Integrative X-ray Structure and Molecular Modeling for the Rationalization of Procaspase-8 Inhibitor Potency and Selectivity

Xu, Janice H.; Eberhardt, Jerome; Hill-Payne, Brianna; González-Páez, Gonzalo E.; Castellón, José Omar; Cravatt, Benjamin F.; Forli, Stefano; Wolan, Dennis W.; Backus, Keriann M.

doi:10.1021/acschembio.0c00019

Title: Integrative X-ray Structure and Molecular Modeling for the Rationalization of Procaspase-8 Inhibitor Potency and Selectivity

Journal Article · 12 January 2020 · ACS Chemical Biology

DOI: https://doi.org/10.1021/acschembio.0c00019 · OSTI ID:1799608

^[1]; Eberhardt, Jerome ^[2]; Hill-Payne, Brianna ^[3];

^[2]; Castellón, José Omar ^[3];

^[2];

^[3]

The Scripps Research Inst., La Jolla, CA (United States); OSTI
The Scripps Research Inst., La Jolla, CA (United States)
Univ. of California, Los Angeles, CA (United States)

Caspases are a critical class of proteases involved in regulating programmed cell death and other biological processes. Selective inhibitors of individual caspases, however, are lacking, due in large part to the high structural similarity found in the active sites of these enzymes. We recently discovered a small-molecule inhibitor, 63-R, that covalently binds the zymogen, or inactive precursor (pro-form), of caspase-8, but not other caspases, pointing to an untapped potential of procaspases as targets for chemical probes. Realizing this goal would benefit from a structural understanding of how small molecules bind to and inhibit caspase zymogens. There have, however, been very few reported procaspase structures. Here, we employ X-ray crystallography to elucidate a procaspase-8 crystal structure in complex with 63-R, which reveals large conformational changes in active-site loops that accommodate the intramolecular cleavage events required for protease activation. Combining these structural insights with molecular modeling and mutagenesis-based biochemical assays, we elucidate key interactions required for 63-R inhibition of procaspase-8. Our findings inform the mechanism of caspase activation and its disruption by small molecules and, more generally, have implications for the development of small molecule inhibitors and/or activators that target alternative (e.g., inactive precursor) protein states to ultimately expand the druggable proteome.

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Research Organization:: University of California, Los Angeles, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: FC02-02ER63421

OSTI ID:: 1799608

Journal Information:: ACS Chemical Biology, Journal Name: ACS Chemical Biology Journal Issue: 2 Vol. 15; ISSN 1554-8929

Publisher:: American Chemical Society (ACS)Copyright Statement

Country of Publication:: United States

Language:: English

References (69)

A Self-Consistent Method for the Analysis of Protein Secondary Structure from Circular Dichroism Sreerama, N.; Woody, R. W. Analytical Biochemistry, Vol. 209, Issue 1 https://doi.org/10.1006/abio.1993.1079	journal	February 1993
Mechanisms of caspase activation Boatright, Kelly M.; Salvesen, Guy S. Current Opinion in Cell Biology, Vol. 15, Issue 6 https://doi.org/10.1016/j.ceb.2003.10.009	journal	December 2003
Caspase Cleavage Is Not for Everyone Johnson, Carrie E.; Kornbluth, Sally Cell, Vol. 134, Issue 5 https://doi.org/10.1016/j.cell.2008.08.019	journal	September 2008
Structural and Biochemical Studies on Procaspase-8: New Insights on Initiator Caspase Activation Keller, Nadine; Mareš, Jiří; Zerbe, Oliver Structure, Vol. 17, Issue 3 https://doi.org/10.1016/j.str.2008.12.019	journal	March 2009
Small Molecule Active Site Directed Tools for Studying Human Caspases Poreba, Marcin; Szalek, Aleksandra; Kasperkiewicz, Paulina Chemical Reviews, Vol. 115, Issue 22 https://doi.org/10.1021/acs.chemrev.5b00434	journal	November 2015
Non-apoptotic functions of caspases in myeloid cell differentiation Solier, Stéphanie; Fontenay, Michaela; Vainchenker, William Cell Death & Differentiation, Vol. 24, Issue 8 https://doi.org/10.1038/cdd.2017.19	journal	February 2017
More alive than dead: non-apoptotic roles for caspases in neuronal development, plasticity and disease Mukherjee, Amrita; Williams, Darren W. Cell Death & Differentiation, Vol. 24, Issue 8 https://doi.org/10.1038/cdd.2017.64	journal	June 2017
Proteome-wide covalent ligand discovery in native biological systems Backus, Keriann M.; Correia, Bruno E.; Lum, Kenneth M. Nature, Vol. 534, Issue 7608 https://doi.org/10.1038/nature18002	journal	June 2016
Computational protein–ligand docking and virtual drug screening with the AutoDock suite Forli, Stefano; Huey, Ruth; Pique, Michael E. Nature Protocols, Vol. 11, Issue 5 https://doi.org/10.1038/nprot.2016.051	journal	April 2016
Glivec (STI571, imatinib), a rationally developed, targeted anticancer drug Capdeville, Renaud; Buchdunger, Elisabeth; Zimmermann, Juerg Nature Reviews Drug Discovery, Vol. 1, Issue 7 https://doi.org/10.1038/nrd839	journal	July 2002
A common allosteric site and mechanism in caspases Scheer, J. M.; Romanowski, M. J.; Wells, J. A. Proceedings of the National Academy of Sciences, Vol. 103, Issue 20 https://doi.org/10.1073/pnas.0602571103	journal	May 2006
Features and development of Coot Emsley, P.; Lohkamp, B.; Scott, W. G. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/s0907444910007493	journal	March 2010
Tailoring Small Molecules for an Allosteric Site on Procaspase-6 Murray, Jeremy; Giannetti, Anthony M.; Steffek, Micah ChemMedChem, Vol. 9, Issue 1 https://doi.org/10.1002/cmdc.201300424	journal	November 2013
AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility Morris, Garrett M.; Huey, Ruth; Lindstrom, William Journal of Computational Chemistry, Vol. 30, Issue 16 https://doi.org/10.1002/jcc.21256	journal	December 2009
MDAnalysis: A toolkit for the analysis of molecular dynamics simulations Michaud-Agrawal, Naveen; Denning, Elizabeth J.; Woolf, Thomas B. Journal of Computational Chemistry, Vol. 32, Issue 10 https://doi.org/10.1002/jcc.21787	journal	April 2011
Covalent docking using autodock: Two-point attractor and flexible side chain methods: Covalent Docking with AutoDock Bianco, Giulia; Forli, Stefano; Goodsell, David S. Protein Science, Vol. 25, Issue 1 https://doi.org/10.1002/pro.2733	journal	July 2015
A Self-Consistent Method for the Analysis of Protein Secondary Structure from Circular Dichroism Sreerama, N.; Woody, R. W. Analytical Biochemistry, Vol. 209, Issue 1 https://doi.org/10.1006/abio.1993.1079	journal	February 1993
Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation 1 1Edited by J. Thornton Word, J. Michael; Lovell, Simon C.; Richardson, Jane S. Journal of Molecular Biology, Vol. 285, Issue 4 https://doi.org/10.1006/jmbi.1998.2401	journal	January 1999
Protein Structure Modeling with MODELLER Webb, Benjamin; Sali, Andrej Methods in Molecular Biology https://doi.org/10.1007/978-1-4939-0366-5_1	book	January 2014
Computer-aided drug design platform using PyMOL Lill, Markus A.; Danielson, Matthew L. Journal of Computer-Aided Molecular Design, Vol. 25, Issue 1 https://doi.org/10.1007/s10822-010-9395-8	journal	October 2010
Caspases: Therapeutic Targets in Neurologic Disease Troy, Carol M.; Jean, Ying Y. Neurotherapeutics, Vol. 12, Issue 1 https://doi.org/10.1007/s13311-014-0307-9	journal	October 2014
Crystal Structure of a Procaspase-7 Zymogen Chai, Jijie; Wu, Qi; Shiozaki, Eric Cell, Vol. 107, Issue 3 https://doi.org/10.1016/S0092-8674(01)00544-X	journal	November 2001
Targeted Disruption of the Mouse Caspase 8 Gene Ablates Cell Death Induction by the TNF Receptors, Fas/Apo1, and DR3 and Is Lethal Prenatally Varfolomeev, Eugene E.; Schuchmann, Marcus; Luria, Victor Immunity, Vol. 9, Issue 2 https://doi.org/10.1016/S1074-7613(00)80609-3	journal	August 1998
A Unified Model for Apical Caspase Activation Boatright, Kelly M.; Renatus, Martin; Scott, Fiona L. Molecular Cell, Vol. 11, Issue 2 https://doi.org/10.1016/S1097-2765(03)00051-0	journal	February 2003
Mechanisms of caspase activation Boatright, Kelly M.; Salvesen, Guy S. Current Opinion in Cell Biology, Vol. 15, Issue 6 https://doi.org/10.1016/j.ceb.2003.10.009	journal	December 2003
Caspase Cleavage Is Not for Everyone Johnson, Carrie E.; Kornbluth, Sally Cell, Vol. 134, Issue 5 https://doi.org/10.1016/j.cell.2008.08.019	journal	September 2008
An Optimized Activity-Based Probe for the Study of Caspase-6 Activation Edgington, Laura E.; van Raam, Bram J.; Verdoes, Martijn Chemistry & Biology, Vol. 19, Issue 3 https://doi.org/10.1016/j.chembiol.2011.12.021	journal	March 2012
An “Omics” based survey of human colon cancer Nambiar, Prashant R.; Gupta, Rishi R.; Misra, Vikas Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, Vol. 693, Issue 1-2 https://doi.org/10.1016/j.mrfmmm.2010.07.008	journal	November 2010
Structural and Biochemical Studies on Procaspase-8: New Insights on Initiator Caspase Activation Keller, Nadine; Mareš, Jiří; Zerbe, Oliver Structure, Vol. 17, Issue 3 https://doi.org/10.1016/j.str.2008.12.019	journal	March 2009
Structure-based design of molecular cancer therapeutics van Montfort, Rob L. M.; Workman, Paul Trends in Biotechnology, Vol. 27, Issue 5 https://doi.org/10.1016/j.tibtech.2009.02.003	journal	May 2009
Small Molecule Active Site Directed Tools for Studying Human Caspases Poreba, Marcin; Szalek, Aleksandra; Kasperkiewicz, Paulina Chemical Reviews, Vol. 115, Issue 22 https://doi.org/10.1021/acs.chemrev.5b00434	journal	November 2015
Information content in the circular dichroism of proteins Hennessey, John P.; Johnson, W. Curtis Biochemistry, Vol. 20, Issue 5, p. 1085-1094 https://doi.org/10.1021/bi00508a007	journal	March 1981
Mutations in the Procaspase-3 Dimer Interface Affect the Activity of the Zymogen ^† Pop, Cristina; Feeney, Brett; Tripathy, Ashutosh Biochemistry, Vol. 42, Issue 42 https://doi.org/10.1021/bi034999p	journal	October 2003
Role of Proteolysis in Caspase-8 Activation and Stabilization Pop, Cristina; Fitzgerald, Patrick; Green, Douglas R. Biochemistry, Vol. 46, Issue 14 https://doi.org/10.1021/bi602623b	journal	March 2007
Selective Detection and Inhibition of Active Caspase-3 in Cells with Optimized Peptides Vickers, Chris J.; González-Páez, Gonzalo E.; Wolan, Dennis W. Journal of the American Chemical Society, Vol. 135, Issue 34 https://doi.org/10.1021/ja406399r	journal	August 2013
DTASelect and Contrast: Tools for Assembling and Comparing Protein Identifications from Shotgun Proteomics Tabb, David L.; McDonald, W. Hayes; Yates, John R. Journal of Proteome Research, Vol. 1, Issue 1, p. 21-26 https://doi.org/10.1021/pr015504q	journal	February 2002
Caspase activation pathways: some recent progress Cullen, S. P.; Martin, S. J. Cell Death & Differentiation, Vol. 16, Issue 7 https://doi.org/10.1038/cdd.2009.59	journal	June 2009
Caspases and cancer Olsson, M.; Zhivotovsky, B. Cell Death & Differentiation, Vol. 18, Issue 9 https://doi.org/10.1038/cdd.2011.30	journal	April 2011
Old, new and emerging functions of caspases Shalini, S.; Dorstyn, L.; Dawar, S. Cell Death & Differentiation, Vol. 22, Issue 4 https://doi.org/10.1038/cdd.2014.216	journal	December 2014
Non-apoptotic functions of caspases in myeloid cell differentiation Solier, Stéphanie; Fontenay, Michaela; Vainchenker, William Cell Death & Differentiation, Vol. 24, Issue 8 https://doi.org/10.1038/cdd.2017.19	journal	February 2017
Caspase-dependent non-apoptotic processes in development Nakajima, Yu-ichiro; Kuranaga, Erina Cell Death & Differentiation, Vol. 24, Issue 8 https://doi.org/10.1038/cdd.2017.36	journal	May 2017
Caspases and their substrates Julien, Olivier; Wells, James A. Cell Death & Differentiation, Vol. 24, Issue 8 https://doi.org/10.1038/cdd.2017.44	journal	May 2017
Killers creating new life: caspases drive apoptosis-induced proliferation in tissue repair and disease Fogarty, Caitlin E.; Bergmann, Andreas Cell Death & Differentiation, Vol. 24, Issue 8 https://doi.org/10.1038/cdd.2017.47	journal	March 2017
More alive than dead: non-apoptotic roles for caspases in neuronal development, plasticity and disease Mukherjee, Amrita; Williams, Darren W. Cell Death & Differentiation, Vol. 24, Issue 8 https://doi.org/10.1038/cdd.2017.64	journal	June 2017
Pleiotropic defects in lymphocyte activation caused by caspase-8 mutations lead to human immunodeficiency Chun, Hyung J.; Zheng, Lixin; Ahmad, Manzoor Nature, Vol. 419, Issue 6905 https://doi.org/10.1038/nature01063	journal	September 2002
Proteome-wide covalent ligand discovery in native biological systems Backus, Keriann M.; Correia, Bruno E.; Lum, Kenneth M. Nature, Vol. 534, Issue 7608 https://doi.org/10.1038/nature18002	journal	June 2016
Computational protein–ligand docking and virtual drug screening with the AutoDock suite Forli, Stefano; Huey, Ruth; Pique, Michael E. Nature Protocols, Vol. 11, Issue 5 https://doi.org/10.1038/nprot.2016.051	journal	April 2016
Glivec (STI571, imatinib), a rationally developed, targeted anticancer drug Capdeville, Renaud; Buchdunger, Elisabeth; Zimmermann, Juerg Nature Reviews Drug Discovery, Vol. 1, Issue 7 https://doi.org/10.1038/nrd839	journal	July 2002
IBD—what role do Proteobacteria play? Mukhopadhya, Indrani; Hansen, Richard; El-Omar, Emad M. Nature Reviews Gastroenterology & Hepatology, Vol. 9, Issue 4 https://doi.org/10.1038/nrgastro.2012.14	journal	February 2012
Converging roles of caspases in inflammasome activation, cell death and innate immunity Man, Si Ming; Kanneganti, Thirumala-Devi Nature Reviews Immunology, Vol. 16, Issue 1 https://doi.org/10.1038/nri.2015.7	journal	December 2015
Caspases in apoptosis and beyond Li, J.; Yuan, J. Oncogene, Vol. 27, Issue 48 https://doi.org/10.1038/onc.2008.297	journal	October 2008
Caspase-8/FLICE functions as an executioner caspase in anticancer drug-induced apoptosis Engels, Ingo H.; Stepczynska, Ania; Stroh, Christopher Oncogene, Vol. 19, Issue 40 https://doi.org/10.1038/sj.onc.1203824	journal	September 2000
Discovery of an allosteric site in the caspases Hardy, J. A.; Lam, J.; Nguyen, J. T. Proceedings of the National Academy of Sciences, Vol. 101, Issue 34 https://doi.org/10.1073/pnas.0404781101	journal	August 2004
A common allosteric site and mechanism in caspases Scheer, J. M.; Romanowski, M. J.; Wells, J. A. Proceedings of the National Academy of Sciences, Vol. 103, Issue 20 https://doi.org/10.1073/pnas.0602571103	journal	May 2006
Explaining why Gleevec is a specific and potent inhibitor of Abl kinase Lin, Y. -L.; Meng, Y.; Jiang, W. Proceedings of the National Academy of Sciences, Vol. 110, Issue 5 https://doi.org/10.1073/pnas.1214330110	journal	January 2013
Structural snapshots reveal distinct mechanisms of procaspase-3 and -7 activation Thomsen, N. D.; Koerber, J. T.; Wells, J. A. Proceedings of the National Academy of Sciences, Vol. 110, Issue 21 https://doi.org/10.1073/pnas.1306759110	journal	May 2013
A Combinatorial Approach Defines Specificities of Members of the Caspase Family and Granzyme B: FUNCTIONAL RELATIONSHIPS ESTABLISHED FOR KEY MEDIATORS OF APOPTOSIS Thornberry, Nancy A.; Rano, Thomas A.; Peterson, Erin P. Journal of Biological Chemistry, Vol. 272, Issue 29 https://doi.org/10.1074/jbc.272.29.17907	journal	July 1997
Crystal Structure of Procaspase-1 Zymogen Domain Reveals Insight into Inflammatory Caspase Autoactivation Elliott, J. Michael; Rouge, Lionel; Wiesmann, Christian Journal of Biological Chemistry, Vol. 284, Issue 10 https://doi.org/10.1074/jbc.M806121200	journal	December 2008
FLICE is activated by association with the CD95 death-inducing signaling complex (DISC) Medema, J. P. The EMBO Journal, Vol. 16, Issue 10 https://doi.org/10.1093/emboj/16.10.2794	journal	May 1997
Essential role for caspase 8 in T-cell homeostasis and T-cell-mediated immunity Salmena, L. Genes & Development, Vol. 17, Issue 7 https://doi.org/10.1101/gad.1063703	journal	March 2003
Phaser crystallographic software McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D. Journal of Applied Crystallography, Vol. 40, Issue 4 https://doi.org/10.1107/S0021889807021206	journal	July 2007
PROCHECK: a program to check the stereochemical quality of protein structures Laskowski, R. A.; MacArthur, M. W.; Moss, D. S. Journal of Applied Crystallography, Vol. 26, Issue 2 https://doi.org/10.1107/S0021889892009944	journal	April 1993
PHENIX: a comprehensive Python-based system for macromolecular structure solution Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221 https://doi.org/10.1107/S0907444909052925	journal	January 2010
Features and development of Coot Emsley, P.; Lohkamp, B.; Scott, W. G. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S0907444910007493	journal	March 2010
Requirement for Caspase-8 in NF- B Activation by Antigen Receptor Su, H. Science, Vol. 307, Issue 5714 https://doi.org/10.1126/science.1104765	journal	March 2005
Caspase-8, association with Alzheimer’s Disease and functional analysis of rare variants Rehker, Jan; Rodhe, Johanna; Nesbitt, Ryan R. PLOS ONE, Vol. 12, Issue 10 https://doi.org/10.1371/journal.pone.0185777	journal	October 2017
Activity of Uncleaved Caspase-8 Controls Anti-bacterial Immune Defense and TLR-Induced Cytokine Production Independent of Cell Death Philip, Naomi H.; DeLaney, Alexandra; Peterson, Lance W. PLOS Pathogens, Vol. 12, Issue 10 https://doi.org/10.1371/journal.ppat.1005910	journal	October 2016
PHENIX: a comprehensive Python-based system for macromolecular structure solution. Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.45787	text	January 2010
Structural and biochemical studies on procaspase-8: New insights on initiator caspase activation Keller, M.; Mares, J.; Zerbe, O. Elsevier https://doi.org/10.5167/uzh-17811	text	January 2009

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59 BASIC BIOLOGICAL SCIENCES
Procaspase-8
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crystallography
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mutational analysis

Title: Integrative X-ray Structure and Molecular Modeling for the Rationalization of Procaspase-8 Inhibitor Potency and Selectivity

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