James A Wells

James A Wells

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Neuronally Enriched RUFY3 Is Required for Caspase-Mediated Axon Degeneration.

Neuron 2019 Aug 17;103(3):412-422.e4. Epub 2019 Jun 17.

Department of Biology, Stanford University, Stanford, CA, USA; Laboratory of Brain Development and Repair, The Rockefeller University, New York, NY, USA. Electronic address:

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http://dx.doi.org/10.1016/j.neuron.2019.05.030DOI Listing
August 2019

Kinase Atlas: Druggability Analysis of Potential Allosteric Sites in Kinases.

J Med Chem 2019 Jul 5;62(14):6512-6524. Epub 2019 Jul 5.

Departments of Pharmaceutical Chemistry and Cellular and Molecular Pharmacology , University of California , 1700 Fourth Street , San Francisco , California 9415 , United States.

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http://dx.doi.org/10.1021/acs.jmedchem.9b00089DOI Listing
July 2019

Multiomics of azacitidine-treated AML cells reveals variable and convergent targets that remodel the cell-surface proteome.

Proc Natl Acad Sci U S A 2019 01 24;116(2):695-700. Epub 2018 Dec 24.

Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143;

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http://dx.doi.org/10.1073/pnas.1813666116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6329958PMC
January 2019

Engineering Improved Antiphosphotyrosine Antibodies Based on an Immunoconvergent Binding Motif.

J Am Chem Soc 2018 12 19;140(48):16615-16624. Epub 2018 Nov 19.

Department of Pharmaceutical Chemistry , University of California, San Francisco , San Francisco , California 94143 , United States.

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http://pubs.acs.org/doi/10.1021/jacs.8b08402
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http://dx.doi.org/10.1021/jacs.8b08402DOI Listing
December 2018

The Unique Cofactor Region of Zika Virus NS2B-NS3 Protease Facilitates Cleavage of Key Host Proteins.

ACS Chem Biol 2018 09 14;13(9):2398-2405. Epub 2018 Aug 14.

Department of Chemistry , University of Massachusetts , Amherst , Massachusetts 01003 , United States.

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http://dx.doi.org/10.1021/acschembio.8b00508DOI Listing
September 2018

Toward a Ferrous Iron-Cleavable Linker for Antibody-Drug Conjugates.

Mol Pharm 2018 05 23;15(5):2054-2059. Epub 2018 Mar 23.

Sutro Biopharma, Inc. , South San Francisco , California 94080 , United States.

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http://dx.doi.org/10.1021/acs.molpharmaceut.8b00242DOI Listing
May 2018

Molecular mechanisms of cell death: recommendations of the Nomenclature Committee on Cell Death 2018.

Authors:
Lorenzo Galluzzi Ilio Vitale Stuart A Aaronson John M Abrams Dieter Adam Patrizia Agostinis Emad S Alnemri Lucia Altucci Ivano Amelio David W Andrews Margherita Annicchiarico-Petruzzelli Alexey V Antonov Eli Arama Eric H Baehrecke Nickolai A Barlev Nicolas G Bazan Francesca Bernassola Mathieu J M Bertrand Katiuscia Bianchi Mikhail V Blagosklonny Klas Blomgren Christoph Borner Patricia Boya Catherine Brenner Michelangelo Campanella Eleonora Candi Didac Carmona-Gutierrez Francesco Cecconi Francis K-M Chan Navdeep S Chandel Emily H Cheng Jerry E Chipuk John A Cidlowski Aaron Ciechanover Gerald M Cohen Marcus Conrad Juan R Cubillos-Ruiz Peter E Czabotar Vincenzo D'Angiolella Ted M Dawson Valina L Dawson Vincenzo De Laurenzi Ruggero De Maria Klaus-Michael Debatin Ralph J DeBerardinis Mohanish Deshmukh Nicola Di Daniele Francesco Di Virgilio Vishva M Dixit Scott J Dixon Colin S Duckett Brian D Dynlacht Wafik S El-Deiry John W Elrod Gian Maria Fimia Simone Fulda Ana J García-Sáez Abhishek D Garg Carmen Garrido Evripidis Gavathiotis Pierre Golstein Eyal Gottlieb Douglas R Green Lloyd A Greene Hinrich Gronemeyer Atan Gross Gyorgy Hajnoczky J Marie Hardwick Isaac S Harris Michael O Hengartner Claudio Hetz Hidenori Ichijo Marja Jäättelä Bertrand Joseph Philipp J Jost Philippe P Juin William J Kaiser Michael Karin Thomas Kaufmann Oliver Kepp Adi Kimchi Richard N Kitsis Daniel J Klionsky Richard A Knight Sharad Kumar Sam W Lee John J Lemasters Beth Levine Andreas Linkermann Stuart A Lipton Richard A Lockshin Carlos López-Otín Scott W Lowe Tom Luedde Enrico Lugli Marion MacFarlane Frank Madeo Michal Malewicz Walter Malorni Gwenola Manic Jean-Christophe Marine Seamus J Martin Jean-Claude Martinou Jan Paul Medema Patrick Mehlen Pascal Meier Sonia Melino Edward A Miao Jeffery D Molkentin Ute M Moll Cristina Muñoz-Pinedo Shigekazu Nagata Gabriel Nuñez Andrew Oberst Moshe Oren Michael Overholtzer Michele Pagano Theocharis Panaretakis Manolis Pasparakis Josef M Penninger David M Pereira Shazib Pervaiz Marcus E Peter Mauro Piacentini Paolo Pinton Jochen H M Prehn Hamsa Puthalakath Gabriel A Rabinovich Markus Rehm Rosario Rizzuto Cecilia M P Rodrigues David C Rubinsztein Thomas Rudel Kevin M Ryan Emre Sayan Luca Scorrano Feng Shao Yufang Shi John Silke Hans-Uwe Simon Antonella Sistigu Brent R Stockwell Andreas Strasser Gyorgy Szabadkai Stephen W G Tait Daolin Tang Nektarios Tavernarakis Andrew Thorburn Yoshihide Tsujimoto Boris Turk Tom Vanden Berghe Peter Vandenabeele Matthew G Vander Heiden Andreas Villunger Herbert W Virgin Karen H Vousden Domagoj Vucic Erwin F Wagner Henning Walczak David Wallach Ying Wang James A Wells Will Wood Junying Yuan Zahra Zakeri Boris Zhivotovsky Laurence Zitvogel Gerry Melino Guido Kroemer

Cell Death Differ 2018 03 23;25(3):486-541. Epub 2018 Jan 23.

Paris Descartes/Paris V University, Paris, France.

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http://dx.doi.org/10.1038/s41418-017-0012-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5864239PMC
March 2018

Human antibody-based chemically induced dimerizers for cell therapeutic applications.

Nat Chem Biol 2018 02 4;14(2):112-117. Epub 2017 Dec 4.

Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA.

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http://dx.doi.org/10.1038/nchembio.2529DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6352901PMC
February 2018

Heat Shock Protein 70 (Hsp70) Suppresses RIP1-Dependent Apoptotic and Necroptotic Cascades.

Mol Cancer Res 2018 01 28;16(1):58-68. Epub 2017 Sep 28.

Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California.

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http://dx.doi.org/10.1158/1541-7786.MCR-17-0408DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6101036PMC
January 2018

Engineering peptide ligase specificity by proteomic identification of ligation sites.

Nat Chem Biol 2018 Jan 20;14(1):50-57. Epub 2017 Nov 20.

Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA.

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http://www.nature.com/doifinder/10.1038/nchembio.2521
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http://dx.doi.org/10.1038/nchembio.2521DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5726896PMC
January 2018

A Split-Abl Kinase for Direct Activation in Cells.

Cell Chem Biol 2017 Oct 14;24(10):1250-1258.e4. Epub 2017 Sep 14.

Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA; Department of Cellular & Molecular Pharmacology, University of California, San Francisco, CA 94158, USA. Electronic address:

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http://dx.doi.org/10.1016/j.chembiol.2017.08.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5650542PMC
October 2017

Engineering a light-activated caspase-3 for precise ablation of neurons in vivo.

Proc Natl Acad Sci U S A 2017 09 11;114(39):E8174-E8183. Epub 2017 Sep 11.

Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158;

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http://dx.doi.org/10.1073/pnas.1705064114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5625904PMC
September 2017

Caspases and their substrates.

Cell Death Differ 2017 08 12;24(8):1380-1389. Epub 2017 May 12.

Department of Pharmaceutical Chemistry and Cellular &Molecular Pharmacology, University of California, San Francisco, CA, USA.

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http://dx.doi.org/10.1038/cdd.2017.44DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5520456PMC
August 2017

Time-Resolved Proteomics Extends Ribosome Profiling-Based Measurements of Protein Synthesis Dynamics.

Cell Syst 2017 06 31;4(6):636-644.e9. Epub 2017 May 31.

Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94107, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2017.05.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5546878PMC
June 2017

Comparative Analysis of Mitochondrial N-Termini from Mouse, Human, and Yeast.

Mol Cell Proteomics 2017 04 25;16(4):512-523. Epub 2017 Jan 25.

From the ‡Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114.

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http://dx.doi.org/10.1074/mcp.M116.063818DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5383775PMC
April 2017

Structure-Activity Relationship and Molecular Mechanics Reveal the Importance of Ring Entropy in the Biosynthesis and Activity of a Natural Product.

J Am Chem Soc 2017 02 13;139(7):2541-2544. Epub 2017 Feb 13.

Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University , Stanford, California 94305, United States.

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http://dx.doi.org/10.1021/jacs.6b10792DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5345905PMC
February 2017

A Novel Tumor-Activated Prodrug Strategy Targeting Ferrous Iron Is Effective in Multiple Preclinical Cancer Models.

J Med Chem 2016 12 12;59(24):11161-11170. Epub 2016 Dec 12.

Department of Pharmaceutical Chemistry, University of California-San Francisco , San Francisco, California 94158, United States.

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http://dx.doi.org/10.1021/acs.jmedchem.6b01470DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5184369PMC
December 2016

Direct Proximity Tagging of Small Molecule Protein Targets Using an Engineered NEDD8 Ligase.

J Am Chem Soc 2016 10 28;138(40):13123-13126. Epub 2016 Sep 28.

Department of Pharmaceutical Chemistry and ‡Department of Cellular and Molecular Pharmacology, University of California , San Francisco, California 94158, United States.

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http://dx.doi.org/10.1021/jacs.6b06828DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5308480PMC
October 2016

A reactivity-based probe of the intracellular labile ferrous iron pool.

Nat Chem Biol 2016 09 4;12(9):680-5. Epub 2016 Jul 4.

Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA.

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http://dx.doi.org/10.1038/nchembio.2116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4990480PMC
September 2016

Caspase-1 causes truncation and aggregation of the Parkinson's disease-associated protein α-synuclein.

Proc Natl Acad Sci U S A 2016 08 1;113(34):9587-92. Epub 2016 Aug 1.

Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202; Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN 46202; Department of Neurology, Indiana University School of Medicine, Indianapolis, IN 46202

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http://dx.doi.org/10.1073/pnas.1610099113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5003239PMC
August 2016

Ligand-binding domains of nuclear receptors facilitate tight control of split CRISPR activity.

Nat Commun 2016 07 1;7:12009. Epub 2016 Jul 1.

Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94158, USA.

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http://dx.doi.org/10.1038/ncomms12009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4932181PMC
July 2016

Reprogramming Caspase-7 Specificity by Regio-Specific Mutations and Selection Provides Alternate Solutions for Substrate Recognition.

ACS Chem Biol 2016 06 31;11(6):1603-12. Epub 2016 Mar 31.

Department of Chemistry, 104 LGRT, 710 N. Pleasant St., University of Massachusetts , Amherst, Massachusetts 01003, United States.

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http://dx.doi.org/10.1021/acschembio.5b00971DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4912419PMC
June 2016

Quantitative MS-based enzymology of caspases reveals distinct protein substrate specificities, hierarchies, and cellular roles.

Proc Natl Acad Sci U S A 2016 Apr 22;113(14):E2001-10. Epub 2016 Mar 22.

Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94143

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http://dx.doi.org/10.1073/pnas.1524900113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4833263PMC
April 2016

CryptoSite: Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites.

J Mol Biol 2016 Feb 5;428(4):709-719. Epub 2016 Feb 5.

Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Pharmaceutical Chemistry and California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA. Electronic address: http://salilab.org.

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http://dx.doi.org/10.1016/j.jmb.2016.01.029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4794384PMC
February 2016

Small-Molecule Allosteric Modulators of the Protein Kinase PDK1 from Structure-Based Docking.

J Med Chem 2015 Oct 12;58(20):8285-8291. Epub 2015 Oct 12.

Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States.

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http://dx.doi.org/10.1021/acs.jmedchem.5b01216DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5099076PMC
October 2015

Engineered cellular gene-replacement platform for selective and inducible proteolytic profiling.

Proc Natl Acad Sci U S A 2015 Jul 23;112(27):8344-9. Epub 2015 Jun 23.

Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94143

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http://dx.doi.org/10.1073/pnas.1504141112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4500269PMC
July 2015

Turning on caspases with genetics and small molecules.

Methods Enzymol 2014 ;544:179-213

Department of Pharmaceutical Chemistry, University of California, San Francisco, California, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA. Electronic address:

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http://dx.doi.org/10.1016/B978-0-12-417158-9.00008-XDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4249682PMC
February 2015

Global analysis of cellular proteolysis by selective enzymatic labeling of protein N-termini.

Methods Enzymol 2014 ;544:327-58

Department of Pharmaceutical Chemistry, University of California, San Francisco, California, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA. Electronic address:

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http://dx.doi.org/10.1016/B978-0-12-417158-9.00013-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4260929PMC
February 2015

An improved single-chain Fab platform for efficient display and recombinant expression.

J Mol Biol 2015 Jan 3;427(2):576-86. Epub 2014 Dec 3.

Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, 94158, USA; Recombinant Antibody Network, University of California, San Francisco, CA, 94158, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00222836140061
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http://dx.doi.org/10.1016/j.jmb.2014.11.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4297586PMC
January 2015

A small-molecule mimic of a peptide docking motif inhibits the protein kinase PDK1.

Proc Natl Acad Sci U S A 2014 Dec 17;111(52):18590-5. Epub 2014 Dec 17.

Department of Pharmaceutical Chemistry, Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158

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http://dx.doi.org/10.1073/pnas.1415365112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4284534PMC
December 2014

Unraveling the mechanism of cell death induced by chemical fibrils.

Nat Chem Biol 2014 Nov 28;10(11):969-76. Epub 2014 Sep 28.

1] Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, California, USA. [2] Department of Cellular and Molecular Pharmacology, University of California-San Francisco, San Francisco, California, USA.

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http://www.nature.com/articles/nchembio.1639
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http://dx.doi.org/10.1038/nchembio.1639DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4201873PMC
November 2014

Small-molecule inhibitors of protein-protein interactions: progressing toward the reality.

Chem Biol 2014 Sep;21(9):1102-14

Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, San Francisco, CA 94158, USA.

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https://linkinghub.elsevier.com/retrieve/pii/S10745521140029
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http://dx.doi.org/10.1016/j.chembiol.2014.09.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4179228PMC
September 2014

Circulating proteolytic signatures of chemotherapy-induced cell death in humans discovered by N-terminal labeling.

Proc Natl Acad Sci U S A 2014 May 12;111(21):7594-9. Epub 2014 May 12.

Pharmaceutical Chemistry, andCellular and Molecular Pharmacology, University of California, San Francisco, CA 94158; and

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http://dx.doi.org/10.1073/pnas.1405987111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4040605PMC
May 2014

Cell biology. New tricks for an old dimer.

Science 2014 May;344(6185):703-4

Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA.

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http://dx.doi.org/10.1126/science.1254799DOI Listing
May 2014

FP Tethering: a screening technique to rapidly identify compounds that disrupt protein-protein interactions.

Medchemcomm 2014 Mar;5:370-375

Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States ; Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States ; Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States.

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http://dx.doi.org/10.1039/C3MD00356FDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4005387PMC
March 2014

K-Ras(G12C) inhibitors allosterically control GTP affinity and effector interactions.

Nature 2013 Nov 20;503(7477):548-51. Epub 2013 Nov 20.

1] Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, California 94158, USA [2].

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http://www.nature.com/articles/nature12796
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http://dx.doi.org/10.1038/nature12796DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4274051PMC
November 2013

Nature-inspired design of motif-specific antibody scaffolds.

Nat Biotechnol 2013 Oct 18;31(10):916-21. Epub 2013 Aug 18.

Department of Pharmaceutical Chemistry, University of California, San Francisco, California, USA.

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http://dx.doi.org/10.1038/nbt.2672DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3795957PMC
October 2013

Global cellular response to chemotherapy-induced apoptosis.

Elife 2013 Oct 29;2:e01236. Epub 2013 Oct 29.

Department of Pharmaceutical Chemistry , University of California, San Francisco , San Francisco , United States ; Department of Laboratory Medicine , University of California, San Francisco , San Francisco , United States.

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http://dx.doi.org/10.7554/eLife.01236DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3808542PMC
October 2013

Next generation therapeutics.

Curr Opin Chem Biol 2013 Jun 14;17(3):317-9. Epub 2013 May 14.

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http://dx.doi.org/10.1016/j.cbpa.2013.04.022DOI Listing
June 2013

Structural snapshots reveal distinct mechanisms of procaspase-3 and -7 activation.

Proc Natl Acad Sci U S A 2013 May 6;110(21):8477-82. Epub 2013 May 6.

Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA.

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http://dx.doi.org/10.1073/pnas.1306759110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3666719PMC
May 2013

Substrate and inhibitor-induced dimerization and cooperativity in caspase-1 but not caspase-3.

J Biol Chem 2013 Apr 5;288(14):9971-81. Epub 2013 Feb 5.

Department of Pharmaceutical Chemistry, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus C, Denmark.

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http://dx.doi.org/10.1074/jbc.M112.426460DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3617296PMC
April 2013

The DegraBase: a database of proteolysis in healthy and apoptotic human cells.

Mol Cell Proteomics 2013 Mar 20;12(3):813-24. Epub 2012 Dec 20.

Department of Pharmaceutical Chemistry, University of California-San Francisco, CA 94158, USA.

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http://dx.doi.org/10.1074/mcp.O112.024372DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3591672PMC
March 2013

Ordering a dynamic protein via a small-molecule stabilizer.

J Am Chem Soc 2013 Mar 22;135(9):3363-6. Epub 2013 Feb 22.

Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States.

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http://dx.doi.org/10.1021/ja3122334DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3607081PMC
March 2013

Substrates of IAP ubiquitin ligases identified with a designed orthogonal E3 ligase, the NEDDylator.

Mol Cell 2013 Jan 29;49(2):273-82. Epub 2012 Nov 29.

Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.

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http://dx.doi.org/10.1016/j.molcel.2012.10.022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3557559PMC
January 2013

Fibrils colocalize caspase-3 with procaspase-3 to foster maturation.

J Biol Chem 2012 Sep 7;287(40):33781-95. Epub 2012 Aug 7.

Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, USA.

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http://dx.doi.org/10.1074/jbc.M112.386128DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3460474PMC
September 2012

Quantitative profiling of caspase-cleaved substrates reveals different drug-induced and cell-type patterns in apoptosis.

Proc Natl Acad Sci U S A 2012 Jul 16;109(31):12432-7. Epub 2012 Jul 16.

Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94114, USA.

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http://dx.doi.org/10.1073/pnas.1208616109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3412033PMC
July 2012

Identification of specific tethered inhibitors for caspase-5.

Chem Biol Drug Des 2012 Feb 28;79(2):209-15. Epub 2011 Nov 28.

Departments of Pharmaceutical Chemistry and Cellular and Molecular Pharmacology, University of California at San Francisco, 1700 4th Street, San Francisco, CA 94143, USA.

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http://doi.wiley.com/10.1111/j.1747-0285.2011.01261.x
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http://dx.doi.org/10.1111/j.1747-0285.2011.01261.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3271850PMC
February 2012

Global kinetic analysis of proteolysis via quantitative targeted proteomics.

Proc Natl Acad Sci U S A 2012 Feb 23;109(6):1913-8. Epub 2012 Jan 23.

Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th Street, San Francisco, CA 94114, USA.

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http://dx.doi.org/10.1073/pnas.1117158109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3277568PMC
February 2012

Self-assembling small molecules form nanofibrils that bind procaspase-3 to promote activation.

J Am Chem Soc 2011 Dec 17;133(49):19630-3. Epub 2011 Nov 17.

Department of Pharmaceutical Chemistry, University of California, San Francisco, California, USA.

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http://dx.doi.org/10.1021/ja208350uDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3253528PMC
December 2011

Caspase substrates and cellular remodeling.

Annu Rev Biochem 2011 ;80:1055-87

Department of Pharmaceutical Chemistry and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158-2330, USA.

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http://dx.doi.org/10.1146/annurev-biochem-061809-121639DOI Listing
October 2011

Structural and enzymatic insights into caspase-2 protein substrate recognition and catalysis.

J Biol Chem 2011 Sep 2;286(39):34147-54. Epub 2011 Aug 2.

Department of Pharmaceutical Chemistry, Small Molecule Discovery Center, University of California, San Francisco, California 94158, USA.

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September 2011

Molecules that modulate Apaf-1 activity.

Med Res Rev 2011 Jul 22;31(4):649-75. Epub 2010 Jan 22.

Peptide and Protein Laboratory, Department of Medicinal Chemistry, Centro de Investigación Príncipe Felipe, Avda Autopista del Saler, Valencia, Spain.

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July 2011

Turning a protein kinase on or off from a single allosteric site via disulfide trapping.

Proc Natl Acad Sci U S A 2011 Apr 23;108(15):6056-61. Epub 2011 Mar 23.

Departments of Pharmaceutical Chemistry and Cellular and Molecular Pharmacology, University of California, 1700 Fourth Street, San Francisco, CA 94158, USA.

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April 2011

Activation of specific apoptotic caspases with an engineered small-molecule-activated protease.

Cell 2010 Aug;142(4):637-46

Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.

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August 2010

Prediction of protease substrates using sequence and structure features.

Bioinformatics 2010 Jul 26;26(14):1714-22. Epub 2010 May 26.

Graduate Group in Bioinformatics, Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA.

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July 2010

Inflammatory stimuli regulate caspase substrate profiles.

Mol Cell Proteomics 2010 May 20;9(5):880-93. Epub 2010 Feb 20.

Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2871421PMC
May 2010

Turning enzymes ON with small molecules.

Nat Chem Biol 2010 Mar;6(3):179-188

Department of Pharmaceutical Chemistry and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA.

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March 2010

Sampling the N-terminal proteome of human blood.

Proc Natl Acad Sci U S A 2010 Mar 19;107(10):4561-6. Epub 2010 Feb 19.

Department of Pharmaceutical Chemistry, University of California, San Francisco, Byers Hall, 1700 4th Street, San Francisco, CA 94158, USA.

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March 2010

Methods for the proteomic identification of protease substrates.

Curr Opin Chem Biol 2009 Dec 2;13(5-6):503-9. Epub 2009 Sep 2.

Department of Pharmaceutical Chemistry, University of California, San Francisco, UCSF MC 2552, 1700 4th St, San Francisco, CA 94158, United States of America.

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December 2009

Warren L. DeLano 21 June 1972-3 November 2009.

Nat Struct Mol Biol 2009 Dec;16(12):1202-3

Howard Hughes Medical Institute and the Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, and Photon Science, Stanford University, Stanford, California, USA. brunger

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December 2009

Small-molecule activators of a proenzyme.

Science 2009 Nov;326(5954):853-8

Department of Pharmaceutical Chemistry, University of California, San Francisco, Byers Hall, 1700 4th Street, San Francisco, CA 94158, USA.

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November 2009

Dissecting an allosteric switch in caspase-7 using chemical and mutational probes.

J Biol Chem 2009 Sep 6;284(38):26063-9. Epub 2009 Jul 6.

Sunesis Pharmaceuticals, South San Francisco, California 94080, USA.

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September 2009

Two-state selection of conformation-specific antibodies.

Proc Natl Acad Sci U S A 2009 Mar 10;106(9):3071-6. Epub 2009 Feb 10.

Department of Pharmaceutical Chemistry, University of California, 1700 4th Street, San Francisco, CA 94143, USA.

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March 2009

Tags for labeling protein N-termini with subtiligase for proteomics.

Bioorg Med Chem Lett 2008 Nov 19;18(22):6000-3. Epub 2008 Aug 19.

Department of Pharmaceutical Chemistry , University of California, San Francisco, CA 94158-2330, USA.

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November 2008

An allosteric circuit in caspase-1.

J Mol Biol 2008 Sep 20;381(5):1157-67. Epub 2008 Jun 20.

Departments of Pharmaceutical Chemistry and Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, CA 94143, USA.

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September 2008

Global sequencing of proteolytic cleavage sites in apoptosis by specific labeling of protein N termini.

Cell 2008 Sep 21;134(5):866-76. Epub 2008 Aug 21.

Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.

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September 2008

Repairing research integrity.

Nature 2008 Jun;453(7198):980-2

Office of Research Integrity, 1101 Wootton Parkway, Suite 750, Rockville, Maryland 20852, USA.

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June 2008

Reaching for high-hanging fruit in drug discovery at protein-protein interfaces.

Nature 2007 Dec;450(7172):1001-9

Department of Pharmaceutical Chemistry, University of California at San Francisco, 1700 4th Street 503A, San Francisco, California 94156, USA.

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December 2007

Computational approach to site-directed ligand discovery.

Proteins 2007 Aug;68(2):551-60

Locus Pharmaceuticals, Blue Bell, Pennsylvania 19422, USA.

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August 2007

Hot-spot mimicry of a cytokine receptor by a small molecule.

Proc Natl Acad Sci U S A 2006 Oct 10;103(42):15422-7. Epub 2006 Oct 10.

Sunesis Pharmaceuticals, 341 Oyster Point Boulevard, South San Francisco, CA 94080, USA.

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October 2006

A common allosteric site and mechanism in caspases.

Proc Natl Acad Sci U S A 2006 May 8;103(20):7595-600. Epub 2006 May 8.

Department of Pharmaceutical Chemistry, University of California, 1700 4th Street, San Francisco, CA 94143, USA.

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May 2006

Malonate-assisted purification of human caspases.

Protein Expr Purif 2005 May;41(1):148-53

Department of Biology, Sunesis Pharmaceuticals, Inc., 341 Oyster Point Boulevard, South San Francisco, CA 94080, USA.

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May 2005

Site-specific disulfide capture of agonist and antagonist peptides on the C5a receptor.

J Biol Chem 2005 Feb 18;280(6):4009-12. Epub 2004 Nov 18.

Sunesis Pharmaceuticals Inc., South San Francisco, California 94080, USA.

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February 2005

Disulfide trapping to localize small-molecule agonists and antagonists for a G protein-coupled receptor.

Proc Natl Acad Sci U S A 2005 Feb 14;102(8):2719-24. Epub 2005 Feb 14.

Sunesis Pharmaceuticals, 341 Oyster Point Boulevard, South San Francisco, CA 94080, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC549436PMC
February 2005

Searching for new allosteric sites in enzymes.

Curr Opin Struct Biol 2004 Dec;14(6):706-15

Sunesis Pharmaceuticals Inc, 341 Oyster Point Boulevard, South San Francisco, California 94080, USA.

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December 2004

Discovery of an allosteric site in the caspases.

Proc Natl Acad Sci U S A 2004 Aug 16;101(34):12461-6. Epub 2004 Aug 16.

Sunesis Pharmaceuticals, Inc., 341 Oyster Point Boulevard, South San Francisco, CA 94080, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC514654PMC
August 2004

Tethering: fragment-based drug discovery.

Annu Rev Biophys Biomol Struct 2004 ;33:199-223

Sunesis Pharmaceuticals, Inc., 341 Oyster Point Boulevard, South San Francisco, California 94080, USA.

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July 2004

Apo cytochrome c inhibits caspases by preventing apoptosome formation.

Biochem Biophys Res Commun 2004 Jul;319(3):944-50

Apoptosis Section, Laboratory of Protein Dynamics and Signaling, NCI-Frederick, Frederick, MD 21702, USA.

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July 2004

Small-molecule inhibitors of protein-protein interactions: progressing towards the dream.

Nat Rev Drug Discov 2004 Apr;3(4):301-17

Sunesis Pharmaceuticals, 341 Oyster Point Boulevard, South San Francisco, California 94080, USA.

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April 2004

Mechanistic diversity of cytokine receptor signaling across cell membranes.

Sci STKE 2004 Apr 28;2004(231):re7. Epub 2004 Apr 28.

Department of Biochemistry and Biophysics, UCSF Genentech Hall, 600 16th Street, University of California, San Francisco, CA 94143-2240, USA.

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April 2004

Potent small-molecule binding to a dynamic hot spot on IL-2.

J Am Chem Soc 2003 Dec;125(50):15280-1

Sunesis Pharmaceuticals, Inc., 341 Oyster Point Boulevard, South San Francisco, CA 94080, USA.

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December 2003

Direct activation of the apoptosis machinery as a mechanism to target cancer cells.

Proc Natl Acad Sci U S A 2003 Jun 13;100(13):7533-8. Epub 2003 Jun 13.

Sunesis Pharmaceuticals, 341 Oyster Point Boulevard, South San Francisco, CA 94080, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC164621PMC
June 2003

Binding of small molecules to an adaptive protein-protein interface.

Proc Natl Acad Sci U S A 2003 Feb 11;100(4):1603-8. Epub 2003 Feb 11.

Department of Biology, Sunesis Pharmaceuticals, South San Francisco, CA 94080-1913, USA.

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February 2003