1
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De Novo Molecular Design of Caspase-6 Inhibitors by a GRU-Based Recurrent Neural Network Combined with a Transfer Learning Approach. Pharmaceuticals (Basel) 2021; 14:ph14121249. [PMID: 34959651 PMCID: PMC8706867 DOI: 10.3390/ph14121249] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 11/21/2021] [Accepted: 11/24/2021] [Indexed: 12/31/2022] Open
Abstract
Due to their potential in the treatment of neurodegenerative diseases, caspase-6 inhibitors have attracted widespread attention. However, the existing caspase-6 inhibitors showed more or less inevitable deficiencies that restrict their clinical development and applications. Therefore, there is an urgent need to develop novel caspase-6 candidate inhibitors. Herein, a gated recurrent unit (GRU)-based recurrent neural network (RNN) combined with transfer learning was used to build a molecular generative model of caspase-6 inhibitors. The results showed that the GRU-based RNN model can accurately learn the SMILES grammars of about 2.4 million chemical molecules including ionic and isomeric compounds and can generate potential caspase-6 inhibitors after transfer learning of the known 433 caspase-6 inhibitors. Based on the novel molecules derived from the molecular generative model, an optimal logistic regression model and Surflex-dock were employed for predicting and ranking the inhibitory activities. According to the prediction results, three potential caspase-6 inhibitors with different scaffolds were selected as the promising candidates for further research. In general, this paper provides an efficient combinational strategy for de novo molecular design of caspase-6 inhibitors.
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2
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Kоbylinska L, Khylyuk D, Subtelna I, Kitsera M, Lesyk R. In silico identification and biochemical validation of plausible molecular targets of 4-thiazolidinone derivative Les-3833 as a potential anticancer agent. UKRAINIAN BIOCHEMICAL JOURNAL 2021. [DOI: 10.15407/ubj93.02.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
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3
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Fernández-Soto P, Casulli J, Solano-Castro D, Rodríguez-Fernández P, Jowitt TA, Travis MA, Cavet JS, Tabernero L. Discovery of uncompetitive inhibitors of SapM that compromise intracellular survival of Mycobacterium tuberculosis. Sci Rep 2021; 11:7667. [PMID: 33828158 PMCID: PMC8027839 DOI: 10.1038/s41598-021-87117-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 02/15/2021] [Indexed: 12/28/2022] Open
Abstract
SapM is a secreted virulence factor from Mycobacterium tuberculosis critical for pathogen survival and persistence inside the host. Its full potential as a target for tuberculosis treatment has not yet been exploited because of the lack of potent inhibitors available. By screening over 1500 small molecules, we have identified new potent and selective inhibitors of SapM with an uncompetitive mechanism of inhibition. The best inhibitors share a trihydroxy-benzene moiety essential for activity. Importantly, the inhibitors significantly reduce mycobacterial burden in infected human macrophages at 1 µM, and they are selective with respect to other mycobacterial and human phosphatases. The best inhibitor also reduces intracellular burden of Francisella tularensis, which secretes the virulence factor AcpA, a homologue of SapM, with the same mechanism of catalysis and inhibition. Our findings demonstrate that inhibition of SapM with small molecule inhibitors is efficient in reducing intracellular mycobacterial survival in host macrophages and confirm SapM as a potential therapeutic target. These initial compounds have favourable physico-chemical properties and provide a basis for exploration towards the development of new tuberculosis treatments. The efficacy of a SapM inhibitor in reducing Francisella tularensis intracellular burden suggests the potential for developing broad-spectrum antivirulence agents to treat microbial infections.
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Affiliation(s)
- Paulina Fernández-Soto
- School of Biological Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, M13 9PT, UK
| | - Joshua Casulli
- School of Biological Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, M13 9PT, UK.,Lydia Becker Institute for Immunology and Inflammation, University of Manchester, Manchester, UK.,Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester, UK
| | - Danilo Solano-Castro
- School of Biological Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, M13 9PT, UK
| | - Pablo Rodríguez-Fernández
- School of Biological Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, M13 9PT, UK
| | - Thomas A Jowitt
- School of Biological Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, M13 9PT, UK.,Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester, UK
| | - Mark A Travis
- School of Biological Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, M13 9PT, UK.,Lydia Becker Institute for Immunology and Inflammation, University of Manchester, Manchester, UK.,Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester, UK
| | - Jennifer S Cavet
- School of Biological Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, M13 9PT, UK
| | - Lydia Tabernero
- School of Biological Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, M13 9PT, UK. .,Lydia Becker Institute for Immunology and Inflammation, University of Manchester, Manchester, UK.
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4
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Wen X, Liu C, Ghislain L, Tovar K, Shah V, Stout SJ, Cifelli S, Satapati S, O’Donnell G, Sheth PR, Wildey MJ, Datwani SS, Covey TR, Bateman KP, McLaren DG. Direct Analysis from Phase-Separated Liquid Samples using ADE-OPI-MS: Applicability to High-Throughput Screening for Inhibitors of Diacylglycerol Acyltransferase 2. Anal Chem 2021; 93:6071-6079. [DOI: 10.1021/acs.analchem.0c04312] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Xiujuan Wen
- Merck & Company, Incorporated, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Chang Liu
- SCIEX, 71 Four Valley Drive, Concord, Ontario L4K 4 V8, Canada
| | - Lucien Ghislain
- Beckman Coulter Life Sciences Incorporated, 170 Rose Orchard Way, San Jose, California 95134, United States
| | - Kiersten Tovar
- Merck & Company, Incorporated, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Vinit Shah
- Merck & Company, Incorporated, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Steven J. Stout
- Merck & Company, Incorporated, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Steven Cifelli
- Merck & Company, Incorporated, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Santhosh Satapati
- Merck & Company, Incorporated, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Gregory O’Donnell
- Merck & Company, Incorporated, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Payal R. Sheth
- Merck & Company, Incorporated, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Mary Jo Wildey
- Merck & Company, Incorporated, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Sammy S. Datwani
- Beckman Coulter Life Sciences Incorporated, 170 Rose Orchard Way, San Jose, California 95134, United States
| | - Thomas R. Covey
- SCIEX, 71 Four Valley Drive, Concord, Ontario L4K 4 V8, Canada
| | - Kevin P. Bateman
- Merck & Company, Incorporated, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - David G. McLaren
- Merck & Company, Incorporated, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
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5
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Campbell AC, Bogner AN, Mao Y, Becker DF, Tanner JJ. Structural analysis of prolines and hydroxyprolines binding to the l-glutamate-γ-semialdehyde dehydrogenase active site of bifunctional proline utilization A. Arch Biochem Biophys 2020; 698:108727. [PMID: 33333077 DOI: 10.1016/j.abb.2020.108727] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/11/2020] [Accepted: 12/12/2020] [Indexed: 01/31/2023]
Abstract
Proline utilization A (PutA) proteins are bifunctional proline catabolic enzymes that catalyze the 4-electron oxidation of l-proline to l-glutamate using spatially-separated proline dehydrogenase and l-glutamate-γ-semialdehyde dehydrogenase (GSALDH, a.k.a. ALDH4A1) active sites. The observation that l-proline inhibits both the GSALDH activity of PutA and monofunctional GSALDHs motivated us to study the inhibition of PutA by proline stereoisomers and analogs. Here we report five high-resolution crystal structures of PutA with the following ligands bound in the GSALDH active site: d-proline, trans-4-hydroxy-d-proline, cis-4-hydroxy-d-proline, l-proline, and trans-4-hydroxy-l-proline. Three of the structures are of ternary complexes of the enzyme with an inhibitor and either NAD+ or NADH. To our knowledge, the NADH complex is the first for any GSALDH. The structures reveal a conserved mode of recognition of the inhibitor carboxylate, which results in the pyrrolidine rings of the d- and l-isomers having different orientations and different hydrogen bonding environments. Activity assays show that the compounds are weak inhibitors with millimolar inhibition constants. Curiously, although the inhibitors occupy the aldehyde binding site, kinetic measurements show the inhibition is uncompetitive. Uncompetitive inhibition may involve proline binding to a remote site or to the enzyme-NADH complex. Together, the structural and kinetic data expand our understanding of how proline-like molecules interact with GSALDH, reveal insight into the relationship between stereochemistry and inhibitor affinity, and demonstrate the pitfalls of inferring the mechanism of inhibition from crystal structures alone.
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Affiliation(s)
- Ashley C Campbell
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, United States
| | - Alexandra N Bogner
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, United States
| | - Yizi Mao
- Department of Biochemistry, Redox Biology Center, University of Nebraska, Lincoln, NE, 68588, United States
| | - Donald F Becker
- Department of Biochemistry, Redox Biology Center, University of Nebraska, Lincoln, NE, 68588, United States
| | - John J Tanner
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, United States; Department of Chemistry, University of Missouri, Columbia, MO, 65211, United States.
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6
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Zhao P, Sun X, Chaggan C, Liao Z, In Wong K, He F, Singh S, Loomba R, Karin M, Witztum JL, Saltiel AR. An AMPK-caspase-6 axis controls liver damage in nonalcoholic steatohepatitis. Science 2020; 367:652-660. [PMID: 32029622 DOI: 10.1126/science.aay0542] [Citation(s) in RCA: 165] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 12/23/2019] [Indexed: 12/14/2022]
Abstract
Liver cell death has an essential role in nonalcoholic steatohepatitis (NASH). The activity of the energy sensor adenosine monophosphate (AMP)-activated protein kinase (AMPK) is repressed in NASH. Liver-specific AMPK knockout aggravated liver damage in mouse NASH models. AMPK phosphorylated proapoptotic caspase-6 protein to inhibit its activation, keeping hepatocyte apoptosis in check. Suppression of AMPK activity relieved this inhibition, rendering caspase-6 activated in human and mouse NASH. AMPK activation or caspase-6 inhibition, even after the onset of NASH, improved liver damage and fibrosis. Once phosphorylation was decreased, caspase-6 was activated by caspase-3 or -7. Active caspase-6 cleaved Bid to induce cytochrome c release, generating a feedforward loop that leads to hepatocyte death. Thus, the AMPK-caspase-6 axis regulates liver damage in NASH, implicating AMPK and caspase-6 as therapeutic targets.
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Affiliation(s)
- Peng Zhao
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Xiaoli Sun
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Cynthia Chaggan
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Zhongji Liao
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kai In Wong
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Feng He
- Department of Pharmacology, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Seema Singh
- NAFLD Research Center, Division of Gastroenterology, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Rohit Loomba
- NAFLD Research Center, Division of Gastroenterology, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Michael Karin
- Department of Pharmacology, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Joseph L Witztum
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Alan R Saltiel
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA. .,Department of Pharmacology, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
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7
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Activation of Caspase-6 Is Promoted by a Mutant Huntingtin Fragment and Blocked by an Allosteric Inhibitor Compound. Cell Chem Biol 2019; 26:1295-1305.e6. [PMID: 31353319 DOI: 10.1016/j.chembiol.2019.07.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 01/08/2019] [Accepted: 06/28/2019] [Indexed: 01/04/2023]
Abstract
Aberrant activation of caspase-6 (C6) in the absence of other hallmarks of apoptosis has been demonstrated in cells and tissues from patients with Huntington disease (HD) and animal models. C6 activity correlates with disease progression in patients with HD and the cleavage of mutant huntingtin (mHTT) protein is thought to strongly contribute to disease pathogenesis. Here we show that the mHTT1-586 fragment generated by C6 cleavage interacts with the zymogen form of the enzyme, stabilizing a conformation that contains an active site and is prone to full activation. This shift toward enhanced activity can be prevented by a small-molecule inhibitor that blocks the interaction between C6 and mHTT1-586. Molecular docking studies suggest that the inhibitor binds an allosteric site in the C6 zymogen. The interaction of mHTT1-586 with C6 may therefore promote a self-reinforcing, feedforward cycle of C6 zymogen activation and mHTT cleavage driving HD pathogenesis.
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8
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Tubeleviciute-Aydin A, Beautrait A, Lynham J, Sharma G, Gorelik A, Deny LJ, Soya N, Lukacs GL, Nagar B, Marinier A, LeBlanc AC. Identification of Allosteric Inhibitors against Active Caspase-6. Sci Rep 2019; 9:5504. [PMID: 30940883 PMCID: PMC6445123 DOI: 10.1038/s41598-019-41930-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 03/21/2019] [Indexed: 01/04/2023] Open
Abstract
Caspase-6 is a cysteine protease that plays essential roles in programmed cell death, axonal degeneration, and development. The excess neuronal activity of Caspase-6 is associated with Alzheimer disease neuropathology and age-dependent cognitive impairment. Caspase-6 inhibition is a promising strategy to stop early stage neurodegenerative events, yet finding potent and selective Caspase-6 inhibitors has been a challenging task due to the overlapping structural and functional similarities between caspase family members. Here, we investigated how four rare non-synonymous missense single-nucleotide polymorphisms (SNPs), resulting in amino acid substitutions outside human Caspase-6 active site, affect enzyme structure and catalytic efficiency. Three investigated SNPs were found to align with a putative allosteric pocket with low sequence conservation among human caspases. Virtual screening of 57,700 compounds against the putative Caspase-6 allosteric pocket, followed by in vitro testing of the best virtual hits in recombinant human Caspase-6 activity assays identified novel allosteric Caspase-6 inhibitors with IC50 and Ki values ranging from ~2 to 13 µM. This report may pave the way towards the development and optimisation of novel small molecule allosteric Caspase-6 inhibitors and illustrates that functional characterisation of rare natural variants holds promise for the identification of allosteric sites on other therapeutic targets in drug discovery.
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Affiliation(s)
- Agne Tubeleviciute-Aydin
- Bloomfield Center for Research in Aging, Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Ch. Cote Ste-Catherine, Montreal, Quebec, H3T 1E2, Canada
- Department of Neurology and Neurosurgery, McGill University, 3775 University St., Montreal, Quebec, H3A 2B4, Canada
| | - Alexandre Beautrait
- Institute for Research in Immunology and Cancer, Université de Montréal, 2590, chemin de Polytechnique, Montreal, Quebec, H3T 1J4, Canada
| | - Jeffrey Lynham
- Bloomfield Center for Research in Aging, Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Ch. Cote Ste-Catherine, Montreal, Quebec, H3T 1E2, Canada
- Department of Anatomy and Cell Biology, McGill University, 3640 University St., Montreal, Quebec, H3A 0C7, Canada
| | - Gyanesh Sharma
- Bloomfield Center for Research in Aging, Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Ch. Cote Ste-Catherine, Montreal, Quebec, H3T 1E2, Canada
- Department of Neurology and Neurosurgery, McGill University, 3775 University St., Montreal, Quebec, H3A 2B4, Canada
| | - Alexei Gorelik
- Department of Biochemistry, McGill University, 3649 promenade Sir-William-Osler, Montreal, Quebec, H3G 0B1, Canada
| | - Ludovic J Deny
- Institute for Research in Immunology and Cancer, Université de Montréal, 2590, chemin de Polytechnique, Montreal, Quebec, H3T 1J4, Canada
| | - Naoto Soya
- Department of Physiology and Biochemistry, McGill University, 3655 Promenade Sir-William-Osler, Montréal, Québec, H3G 1Y6, Canada
| | - Gergely L Lukacs
- Department of Physiology and Biochemistry, McGill University, 3655 Promenade Sir-William-Osler, Montréal, Québec, H3G 1Y6, Canada
| | - Bhushan Nagar
- Department of Biochemistry, McGill University, 3649 promenade Sir-William-Osler, Montreal, Quebec, H3G 0B1, Canada
| | - Anne Marinier
- Institute for Research in Immunology and Cancer, Université de Montréal, 2590, chemin de Polytechnique, Montreal, Quebec, H3T 1J4, Canada
| | - Andrea C LeBlanc
- Bloomfield Center for Research in Aging, Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Ch. Cote Ste-Catherine, Montreal, Quebec, H3T 1E2, Canada.
- Department of Neurology and Neurosurgery, McGill University, 3775 University St., Montreal, Quebec, H3A 2B4, Canada.
- Department of Anatomy and Cell Biology, McGill University, 3640 University St., Montreal, Quebec, H3A 0C7, Canada.
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9
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Di Trani JM, Moitessier N, Mittermaier AK. Complete Kinetic Characterization of Enzyme Inhibition in a Single Isothermal Titration Calorimetric Experiment. Anal Chem 2018; 90:8430-8435. [DOI: 10.1021/acs.analchem.8b00993] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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10
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Abstract
The cysteine protease Caspase-6 (Casp6) is a potential therapeutic target of Alzheimer Disease (AD) and age-dependent cognitive impairment. To assess if Casp6 is essential to human health, we investigated the effect of CASP6 variants sequenced from healthy humans on Casp6 activity. Here, we report the effects of two rare Casp6 amino acid polymorphisms, R65W and G66R, on the catalytic function and structure of Casp6. The G66R substitution eliminated and R65W substitution significantly reduced Casp6 catalytic activity through impaired substrate binding. In contrast to wild-type Casp6, both Casp6 variants were unstable and inactive in transfected mammalian cells. In addition, Casp6-G66R acted as a dominant negative inhibitor of wild-type Casp6. The R65W and G66R substitutions caused perturbations in substrate recognition and active site organization as revealed by molecular dynamics simulations. Our results suggest that full Casp6 activity may not be essential for healthy humans and support the use of Casp6 inhibitors against Casp6-dependent neurodegeneration in age-dependent cognitive impairment and AD. Furthermore, this work illustrates that studying natural single amino acid polymorphisms of enzyme drug targets is a promising approach to uncover previously uncharacterized regulatory sites important for enzyme activity.
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11
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O'Brien M, Moehring D, Muñoz-Planillo R, Núñez G, Callaway J, Ting J, Scurria M, Ugo T, Bernad L, Cali J, Lazar D. A bioluminescent caspase-1 activity assay rapidly monitors inflammasome activation in cells. J Immunol Methods 2017; 447:1-13. [PMID: 28268194 DOI: 10.1016/j.jim.2017.03.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 02/13/2017] [Accepted: 03/03/2017] [Indexed: 01/01/2023]
Abstract
Inflammasomes are protein complexes induced by diverse inflammatory stimuli that activate caspase-1, resulting in the processing and release of cytokines, IL-1β and IL-18, and pyroptosis, an immunogenic form of cell death. To provide a homogeneous method for detecting caspase-1 activity, we developed a bioluminescent, plate-based assay that combines a substrate, Z-WEHD-aminoluciferin, with a thermostable luciferase in an optimized lytic reagent added directly to cultured cells. Assay specificity for caspase-1 is conferred by inclusion of a proteasome inhibitor in the lytic reagent and by use of a caspase-1 inhibitor to confirm activity. This approach enables a specific and rapid determination of caspase-1 activation. Caspase-1 activity is stable in the reagent thereby providing assay convenience and flexibility. Using this assay system, caspase-1 activation has been determined in THP-1 cells following treatment with α-hemolysin, LPS, nigericin, gramicidin, MSU, R848, Pam3CSK4, and flagellin. Caspase-1 activation has also been demonstrated in treated J774A.1 mouse macrophages, bone marrow-derived macrophages (BMDMs) from mice, as well as in human primary monocytes. Caspase-1 activity was not detected in treated BMDMs derived from Casp1-/- mice, further confirming the specificity of the assay. Caspase-1 activity can be measured directly in cultured cells using the lytic reagent, or caspase-1 activity released into medium can be monitored by assay of transferred supernatant. The caspase-1 assay can be multiplexed with other assays to monitor additional parameters from the same cells, such as IL-1β release or cell death. The caspase-1 assay in combination with a sensitive real-time monitor of cell death allows one to accurately establish pyroptosis. This assay system provides a rapid, convenient, and flexible method to specifically and quantitatively monitor caspase-1 activation in cells in a plate-based format. This will allow a more efficient and effective assessment of inflammasome activation as well as enable high-throughput screening for inflammasome modulators.
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Affiliation(s)
- Martha O'Brien
- Promega Corporation, 2800 Woods Hollow Rd, Madison, WI 53711, USA.
| | | | - Raúl Muñoz-Planillo
- Dept. of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Gabriel Núñez
- Dept. of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Justin Callaway
- Dept. of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jenny Ting
- Dept. of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Mike Scurria
- Promega Biosciences LLC, 277 Granada Dr, San Luis Obispo, CA 93401, USA
| | - Tim Ugo
- Promega Biosciences LLC, 277 Granada Dr, San Luis Obispo, CA 93401, USA
| | - Laurent Bernad
- Promega Biosciences LLC, 277 Granada Dr, San Luis Obispo, CA 93401, USA
| | - James Cali
- Promega Corporation, 2800 Woods Hollow Rd, Madison, WI 53711, USA
| | - Dan Lazar
- Promega Corporation, 2800 Woods Hollow Rd, Madison, WI 53711, USA
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12
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Skotte NH, Sanders SS, Singaraja RR, Ehrnhoefer DE, Vaid K, Qiu X, Kannan S, Verma C, Hayden MR. Palmitoylation of caspase-6 by HIP14 regulates its activation. Cell Death Differ 2017; 24:433-444. [PMID: 27911442 PMCID: PMC5344205 DOI: 10.1038/cdd.2016.139] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 10/03/2016] [Accepted: 10/25/2016] [Indexed: 02/06/2023] Open
Abstract
Caspase-6 (CASP6) has an important role in axonal degeneration during neuronal apoptosis and in the neurodegenerative diseases Alzheimer and Huntington disease. Decreasing CASP6 activity may help to restore neuronal function in these and other diseases such as stroke and ischemia, where increased CASP6 activity has been implicated. The key to finding approaches to decrease CASP6 activity is a deeper understanding of the mechanisms regulating CASP6 activation. We show that CASP6 is posttranslationally palmitoylated by the palmitoyl acyltransferase HIP14 and that the palmitoylation of CASP6 inhibits its activation. Palmitoylation of CASP6 is decreased both in Hip14-/- mice, where HIP14 is absent, and in YAC128 mice, a model of Huntington disease, where HIP14 is dysfunctional and where CASP6 activity is increased. Molecular modeling suggests that palmitoylation of CASP6 may inhibit its activation via steric blockage of the substrate-binding groove and inhibition of CASP6 dimerization, both essential for CASP6 function. Our studies identify palmitoylation as a novel CASP6 modification and as a key regulator of CASP6 activity.
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Affiliation(s)
- Niels H Skotte
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Shaun S Sanders
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Roshni R Singaraja
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada
- Translational Laboratories in Genetic Medicine, Agency for Science, Technology and Research, Singapore, Singapore
- Department of Medicine at Yong Loo Lin School of Medicine, National University of Singapore, Singapore 138648, Singapore
| | - Dagmar E Ehrnhoefer
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Kuljeet Vaid
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Xiaofan Qiu
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Srinivasaragavan Kannan
- Bioinformatics Institute, Agency for Science, Technology and Research, 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
| | - Chandra Verma
- Bioinformatics Institute, Agency for Science, Technology and Research, 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
- School of Biological Sciences, Nanyang Technological University, 50 Nanyang Drive, Singapore 637551, Singapore
| | - Michael R Hayden
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada
- Translational Laboratories in Genetic Medicine, Agency for Science, Technology and Research, Singapore, Singapore
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13
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Pakavathkumar P, Noël A, Lecrux C, Tubeleviciute-Aydin A, Hamel E, Ahlfors JE, LeBlanc AC. Caspase vinyl sulfone small molecule inhibitors prevent axonal degeneration in human neurons and reverse cognitive impairment in Caspase-6-overexpressing mice. Mol Neurodegener 2017; 12:22. [PMID: 28241839 PMCID: PMC5329948 DOI: 10.1186/s13024-017-0166-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 02/22/2017] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND The activation of the aspartate-specific cysteinyl protease, Caspase-6, is proposed as an early pathogenic event of Alzheimer disease (AD) and Huntington's disease. Caspase-6 inhibitors could be useful against these neurodegenerative diseases but most Caspase-6 inhibitors have been exclusively studied in vitro or show acute liver toxicity in humans. Here, we assessed vinyl sulfone small molecule peptide caspase inhibitors for potential use in vivo. METHODS The IC50 of NWL vinyl sulfone small molecule caspase inhibitors were determined on Caspase-1 to 10, and Caspase-6-transfected human colon carcinoma HCT116 cells. Inhibition of Caspase-6-mediated axonal degeneration was assessed in serum-deprived or amyloid precursor protein-transfected primary human CNS neurons. Cellular toxicity was measured by phase contrast microscopy, mitochondrial and lactate dehydrogenase colorimetric activity assays, or flow cytometry. Caspase inhibition was measured by fluorogenic activity assays, fluorescence microscopy, and western blot analyses. The effect of inhibitors on age-dependent cognitive deficits in Caspase-6 transgenic mice was assessed by the novel object recognition task. Liquid chromatography coupled to tandem mass spectrometry assessed the blood-brain barrier permeability of inhibitors in Caspase-6 mice. RESULTS Vinyl sulfone NWL-117 caspase inhibitor has a higher selectivity against Caspase-6, -4, -8, -9, and -10 whereas NWL-154 has higher selectivity against Caspase-6, -8, and -10. The half-maximal inhibitory concentrations (IC50) of NWL-117 and NWL-154 is 192 nM and 100 nM against Caspase-6 in vitro, and 4.82 μM and 3.63 μM in Caspase-6-transfected HCT116 cells, respectively. NWL inhibitors are not toxic to HCT116 cells or to human primary neurons. NWL-117 and NWL-154 inhibit serum deprivation-induced Caspase-6 activity and prevent amyloid precursor protein-mediated neurite degeneration in human primary CNS neurons. NWL-117 crosses the blood brain barrier and reverses age-dependent episodic memory deficits in Caspase-6 mice. CONCLUSIONS NWL peptidic vinyl methyl sulfone inhibitors are potent, non-toxic, blood-brain barrier permeable, and irreversible caspase inhibitors with neuroprotective effects in HCT116 cells, in primary human CNS neurons, and in Caspase-6 mice. These results highlight the therapeutic potential of vinyl sulfone inhibitors as caspase inhibitors against neurodegenerative diseases and sanction additional work to improve their selectivity against different caspases.
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Affiliation(s)
- Prateep Pakavathkumar
- Bloomfield Center for Research in Aging, Lady Davis Institute for Medical Research, Jewish General Hospital, 3999 Ch. Cote Ste-Catherine, Montreal, QC, H3T 1E2, Canada
- Department of Neurology and Neurosurgery, McGill University, 845 Sherbrooke O, Montreal, QC, H3A 0G4, Canada
| | - Anastasia Noël
- Bloomfield Center for Research in Aging, Lady Davis Institute for Medical Research, Jewish General Hospital, 3999 Ch. Cote Ste-Catherine, Montreal, QC, H3T 1E2, Canada
- Department of Neurology and Neurosurgery, McGill University, 845 Sherbrooke O, Montreal, QC, H3A 0G4, Canada
| | - Clotilde Lecrux
- Laboratory of Cerebrovascular Research, Montreal Neurological Institute, 3801 University Street, Montreal, QC, H3A 2B4, Canada
| | - Agne Tubeleviciute-Aydin
- Bloomfield Center for Research in Aging, Lady Davis Institute for Medical Research, Jewish General Hospital, 3999 Ch. Cote Ste-Catherine, Montreal, QC, H3T 1E2, Canada
- Department of Neurology and Neurosurgery, McGill University, 845 Sherbrooke O, Montreal, QC, H3A 0G4, Canada
| | - Edith Hamel
- Laboratory of Cerebrovascular Research, Montreal Neurological Institute, 3801 University Street, Montreal, QC, H3A 2B4, Canada
| | - Jan-Eric Ahlfors
- New World Laboratories, 500 Boulevard Cartier Ouest, Laval, QC, H7V 5B7, Canada
| | - Andrea C LeBlanc
- Bloomfield Center for Research in Aging, Lady Davis Institute for Medical Research, Jewish General Hospital, 3999 Ch. Cote Ste-Catherine, Montreal, QC, H3T 1E2, Canada.
- Department of Neurology and Neurosurgery, McGill University, 845 Sherbrooke O, Montreal, QC, H3A 0G4, Canada.
- Molecular and Regenerative Medicine Axis, Lady Davis Institute for Medical Research, Sir Mortimer B Davis Jewish General Hospital, 3755 ch. Côte Ste-Catherine, Montréal, QC, H3T 1E2, Canada.
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Xu D, Jalal SI, Sledge GW, Meroueh SO. Small-molecule binding sites to explore protein-protein interactions in the cancer proteome. MOLECULAR BIOSYSTEMS 2016; 12:3067-87. [PMID: 27452673 DOI: 10.1039/c6mb00231e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The Cancer Genome Atlas (TCGA) offers an unprecedented opportunity to identify small-molecule binding sites on proteins with overexpressed mRNA levels that correlate with poor survival. Here, we analyze RNA-seq and clinical data for 10 tumor types to identify genes that are both overexpressed and correlate with patient survival. Protein products of these genes were scanned for binding sites that possess shape and physicochemical properties that can accommodate small-molecule probes or therapeutic agents (druggable). These binding sites were classified as enzyme active sites (ENZ), protein-protein interaction sites (PPI), or other sites whose function is unknown (OTH). Interestingly, the overwhelming majority of binding sites were classified as OTH. We find that ENZ, PPI, and OTH binding sites often occurred on the same structure suggesting that many of these OTH cavities can be used for allosteric modulation of enzyme activity or protein-protein interactions with small molecules. We discovered several ENZ (PYCR1, QPRT, and HSPA6) and PPI (CASC5, ZBTB32, and CSAD) binding sites on proteins that have been seldom explored in cancer. We also found proteins that have been extensively studied in cancer that have not been previously explored with small molecules that harbor ENZ (PKMYT1, STEAP3, and NNMT) and PPI (HNF4A, MEF2B, and CBX2) binding sites. All binding sites were classified by the signaling pathways to which the protein that harbors them belongs using KEGG. In addition, binding sites were mapped onto structural protein-protein interaction networks to identify promising sites for drug discovery. Finally, we identify pockets that harbor missense mutations previously identified from analysis of TCGA data. The occurrence of mutations in these binding sites provides new opportunities to develop small-molecule probes to explore their function in cancer.
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Affiliation(s)
- David Xu
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
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15
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16
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Poreba M, Szalek A, Kasperkiewicz P, Rut W, Salvesen GS, Drag M. Small Molecule Active Site Directed Tools for Studying Human Caspases. Chem Rev 2015; 115:12546-629. [PMID: 26551511 DOI: 10.1021/acs.chemrev.5b00434] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Caspases are proteases of clan CD and were described for the first time more than two decades ago. They play critical roles in the control of regulated cell death pathways including apoptosis and inflammation. Due to their involvement in the development of various diseases like cancer, neurodegenerative diseases, or autoimmune disorders, caspases have been intensively investigated as potential drug targets, both in academic and industrial laboratories. This review presents a thorough, deep, and systematic assessment of all technologies developed over the years for the investigation of caspase activity and specificity using substrates and inhibitors, as well as activity based probes, which in recent years have attracted considerable interest due to their usefulness in the investigation of biological functions of this family of enzymes.
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Affiliation(s)
- Marcin Poreba
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Technology , Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Aleksandra Szalek
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Technology , Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Paulina Kasperkiewicz
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Technology , Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Wioletta Rut
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Technology , Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Guy S Salvesen
- Program in Cell Death and Survival Networks, Sanford Burnham Prebys Medical Discovery Institute , La Jolla, California 92037, United States
| | - Marcin Drag
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Technology , Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
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17
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Targeting caspase-6 and caspase-8 to promote neuronal survival following ischemic stroke. Cell Death Dis 2015; 6:e1967. [PMID: 26539914 PMCID: PMC4670918 DOI: 10.1038/cddis.2015.272] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 08/18/2015] [Accepted: 08/24/2015] [Indexed: 01/06/2023]
Abstract
Previous studies show that caspase-6 and caspase-8 are involved in neuronal apoptosis and regenerative failure after trauma of the adult central nervous system (CNS). In this study, we evaluated whether caspase-6 or -8 inhibitors can reduce cerebral or retinal injury after ischemia. Cerebral infarct volume, relative to appropriate controls, was significantly reduced in groups treated with caspase-6 or -8 inhibitors. Concomitantly, these treatments also reduced neurological deficits, reduced edema, increased cell proliferation, and increased neurofilament levels in the injured cerebrum. Caspase-6 and -8 inhibitors, or siRNAs, also increased retinal ganglion cell survival at 14 days after ischemic injury. Caspase-6 or -8 inhibition also decreased caspase-3, -6, and caspase-8 cleavage when assayed by western blot and reduced caspase-3 and -6 activities in colorimetric assays. We have shown that caspase-6 or caspase-8 inhibition decreases the neuropathological consequences of cerebral or retinal infarction, thereby emphasizing their importance in ischemic neuronal degeneration. As such, caspase-6 and -8 are potential targets for future therapies aimed at attenuating the devastating functional losses that result from retinal or cerebral stroke.
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18
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Meng J, Lai MT, Munshi V, Grobler J, McCauley J, Zuck P, Johnson EN, Uebele VN, Hermes JD, Adam GC. Screening of HIV-1 Protease Using a Combination of an Ultra-High-Throughput Fluorescent-Based Assay and RapidFire Mass Spectrometry. ACTA ACUST UNITED AC 2015; 20:606-15. [PMID: 25681434 DOI: 10.1177/1087057115570838] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 01/12/2015] [Indexed: 12/19/2022]
Abstract
HIV-1 protease (PR) represents one of the primary targets for developing antiviral agents for the treatment of HIV-infected patients. To identify novel PR inhibitors, a label-free, high-throughput mass spectrometry (HTMS) assay was developed using the RapidFire platform and applied as an orthogonal assay to confirm hits identified in a fluorescence resonance energy transfer (FRET)-based primary screen of > 1 million compounds. For substrate selection, a panel of peptide substrates derived from natural processing sites for PR was evaluated on the RapidFire platform. As a result, KVSLNFPIL, a new substrate measured to have a ~ 20- and 60-fold improvement in k cat/K m over the frequently used sequences SQNYPIVQ and SQNYPIV, respectively, was identified for the HTMS screen. About 17% of hits from the FRET-based primary screen were confirmed in the HTMS confirmatory assay including all 304 known PR inhibitors in the set, demonstrating that the HTMS assay is effective at triaging false-positives while capturing true hits. Hence, with a sampling rate of ~7 s per well, the RapidFire HTMS assay enables the high-throughput evaluation of peptide substrates and functions as an efficient tool for hits triage in the discovery of novel PR inhibitors.
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Affiliation(s)
- Juncai Meng
- Screening and Protein Sciences, Merck Research Labs, North Wales, PA, USA
| | - Ming-Tain Lai
- Department of Infectious Disease, Merck Research Labs, West Point, PA, USA
| | - Vandna Munshi
- Department of Infectious Disease, Merck Research Labs, West Point, PA, USA
| | - Jay Grobler
- Department of Infectious Disease, Merck Research Labs, West Point, PA, USA
| | - John McCauley
- Medicinal Chemistry, Merck Research Labs, West Point, PA, USA
| | - Paul Zuck
- Screening and Protein Sciences, Merck Research Labs, North Wales, PA, USA
| | - Eric N Johnson
- Screening and Protein Sciences, Merck Research Labs, North Wales, PA, USA Wuxi Apptech
| | - Victor N Uebele
- Screening and Protein Sciences, Merck Research Labs, North Wales, PA, USA
| | - Jeffrey D Hermes
- Screening and Protein Sciences, Merck Research Labs, North Wales, PA, USA
| | - Gregory C Adam
- Screening and Protein Sciences, Merck Research Labs, North Wales, PA, USA
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19
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Adam GC, Meng J, Rizzo JM, Amoss A, Lusen JW, Patel A, Riley D, Hunt R, Zuck P, Johnson EN, Uebele VN, Hermes JD. Use of high-throughput mass spectrometry to reduce false positives in protease uHTS screens. ACTA ACUST UNITED AC 2014; 20:212-22. [PMID: 25336354 DOI: 10.1177/1087057114555832] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
As a label-free technology, mass spectrometry (MS) enables assays to be generated that monitor the conversion of substrates with native sequences to products without the requirement for substrate modifications or indirect detection methods. Although traditional liquid chromatography (LC)-MS methods are relatively slow for a high-throughput screening (HTS) paradigm, with cycle times typically ≥ 60 s per sample, the Agilent RapidFire High-Throughput Mass Spectrometry (HTMS) System, with a cycle time of 5-7 s per sample, enables rapid analysis of compound numbers compatible with HTS. By monitoring changes in mass directly, HTMS assays can be used as a triaging tool by eliminating large numbers of false positives resulting from fluorescent compound interference or from compounds interacting with hydrophobic fluorescent dyes appended to substrates. Herein, HTMS assays were developed for multiple protease programs, including cysteine, serine, and aspartyl proteases, and applied as a confirmatory assay. The confirmation rate for each protease assay averaged <30%, independent of the primary assay technology used (i.e., luminescent, fluorescent, and time-resolved fluorescent technologies). Importantly, >99% of compounds designed to inhibit the enzymes were confirmed by the corresponding HTMS assay. Hence, HTMS is an effective tool for removing detection-based false positives from ultrahigh-throughput screening, resulting in hit lists enriched in true actives for downstream dose response titrations and hit-to-lead efforts.
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Affiliation(s)
- Gregory C Adam
- Screening and Protein Sciences, Merck Research Labs, North Wales, PA, USA
| | - Juncai Meng
- Screening and Protein Sciences, Merck Research Labs, North Wales, PA, USA
| | - Joseph M Rizzo
- Screening and Protein Sciences, Merck Research Labs, North Wales, PA, USA
| | - Adam Amoss
- Screening and Protein Sciences, Merck Research Labs, North Wales, PA, USA
| | - Jeffrey W Lusen
- Screening and Protein Sciences, Merck Research Labs, North Wales, PA, USA
| | - Amita Patel
- Screening and Protein Sciences, Merck Research Labs, North Wales, PA, USA
| | - Daniel Riley
- Screening and Protein Sciences, Merck Research Labs, North Wales, PA, USA
| | - Rachel Hunt
- Screening and Protein Sciences, Merck Research Labs, North Wales, PA, USA
| | - Paul Zuck
- Screening and Protein Sciences, Merck Research Labs, North Wales, PA, USA
| | - Eric N Johnson
- Screening and Protein Sciences, Merck Research Labs, North Wales, PA, USA Wuxi Apptech
| | - Victor N Uebele
- Screening and Protein Sciences, Merck Research Labs, North Wales, PA, USA
| | - Jeffrey D Hermes
- Screening and Protein Sciences, Merck Research Labs, North Wales, PA, USA
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20
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Wang XJ, Cao Q, Zhang Y, Su XD. Activation and regulation of caspase-6 and its role in neurodegenerative diseases. Annu Rev Pharmacol Toxicol 2014; 55:553-72. [PMID: 25340928 DOI: 10.1146/annurev-pharmtox-010814-124414] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Caspases, a family of cysteine proteases, are major mediators of apoptosis and inflammation. Caspase-6 is classified as an apoptotic effector, and it mediates nuclear shrinkage during apoptosis, but it possesses unique activation and regulation mechanisms that differ from those of other effector caspases. Furthermore, increasing evidence has shown that caspase-6 is highly involved in axon degeneration and neurodegenerative diseases, such as Huntington's disease and Alzheimer's disease. Cleavage at the caspase-6 site in mutated huntingtin protein is a prerequisite for the development of the characteristic behavioral and neuropathological features of Huntington's disease. Active caspase-6 is present in early stages of Alzheimer's disease, and caspase-6 activity is associated with the disease's pathological lesions. In this review, we discuss the evidence relevant to the role of caspase-6 in neurodegenerative diseases and summarize its activation and regulation mechanisms. In doing so, we provide new insight about potential therapeutic approaches that incorporate the modulation of caspase-6 function for the treatment of neurodegenerative diseases.
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Affiliation(s)
- Xiao-Jun Wang
- State Key Laboratory of Protein and Plant Gene Research and
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21
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Cappiello M, Moschini R, Balestri F, Mura U, Del-Corso A. Basic models for differential inhibition of enzymes. Biochem Biophys Res Commun 2014; 445:556-60. [DOI: 10.1016/j.bbrc.2014.02.030] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 02/06/2014] [Indexed: 10/25/2022]
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22
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Dagbay K, Eron SJ, Serrano BP, Velázquez-Delgado EM, Zhao Y, Lin D, Vaidya S, Hardy JA. A multipronged approach for compiling a global map of allosteric regulation in the apoptotic caspases. Methods Enzymol 2014; 544:215-49. [PMID: 24974292 DOI: 10.1016/b978-0-12-417158-9.00009-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
One of the most promising and as yet underutilized means of regulating protein function is exploitation of allosteric sites. All caspases catalyze the same overall reaction, but they perform different biological roles and are differentially regulated. It is our hypothesis that many allosteric sites exist on various caspases and that understanding both the distinct and overlapping mechanisms by which each caspase can be allosterically controlled should ultimately enable caspase-specific inhibition. Here we describe the ongoing work and methods for compiling a comprehensive map of apoptotic caspase allostery. Central to this approach are the use of (i) the embedded record of naturally evolved allosteric sites that are sensitive to zinc-mediated inhibition, phosphorylation, and other posttranslational modifications, (ii) structural and mutagenic approaches, and (iii) novel binding sites identified by both rationally-designed and screening-derived small-molecule inhibitors.
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Affiliation(s)
- Kevin Dagbay
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts, USA
| | - Scott J Eron
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts, USA
| | - Banyuhay P Serrano
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts, USA
| | | | - Yunlong Zhao
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts, USA
| | - Di Lin
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts, USA
| | - Sravanti Vaidya
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts, USA
| | - Jeanne A Hardy
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts, USA.
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23
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Cao Q, Wang XJ, Li LF, Su XD. The regulatory mechanism of the caspase 6 pro-domain revealed by crystal structure and biochemical assays. ACTA ACUST UNITED AC 2013; 70:58-67. [PMID: 24419379 DOI: 10.1107/s1399004713024218] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 08/29/2013] [Indexed: 11/10/2022]
Abstract
Caspase 6 (CASP6) is a neuron degeneration-related protease and is widely considered to be a potential drug-design target against neurodegenerative diseases such as Huntington's disease and Alzheimer's disease. The N-terminal pro-peptide of CASP6, also referred to as the pro-domain, contains 23 residues and its functional role remains elusive. In this study, the crystal structure of a full-length CASP6 zymogen mutant, proCASP6H121A, was solved. Although the pro-domain was flexible in the crystal, without visible electron density, structural analyses combined with biochemical assays revealed that the pro-domain inhibited CASP6 auto-activation by inhibiting intramolecular cleavage at the intersubunit cleavage site TEVD(193) and also by preventing this site from intermolecular cleavage at low protein concentration through a so-called `suicide-protection' mechanism. Further experiments showed that the length of the pro-domain and the side chain of Asn18 played critical roles in suicide protection. These results disclosed a new inhibitory mechanism of CASP6 and shed light on the pathogenesis and therapeutically relevant study of CASP6-related neurodegenerative diseases.
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Affiliation(s)
- Qin Cao
- State Key Laboratory of Protein and Plant Gene Research, and Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Xiao-Jun Wang
- State Key Laboratory of Protein and Plant Gene Research, and Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Lan-Fen Li
- State Key Laboratory of Protein and Plant Gene Research, and Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Xiao-Dong Su
- State Key Laboratory of Protein and Plant Gene Research, and Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, People's Republic of China
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24
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Modulating caspase activity: beyond the active site. Curr Opin Struct Biol 2013; 23:812-9. [DOI: 10.1016/j.sbi.2013.10.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 10/14/2013] [Indexed: 12/16/2022]
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25
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Murray J, Giannetti AM, Steffek M, Gibbons P, Hearn BR, Cohen F, Tam C, Pozniak C, Bravo B, Lewcock J, Jaishankar P, Ly CQ, Zhao X, Tang Y, Chugha P, Arkin MR, Flygare J, Renslo AR. Tailoring small molecules for an allosteric site on procaspase-6. ChemMedChem 2013; 9:73-7, 2. [PMID: 24259468 DOI: 10.1002/cmdc.201300424] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Indexed: 12/20/2022]
Abstract
Although they represent attractive therapeutic targets, caspases have so far proven recalcitrant to the development of drugs targeting the active site. Allosteric modulation of caspase activity is an alternate strategy that potentially avoids the need for anionic and electrophilic functionality present in most active-site inhibitors. Caspase-6 has been implicated in neurodegenerative disease, including Huntington's and Alzheimer's diseases. Herein we describe a fragment-based lead discovery effort focused on caspase-6 in its active and zymogen forms. Fragments were identified for procaspase-6 using surface plasmon resonance methods and subsequently shown by X-ray crystallography to bind a putative allosteric site at the dimer interface. A fragment-merging strategy was employed to produce nanomolar-affinity ligands that contact residues in the L2 loop at the dimer interface, significantly stabilizing procaspase-6. Because rearrangement of the L2 loop is required for caspase-6 activation, our results suggest a strategy for the allosteric control of caspase activation with drug-like small molecules.
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Affiliation(s)
- Jeremy Murray
- Departments of Structural Biology, Biochemical Pharmacology, Neuroscience, and Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080 (USA).
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26
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Resistance mechanism to an uncompetitive inhibitor of a single-substrate, single-product enzyme: a study of Helicobacter pylori glutamate racemase. Future Med Chem 2013; 5:1203-14. [DOI: 10.4155/fmc.13.94] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Two independent series of inhibitors of Helicobacter pylori glutamate racemase (MurI) were characterized for their kinetic mechanism, and one was used to generate resistant mutants in vitro. Mutant MurI enzymes from these strains were characterized by structural, genetic, kinetic and biophysical methods. Both inhibitor series, pyrazolopyrimidinediones and benzodiazepines, are uncompetitive with respect to the glutamate substrate, and the resistance mutations were found to act by reducing the affinity of MurI for substrate, thereby reducing the pool of enzyme–substrate complex available for binding inhibitor, while still allowing sufficient glutamate racemase activity for peptidoglycan construction. Uncompetitive inhibitors of a single-substrate, single-product enzyme are rare, and this work gives insight into an remarkable resistance mechanism. This article will discuss the projected clinical impact of H. pylori MurI resistance on these types of inhibitors.
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27
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LeBlanc AC. Caspase-6 as a novel early target in the treatment of Alzheimer's disease. Eur J Neurosci 2013; 37:2005-18. [DOI: 10.1111/ejn.12250] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 04/01/2013] [Accepted: 04/06/2013] [Indexed: 12/16/2022]
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28
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Hasson SA, Inglese J. Innovation in academic chemical screening: filling the gaps in chemical biology. Curr Opin Chem Biol 2013; 17:329-38. [PMID: 23683346 PMCID: PMC3719966 DOI: 10.1016/j.cbpa.2013.04.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2013] [Revised: 03/26/2013] [Accepted: 04/15/2013] [Indexed: 12/12/2022]
Abstract
Academic screening centers across the world have endeavored to discover small molecules that can modulate biological systems. To increase the reach of functional-genomic and chemical screening programs, universities, research institutes, and governments have followed their industrial counterparts in adopting high-throughput paradigms. As academic screening efforts have steadily grown in scope and complexity, so have the ideas of what is possible with the union of technology and biology. This review addresses the recent conceptual and technological innovation that has been propelling academic screening into its own unique niche. In particular, high-content and whole-organism screening are changing how academics search for novel bioactive compounds. Importantly, we recognize examples of successful chemical probe development that have punctuated the changing technology landscape.
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Affiliation(s)
- Samuel A Hasson
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
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