis was used to identify the catalytic residues of OVCA2 with a Ser117-His206-Asp179 classic catalytic triad. Comparison of the substrate specificity of OVCA2 to the model homologue FSH1 from Saccharomyces cerevisiae illustrated the tighter substrate selectivity of OVCA2, but their overlapping substrate preference for extended straight-chain alkyl esters. Conformation of the overlapping biochemical properties of OVCA2 and FSH1 was used to model structural information about OVCA2. Together our analysis provides detailed substrate specificity information about a previously, uncharacterized human serine hydrolase and begins to define the biological properties of OVCA2.
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Affiliation(s)
- Jessica S. Bun
- Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana, United States of America
| | - Michael D. Slack
- Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana, United States of America
| | - Daniel E. Schemenauer
- Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana, United States of America
| | - R. Jeremy Johnson
- Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana, United States of America
- * E-mail:
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23
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High-Resolution Confocal Fluorescence Imaging of Serine Hydrolase Activity in Cryosections - Application to Glioma Brain Unveils Activity Hotspots Originating from Tumor-Associated Neutrophils. Biol Proced Online 2020; 22:6. [PMID: 32190011 PMCID: PMC7073015 DOI: 10.1186/s12575-020-00118-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 02/19/2020] [Indexed: 12/18/2022] Open
Abstract
Background Serine hydrolases (SHs) are a functionally diverse family of enzymes playing pivotal roles in health and disease and have emerged as important therapeutic targets in many clinical conditions. Activity-based protein profiling (ABPP) using fluorophosphonate (FP) probes has been a powerful chemoproteomic approach in studies unveiling roles of SHs in various biological systems. ABPP utilizes cell/tissue proteomes and features the FP-warhead, linked to a fluorescent reporter for in-gel fluorescence imaging or a biotin tag for streptavidin enrichment and LC-MS/MS-based target identification. Existing ABPP approaches characterize global SH activity based on mobility in gel or MS-based target identification and cannot reveal the identity of the cell-type responsible for an individual SH activity originating from complex proteomes. Results Here, by using an activity probe with broad reactivity towards the SH family, we advance the ABPP methodology to glioma brain cryosections, enabling for the first time high-resolution confocal fluorescence imaging of global SH activity in the tumor microenvironment. Tumor-associated cell types were identified by extensive immunohistochemistry on activity probe-labeled sections. Tissue-ABPP indicated heightened SH activity in glioma vs. normal brain and unveiled activity hotspots originating from tumor-associated neutrophils (TANs), rather than tumor-associated macrophages (TAMs). Thorough optimization and validation was provided by parallel gel-based ABPP combined with LC-MS/MS-based target verification. Conclusions Our study advances the ABPP methodology to tissue sections, enabling high-resolution confocal fluorescence imaging of global SH activity in anatomically preserved complex native cellular environment. To achieve global portrait of SH activity throughout the section, a probe with broad reactivity towards the SH family members was employed. As ABPP requires no a priori knowledge of the identity of the target, we envisage no imaginable reason why the presently described approach would not work for sections regardless of species and tissue source.
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24
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Griswold AR, Ball DP, Bhattacharjee A, Chui AJ, Rao SD, Taabazuing CY, Bachovchin DA. DPP9's Enzymatic Activity and Not Its Binding to CARD8 Inhibits Inflammasome Activation. ACS Chem Biol 2019; 14:2424-2429. [PMID: 31525884 PMCID: PMC6862324 DOI: 10.1021/acschembio.9b00462] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
Inflammasomes
are multiprotein complexes formed in response to
pathogens. NLRP1 and CARD8 are related proteins that form inflammasomes,
but the pathogen-associated signal(s) and the molecular mechanisms
controlling their activation have not been established. Inhibitors
of the serine dipeptidyl peptidases DPP8 and DPP9 (DPP8/9) activate
both NLRP1 and CARD8. Interestingly, DPP9 binds directly to NLRP1
and CARD8, and this interaction may contribute to the inhibition of
NLRP1. Here, we use activity-based probes, reconstituted inflammasome
assays, and mass spectrometry-based proteomics to further investigate
the DPP9–CARD8 interaction. We show that the DPP9–CARD8
interaction, unlike the DPP9–NLRP1 interaction, is not disrupted
by DPP9 inhibitors or CARD8 mutations that block autoproteolysis.
Moreover, wild-type, but not catalytically inactive mutant, DPP9 rescues
CARD8-mediated cell death in DPP9 knockout cells.
Together, this work reveals that DPP9’s catalytic activity
and not its binding to CARD8 restrains the CARD8 inflammasome and
thus suggests the binding interaction likely serves some other biological
purpose.
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Affiliation(s)
- Andrew R. Griswold
- Tri-Institutional M.D.−Ph.D. Program, Memorial Sloan Kettering Cancer Center, Rockefeller University, Weill Cornell Medical College, New York, New York 10065, United States
- Pharmacology Program, Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Daniel P. Ball
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Abir Bhattacharjee
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Ashley J. Chui
- Tri-Institutional Ph.D. Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Sahana D. Rao
- Tri-Institutional Ph.D. Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Cornelius Y. Taabazuing
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Daniel A. Bachovchin
- Pharmacology Program, Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
- Tri-Institutional Ph.D. Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
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25
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Buckley BJ, Majed H, Aboelela A, Minaei E, Jiang L, Fildes K, Cheung CY, Johnson D, Bachovchin D, Cook GM, Huang M, Ranson M, Kelso MJ. 6-Substituted amiloride derivatives as inhibitors of the urokinase-type plasminogen activator for use in metastatic disease. Bioorg Med Chem Lett 2019; 29:126753. [PMID: 31679971 DOI: 10.1016/j.bmcl.2019.126753] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 10/10/2019] [Accepted: 10/11/2019] [Indexed: 11/25/2022]
Abstract
The oral K+-sparing diuretic amiloride shows anti-cancer side-activities in multiple rodent models. These effects appear to arise, at least in part, through moderate inhibition of the urokinase-type plasminogen activator (uPA, Ki = 2.4 µM), a pro-metastatic trypsin-like serine protease that is upregulated in many aggressive solid malignancies. In applying the selective optimization of side-activity (SOSA) approach, a focused library of twenty two 6-substituted amiloride derivatives were prepared, with multiple examples displaying uPA inhibitory potencies in the nM range. X-ray co-crystal structures revealed that the potency increases relative to amiloride arise from increased occupancy of uPA's S1β subsite by the appended 6-substituents. Leading compounds were shown to have high selectivity over related trypsin-like serine proteases and no diuretic or anti-kaliuretic effects in rats. Compound 15 showed anti-metastatic effects in a xenografted mouse model of late-stage lung metastasis.
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Affiliation(s)
- Benjamin J Buckley
- School of Chemistry and Molecular Bioscience, University of Wollongong, NSW 2522, Australia; Illawarra Health and Medical Research Institute, NSW 2522, Australia; Molecular Horizons, University of Wollongong, NSW 2522, Australia
| | - Hiwa Majed
- School of Chemistry and Molecular Bioscience, University of Wollongong, NSW 2522, Australia; Illawarra Health and Medical Research Institute, NSW 2522, Australia; Molecular Horizons, University of Wollongong, NSW 2522, Australia
| | - Ashraf Aboelela
- School of Chemistry and Molecular Bioscience, University of Wollongong, NSW 2522, Australia; Illawarra Health and Medical Research Institute, NSW 2522, Australia; Molecular Horizons, University of Wollongong, NSW 2522, Australia
| | - Elahe Minaei
- Illawarra Health and Medical Research Institute, NSW 2522, Australia; Molecular Horizons, University of Wollongong, NSW 2522, Australia
| | - Longguang Jiang
- National Joint Biomdical Engineering Research Centre on Photodynamic Technologies, Fuzhou University, Fuzhou 350116, China
| | - Karen Fildes
- Illawarra Health and Medical Research Institute, NSW 2522, Australia; Graduate School of Medicine, University of Wollongong, NSW 2522, Australia
| | - Chen-Yi Cheung
- Department of Microbiology and Immunology, University of Otago, Otago 9016, New Zealand
| | - Darren Johnson
- Tri-institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, NY 10065, USA
| | - Daniel Bachovchin
- Tri-institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, NY 10065, USA; Chemical Biology Program, Memorial Sloan Kettering Cancer Centre, NY 10065, USA
| | - Gregory M Cook
- Department of Microbiology and Immunology, University of Otago, Otago 9016, New Zealand
| | - Mingdong Huang
- National Joint Biomdical Engineering Research Centre on Photodynamic Technologies, Fuzhou University, Fuzhou 350116, China
| | - Marie Ranson
- School of Chemistry and Molecular Bioscience, University of Wollongong, NSW 2522, Australia; Illawarra Health and Medical Research Institute, NSW 2522, Australia; Molecular Horizons, University of Wollongong, NSW 2522, Australia.
| | - Michael J Kelso
- School of Chemistry and Molecular Bioscience, University of Wollongong, NSW 2522, Australia; Illawarra Health and Medical Research Institute, NSW 2522, Australia; Molecular Horizons, University of Wollongong, NSW 2522, Australia.
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26
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Abstract
The ubiquitin proteasome system (UPS) degrades individual proteins in a highly regulated fashion and is responsible for the degradation of misfolded, damaged, or unneeded cellular proteins. During the past 20 years, investigators have established a critical role for the UPS in essentially every cellular process, including cell cycle progression, transcriptional regulation, genome integrity, apoptosis, immune responses, and neuronal plasticity. At the center of the UPS is the proteasome, a large and complex molecular machine containing a multicatalytic protease complex. When the efficiency of this proteostasis system is perturbed, misfolded and damaged protein aggregates can accumulate to toxic levels and cause neuronal dysfunction, which may underlie many neurodegenerative diseases. In addition, many cancers rely on robust proteasome activity for degrading tumor suppressors and cell cycle checkpoint inhibitors necessary for rapid cell division. Thus, proteasome inhibitors have proven clinically useful to treat some types of cancer, especially multiple myeloma. Numerous cellular processes rely on finely tuned proteasome function, making it a crucial target for future therapeutic intervention in many diseases, including neurodegenerative diseases, cystic fibrosis, atherosclerosis, autoimmune diseases, diabetes, and cancer. In this review, we discuss the structure and function of the proteasome, the mechanisms of action of different proteasome inhibitors, various techniques to evaluate proteasome function in vitro and in vivo, proteasome inhibitors in preclinical and clinical development, and the feasibility for pharmacological activation of the proteasome to potentially treat neurodegenerative disease.
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Affiliation(s)
- Tiffany A Thibaudeau
- Department of Biochemistry, West Virginia University School of Medicine, Morgantown, West Virginia
| | - David M Smith
- Department of Biochemistry, West Virginia University School of Medicine, Morgantown, West Virginia
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27
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Vasudevan A, Argiriadi MA, Baranczak A, Friedman MM, Gavrilyuk J, Hobson AD, Hulce JJ, Osman S, Wilson NS. Covalent binders in drug discovery. PROGRESS IN MEDICINAL CHEMISTRY 2019; 58:1-62. [PMID: 30879472 DOI: 10.1016/bs.pmch.2018.12.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covalent modulation of protein function can have multiple utilities including therapeutics, and probes to interrogate biology. While this field is still viewed with scepticism due to the potential for (idiosyncratic) toxicities, significant strides have been made in terms of understanding how to tune electrophilicity to selectively target specific residues. Progress has also been made in harnessing the potential of covalent binders to uncover novel biology and to provide an enhanced utility as payloads for Antibody Drug Conjugates. This perspective covers the tenets and applications of covalent binders.
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Affiliation(s)
| | | | | | | | - Julia Gavrilyuk
- AbbVie Stemcentrx, LLC, South San Francisco, CA, United States
| | | | | | - Sami Osman
- AbbVie Bioresearch Center, Worcester, MA, United States
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28
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Panaro BL, Coppage AL, Beaudry JL, Varin EM, Kaur K, Lai JH, Wu W, Liu Y, Bachovchin WW, Drucker DJ. Fibroblast activation protein is dispensable for control of glucose homeostasis and body weight in mice. Mol Metab 2018; 19:65-74. [PMID: 30477988 PMCID: PMC6323180 DOI: 10.1016/j.molmet.2018.10.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 10/30/2018] [Accepted: 10/30/2018] [Indexed: 12/12/2022] Open
Abstract
Objective Fibroblast Activation Protein (FAP), an enzyme structurally related to dipeptidyl peptidase-4 (DPP-4), has garnered interest as a potential metabolic drug target due to its ability to cleave and inactivate FGF-21 as well as other peptide substrates. Here we investigated the metabolic importance of FAP for control of body weight and glucose homeostasis in regular chow-fed and high fat diet-fed mice. Methods FAP enzyme activity was transiently attenuated using a highly-specific inhibitor CPD60 and permanently ablated by genetic inactivation of the mouse Fap gene. We also assessed the FAP-dependence of CPD60 and talabostat (Val-boroPro), a chemical inhibitor reportedly targeting both FAP and dipeptidyl peptidase-4 Results CPD60 robustly inhibited plasma FAP activity with no effect on DPP-4 activity. Fap gene disruption was confirmed by assessment of genomic DNA, and loss of FAP enzyme activity in plasma and tissues. CPD60 did not improve lipid tolerance but modestly improved acute oral and intraperitoneal glucose tolerance in a FAP-dependent manner. Genetic inactivation of Fap did not improve glucose or lipid tolerance nor confer resistance to weight gain in male or female Fap−/− mice fed regular chow or high-fat diets. Moreover, talabostat markedly improved glucose homeostasis in a FAP- and FGF-21-independent, DPP-4 dependent manner. Conclusion Although pharmacological FAP inhibition improves glucose tolerance, the absence of a metabolic phenotype in Fap−/−mice suggest that endogenous FAP is dispensable for the regulation of murine glucose homeostasis and body weight. These findings highlight the importance of characterizing the specificity and actions of FAP inhibitors in different species and raise important questions about the feasibility of mouse models for targeting FAP as a treatment for diabetes and related metabolic disorders. Acute inhibition of FAP enzyme activity improves glucose tolerance in mice. Fap knockout mice exhibit normal glucose and lipid tolerance. Fap knockout mice do not resist obesity after high fat feeding. Talabostat robustly lowers glucose in a FAP and FGF21-independent manner. Talabostat, but not CPD60, requires DPP4 to exert its full metabolic activity.
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Affiliation(s)
- Brandon L Panaro
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | - Andrew L Coppage
- Sackler School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA, 02111, USA
| | - Jacqueline L Beaudry
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | - Elodie M Varin
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | - Kirandeep Kaur
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | - Jack H Lai
- Sackler School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA, 02111, USA
| | - Wengen Wu
- Sackler School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA, 02111, USA
| | - Yuxin Liu
- Sackler School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA, 02111, USA
| | - William W Bachovchin
- Sackler School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA, 02111, USA
| | - Daniel J Drucker
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada.
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29
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Buckley BJ, Aboelela A, Minaei E, Jiang LX, Xu Z, Ali U, Fildes K, Cheung CY, Cook SM, Johnson DC, Bachovchin DA, Cook GM, Apte M, Huang M, Ranson M, Kelso MJ. 6-Substituted Hexamethylene Amiloride (HMA) Derivatives as Potent and Selective Inhibitors of the Human Urokinase Plasminogen Activator for Use in Cancer. J Med Chem 2018; 61:8299-8320. [PMID: 30130401 DOI: 10.1021/acs.jmedchem.8b00838] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Metastasis is the cause of death in the majority (∼90%) of malignant cancers. The oral potassium-sparing diuretic amiloride and its 5-substituted derivative 5 -N, N-(hexamethylene)amiloride (HMA) reportedly show robust antitumor/metastasis effects in multiple in vitro and animal models. These effects are likely due, at least in part, to inhibition of the urokinase plasminogen activator (uPA), a key protease determinant of cell invasiveness and metastasis. This study reports the discovery of 6-substituted HMA analogs that show nanomolar potency against uPA, high selectivity over related trypsin-like serine proteases, and minimal inhibitory effects against epithelial sodium channels (ENaC), the diuretic and antikaliuretic target of amiloride. Reductions in lung metastases were demonstrated for two analogs in a late-stage experimental mouse metastasis model, and one analog completely inhibited formation of liver metastases in an orthotopic xenograft mouse model of pancreatic cancer. The results support further evaluation of 6-substituted HMA derivatives as uPA-targeting anticancer drugs.
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Affiliation(s)
- Benjamin J Buckley
- Molecular Horizons and School of Chemistry & Molecular Bioscience , University of Wollongong , Wollongong , NSW 2522 , Australia.,Illawarra Health & Medical Research Institute , Wollongong , NSW 2522 , Australia
| | - Ashraf Aboelela
- Molecular Horizons and School of Chemistry & Molecular Bioscience , University of Wollongong , Wollongong , NSW 2522 , Australia.,Illawarra Health & Medical Research Institute , Wollongong , NSW 2522 , Australia
| | - Elahe Minaei
- Molecular Horizons and School of Chemistry & Molecular Bioscience , University of Wollongong , Wollongong , NSW 2522 , Australia.,Illawarra Health & Medical Research Institute , Wollongong , NSW 2522 , Australia
| | - Longguang X Jiang
- National Joint Biomedical Engineering Research Centre on Photodynamic Technologies , Fuzhou University , Fujian 350116 , China
| | - Zhihong Xu
- Pancreatic Research Group, South Western Sydney Clinical School , University of New South Wales, and Ingham Institute for Applied Medical Research , Liverpool , NSW 2170 , Australia
| | - Umar Ali
- Molecular Horizons and School of Chemistry & Molecular Bioscience , University of Wollongong , Wollongong , NSW 2522 , Australia.,Illawarra Health & Medical Research Institute , Wollongong , NSW 2522 , Australia
| | - Karen Fildes
- Illawarra Health & Medical Research Institute , Wollongong , NSW 2522 , Australia.,Graduate School of Medicine , University of Wollongong , Wollongong , NSW 2522 , Australia
| | - Chen-Yi Cheung
- Department of Microbiology and Immunology , University of Otago , Otago 9016 , New Zealand
| | - Simon M Cook
- Illawarra Health & Medical Research Institute , Wollongong , NSW 2522 , Australia
| | - Darren C Johnson
- Tri-Institutional PhD Program in Chemical Biology , Memorial Sloan Kettering Cancer Center , New York , New York 10065 , United States
| | - Daniel A Bachovchin
- Tri-Institutional PhD Program in Chemical Biology , Memorial Sloan Kettering Cancer Center , New York , New York 10065 , United States.,Chemical Biology Program , Memorial Sloan Kettering Cancer Center , New York , New York 10065 , United States
| | - Gregory M Cook
- Department of Microbiology and Immunology , University of Otago , Otago 9016 , New Zealand
| | - Minoti Apte
- Pancreatic Research Group, South Western Sydney Clinical School , University of New South Wales, and Ingham Institute for Applied Medical Research , Liverpool , NSW 2170 , Australia
| | - Mingdong Huang
- National Joint Biomedical Engineering Research Centre on Photodynamic Technologies , Fuzhou University , Fujian 350116 , China
| | - Marie Ranson
- Molecular Horizons and School of Chemistry & Molecular Bioscience , University of Wollongong , Wollongong , NSW 2522 , Australia.,Illawarra Health & Medical Research Institute , Wollongong , NSW 2522 , Australia
| | - Michael J Kelso
- Molecular Horizons and School of Chemistry & Molecular Bioscience , University of Wollongong , Wollongong , NSW 2522 , Australia.,Illawarra Health & Medical Research Institute , Wollongong , NSW 2522 , Australia
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30
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Johnson DC, Taabazuing CY, Okondo MC, Chui AJ, Rao SD, Brown FC, Reed C, Peguero E, de Stanchina E, Kentsis A, Bachovchin DA. DPP8/DPP9 inhibitor-induced pyroptosis for treatment of acute myeloid leukemia. Nat Med 2018; 24:1151-1156. [PMID: 29967349 PMCID: PMC6082709 DOI: 10.1038/s41591-018-0082-y] [Citation(s) in RCA: 227] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 04/30/2018] [Indexed: 12/26/2022]
Abstract
Small-molecule inhibitors of the serine dipeptidases DPP8 and DPP9 (DPP8/9) induce a lytic form of cell death called pyroptosis in mouse and human monocytes and macrophages1,2. In mouse myeloid cells, Dpp8/9 inhibition activates the inflammasome sensor Nlrp1b, which in turn activates pro-caspase-1 to mediate cell death3, but the mechanism of DPP8/9 inhibitor-induced pyroptosis in human myeloid cells is not yet known. Here we show that the CARD-containing protein CARD8 mediates DPP8/9 inhibitor-induced pro-caspase-1-dependent pyroptosis in human myeloid cells. We further show that DPP8/9 inhibitors induce pyroptosis in the majority of human acute myeloid leukemia (AML) cell lines and primary AML samples, but not in cells from many other lineages, and that these inhibitors inhibit human AML progression in mouse models. Overall, this work identifies an activator of CARD8 in human cells and indicates that its activation by small-molecule DPP8/9 inhibitors represents a new potential therapeutic strategy for AML.
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Affiliation(s)
- Darren C Johnson
- Tri-institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Marian C Okondo
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ashley J Chui
- Tri-institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sahana D Rao
- Tri-institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fiona C Brown
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Casie Reed
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elizabeth Peguero
- Antitumor Assessment Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elisa de Stanchina
- Antitumor Assessment Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alex Kentsis
- Tri-institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Pharmacology Program of the Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel A Bachovchin
- Tri-institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Pharmacology Program of the Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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31
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Kim D, Jetson RR, Krusemark CJ. A DNA-assisted immunoassay for enzyme activity via a DNA-linked, activity-based probe. Chem Commun (Camb) 2018; 53:9474-9477. [PMID: 28795701 DOI: 10.1039/c7cc05236g] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Here, we describe an immunoassay approach for the detection of enzyme activity by quantitative PCR (qPCR) or parallel DNA sequencing which relies on activity-based probes linked to barcoding DNAs. We demonstrate this technique in the detection of serine hydrolase activities using a fluorophosphonate-oligonucleotide conjugate.
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Affiliation(s)
- Dongwook Kim
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA.
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32
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Dudani JS, Warren AD, Bhatia SN. Harnessing Protease Activity to Improve Cancer Care. ANNUAL REVIEW OF CANCER BIOLOGY-SERIES 2018. [DOI: 10.1146/annurev-cancerbio-030617-050549] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jaideep S. Dudani
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;, ,
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Andrew D. Warren
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;, ,
- Harvard–MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Sangeeta N. Bhatia
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;, ,
- Harvard–MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02139, USA
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33
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Ivry SL, Meyer NO, Winter MB, Bohn MF, Knudsen GM, O'Donoghue AJ, Craik CS. Global substrate specificity profiling of post-translational modifying enzymes. Protein Sci 2018; 27:584-594. [PMID: 29168252 PMCID: PMC5818756 DOI: 10.1002/pro.3352] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 11/09/2017] [Accepted: 11/13/2017] [Indexed: 12/14/2022]
Abstract
Enzymes that modify the proteome, referred to as post-translational modifying (PTM) enzymes, are central regulators of cellular signaling. Determining the substrate specificity of PTM enzymes is a critical step in unraveling their biological functions both in normal physiological processes and in disease states. Advances in peptide chemistry over the last century have enabled the rapid generation of peptide libraries for querying substrate recognition by PTM enzymes. In this article, we highlight various peptide-based approaches for analysis of PTM enzyme substrate specificity. We focus on the application of these technologies to proteases and also discuss specific examples in which they have been used to uncover the substrate specificity of other types of PTM enzymes, such as kinases. In particular, we highlight our multiplex substrate profiling by mass spectrometry (MSP-MS) assay, which uses a rationally designed, physicochemically diverse library of tetradecapeptides. We show how this method has been applied to PTM enzymes to uncover biological function, and guide substrate and inhibitor design. We also briefly discuss how this technique can be combined with other methods to gain a systems-level understanding of PTM enzyme regulation and function.
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Affiliation(s)
- Sam L. Ivry
- Department of Pharmaceutical ChemistryUniversity of California, San FranciscoSan FranciscoCalifornia
- Pharmaceutical Sciences and Pharmacogenomics Graduate ProgramUniversity of California, San FranciscoSan FranciscoCalifornia
| | - Nicole O. Meyer
- Department of Pharmaceutical ChemistryUniversity of California, San FranciscoSan FranciscoCalifornia
| | - Michael B. Winter
- Department of Pharmaceutical ChemistryUniversity of California, San FranciscoSan FranciscoCalifornia
| | - Markus F. Bohn
- Department of Pharmaceutical ChemistryUniversity of California, San FranciscoSan FranciscoCalifornia
| | - Giselle M. Knudsen
- Department of Pharmaceutical ChemistryUniversity of California, San FranciscoSan FranciscoCalifornia
| | - Anthony J. O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San DiegoLa JollaCalifornia
| | - Charles S. Craik
- Department of Pharmaceutical ChemistryUniversity of California, San FranciscoSan FranciscoCalifornia
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34
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Daniels BE, Stivala CE. A solid-phase approach for the synthesis of α-aminoboronic acid peptides. RSC Adv 2018; 8:3343-3347. [PMID: 35541192 PMCID: PMC9077542 DOI: 10.1039/c7ra13479g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 01/10/2018] [Indexed: 01/06/2023] Open
Abstract
A solid-phase synthesis of α-aminoboronic acid peptides using a 1-glycerol polystyrene resin is described.
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35
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Abstract
The activity of proteases is tightly regulated, and dysregulation is linked to a variety of human diseases. For this reason, ABPP is a well-suited method to study protease biology and the design of protease probes has pushed the boundaries of ABPP. The development of highly selective protease probes is still a challenging task. After an introduction, the first section of this chapter discusses several strategies to enable detection of a single active protease species. These range from the usage of non-natural amino acids, combination of probes with antibodies, and engineering of the target proteases. A next section describes the different types of detection tags that facilitate the read-out possibilities including various types of imaging methods and mass spectrometry-based target identification. The power of protease ABPP is illustrated by examples for a selected number of proteases. It is expected that some protease probes that have been evaluated in animal models of human disease will find translation into clinical application in the near future.
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36
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Goel P, Jumpertz T, Mikles DC, Tichá A, Nguyen MTN, Verhelst S, Hubalek M, Johnson DC, Bachovchin DA, Ogorek I, Pietrzik CU, Strisovsky K, Schmidt B, Weggen S. Discovery and Biological Evaluation of Potent and Selective N-Methylene Saccharin-Derived Inhibitors for Rhomboid Intramembrane Proteases. Biochemistry 2017; 56:6713-6725. [PMID: 29185711 DOI: 10.1021/acs.biochem.7b01066] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Rhomboids are intramembrane serine proteases and belong to the group of structurally and biochemically most comprehensively characterized membrane proteins. They are highly conserved and ubiquitously distributed in all kingdoms of life and function in a wide range of biological processes, including epidermal growth factor signaling, mitochondrial dynamics, and apoptosis. Importantly, rhomboids have been associated with multiple diseases, including Parkinson's disease, type 2 diabetes, and malaria. However, despite a thorough understanding of many structural and functional aspects of rhomboids, potent and selective inhibitors of these intramembrane proteases are still not available. In this study, we describe the computer-based rational design, chemical synthesis, and biological evaluation of novel N-methylene saccharin-based rhomboid protease inhibitors. Saccharin inhibitors displayed inhibitory potency in the submicromolar range, effectiveness against rhomboids both in vitro and in live Escherichia coli cells, and substantially improved selectivity against human serine hydrolases compared to those of previously known rhomboid inhibitors. Consequently, N-methylene saccharins are promising new templates for the development of rhomboid inhibitors, providing novel tools for probing rhomboid functions in physiology and disease.
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Affiliation(s)
- Parul Goel
- Department of Neuropathology, Heinrich-Heine University Duesseldorf , Moorenstrasse 5, 40225 Duesseldorf, Germany.,Clemens Schoepf Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt , Alarich-Weiss-Strasse 4-8, 64287 Darmstadt, Germany
| | - Thorsten Jumpertz
- Department of Neuropathology, Heinrich-Heine University Duesseldorf , Moorenstrasse 5, 40225 Duesseldorf, Germany
| | - David C Mikles
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo n. 2, 166 10 Praha 6, Czech Republic
| | - Anežka Tichá
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo n. 2, 166 10 Praha 6, Czech Republic
| | - Minh T N Nguyen
- Chemical Proteomics Group, Leibnitz Institute for Analytical Sciences (ISAS) e.V. , Otto-Hahn-Strasse 6b, 44227 Dortmund, Germany
| | - Steven Verhelst
- Chemical Proteomics Group, Leibnitz Institute for Analytical Sciences (ISAS) e.V. , Otto-Hahn-Strasse 6b, 44227 Dortmund, Germany.,Laboratory of Chemical Biology, Department of Cellular and Molecular Medicine, University of Leuven , Herestraat 49, Box 802, 3000 Leuven, Belgium
| | - Martin Hubalek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo n. 2, 166 10 Praha 6, Czech Republic
| | - Darren C Johnson
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center , 1275 York Avenue, Box 428, New York, New York 10065, United States
| | - Daniel A Bachovchin
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center , 1275 York Avenue, Box 428, New York, New York 10065, United States
| | - Isabella Ogorek
- Department of Neuropathology, Heinrich-Heine University Duesseldorf , Moorenstrasse 5, 40225 Duesseldorf, Germany
| | - Claus U Pietrzik
- Institute for Pathobiochemistry, University Medical Center of the Johannes Gutenberg University Mainz , Duesbergweg 6, 55128 Mainz, Germany
| | - Kvido Strisovsky
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo n. 2, 166 10 Praha 6, Czech Republic
| | - Boris Schmidt
- Clemens Schoepf Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt , Alarich-Weiss-Strasse 4-8, 64287 Darmstadt, Germany
| | - Sascha Weggen
- Department of Neuropathology, Heinrich-Heine University Duesseldorf , Moorenstrasse 5, 40225 Duesseldorf, Germany
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37
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Yang W, Yaggie RE, Jiang MC, Rudick CN, Done J, Heckman CJ, Rosen JM, Schaeffer AJ, Klumpp DJ. Acyloxyacyl hydrolase modulates pelvic pain severity. Am J Physiol Regul Integr Comp Physiol 2017; 314:R353-R365. [PMID: 29118019 DOI: 10.1152/ajpregu.00239.2017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Chronic pelvic pain causes significant patient morbidity and is a challenge to clinicians. Using a murine neurogenic cystitis model that recapitulates key aspects of interstitial cystitis/bladder pain syndrome (IC), we recently showed that pseudorabies virus (PRV) induces severe pelvic allodynia in BALB/c mice relative to C57BL/6 mice. Here, we report that a quantitative trait locus (QTL) analysis of PRV-induced allodynia in F2CxB progeny identified a polymorphism on chromosome 13, rs6314295 , significantly associated with allodynia (logarithm of odds = 3.11). The nearby gene encoding acyloxyacyl hydrolase ( Aoah) was induced in the sacral spinal cord of PRV-infected mice. AOAH-deficient mice exhibited increased vesicomotor reflex in response to bladder distension, consistent with spontaneous bladder hypersensitivity, and increased pelvic allodynia in neurogenic cystitis and postbacterial chronic pain models. AOAH deficiency resulted in greater bladder pathology and tumor necrosis factor production in PRV neurogenic cystitis, markers of increased bladder mast cell activation. AOAH immunoreactivity was detectable along the bladder-brain axis, including in brain sites previously correlated with human chronic pelvic pain. Finally, AOAH-deficient mice had significantly higher levels of bladder vascular endothelial growth factor, an emerging marker of chronic pelvic pain in humans. These findings indicate that AOAH modulates pelvic pain severity, suggesting that allelic variation in Aoah influences pelvic pain in IC.
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Affiliation(s)
- Wenbin Yang
- Department of Urology, Feinberg School of Medicine, Northwestern University , Chicago, Illinois
| | - Ryan E Yaggie
- Department of Urology, Feinberg School of Medicine, Northwestern University , Chicago, Illinois
| | - Mingchen C Jiang
- Department of Physiology, Feinberg School of Medicine, Northwestern University , Chicago, Illinois
| | - Charles N Rudick
- Department of Urology, Feinberg School of Medicine, Northwestern University , Chicago, Illinois
| | - Joseph Done
- Department of Urology, Feinberg School of Medicine, Northwestern University , Chicago, Illinois
| | - Charles J Heckman
- Department of Physiology, Feinberg School of Medicine, Northwestern University , Chicago, Illinois.,Department of Physical Medicine and Rehabilitation, Feinberg School of Medicine, Northwestern University , Chicago, Illinois
| | - John M Rosen
- Department of Pediatric Gastroenterology, Children's Mercy, Kansas City, Missouri
| | - Anthony J Schaeffer
- Department of Urology, Feinberg School of Medicine, Northwestern University , Chicago, Illinois
| | - David J Klumpp
- Department of Urology, Feinberg School of Medicine, Northwestern University , Chicago, Illinois.,Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University , Chicago, Illinois
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38
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Tichá A, Stanchev S, Vinothkumar KR, Mikles DC, Pachl P, Began J, Škerle J, Švehlová K, Nguyen MTN, Verhelst SHL, Johnson DC, Bachovchin DA, Lepšík M, Majer P, Strisovsky K. General and Modular Strategy for Designing Potent, Selective, and Pharmacologically Compliant Inhibitors of Rhomboid Proteases. Cell Chem Biol 2017; 24:1523-1536.e4. [PMID: 29107700 PMCID: PMC5746060 DOI: 10.1016/j.chembiol.2017.09.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 08/19/2017] [Accepted: 09/18/2017] [Indexed: 12/19/2022]
Abstract
Rhomboid-family intramembrane proteases regulate important biological processes and have been associated with malaria, cancer, and Parkinson's disease. However, due to the lack of potent, selective, and pharmacologically compliant inhibitors, the wide therapeutic potential of rhomboids is currently untapped. Here, we bridge this gap by discovering that peptidyl α-ketoamides substituted at the ketoamide nitrogen by hydrophobic groups are potent rhomboid inhibitors active in the nanomolar range, surpassing the currently used rhomboid inhibitors by up to three orders of magnitude. Such peptidyl ketoamides show selectivity for rhomboids, leaving most human serine hydrolases unaffected. Crystal structures show that these compounds bind the active site of rhomboid covalently and in a substrate-like manner, and kinetic analysis reveals their reversible, slow-binding, non-competitive mechanism. Since ketoamides are clinically used pharmacophores, our findings uncover a straightforward modular way for the design of specific inhibitors of rhomboid proteases, which can be widely applicable in cell biology and drug discovery. N-substituted peptidyl α-ketoamides are nanomolar inhibitors of rhomboid proteases Peptidyl ketoamides inhibit rhomboids covalently, reversibly, and non-competitively The peptide and ketoamide substituent independently modulate potency and selectivity Peptidyl ketoamides are selective for rhomboids, sparing most human serine proteases
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Affiliation(s)
- Anežka Tichá
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo n. 2, Prague 166 10, Czech Republic; First Faculty of Medicine, Charles University, Kateřinská 32, Prague 121 08, Czech Republic
| | - Stancho Stanchev
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo n. 2, Prague 166 10, Czech Republic
| | - Kutti R Vinothkumar
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - David C Mikles
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo n. 2, Prague 166 10, Czech Republic
| | - Petr Pachl
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo n. 2, Prague 166 10, Czech Republic
| | - Jakub Began
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo n. 2, Prague 166 10, Czech Republic; Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, Prague 128 44, Czech Republic
| | - Jan Škerle
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo n. 2, Prague 166 10, Czech Republic; Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, Prague 128 43, Czech Republic
| | - Kateřina Švehlová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo n. 2, Prague 166 10, Czech Republic
| | - Minh T N Nguyen
- Leibniz Institute for Analytical Sciences ISAS, Otto-Hahn-Strasse 6b, 44227 Dortmund, Germany
| | - Steven H L Verhelst
- Leibniz Institute for Analytical Sciences ISAS, Otto-Hahn-Strasse 6b, 44227 Dortmund, Germany; KU Leuven - University of Leuven, Herestraat 49, Box 802, 3000 Leuven, Belgium
| | - Darren C Johnson
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 428, New York, NY 10065, USA
| | - Daniel A Bachovchin
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 428, New York, NY 10065, USA
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo n. 2, Prague 166 10, Czech Republic
| | - Pavel Majer
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo n. 2, Prague 166 10, Czech Republic
| | - Kvido Strisovsky
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo n. 2, Prague 166 10, Czech Republic.
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39
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Keckesova Z, Donaher JL, De Cock J, Freinkman E, Lingrell S, Bachovchin DA, Bierie B, Tischler V, Noske A, Okondo MC, Reinhardt F, Thiru P, Golub TR, Vance JE, Weinberg RA. LACTB is a tumour suppressor that modulates lipid metabolism and cell state. Nature 2017; 543:681-686. [PMID: 28329758 PMCID: PMC6246920 DOI: 10.1038/nature21408] [Citation(s) in RCA: 120] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 01/18/2017] [Indexed: 02/05/2023]
Abstract
Post-mitotic, differentiated cells exhibit a variety of characteristics that contrast with those of actively growing neoplastic cells, such as the expression of cell-cycle inhibitors and differentiation factors. We hypothesized that the gene expression profiles of these differentiated cells could reveal the identities of genes that may function as tumour suppressors. Here we show, using in vitro and in vivo studies in mice and humans, that the mitochondrial protein LACTB potently inhibits the proliferation of breast cancer cells. Its mechanism of action involves alteration of mitochondrial lipid metabolism and differentiation of breast cancer cells. This is achieved, at least in part, through reduction of the levels of mitochondrial phosphatidylserine decarboxylase, which is involved in the synthesis of mitochondrial phosphatidylethanolamine. These observations uncover a novel mitochondrial tumour suppressor and demonstrate a connection between mitochondrial lipid metabolism and the differentiation program of breast cancer cells, thereby revealing a previously undescribed mechanism of tumour suppression.
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Affiliation(s)
- Zuzana Keckesova
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
| | - Joana Liu Donaher
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
| | - Jasmine De Cock
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
| | - Elizaveta Freinkman
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
- Metabolon, Inc., PO Box 110407, Research Triangle Park, North Carolina 27709, USA
| | - Susanne Lingrell
- Department of Medicine and the Group on Molecular and Cell Biology of Lipids, University of Alberta, Edmonton, Alberta T6G 2S2, Canada
| | - Daniel A Bachovchin
- Broad Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Brian Bierie
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
| | - Verena Tischler
- Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Aurelia Noske
- Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Marian C Okondo
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Ferenc Reinhardt
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
| | - Prathapan Thiru
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
| | - Todd R Golub
- Broad Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Jean E Vance
- Department of Medicine and the Group on Molecular and Cell Biology of Lipids, University of Alberta, Edmonton, Alberta T6G 2S2, Canada
| | - Robert A Weinberg
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- MIT Ludwig Center for Molecular Oncology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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40
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Kulkarni RA, Worth AJ, Zengeya TT, Shrimp JH, Garlick JM, Roberts AM, Montgomery DC, Sourbier C, Gibbs BK, Mesaros C, Tsai YC, Das S, Chan KC, Zhou M, Andresson T, Weissman AM, Linehan WM, Blair IA, Snyder NW, Meier JL. Discovering Targets of Non-enzymatic Acylation by Thioester Reactivity Profiling. Cell Chem Biol 2017; 24:231-242. [PMID: 28163016 DOI: 10.1016/j.chembiol.2017.01.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 10/14/2016] [Accepted: 01/10/2017] [Indexed: 01/15/2023]
Abstract
Non-enzymatic protein modification driven by thioester reactivity is thought to play a major role in the establishment of cellular lysine acylation. However, the specific protein targets of this process are largely unknown. Here we report an experimental strategy to investigate non-enzymatic acylation in cells. Specifically, we develop a chemoproteomic method that separates thioester reactivity from enzymatic utilization, allowing selective enrichment of non-enzymatic acylation targets. Applying this method to cancer cell lines identifies numerous candidate targets of non-enzymatic acylation, including several enzymes in lower glycolysis. Functional studies highlight malonyl-CoA as a reactive thioester metabolite that can modify and inhibit glycolytic enzyme activity. Finally, we show that synthetic thioesters can be used as novel reagents to probe non-enzymatic acylation in living cells. Our studies provide new insights into the targets and drivers of non-enzymatic acylation, and demonstrate the utility of reactivity-based methods to experimentally investigate this phenomenon in biology and disease.
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Affiliation(s)
- Rhushikesh A Kulkarni
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Andrew J Worth
- Penn SRP Center, Center for Excellence in Environmental Toxicology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Thomas T Zengeya
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Jonathan H Shrimp
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Julie M Garlick
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Allison M Roberts
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - David C Montgomery
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Carole Sourbier
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20817, USA
| | - Benjamin K Gibbs
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20817, USA
| | - Clementina Mesaros
- Penn SRP Center, Center for Excellence in Environmental Toxicology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yien Che Tsai
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Sudipto Das
- Protein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - King C Chan
- Protein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - Ming Zhou
- Protein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - Thorkell Andresson
- Protein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - Allan M Weissman
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - W Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20817, USA
| | - Ian A Blair
- Penn SRP Center, Center for Excellence in Environmental Toxicology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nathaniel W Snyder
- Drexel University, A.J. Drexel Autism Institute, 3020 Market Street, Philadelphia, PA 19104, USA
| | - Jordan L Meier
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA.
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41
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Wooden B, Goossens N, Hoshida Y, Friedman SL. Using Big Data to Discover Diagnostics and Therapeutics for Gastrointestinal and Liver Diseases. Gastroenterology 2017; 152:53-67.e3. [PMID: 27773806 PMCID: PMC5193106 DOI: 10.1053/j.gastro.2016.09.065] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 09/15/2016] [Accepted: 09/25/2016] [Indexed: 12/13/2022]
Abstract
Technologies such as genome sequencing, gene expression profiling, proteomic and metabolomic analyses, electronic medical records, and patient-reported health information have produced large amounts of data from various populations, cell types, and disorders (big data). However, these data must be integrated and analyzed if they are to produce models or concepts about physiological function or mechanisms of pathogenesis. Many of these data are available to the public, allowing researchers anywhere to search for markers of specific biological processes or therapeutic targets for specific diseases or patient types. We review recent advances in the fields of computational and systems biology and highlight opportunities for researchers to use big data sets in the fields of gastroenterology and hepatology to complement traditional means of diagnostic and therapeutic discovery.
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Affiliation(s)
- Benjamin Wooden
- Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Nicolas Goossens
- Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York; Division of Gastroenterology and Hepatology, Department of Medical Specialties, Geneva University Hospital, Geneva, Switzerland
| | - Yujin Hoshida
- Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York.
| | - Scott L Friedman
- Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
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42
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Baier F, Copp JN, Tokuriki N. Evolution of Enzyme Superfamilies: Comprehensive Exploration of Sequence–Function Relationships. Biochemistry 2016; 55:6375-6388. [DOI: 10.1021/acs.biochem.6b00723] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- F. Baier
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - J. N. Copp
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - N. Tokuriki
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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43
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Okondo MC, Johnson DC, Sridharan R, Go EB, Chui AJ, Wang MS, Poplawski SE, Wu W, Liu Y, Lai JH, Sanford DG, Arciprete MO, Golub TR, Bachovchin WW, Bachovchin DA. DPP8 and DPP9 inhibition induces pro-caspase-1-dependent monocyte and macrophage pyroptosis. Nat Chem Biol 2016; 13:46-53. [PMID: 27820798 DOI: 10.1038/nchembio.2229] [Citation(s) in RCA: 186] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 08/30/2016] [Indexed: 12/12/2022]
Abstract
Val-boroPro (Talabostat, PT-100), a nonselective inhibitor of post-proline cleaving serine proteases, stimulates mammalian immune systems through an unknown mechanism of action. Despite this lack of mechanistic understanding, Val-boroPro has attracted substantial interest as a potential anticancer agent, reaching phase 3 trials in humans. Here we show that Val-boroPro stimulates the immune system by triggering a proinflammatory form of cell death in monocytes and macrophages known as pyroptosis. We demonstrate that the inhibition of two serine proteases, DPP8 and DPP9, activates the pro-protein form of caspase-1 independent of the inflammasome adaptor ASC. Activated pro-caspase-1 does not efficiently process itself or IL-1β but does cleave and activate gasdermin D to induce pyroptosis. Mice lacking caspase-1 do not show immune stimulation after treatment with Val-boroPro. Our data identify what is to our knowledge the first small molecule that induces pyroptosis and reveals a new checkpoint that controls the activation of the innate immune system.
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Affiliation(s)
- Marian C Okondo
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Darren C Johnson
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ramya Sridharan
- Graduate Program in Pharmacology, Weill Cornell Graduate School of Medical Sciences, New York, New York, USA
| | - Eun Bin Go
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ashley J Chui
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Mitchell S Wang
- Graduate Program in Pharmacology, Weill Cornell Graduate School of Medical Sciences, New York, New York, USA
| | - Sarah E Poplawski
- Department of Developmental, Chemical &Molecular Biology, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, Massachusetts, USA
| | - Wengen Wu
- Department of Developmental, Chemical &Molecular Biology, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, Massachusetts, USA
| | - Yuxin Liu
- Department of Developmental, Chemical &Molecular Biology, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, Massachusetts, USA
| | - Jack H Lai
- Department of Developmental, Chemical &Molecular Biology, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, Massachusetts, USA
| | - David G Sanford
- Department of Developmental, Chemical &Molecular Biology, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, Massachusetts, USA
| | - Michael O Arciprete
- Department of Developmental, Chemical &Molecular Biology, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, Massachusetts, USA
| | - Todd R Golub
- The Eli and Edythe L. Broad Institute, Cambridge, Massachusetts, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - William W Bachovchin
- Department of Developmental, Chemical &Molecular Biology, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, Massachusetts, USA.,Arisaph Pharmaceuticals, Boston, Massachusetts, USA
| | - Daniel A Bachovchin
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Graduate Program in Pharmacology, Weill Cornell Graduate School of Medical Sciences, New York, New York, USA
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44
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Diaz DB, Scully CCG, Liew SK, Adachi S, Trinchera P, St Denis JD, Yudin AK. Synthesis of Aminoboronic Acid Derivatives from Amines and Amphoteric Boryl Carbonyl Compounds. Angew Chem Int Ed Engl 2016; 55:12659-63. [PMID: 27584917 DOI: 10.1002/anie.201605754] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Indexed: 12/17/2022]
Abstract
Herein, we demonstrate the use of α-boryl aldehydes and acyl boronates in the synthesis of aminoboronic acid derivatives. This work highlights the untapped potential of boron-substituted iminium ions and offers insights into the behavior of N-methyliminodiacetyl (MIDA) boronates during condensation and tautomerization processes. The preparative value of this contribution lies in the demonstration that various amines, including linear and cyclic peptides, can be readily conjugated with boron-containing fragments. A mild deprotection of amino MIDA-boronates enables access to α- and β-aminoboronic acids in high chemical yields. This simple process should be applicable to the synthesis of a wide range of bioactive molecules as well as precursors for cross-coupling reactions.
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Affiliation(s)
- Diego B Diaz
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George St., Toronto, ON, M5S 3H6, Canada
| | - Conor C G Scully
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George St., Toronto, ON, M5S 3H6, Canada
| | - Sean K Liew
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George St., Toronto, ON, M5S 3H6, Canada
| | - Shinya Adachi
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George St., Toronto, ON, M5S 3H6, Canada
| | - Piera Trinchera
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George St., Toronto, ON, M5S 3H6, Canada
| | - Jeffrey D St Denis
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George St., Toronto, ON, M5S 3H6, Canada
| | - Andrei K Yudin
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George St., Toronto, ON, M5S 3H6, Canada.
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45
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Diaz DB, Scully CCG, Liew SK, Adachi S, Trinchera P, St. Denis JD, Yudin AK. Synthesis of Aminoboronic Acid Derivatives from Amines and Amphoteric Boryl Carbonyl Compounds. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201605754] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Diego B. Diaz
- Davenport Research Laboratories; Department of Chemistry; University of Toronto; 80 St. George St. Toronto ON M5S 3H6 Canada
| | - Conor C. G. Scully
- Davenport Research Laboratories; Department of Chemistry; University of Toronto; 80 St. George St. Toronto ON M5S 3H6 Canada
| | - Sean K. Liew
- Davenport Research Laboratories; Department of Chemistry; University of Toronto; 80 St. George St. Toronto ON M5S 3H6 Canada
| | - Shinya Adachi
- Davenport Research Laboratories; Department of Chemistry; University of Toronto; 80 St. George St. Toronto ON M5S 3H6 Canada
| | - Piera Trinchera
- Davenport Research Laboratories; Department of Chemistry; University of Toronto; 80 St. George St. Toronto ON M5S 3H6 Canada
| | - Jeffrey D. St. Denis
- Davenport Research Laboratories; Department of Chemistry; University of Toronto; 80 St. George St. Toronto ON M5S 3H6 Canada
| | - Andrei K. Yudin
- Davenport Research Laboratories; Department of Chemistry; University of Toronto; 80 St. George St. Toronto ON M5S 3H6 Canada
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46
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Csizmadia V, Hales P, Tsu C, Ma J, Chen J, Shah P, Fleming P, Senn JJ, Kadambi VJ, Dick L, Wolenski FS. Proteasome inhibitors bortezomib and carfilzomib used for the treatment of multiple myeloma do not inhibit the serine protease HtrA2/Omi. Toxicol Res (Camb) 2016; 5:1619-1628. [PMID: 30090462 PMCID: PMC6062231 DOI: 10.1039/c6tx00220j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 08/23/2016] [Indexed: 12/26/2022] Open
Abstract
The proteasome inhibitor bortezomib is associated with the development of peripheral neuropathy in patients, but the mechanism is not fully understood.
The proteasome inhibitor bortezomib is associated with the development of peripheral neuropathy in patients, but the mechanism by which bortezomib can induce peripheral neuropathy is not fully understood. One study suggested that off-target inhibition of proteases other than the proteasome, particularly HtraA2/Omi, may be the underlying mechanism of the neuropathy. The same study also concluded that carfilzomib, a second proteasome inhibitor that is associated with less peripheral neuropathy in patients than bortezomib, showed no inhibition of HtrA2/Omi. The goal of the work described here was to determine whether either proteasome inhibitors truly affected HtrA2/Omi activity. A variety of methods were used to test the effects of both bortezomib and carfilzomib on HtrA2/Omi activity that included in vitro recombinant enzyme assays, and studies with the human neuroblastoma SH-SY5Y cell line and HtrA2/Omi-knockout mouse embryonic fibroblasts. The compound ucf-101 was used to assess the effects of specific HtrA2/Omi inhibition. In contrast to previously published data, our results clearly demonstrated that neither bortezomib nor carfilzomib inhibited HtrA2/Omi activity in recombinant enzyme assays at concentrations up to 100 μM, while the specific inhibitor ucf-101 did inhibit the enzyme. The proteasome inhibitors did not inhibit HtrA2/Omi activity in either SH-SY5Y cells or mouse embryonic fibroblasts, as determined by expression of the HtrA2/Omi substrates eIF4G1 and UCH-L1. Based on our biochemical and cell-based assays, we conclude that neither bortezomib nor carfilzomib inhibited HtrA2/Omi activity. Therefore, it is unlikely that bortezomib associated peripheral neuropathy is a direct result of off-target inhibition of HtrA2/Omi.
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Affiliation(s)
- Vilmos Csizmadia
- Millennium Pharmaceuticals , Inc (a wholly owned subsidiary of Takeda Pharmaceutical Company Limited) , Cambridge , MA 02139 , USA . ; ; Tel: +1 617-551-3620
| | - Paul Hales
- Millennium Pharmaceuticals , Inc (a wholly owned subsidiary of Takeda Pharmaceutical Company Limited) , Cambridge , MA 02139 , USA . ; ; Tel: +1 617-551-3620
| | - Christopher Tsu
- Millennium Pharmaceuticals , Inc (a wholly owned subsidiary of Takeda Pharmaceutical Company Limited) , Cambridge , MA 02139 , USA . ; ; Tel: +1 617-551-3620
| | - Jingya Ma
- Millennium Pharmaceuticals , Inc (a wholly owned subsidiary of Takeda Pharmaceutical Company Limited) , Cambridge , MA 02139 , USA . ; ; Tel: +1 617-551-3620
| | - Jiejin Chen
- Millennium Pharmaceuticals , Inc (a wholly owned subsidiary of Takeda Pharmaceutical Company Limited) , Cambridge , MA 02139 , USA . ; ; Tel: +1 617-551-3620
| | - Pooja Shah
- Millennium Pharmaceuticals , Inc (a wholly owned subsidiary of Takeda Pharmaceutical Company Limited) , Cambridge , MA 02139 , USA . ; ; Tel: +1 617-551-3620
| | - Paul Fleming
- Millennium Pharmaceuticals , Inc (a wholly owned subsidiary of Takeda Pharmaceutical Company Limited) , Cambridge , MA 02139 , USA . ; ; Tel: +1 617-551-3620
| | - Joseph J Senn
- Millennium Pharmaceuticals , Inc (a wholly owned subsidiary of Takeda Pharmaceutical Company Limited) , Cambridge , MA 02139 , USA . ; ; Tel: +1 617-551-3620
| | - Vivek J Kadambi
- Millennium Pharmaceuticals , Inc (a wholly owned subsidiary of Takeda Pharmaceutical Company Limited) , Cambridge , MA 02139 , USA . ; ; Tel: +1 617-551-3620
| | - Larry Dick
- Millennium Pharmaceuticals , Inc (a wholly owned subsidiary of Takeda Pharmaceutical Company Limited) , Cambridge , MA 02139 , USA . ; ; Tel: +1 617-551-3620
| | - Francis S Wolenski
- Millennium Pharmaceuticals , Inc (a wholly owned subsidiary of Takeda Pharmaceutical Company Limited) , Cambridge , MA 02139 , USA . ; ; Tel: +1 617-551-3620
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Janssen FJ, van der Stelt M. Inhibitors of diacylglycerol lipases in neurodegenerative and metabolic disorders. Bioorg Med Chem Lett 2016; 26:3831-7. [DOI: 10.1016/j.bmcl.2016.06.076] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 06/22/2016] [Accepted: 06/26/2016] [Indexed: 01/11/2023]
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Kuang ZK, Feng SY, Hu B, Wang D, He SB, Kong DX. Predicting subtype selectivity of dopamine receptor ligands with three-dimensional biologically relevant spectrum. Chem Biol Drug Des 2016; 88:859-872. [PMID: 27390270 DOI: 10.1111/cbdd.12815] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 06/28/2016] [Accepted: 07/02/2016] [Indexed: 12/11/2022]
Abstract
We applied a novel molecular descriptor, three-dimensional biologically relevant spectrum (BRS-3D), in subtype selectivity prediction of dopamine receptor (DR) ligands. BRS-3D is a shape similarity profile calculated by superimposing the objective compounds against 300 template ligands from sc-PDB. First, we constructed five subtype selectivity regression models between DR subtypes D1-D2, D1-D3, D2-D3, D2-D4, and D3-D4. The models' 10-fold cross-validation-squared correlation coefficient (Q2 , for training sets) and determination coefficient (R2 , for test sets) were in the range of 0.5-0.7 and 0.6-0.8, respectively. Then, four pair-wise (D1-D2, D2-D3, D2-D4, and D3-D4) and a multitype (D2, D3, and D4) classification models were developed with the prediction accuracies around or over 90% (for test sets). Lastly, we compared the performances of the models developed on BRS-3D and classical descriptors. The results showed that BRS-3D performed similarly to classical 2D descriptors and better than other 3D descriptors. Combining BRS-3D and 2D descriptors can further improve the prediction performance. These results confirmed the capacity of BRS-3D in the prediction of DR subtype-selective ligands.
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Affiliation(s)
- Zheng-Kun Kuang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Agricultural Bioinformatics Key Laboratory of Hubei Province, College of informatics, Huazhong Agricultural University, Wuhan, China
| | - Shi-Yu Feng
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of informatics, Huazhong Agricultural University, Wuhan, China
| | - Ben Hu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Agricultural Bioinformatics Key Laboratory of Hubei Province, College of informatics, Huazhong Agricultural University, Wuhan, China
| | - Dong Wang
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of informatics, Huazhong Agricultural University, Wuhan, China
| | - Song-Bing He
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of informatics, Huazhong Agricultural University, Wuhan, China
| | - De-Xin Kong
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China. .,Agricultural Bioinformatics Key Laboratory of Hubei Province, College of informatics, Huazhong Agricultural University, Wuhan, China.
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49
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Kim RS, Goossens N, Hoshida Y. Use of big data in drug development for precision medicine. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2016; 1:245-253. [PMID: 27430024 DOI: 10.1080/23808993.2016.1174062] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Drug development has been a costly and lengthy process with an extremely low success rate and lack of consideration of individual diversity in drug response and toxicity. Over the past decade, an alternative "big data" approach has been expanding at an unprecedented pace based on the development of electronic databases of chemical substances, disease gene/protein targets, functional readouts, and clinical information covering inter-individual genetic variations and toxicities. This paradigm shift has enabled systematic, high-throughput, and accelerated identification of novel drugs or repurposed indications of existing drugs for pathogenic molecular aberrations specifically present in each individual patient. The exploding interest from the information technology and direct-to-consumer genetic testing industries has been further facilitating the use of big data to achieve personalized Precision Medicine. Here we overview currently available resources and discuss future prospects.
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Affiliation(s)
- Rosa S Kim
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Nicolas Goossens
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, USA; Division of Gastroenterology and Hepatology, Geneva University Hospital, Geneva, Switzerland
| | - Yujin Hoshida
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, USA
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50
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Hatzios SK, Abel S, Martell J, Hubbard T, Sasabe J, Munera D, Clark L, Bachovchin DA, Qadri F, Ryan ET, Davis BM, Weerapana E, Waldor MK. Chemoproteomic profiling of host and pathogen enzymes active in cholera. Nat Chem Biol 2016; 12:268-274. [PMID: 26900865 PMCID: PMC4765928 DOI: 10.1038/nchembio.2025] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 12/31/2015] [Indexed: 12/15/2022]
Abstract
Activity-based protein profiling (ABPP) is a chemoproteomic tool for detecting active enzymes in complex biological systems. We used ABPP to identify secreted bacterial and host serine hydrolases that are active in animals infected with the cholera pathogen Vibrio cholerae. Four V. cholerae proteases were consistently active in infected rabbits, and one, VC0157 (renamed IvaP), was also active in human choleric stool. Inactivation of IvaP influenced the activity of other secreted V. cholerae and rabbit enzymes in vivo, and genetic disruption of all four proteases increased the abundance of intelectin, an intestinal lectin, and its binding to V. cholerae in infected rabbits. Intelectin also bound to other enteric bacterial pathogens, suggesting that it may constitute a previously unrecognized mechanism of bacterial surveillance in the intestine that is inhibited by pathogen-secreted proteases. Our work demonstrates the power of activity-based proteomics to reveal host-pathogen enzymatic dialog in an animal model of infection.
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Affiliation(s)
- Stavroula K. Hatzios
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Sören Abel
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
- Department of Pharmacy, University of Tromsø (UiT), The Arctic University of Norway, Tromsø, Norway
| | | | - Troy Hubbard
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Jumpei Sasabe
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Diana Munera
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Lars Clark
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | | | - Firdausi Qadri
- International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR,B), Dhaka, Bangladesh
| | - Edward T. Ryan
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Brigid M. Davis
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | | | - Matthew K. Waldor
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
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