1
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Crawford JJ, Feng J, Brightbill HD, Johnson AR, Wright M, Kolesnikov A, Lee W, Castanedo GM, Do S, Blaquiere N, Staben ST, Chiang PC, Fan PW, Baumgardner M, Wong S, Godemann R, Grabbe A, Wiegel C, Sujatha-Bhaskar S, Hymowitz SG, Liau N, Hsu PL, McEwan PA, Ismaili MHA, Landry ML. Filling a nick in NIK: extending the half-life of a NIK inhibitor through structure-based drug design. Bioorg Med Chem Lett 2023; 89:129277. [PMID: 37105490 DOI: 10.1016/j.bmcl.2023.129277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/04/2023] [Accepted: 04/04/2023] [Indexed: 04/29/2023]
Abstract
Inhibition of NF-κB inducing kinase (NIK) has been pursued as a promising therapeutic target for autoimmune disorders due to its highly regulated role in key steps of the NF-κB signaling pathway. Previously reported NIK inhibitors from our group were shown to be potent, selective, and efficacious, but had higher human dose projections than desirable for immunology indications. Herein we report the clearance-driven optimization of a NIK inhibitor guided by metabolite identification studies and structure-based drug design. This led to the identification of an azabicyclo[3.1.0]hexanone motif that attenuated in vitro and in vivo clearance while maintaining NIK potency and increasing selectivity over other kinases, resulting in a greater than ten-fold reduction in predicted human dose.
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Affiliation(s)
- James J Crawford
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Jianwen Feng
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Hans D Brightbill
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Adam R Johnson
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Matthew Wright
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Aleksandr Kolesnikov
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Wendy Lee
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | | | - Steven Do
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Nicole Blaquiere
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Steven T Staben
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Po-Chang Chiang
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Peter W Fan
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Matt Baumgardner
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Susan Wong
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Robert Godemann
- Evotec SE., Manfred Eigen Campus, Essener Bogen 7, Hamburg 22419, Germany
| | - Alice Grabbe
- Evotec SE., Manfred Eigen Campus, Essener Bogen 7, Hamburg 22419, Germany
| | - Catharina Wiegel
- Evotec SE., Manfred Eigen Campus, Essener Bogen 7, Hamburg 22419, Germany
| | | | - Sarah G Hymowitz
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Nicholas Liau
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Peter L Hsu
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Paul A McEwan
- Evotec SE., Manfred Eigen Campus, Essener Bogen 7, Hamburg 22419, Germany
| | | | - Matthew L Landry
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
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2
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Liau NPD, Johnson MC, Izadi S, Gerosa L, Hammel M, Bruning JM, Wendorff TJ, Phung W, Hymowitz SG, Sudhamsu J. Structural basis for SHOC2 modulation of RAS signalling. Nature 2022; 609:400-407. [PMID: 35768504 PMCID: PMC9452301 DOI: 10.1038/s41586-022-04838-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 05/05/2022] [Indexed: 12/12/2022]
Abstract
The RAS-RAF pathway is one of the most commonly dysregulated in human cancers1-3. Despite decades of study, understanding of the molecular mechanisms underlying dimerization and activation4 of the kinase RAF remains limited. Recent structures of inactive RAF monomer5 and active RAF dimer5-8 bound to 14-3-39,10 have revealed the mechanisms by which 14-3-3 stabilizes both RAF conformations via specific phosphoserine residues. Prior to RAF dimerization, the protein phosphatase 1 catalytic subunit (PP1C) must dephosphorylate the N-terminal phosphoserine (NTpS) of RAF11 to relieve inhibition by 14-3-3, although PP1C in isolation lacks intrinsic substrate selectivity. SHOC2 is as an essential scaffolding protein that engages both PP1C and RAS to dephosphorylate RAF NTpS11-13, but the structure of SHOC2 and the architecture of the presumptive SHOC2-PP1C-RAS complex remain unknown. Here we present a cryo-electron microscopy structure of the SHOC2-PP1C-MRAS complex to an overall resolution of 3 Å, revealing a tripartite molecular architecture in which a crescent-shaped SHOC2 acts as a cradle and brings together PP1C and MRAS. Our work demonstrates the GTP dependence of multiple RAS isoforms for complex formation, delineates the RAS-isoform preference for complex assembly, and uncovers how the SHOC2 scaffold and RAS collectively drive specificity of PP1C for RAF NTpS. Our data indicate that disease-relevant mutations affect complex assembly, reveal the simultaneous requirement of two RAS molecules for RAF activation, and establish rational avenues for discovery of new classes of inhibitors to target this pathway.
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Affiliation(s)
- Nicholas P D Liau
- Department of Structural Biology, Genentech, South San Francisco, CA, USA
| | - Matthew C Johnson
- Department of Structural Biology, Genentech, South San Francisco, CA, USA
| | - Saeed Izadi
- Pharmaceutical Development, Genentech, South San Francisco, CA, USA
| | - Luca Gerosa
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA, USA
| | - Michal Hammel
- Physical Bioscience Division, Lawrence Berkeley National Labs, Berkeley, CA, USA
| | - John M Bruning
- Department of Biochemical and Cellular Pharmacology, Genentech, South San Francisco, CA, USA
| | - Timothy J Wendorff
- Department of Structural Biology, Genentech, South San Francisco, CA, USA
| | - Wilson Phung
- Department of Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, CA, USA
| | - Sarah G Hymowitz
- Department of Structural Biology, Genentech, South San Francisco, CA, USA.
- The Column Group, San Francisco, CA, USA.
| | - Jawahar Sudhamsu
- Department of Structural Biology, Genentech, South San Francisco, CA, USA.
- Department of Discovery Oncology, Genentech, South San Francisco, CA, USA.
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3
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Tilegenova C, Izadi S, Yin J, Huang CS, Wu J, Ellerman D, Hymowitz SG, Walters B, Salisbury C, Carter PJ. Dissecting the molecular basis of high viscosity of monospecific and bispecific IgG antibodies. MAbs 2021; 12:1692764. [PMID: 31779513 PMCID: PMC6927759 DOI: 10.1080/19420862.2019.1692764] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Some antibodies exhibit elevated viscosity at high concentrations, making them poorly suited for therapeutic applications requiring administration by injection such as subcutaneous or ocular delivery. Here we studied an anti-IL-13/IL-17 bispecific IgG4 antibody, which has anomalously high viscosity compared to its parent monospecific antibodies. The viscosity of the bispecific IgG4 in solution was decreased by only ~30% in the presence of NaCl, suggesting electrostatic interactions are insufficient to fully explain the drivers of viscosity. Intriguingly, addition of arginine-HCl reduced the viscosity of the bispecific IgG4 by ~50% to its parent IgG level. These data suggest that beyond electrostatics, additional types of interactions such as cation-π and/or π-π may contribute to high viscosity more significantly than previously understood. Molecular dynamics simulations of antibody fragments in the mixed solution of free arginine and explicit water were conducted to identify hotspots involved in self-interactions. Exposed surface aromatic amino acids displayed an increased number of contacts with arginine. Mutagenesis of the majority of aromatic residues pinpointed by molecular dynamics simulations effectively decreased the solution's viscosity when tested experimentally. This mutational method to reduce the viscosity of a bispecific antibody was extended to a monospecific anti-GCGR IgG1 antibody with elevated viscosity. In all cases, point mutants were readily identified that both reduced viscosity and retained antigen-binding affinity. These studies demonstrate a new approach to mitigate high viscosity of some antibodies by mutagenesis of surface-exposed aromatic residues on complementarity-determining regions that may facilitate some clinical applications.
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Affiliation(s)
| | - Saeed Izadi
- Early Stage Pharmaceutical Development, Genentech Inc., South San Francisco, CA, USA
| | - Jianping Yin
- Structural Biology, Genentech Inc., South San Francisco, CA, USA
| | | | - Jiansheng Wu
- Protein Chemistry, Genentech Inc., South San Francisco, CA, USA
| | - Diego Ellerman
- Protein Chemistry, Genentech Inc., South San Francisco, CA, USA
| | - Sarah G Hymowitz
- Structural Biology, Genentech Inc., South San Francisco, CA, USA
| | - Benjamin Walters
- Biochemical and Cellular Pharmacology, Genentech Inc., South San Francisco, CA, USA
| | - Cleo Salisbury
- Early Stage Pharmaceutical Development, Genentech Inc., South San Francisco, CA, USA
| | - Paul J Carter
- Antibody Engineering, Genentech Inc., South San Francisco, CA, USA
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4
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Liau NPD, Venkatanarayan A, Quinn JG, Phung W, Malek S, Hymowitz SG, Sudhamsu J. Dimerization Induced by C-Terminal 14-3-3 Binding Is Sufficient for BRAF Kinase Activation. Biochemistry 2020; 59:3982-3992. [PMID: 32970425 DOI: 10.1021/acs.biochem.0c00517] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The Ras-RAF-MEK-ERK signaling axis, commonly mutated in human cancers, is highly regulated to prevent aberrant signaling in healthy cells. One of the pathway modulators, 14-3-3, a constitutive dimer, induces RAF dimerization and activation by binding to a phosphorylated motif C-terminal to the RAF kinase domain. Recent work has suggested that a C-terminal "DTS" region in BRAF is necessary for this 14-3-3-mediated activation. We show that the catalytic activity and ATP binding affinity of the BRAF:14-3-3 complex is insensitive to the presence or absence of the DTS, while the ATP sites of both BRAF molecules are identical and available for binding. We also present a crystal structure of the apo BRAF:14-3-3 complex showing that the DTS is not required to attain the catalytically active conformation of BRAF. Rather, BRAF dimerization induced by 14-3-3 is the key step in activation, allowing the active BRAF:14-3-3 tetramer to achieve catalytic activity comparable to the constitutively active oncogenic BRAF V600E mutant.
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5
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Abstract
Despite decades of extensive drug discovery efforts, there are currently no targeted therapies approved to treat KRAS mutant cancers. In this review, we highlight the challenges and opportunities in targeting KRAS mutant tumors through inhibition of mitogen-activated protein kinase (MAPK) signaling with conformation-specific kinase inhibitors. Through structural analysis and mechanistic studies with BRAF and mitogen-activated protein kinase (MEK) inhibitors, we describe how kinase-dependent and -independent functions of MAPK signaling components regulate KRAS-driven tumorigenesis and how these insights can be used to treat RAS mutant cancers with small molecule kinase inhibitors.
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Affiliation(s)
- Sarah G Hymowitz
- Department of Structural Biology, Genentech Inc., South San Francisco, California 94080
| | - Shiva Malek
- Department of Discovery Oncology, Genentech Inc., South San Francisco, California 94080
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6
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Blaquiere N, Castanedo GM, Burch JD, Berezhkovskiy LM, Brightbill H, Brown S, Chan C, Chiang PC, Crawford JJ, Dong T, Fan P, Feng J, Ghilardi N, Godemann R, Gogol E, Grabbe A, Hole AJ, Hu B, Hymowitz SG, Alaoui Ismaili MH, Le H, Lee P, Lee W, Lin X, Liu N, McEwan PA, McKenzie B, Silvestre HL, Suto E, Sujatha-Bhaskar S, Wu G, Wu LC, Zhang Y, Zhong Z, Staben ST. Scaffold-Hopping Approach To Discover Potent, Selective, and Efficacious Inhibitors of NF-κB Inducing Kinase. J Med Chem 2018; 61:6801-6813. [PMID: 29940120 DOI: 10.1021/acs.jmedchem.8b00678] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
NF-κB-inducing kinase (NIK) is a protein kinase central to the noncanonical NF-κB pathway downstream from multiple TNF receptor family members, including BAFF, which has been associated with B cell survival and maturation, dendritic cell activation, secondary lymphoid organ development, and bone metabolism. We report herein the discovery of lead chemical series of NIK inhibitors that were identified through a scaffold-hopping strategy using structure-based design. Electronic and steric properties of lead compounds were modified to address glutathione conjugation and amide hydrolysis. These highly potent compounds exhibited selective inhibition of LTβR-dependent p52 translocation and transcription of NF-κB2 related genes. Compound 4f is shown to have a favorable pharmacokinetic profile across species and to inhibit BAFF-induced B cell survival in vitro and reduce splenic marginal zone B cells in vivo.
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Affiliation(s)
- Nicole Blaquiere
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Georgette M Castanedo
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Jason D Burch
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | | | - Hans Brightbill
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Suzanne Brown
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Connie Chan
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Po-Chang Chiang
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - James J Crawford
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Teresa Dong
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Peter Fan
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Jianwen Feng
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Nico Ghilardi
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Robert Godemann
- Evotec AG , Manfred Eigen Campus, Essener Bogen , Hamburg 22419 , Germany
| | - Emily Gogol
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Alice Grabbe
- Evotec AG , Manfred Eigen Campus, Essener Bogen , Hamburg 22419 , Germany
| | - Alison J Hole
- Evotec AG , Manfred Eigen Campus, Essener Bogen , Hamburg 22419 , Germany
| | - Baihua Hu
- Pharmaron Beijing Co., Ltd. , 6 Taihe Road, BDA , Beijing 100176 , P. R. China
| | - Sarah G Hymowitz
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | | | - Hoa Le
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Patrick Lee
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Wyne Lee
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Xingyu Lin
- Pharmaron Beijing Co., Ltd. , 6 Taihe Road, BDA , Beijing 100176 , P. R. China
| | - Ning Liu
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Paul A McEwan
- Evotec AG , Manfred Eigen Campus, Essener Bogen , Hamburg 22419 , Germany
| | - Brent McKenzie
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | | | - Eric Suto
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | | | - Guosheng Wu
- Pharmaron Beijing Co., Ltd. , 6 Taihe Road, BDA , Beijing 100176 , P. R. China
| | - Lawren C Wu
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Yamin Zhang
- Pharmaron Beijing Co., Ltd. , 6 Taihe Road, BDA , Beijing 100176 , P. R. China
| | - Zoe Zhong
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Steven T Staben
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
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7
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Huang CS, Oberbeck N, Hsiao YC, Liu P, Johnson AR, Dixit VM, Hymowitz SG. Crystal Structure of Ripk4 Reveals Dimerization-Dependent Kinase Activity. Structure 2018; 26:767-777.e5. [PMID: 29706531 DOI: 10.1016/j.str.2018.04.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 03/01/2018] [Accepted: 04/05/2018] [Indexed: 12/16/2022]
Abstract
Receptor-interacting protein kinase 4 (RIPK4) is a highly conserved regulator of epidermal differentiation. Members of the RIPK family possess a common kinase domain as well as unique accessory domains that likely dictate subcellular localization and substrate preferences. Mutations in human RIPK4 manifest as Bartsocas-Papas syndrome (BPS), a genetic disorder characterized by severe craniofacial and limb abnormalities. We describe the structure of the murine Ripk4 (MmRipk4) kinase domain, in ATP- and inhibitor-bound forms. The crystallographic dimer of MmRipk4 is similar to those of RIPK2 and BRAF, and we show that the intact dimeric entity is required for MmRipk4 catalytic activity through a series of engineered mutations and cell-based assays. We also assess the impact of BPS mutations on protein structure and activity to elucidate the molecular origins of the disease.
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Affiliation(s)
- Christine S Huang
- Department of Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Nina Oberbeck
- Department of Physiological Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Yi-Chun Hsiao
- Department of Antibody Engineering, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Peter Liu
- Department of Microchemistry, Proteomics, and Lipidomics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Adam R Johnson
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Vishva M Dixit
- Department of Physiological Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Sarah G Hymowitz
- Department of Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
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8
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Abstract
In this issue of Structure, Castañeda et al. (2016b) use multi-disciplinary approaches including NMR techniques, small-angle neutron scattering, and docking to convincingly demonstrate that K27-linked diubiquitin is relatively rigid with unexpected similarity to the conformation of K48-linked diubiquitin bound to the UBA2 domain of hHR23a.
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Affiliation(s)
- Paola Di Lello
- Department of Protein Chemistry & Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Sarah G Hymowitz
- Department of Protein Chemistry & Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
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9
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Foster SA, Whalen DM, Özen A, Wongchenko MJ, Yin J, Yen I, Schaefer G, Mayfield JD, Chmielecki J, Stephens PJ, Albacker LA, Yan Y, Song K, Hatzivassiliou G, Eigenbrot C, Yu C, Shaw AS, Manning G, Skelton NJ, Hymowitz SG, Malek S. Activation Mechanism of Oncogenic Deletion Mutations in BRAF, EGFR, and HER2. Cancer Cell 2016; 29:477-493. [PMID: 26996308 DOI: 10.1016/j.ccell.2016.02.010] [Citation(s) in RCA: 151] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 01/11/2016] [Accepted: 02/13/2016] [Indexed: 12/11/2022]
Abstract
Activating mutations in protein kinases drive many cancers. While how recurring point mutations affect kinase activity has been described, the effect of in-frame deletions is not well understood. We show that oncogenic deletions within the β3-αC loop of HER2 and BRAF are analogous to the recurrent EGFR exon 19 deletions. We identify pancreatic carcinomas with BRAF deletions mutually exclusive with KRAS mutations. Crystal structures of BRAF deletions reveal the truncated loop restrains αC in an active "in" conformation, imparting resistance to inhibitors like vemurafenib that bind the αC "out" conformation. Characterization of loop length explains the prevalence of five amino acid deletions in BRAF, EGFR, and HER2 and highlights the importance of this region for kinase activity and inhibitor efficacy.
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Affiliation(s)
- Scott A Foster
- Department of Discovery Oncology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Daniel M Whalen
- Department of Protein Chemistry & Structural Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Ayşegül Özen
- Department of Discovery Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA; Department of Early Discovery Biochemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Matthew J Wongchenko
- Department of Oncology Biomarker Development, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - JianPing Yin
- Department of Protein Chemistry & Structural Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Ivana Yen
- Department of Discovery Oncology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Gabriele Schaefer
- Department of Translational Oncology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - John D Mayfield
- Foundation Medicine, 150 Second Street, Cambridge, MA 02141, USA
| | | | | | - Lee A Albacker
- Foundation Medicine, 150 Second Street, Cambridge, MA 02141, USA
| | - Yibing Yan
- Department of Oncology Biomarker Development, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Kyung Song
- Department of Translational Oncology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Georgia Hatzivassiliou
- Department of Cancer Immunology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Charles Eigenbrot
- Department of Protein Chemistry & Structural Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Christine Yu
- Department of Protein Chemistry & Structural Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Andrey S Shaw
- Department of Discovery Oncology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Gerard Manning
- Department of Bioinformatics & Computational Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Nicholas J Skelton
- Department of Discovery Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Sarah G Hymowitz
- Department of Protein Chemistry & Structural Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Shiva Malek
- Department of Discovery Oncology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
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10
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Abstract
In this issue of Structure, Liu and colleagues report the structure of the TNF superfamily member LIGHT bound to decoy receptor 3 (DcR3). Both LIGHT and DcR3 interact with multiple binding partners. The authors identify a conserved interaction important for affinity as well as additional interactions that can be targeted to introduce selectivity.
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Affiliation(s)
- Daniel M Whalen
- Department of Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Sarah G Hymowitz
- Department of Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
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11
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René O, Fauber B, Boenig GL, Burton B, Eidenschenk C, Everett C, Gobbi A, Hymowitz SG, Johnson AR, Kiefer JR, Liimatta M, Lockey P, Norman M, Ouyang W, Wallweber HA, Wong H. Minor Structural Change to Tertiary Sulfonamide RORc Ligands Led to Opposite Mechanisms of Action. ACS Med Chem Lett 2015; 6:276-81. [PMID: 25815138 PMCID: PMC4360161 DOI: 10.1021/ml500420y] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 12/04/2014] [Indexed: 12/21/2022] Open
Abstract
A minor structural change to tertiary sulfonamide RORc ligands led to distinct mechanisms of action. Co-crystal structures of two compounds revealed mechanistically consistent protein conformational changes. Optimized phenylsulfonamides were identified as RORc agonists while benzylsulfonamides exhibited potent inverse agonist activity. Compounds behaving as agonists in our biochemical assay also gave rise to an increased production of IL-17 in human PBMCs whereas inverse agonists led to significant suppression of IL-17 under the same assay conditions. The most potent inverse agonist compound showed >180-fold selectivity over the ROR isoforms as well as all other nuclear receptors that were profiled.
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Affiliation(s)
- Olivier René
- Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
| | - Benjamin
P. Fauber
- Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
| | | | - Brenda Burton
- Argenta, Early
Discovery, Charles River, 7-9 Spire
Green Centre, Flex Meadow, Harlow, Essex CM19 5TR, U.K.
| | - Céline Eidenschenk
- Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
| | - Christine Everett
- Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
| | - Alberto Gobbi
- Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
| | - Sarah G. Hymowitz
- Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
| | - Adam R. Johnson
- Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
| | - James R. Kiefer
- Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
| | - Marya Liimatta
- Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
| | - Peter Lockey
- Argenta, Early
Discovery, Charles River, 7-9 Spire
Green Centre, Flex Meadow, Harlow, Essex CM19 5TR, U.K.
| | - Maxine Norman
- Argenta, Early
Discovery, Charles River, 7-9 Spire
Green Centre, Flex Meadow, Harlow, Essex CM19 5TR, U.K.
| | - Wenjun Ouyang
- Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
| | - Heidi A. Wallweber
- Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
| | - Harvey Wong
- Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
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12
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Young WB, Barbosa J, Blomgren P, Bremer MC, Crawford JJ, Dambach D, Gallion S, Hymowitz SG, Kropf JE, Lee SH, Liu L, Lubach JW, Macaluso J, Maciejewski P, Maurer B, Mitchell SA, Ortwine DF, Di Paolo J, Reif K, Scheerens H, Schmitt A, Sowell CG, Wang X, Wong H, Xiong JM, Xu J, Zhao Z, Currie KS. Potent and selective Bruton's tyrosine kinase inhibitors: discovery of GDC-0834. Bioorg Med Chem Lett 2015; 25:1333-7. [PMID: 25701252 DOI: 10.1016/j.bmcl.2015.01.032] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2014] [Revised: 01/11/2015] [Accepted: 01/16/2015] [Indexed: 10/24/2022]
Abstract
SAR studies focused on improving the pharmacokinetic (PK) properties of the previously reported potent and selective Btk inhibitor CGI-1746 (1) resulted in the clinical candidate GDC-0834 (2), which retained the potency and selectivity of CGI-1746, but with much improved PK in preclinical animal models. Structure based design efforts drove this work as modifications to 1 were investigated at both the solvent exposed region as well as 'H3 binding pocket'. However, in vitro metabolic evaluation of 2 revealed a non CYP-mediated metabolic process that was more prevalent in human than preclinical species (mouse, rat, dog, cyno), leading to a high-level of uncertainly in predicting human pharmacokinetics. Due to its promising potency, selectivity, and preclinical efficacy, a single dose IND was filed and 2 was taken in to a single dose phase I trial in healthy volunteers to quickly evaluate the human pharmacokinetics. In human, 2 was found to be highly labile at the exo-cyclic amide bond that links the tetrahydrobenzothiophene moiety to the central aniline ring, resulting in insufficient parent drug exposure. This information informed the back-up program and discovery of improved inhibitors.
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Affiliation(s)
- Wendy B Young
- Genentech, 1 DNA Way, South San Francisco, CA 94080, United States
| | - James Barbosa
- Gilead Sciences, 36 East Industrial Rd., Branford, CT 06405, United States (formerly CGI Pharmaceuticals)
| | - Peter Blomgren
- Gilead Sciences, 36 East Industrial Rd., Branford, CT 06405, United States (formerly CGI Pharmaceuticals)
| | - Meire C Bremer
- Genentech, 1 DNA Way, South San Francisco, CA 94080, United States
| | - James J Crawford
- Genentech, 1 DNA Way, South San Francisco, CA 94080, United States
| | - Donna Dambach
- Genentech, 1 DNA Way, South San Francisco, CA 94080, United States
| | - Steve Gallion
- St. Andrews Circle, Wallingford, CT 06492, United States
| | - Sarah G Hymowitz
- Genentech, 1 DNA Way, South San Francisco, CA 94080, United States
| | - Jeffrey E Kropf
- Gilead Sciences, 36 East Industrial Rd., Branford, CT 06405, United States (formerly CGI Pharmaceuticals)
| | - Seung H Lee
- Gilead Sciences, 36 East Industrial Rd., Branford, CT 06405, United States (formerly CGI Pharmaceuticals)
| | - Lichuan Liu
- Genentech, 1 DNA Way, South San Francisco, CA 94080, United States
| | - Joseph W Lubach
- Genentech, 1 DNA Way, South San Francisco, CA 94080, United States
| | - Jen Macaluso
- Gilead Sciences, 36 East Industrial Rd., Branford, CT 06405, United States (formerly CGI Pharmaceuticals)
| | - Pat Maciejewski
- Gilead Sciences, 36 East Industrial Rd., Branford, CT 06405, United States (formerly CGI Pharmaceuticals)
| | - Brigitte Maurer
- Genentech, 1 DNA Way, South San Francisco, CA 94080, United States
| | - Scott A Mitchell
- Gilead Sciences, 36 East Industrial Rd., Branford, CT 06405, United States (formerly CGI Pharmaceuticals)
| | - Daniel F Ortwine
- Genentech, 1 DNA Way, South San Francisco, CA 94080, United States
| | - Julie Di Paolo
- Gilead Sciences, 36 East Industrial Rd., Branford, CT 06405, United States (formerly CGI Pharmaceuticals)
| | - Karin Reif
- Genentech, 1 DNA Way, South San Francisco, CA 94080, United States
| | - Heleen Scheerens
- Genentech, 1 DNA Way, South San Francisco, CA 94080, United States
| | - Aaron Schmitt
- Gilead Sciences, 36 East Industrial Rd., Branford, CT 06405, United States (formerly CGI Pharmaceuticals)
| | - C Gregory Sowell
- Genentech, 1 DNA Way, South San Francisco, CA 94080, United States
| | - Xiaojing Wang
- Genentech, 1 DNA Way, South San Francisco, CA 94080, United States
| | - Harvey Wong
- Genentech, 1 DNA Way, South San Francisco, CA 94080, United States
| | - Jin-Ming Xiong
- Gilead Sciences, 36 East Industrial Rd., Branford, CT 06405, United States (formerly CGI Pharmaceuticals)
| | - Jianjun Xu
- Gilead Sciences, 36 East Industrial Rd., Branford, CT 06405, United States (formerly CGI Pharmaceuticals)
| | - Zhongdong Zhao
- Gilead Sciences, 36 East Industrial Rd., Branford, CT 06405, United States (formerly CGI Pharmaceuticals)
| | - Kevin S Currie
- Gilead Sciences, 36 East Industrial Rd., Branford, CT 06405, United States (formerly CGI Pharmaceuticals)
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13
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Tao ZF, Hasvold L, Wang L, Wang X, Petros AM, Park CH, Boghaert ER, Catron ND, Chen J, Colman PM, Czabotar PE, Deshayes K, Fairbrother WJ, Flygare JA, Hymowitz SG, Jin S, Judge RA, Koehler MFT, Kovar PJ, Lessene G, Mitten MJ, Ndubaku CO, Nimmer P, Purkey HE, Oleksijew A, Phillips DC, Sleebs BE, Smith BJ, Smith ML, Tahir SK, Watson KG, Xiao Y, Xue J, Zhang H, Zobel K, Rosenberg SH, Tse C, Leverson JD, Elmore SW, Souers AJ. Discovery of a Potent and Selective BCL-XL Inhibitor with in Vivo Activity. ACS Med Chem Lett 2014; 5:1088-93. [PMID: 25313317 DOI: 10.1021/ml5001867] [Citation(s) in RCA: 215] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 08/26/2014] [Indexed: 11/30/2022] Open
Abstract
A-1155463, a highly potent and selective BCL-XL inhibitor, was discovered through nuclear magnetic resonance (NMR) fragment screening and structure-based design. This compound is substantially more potent against BCL-XL-dependent cell lines relative to our recently reported inhibitor, WEHI-539, while possessing none of its inherent pharmaceutical liabilities. A-1155463 caused a mechanism-based and reversible thrombocytopenia in mice and inhibited H146 small cell lung cancer xenograft tumor growth in vivo following multiple doses. A-1155463 thus represents an excellent tool molecule for studying BCL-XL biology as well as a productive lead structure for further optimization.
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Affiliation(s)
- Zhi-Fu Tao
- AbbVie, Inc., 1 North Waukegan
Road, North Chicago, Illinois 60064 United States
| | - Lisa Hasvold
- AbbVie, Inc., 1 North Waukegan
Road, North Chicago, Illinois 60064 United States
| | - Le Wang
- AbbVie, Inc., 1 North Waukegan
Road, North Chicago, Illinois 60064 United States
| | - Xilu Wang
- AbbVie, Inc., 1 North Waukegan
Road, North Chicago, Illinois 60064 United States
| | - Andrew M. Petros
- AbbVie, Inc., 1 North Waukegan
Road, North Chicago, Illinois 60064 United States
| | - Chang H. Park
- AbbVie, Inc., 1 North Waukegan
Road, North Chicago, Illinois 60064 United States
| | - Erwin R. Boghaert
- AbbVie, Inc., 1 North Waukegan
Road, North Chicago, Illinois 60064 United States
| | - Nathaniel D. Catron
- AbbVie, Inc., 1 North Waukegan
Road, North Chicago, Illinois 60064 United States
| | - Jun Chen
- AbbVie, Inc., 1 North Waukegan
Road, North Chicago, Illinois 60064 United States
| | - Peter M. Colman
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
- Department
of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Peter E. Czabotar
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
- Department
of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Kurt Deshayes
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080 United States
| | | | - John A. Flygare
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080 United States
| | - Sarah G. Hymowitz
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080 United States
| | - Sha Jin
- AbbVie, Inc., 1 North Waukegan
Road, North Chicago, Illinois 60064 United States
| | - Russell A. Judge
- AbbVie, Inc., 1 North Waukegan
Road, North Chicago, Illinois 60064 United States
| | | | - Peter J. Kovar
- AbbVie, Inc., 1 North Waukegan
Road, North Chicago, Illinois 60064 United States
| | - Guillaume Lessene
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
- Department
of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
- Department
of Pharmacology and Therapeutics, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Michael J. Mitten
- AbbVie, Inc., 1 North Waukegan
Road, North Chicago, Illinois 60064 United States
| | - Chudi O. Ndubaku
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080 United States
| | - Paul Nimmer
- AbbVie, Inc., 1 North Waukegan
Road, North Chicago, Illinois 60064 United States
| | - Hans E. Purkey
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080 United States
| | - Anatol Oleksijew
- AbbVie, Inc., 1 North Waukegan
Road, North Chicago, Illinois 60064 United States
| | - Darren C. Phillips
- AbbVie, Inc., 1 North Waukegan
Road, North Chicago, Illinois 60064 United States
| | - Brad E. Sleebs
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
- Department
of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Brian J. Smith
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
- Department
of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Morey L. Smith
- AbbVie, Inc., 1 North Waukegan
Road, North Chicago, Illinois 60064 United States
| | - Stephen K. Tahir
- AbbVie, Inc., 1 North Waukegan
Road, North Chicago, Illinois 60064 United States
| | - Keith G. Watson
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
- Department
of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Yu Xiao
- AbbVie, Inc., 1 North Waukegan
Road, North Chicago, Illinois 60064 United States
| | - John Xue
- AbbVie, Inc., 1 North Waukegan
Road, North Chicago, Illinois 60064 United States
| | - Haichao Zhang
- AbbVie, Inc., 1 North Waukegan
Road, North Chicago, Illinois 60064 United States
| | - Kerry Zobel
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080 United States
| | - Saul H. Rosenberg
- AbbVie, Inc., 1 North Waukegan
Road, North Chicago, Illinois 60064 United States
| | - Chris Tse
- AbbVie, Inc., 1 North Waukegan
Road, North Chicago, Illinois 60064 United States
| | - Joel D. Leverson
- AbbVie, Inc., 1 North Waukegan
Road, North Chicago, Illinois 60064 United States
| | - Steven W. Elmore
- AbbVie, Inc., 1 North Waukegan
Road, North Chicago, Illinois 60064 United States
| | - Andrew J. Souers
- AbbVie, Inc., 1 North Waukegan
Road, North Chicago, Illinois 60064 United States
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14
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Haling JR, Sudhamsu J, Yen I, Sideris S, Sandoval W, Phung W, Bravo BJ, Giannetti AM, Peck A, Masselot A, Morales T, Smith D, Brandhuber BJ, Hymowitz SG, Malek S. Structure of the BRAF-MEK complex reveals a kinase activity independent role for BRAF in MAPK signaling. Cancer Cell 2014; 26:402-413. [PMID: 25155755 DOI: 10.1016/j.ccr.2014.07.007] [Citation(s) in RCA: 141] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 04/15/2014] [Accepted: 07/11/2014] [Indexed: 01/07/2023]
Abstract
Numerous oncogenic mutations occur within the BRAF kinase domain (BRAF(KD)). Here we show that stable BRAF-MEK1 complexes are enriched in BRAF(WT) and KRAS mutant (MT) cells but not in BRAF(MT) cells. The crystal structure of the BRAF(KD) in a complex with MEK1 reveals a face-to-face dimer sensitive to MEK1 phosphorylation but insensitive to BRAF dimerization. Structure-guided studies reveal that oncogenic BRAF mutations function by bypassing the requirement for BRAF dimerization for activity or weakening the interaction with MEK1. Finally, we show that conformation-specific BRAF inhibitors can sequester a dormant BRAF-MEK1 complex resulting in pathway inhibition. Taken together, these findings reveal a regulatory role for BRAF in the MAPK pathway independent of its kinase activity but dependent on interaction with MEK.
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Affiliation(s)
- Jacob R Haling
- Department of Biochemical and Cellular Pharmacology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jawahar Sudhamsu
- Department of Structural Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Ivana Yen
- Department of Biochemical and Cellular Pharmacology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Steve Sideris
- Department of Biochemical and Cellular Pharmacology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Wendy Sandoval
- Department of Protein Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Wilson Phung
- Department of Protein Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Brandon J Bravo
- Department of Biochemical and Cellular Pharmacology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Anthony M Giannetti
- Department of Biochemical and Cellular Pharmacology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Ariana Peck
- Department of Biochemical and Cellular Pharmacology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Alexandre Masselot
- Department of Bioinformatics, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Tony Morales
- Department of Structural Biology, Array BioPharma, Inc., 3200 Walnut Street, Boulder, CO 80301, USA
| | - Darin Smith
- Department of Structural Biology, Array BioPharma, Inc., 3200 Walnut Street, Boulder, CO 80301, USA
| | - Barbara J Brandhuber
- Department of Structural Biology, Array BioPharma, Inc., 3200 Walnut Street, Boulder, CO 80301, USA
| | - Sarah G Hymowitz
- Department of Structural Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
| | - Shiva Malek
- Department of Biochemical and Cellular Pharmacology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
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15
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Fauber BP, René O, de Leon Boenig G, Burton B, Deng Y, Eidenschenk C, Everett C, Gobbi A, Hymowitz SG, Johnson AR, La H, Liimatta M, Lockey P, Norman M, Ouyang W, Wang W, Wong H. Reduction in lipophilicity improved the solubility, plasma–protein binding, and permeability of tertiary sulfonamide RORc inverse agonists. Bioorg Med Chem Lett 2014; 24:3891-7. [DOI: 10.1016/j.bmcl.2014.06.048] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 06/16/2014] [Accepted: 06/18/2014] [Indexed: 12/18/2022]
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16
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Huang X, McGann JC, Liu BY, Hannoush RN, Lill JR, Pham V, Newton K, Kakunda M, Liu J, Yu C, Hymowitz SG, Hongo JA, Wynshaw-Boris A, Polakis P, Harland RM, Dixit VM. Phosphorylation of Dishevelled by protein kinase RIPK4 regulates Wnt signaling. Science 2013; 339:1441-5. [PMID: 23371553 DOI: 10.1126/science.1232253] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Receptor-interacting protein kinase 4 (RIPK4) is required for epidermal differentiation and is mutated in Bartsocas-Papas syndrome. RIPK4 binds to protein kinase C, but its signaling mechanisms are largely unknown. Ectopic RIPK4, but not catalytically inactive or Bartsocas-Papas RIPK4 mutants, induced accumulation of cytosolic β-catenin and a transcriptional program similar to that caused by Wnt3a. In Xenopus embryos, Ripk4 synergized with coexpressed Xwnt8, whereas Ripk4 morpholinos or catalytic inactive Ripk4 antagonized Wnt signaling. RIPK4 interacted constitutively with the adaptor protein DVL2 and, after Wnt3a stimulation, with the co-receptor LRP6. Phosphorylation of DVL2 by RIPK4 favored canonical Wnt signaling. Wnt-dependent growth of xenografted human tumor cells was suppressed by RIPK4 knockdown, suggesting that RIPK4 overexpression may contribute to the growth of certain tumor types.
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Affiliation(s)
- XiaoDong Huang
- Department of Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
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17
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Souers AJ, Leverson JD, Boghaert ER, Ackler SL, Catron ND, Chen J, Dayton BD, Ding H, Enschede SH, Fairbrother WJ, Huang DCS, Hymowitz SG, Jin S, Khaw SL, Kovar PJ, Lam LT, Lee J, Maecker HL, Marsh KC, Mason KD, Mitten MJ, Nimmer PM, Oleksijew A, Park CH, Park CM, Phillips DC, Roberts AW, Sampath D, Seymour JF, Smith ML, Sullivan GM, Tahir SK, Tse C, Wendt MD, Xiao Y, Xue JC, Zhang H, Humerickhouse RA, Rosenberg SH, Elmore SW. ABT-199, a potent and selective BCL-2 inhibitor, achieves antitumor activity while sparing platelets. Nat Med 2013; 19:202-8. [PMID: 23291630 DOI: 10.1038/nm.3048] [Citation(s) in RCA: 2135] [Impact Index Per Article: 194.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 11/29/2012] [Indexed: 01/28/2023]
Abstract
Proteins in the B cell CLL/lymphoma 2 (BCL-2) family are key regulators of the apoptotic process. This family comprises proapoptotic and prosurvival proteins, and shifting the balance toward the latter is an established mechanism whereby cancer cells evade apoptosis. The therapeutic potential of directly inhibiting prosurvival proteins was unveiled with the development of navitoclax, a selective inhibitor of both BCL-2 and BCL-2-like 1 (BCL-X(L)), which has shown clinical efficacy in some BCL-2-dependent hematological cancers. However, concomitant on-target thrombocytopenia caused by BCL-X(L) inhibition limits the efficacy achievable with this agent. Here we report the re-engineering of navitoclax to create a highly potent, orally bioavailable and BCL-2-selective inhibitor, ABT-199. This compound inhibits the growth of BCL-2-dependent tumors in vivo and spares human platelets. A single dose of ABT-199 in three patients with refractory chronic lymphocytic leukemia resulted in tumor lysis within 24 h. These data indicate that selective pharmacological inhibition of BCL-2 shows promise for the treatment of BCL-2-dependent hematological cancers.
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18
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de Leon-Boenig G, Bowman KK, Feng JA, Crawford T, Everett C, Franke Y, Oh A, Stanley M, Staben ST, Starovasnik MA, Wallweber HJA, Wu J, Wu LC, Johnson AR, Hymowitz SG. The crystal structure of the catalytic domain of the NF-κB inducing kinase reveals a narrow but flexible active site. Structure 2012; 20:1704-14. [PMID: 22921830 DOI: 10.1016/j.str.2012.07.013] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Revised: 07/20/2012] [Accepted: 07/23/2012] [Indexed: 11/18/2022]
Abstract
The NF-κB inducing kinase (NIK) regulates the non-canonical NF-κB pathway downstream of important clinical targets including BAFF, RANKL, and LTβ. Despite numerous genetic studies associating dysregulation of this pathway with autoimmune diseases and hematological cancers, detailed molecular characterization of this central signaling node has been lacking. We undertook a systematic cloning and expression effort to generate soluble, well-behaved proteins encompassing the kinase domains of human and murine NIK. Structures of the apo NIK kinase domain from both species reveal an active-like conformation in the absence of phosphorylation. ATP consumption and peptide phosphorylation assays confirm that phosphorylation of NIK does not increase enzymatic activity. Structures of murine NIK bound to inhibitors possessing two different chemotypes reveal conformational flexibility in the gatekeeper residue controlling access to a hydrophobic pocket. Finally, a single amino acid difference affects the ability of some inhibitors to bind murine and human NIK with the same affinity.
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Affiliation(s)
- Gladys de Leon-Boenig
- Department of Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
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19
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Flygare JA, Beresini M, Budha N, Chan H, Chan IT, Cheeti S, Cohen F, Deshayes K, Doerner K, Eckhardt SG, Elliott LO, Feng B, Franklin MC, Reisner SF, Gazzard L, Halladay J, Hymowitz SG, La H, LoRusso P, Maurer B, Murray L, Plise E, Quan C, Stephan JP, Young SG, Tom J, Tsui V, Um J, Varfolomeev E, Vucic D, Wagner AJ, Wallweber HJA, Wang L, Ware J, Wen Z, Wong H, Wong JM, Wong M, Wong S, Yu R, Zobel K, Fairbrother WJ. Discovery of a potent small-molecule antagonist of inhibitor of apoptosis (IAP) proteins and clinical candidate for the treatment of cancer (GDC-0152). J Med Chem 2012; 55:4101-13. [PMID: 22413863 DOI: 10.1021/jm300060k] [Citation(s) in RCA: 175] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A series of compounds were designed and synthesized as antagonists of cIAP1/2, ML-IAP, and XIAP based on the N-terminus, AVPI, of mature Smac. Compound 1 (GDC-0152) has the best profile of these compounds; it binds to the XIAP BIR3 domain, the BIR domain of ML-IAP, and the BIR3 domains of cIAP1 and cIAP2 with K(i) values of 28, 14, 17, and 43 nM, respectively. These compounds promote degradation of cIAP1, induce activation of caspase-3/7, and lead to decreased viability of breast cancer cells without affecting normal mammary epithelial cells. Compound 1 inhibits tumor growth when dosed orally in the MDA-MB-231 breast cancer xenograft model. Compound 1 was advanced to human clinical trials, and it exhibited linear pharmacokinetics over the dose range (0.049 to 1.48 mg/kg) tested. Mean plasma clearance in humans was 9 ± 3 mL/min/kg, and the volume of distribution was 0.6 ± 0.2 L/kg.
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Affiliation(s)
- John A Flygare
- Department of Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, USA.
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20
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Matsumoto ML, Dong KC, Yu C, Phu L, Gao X, Hannoush RN, Hymowitz SG, Kirkpatrick DS, Dixit VM, Kelley RF. Engineering and structural characterization of a linear polyubiquitin-specific antibody. J Mol Biol 2011; 418:134-44. [PMID: 22227388 DOI: 10.1016/j.jmb.2011.12.053] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Revised: 12/20/2011] [Accepted: 12/22/2011] [Indexed: 10/14/2022]
Abstract
Polyubiquitination is an essential posttranslational modification that plays critical roles in cellular signaling. PolyUb (polyubiquitin) chains are formed by linking the carboxyl-terminus of one Ub (ubiquitin) subunit to either a lysine residue or the amino-terminus of an adjacent Ub. Linkage through the amino-terminus results in linear polyubiquitination that has recently been demonstrated to be a key step in nuclear factor κB activation; however, tools to study linear chains have been lacking. We therefore engineered a linear-linkage-specific antibody that is functional in Western blot, immunoprecipitation, and immunofluorescence applications. A crystal structure of the linear-linkage-specific antibody Fab fragment in complex with linear diubiquitin provides molecular insight into the nature of linear chain specificity. We use the antibody to demonstrate that linear polyUb is up-regulated upon tumor necrosis factor α stimulation of cells, consistent with a critical role in nuclear factor κB signaling. This antibody provides an essential tool for further investigation of the function of linear chains.
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Affiliation(s)
- Marissa L Matsumoto
- Department of Antibody Engineering, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
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21
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Abstract
The IL-10 family of cytokines consists of nine members: IL-10, IL-19, IL-20, IL-22, IL-24, IL-26, and the more distantly related IL-28A, IL-28B, and IL-29. Evolutionarily, IL-10 family cytokines emerged before the adaptive immune response. These cytokines elicit diverse host defense mechanisms, especially from epithelial cells, during various infections. IL-10 family cytokines are essential for maintaining the integrity and homeostasis of tissue epithelial layers. Members of this family can promote innate immune responses from tissue epithelia to limit the damage caused by viral and bacterial infections. These cytokines can also facilitate the tissue-healing process in injuries caused by infection or inflammation. Finally, IL-10 itself can repress proinflammatory responses and limit unnecessary tissue disruptions caused by inflammation. Thus, IL-10 family cytokines have indispensable functions in many infectious and inflammatory diseases.
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Affiliation(s)
- Wenjun Ouyang
- Department of Immunology, Genentech, Inc., South San Francisco, California 94080, USA.
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22
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Bosanac I, Phu L, Pan B, Zilberleyb I, Maurer B, Dixit VM, Hymowitz SG, Kirkpatrick DS. Modulation of K11-linkage formation by variable loop residues within UbcH5A. J Mol Biol 2011; 408:420-31. [PMID: 21396940 DOI: 10.1016/j.jmb.2011.03.011] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2010] [Revised: 03/02/2011] [Accepted: 03/03/2011] [Indexed: 01/04/2023]
Abstract
Ubiquitination refers to the covalent addition of ubiquitin (Ub) to substrate proteins or other Ub molecules via the sequential action of three enzymes (E1, E2, and E3). Recent advances in mass spectrometry proteomics have made it possible to identify and quantify Ub linkages in biochemical and cellular systems. We used these tools to probe the mechanisms controlling linkage specificity for UbcH5A. UbcH5A is a promiscuous E2 enzyme with an innate preference for forming polyubiquitin chains through lysine 11 (K11), lysine 48 (K48), and lysine 63 (K63) of Ub. We present the crystal structure of a noncovalent complex between Ub and UbcH5A. This structure reveals an interaction between the Ub surface flanking K11 and residues adjacent to the E2 catalytic cysteine and suggests a possible role for this surface in formation of K11 linkages. Structure-guided mutagenesis, in vitro ubiquitination and quantitative mass spectrometry have been used to characterize the ability of residues in the vicinity of the E2 active site to direct synthesis of K11- and K63-linked polyubiquitin. Mutation of critical residues in the interface modulated the linkage specificity of UbcH5A, resulting in generation of more K63-linked chains at the expense of K11-linkage synthesis. This study provides direct evidence that the linkage specificity of E2 enzymes may be altered through active-site mutagenesis.
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Affiliation(s)
- Ivan Bosanac
- Department of Structural Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
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23
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Beachy PA, Hymowitz SG, Lazarus RA, Leahy DJ, Siebold C. Interactions between Hedgehog proteins and their binding partners come into view. Genes Dev 2010; 24:2001-12. [PMID: 20844013 DOI: 10.1101/gad.1951710] [Citation(s) in RCA: 153] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Hedgehog (Hh) proteins are secreted signaling molecules that mediate essential tissue-patterning events during embryonic development and function in tissue homeostasis and regeneration throughout life. Hh signaling is regulated by multiple mechanisms, including covalent lipid modification of the Hh protein and interactions with multiple protein and glycan partners. Unraveling the nature and effects of these interactions has proven challenging, but recent structural and biophysical studies of Hh proteins and active fragments of heparin, Ihog, Cdo, Boc, Hedgehog-interacting protein (Hhip), Patched (Ptc), and the monoclonal antibody 5E1 have added a new level of molecular detail to our understanding of how Hh signal response and distribution are regulated within tissues. We review these results and discuss their implications for understanding Hh signaling in normal and disease states.
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Affiliation(s)
- Philip A Beachy
- Department of Developmental Biology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
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24
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25
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Bosanac I, Wertz IE, Pan B, Yu C, Kusam S, Lam C, Phu L, Phung Q, Maurer B, Arnott D, Kirkpatrick DS, Dixit VM, Hymowitz SG. Ubiquitin Binding to A20 ZnF4 Is Required for Modulation of NF-κB Signaling. Mol Cell 2010; 40:548-57. [DOI: 10.1016/j.molcel.2010.10.009] [Citation(s) in RCA: 133] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Revised: 07/07/2010] [Accepted: 08/27/2010] [Indexed: 01/27/2023]
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26
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Matsumoto ML, Wickliffe KE, Dong KC, Yu C, Bosanac I, Bustos D, Phu L, Kirkpatrick DS, Hymowitz SG, Rape M, Kelley RF, Dixit VM. K11-linked polyubiquitination in cell cycle control revealed by a K11 linkage-specific antibody. Mol Cell 2010; 39:477-84. [PMID: 20655260 DOI: 10.1016/j.molcel.2010.07.001] [Citation(s) in RCA: 306] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2010] [Revised: 06/02/2010] [Accepted: 06/29/2010] [Indexed: 01/12/2023]
Abstract
Polyubiquitination is a posttranslational modification where ubiquitin chains containing isopeptide bonds linking one of seven ubiquitin lysines with the C terminus of an adjoining ubiquitin are covalently attached to proteins. While functions of K48- and K63-linked polyubiquitin are understood, the role(s) of noncanonical K11-linked chains is less clear. A crystal structure of K11-linked diubiquitin demonstrates a distinct conformation from K48- or K63-linked diubiquitin. We engineered a K11 linkage-specific antibody and use it to demonstrate that K11 chains are highly upregulated in mitotic human cells precisely when substrates of the ubiquitin ligase anaphase-promoting complex (APC/C) are degraded. These chains increased with proteasomal inhibition, suggesting they act as degradation signals in vivo. Inhibition of the APC/C strongly impeded the formation of K11-linked chains, suggesting that a single ubiquitin ligase is the major source of mitotic K11-linked chains. Our results underscore the importance of K11-linked ubiquitin chains as critical regulators of mitotic protein degradation.
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Affiliation(s)
- Marissa L Matsumoto
- Department of Antibody Engineering, Genentech, Inc., South San Francisco, CA 94080, USA
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27
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Wu Y, Cain-Hom C, Choy L, Hagenbeek TJ, de Leon GP, Chen Y, Finkle D, Venook R, Wu X, Ridgway J, Schahin-Reed D, Dow GJ, Shelton A, Stawicki S, Watts RJ, Zhang J, Choy R, Howard P, Kadyk L, Yan M, Zha J, Callahan CA, Hymowitz SG, Siebel CW. Therapeutic antibody targeting of individual Notch receptors. Nature 2010; 464:1052-7. [PMID: 20393564 DOI: 10.1038/nature08878] [Citation(s) in RCA: 549] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Accepted: 01/28/2010] [Indexed: 12/11/2022]
Abstract
The four receptors of the Notch family are widely expressed transmembrane proteins that function as key conduits through which mammalian cells communicate to regulate cell fate and growth. Ligand binding triggers a conformational change in the receptor negative regulatory region (NRR) that enables ADAM protease cleavage at a juxtamembrane site that otherwise lies buried within the quiescent NRR. Subsequent intramembrane proteolysis catalysed by the gamma-secretase complex liberates the intracellular domain (ICD) to initiate the downstream Notch transcriptional program. Aberrant signalling through each receptor has been linked to numerous diseases, particularly cancer, making the Notch pathway a compelling target for new drugs. Although gamma-secretase inhibitors (GSIs) have progressed into the clinic, GSIs fail to distinguish individual Notch receptors, inhibit other signalling pathways and cause intestinal toxicity, attributed to dual inhibition of Notch1 and 2 (ref. 11). To elucidate the discrete functions of Notch1 and Notch2 and develop clinically relevant inhibitors that reduce intestinal toxicity, we used phage display technology to generate highly specialized antibodies that specifically antagonize each receptor paralogue and yet cross-react with the human and mouse sequences, enabling the discrimination of Notch1 versus Notch2 function in human patients and rodent models. Our co-crystal structure shows that the inhibitory mechanism relies on stabilizing NRR quiescence. Selective blocking of Notch1 inhibits tumour growth in pre-clinical models through two mechanisms: inhibition of cancer cell growth and deregulation of angiogenesis. Whereas inhibition of Notch1 plus Notch2 causes severe intestinal toxicity, inhibition of either receptor alone reduces or avoids this effect, demonstrating a clear advantage over pan-Notch inhibitors. Our studies emphasize the value of paralogue-specific antagonists in dissecting the contributions of distinct Notch receptors to differentiation and disease and reveal the therapeutic promise in targeting Notch1 and Notch2 independently.
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Affiliation(s)
- Yan Wu
- Department of Antibody Engineering, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, USA
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28
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Maun HR, Wen X, Lingel A, de Sauvage FJ, Lazarus RA, Scales SJ, Hymowitz SG. Hedgehog pathway antagonist 5E1 binds hedgehog at the pseudo-active site. J Biol Chem 2010; 285:26570-80. [PMID: 20504762 DOI: 10.1074/jbc.m110.112284] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Proper hedgehog (Hh) signaling is crucial for embryogenesis and tissue regeneration. Dysregulation of this pathway is associated with several types of cancer. The monoclonal antibody 5E1 is a Hh pathway inhibitor that has been extensively used to elucidate vertebrate Hh biology due to its ability to block binding of the three mammalian Hh homologs to the receptor, Patched1 (Ptc1). Here, we engineered a murine:human chimeric 5E1 (ch5E1) with similar Hh-binding properties to the original murine antibody. Using biochemical, biophysical, and x-ray crystallographic studies, we show that, like the regulatory receptors Cdon and Hedgehog-interacting protein (Hhip), ch5E1 binding to Sonic hedgehog (Shh) is enhanced by calcium ions. In the presence of calcium and zinc ions, the ch5E1 binding affinity increases 10-20-fold to tighter than 1 nm primarily because of a decrease in the dissociation rate. The co-crystal structure of Shh bound to the Fab fragment of ch5E1 reveals that 5E1 binds at the pseudo-active site groove of Shh with an epitope that largely overlaps with the binding site of its natural receptor antagonist Hhip. Unlike Hhip, the side chains of 5E1 do not directly coordinate the Zn(2+) cation in the pseudo-active site, despite the modest zinc-dependent increase in 5E1 affinity for Shh. Furthermore, to our knowledge, the ch5E1 Fab-Shh complex represents the first structure of an inhibitor antibody bound to a metalloprotease fold.
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Affiliation(s)
- Henry R Maun
- Department of Protein Engineering, Genentech, Inc., South San Francisco, California 94080, USA
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29
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Abstract
Clinicians have suspected for hundreds of years that chronic activation of the immune system contributes to the development of cancer. However, the molecular mechanisms that mediate this precarious interplay are only now being elucidated. Recent reports have identified A20 as a crucial tumour suppressor in various lymphomas. A20 is a ubiquitin-editing enzyme that attenuates the activity of proximal signalling complexes at pro-inflammatory receptors. In this Review we summarize the evidence linking chronic inflammation with tumorigenesis and consider how A20 modulates inflammatory signalling cascades, thereby providing a mechanism to explain how deregulation of ubiquitylation can promote tumorigenesis.
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Affiliation(s)
- Sarah G Hymowitz
- Department of Structural Biology, Genentech, Inc.1 DNA Way, M/S 40, South San Francisco, CA 94080, USA
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30
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Ndubaku C, Varfolomeev E, Wang L, Zobel K, Lau K, Elliott LO, Maurer B, Fedorova AV, Dynek JN, Koehler M, Hymowitz SG, Tsui V, Deshayes K, Fairbrother WJ, Flygare JA, Vucic D. Antagonism of c-IAP and XIAP proteins is required for efficient induction of cell death by small-molecule IAP antagonists. ACS Chem Biol 2009; 4:557-66. [PMID: 19492850 DOI: 10.1021/cb900083m] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The inhibitor of apoptosis (IAP) proteins are critical regulators of cancer cell survival, which makes them attractive targets for therapeutic intervention in cancers. Herein, we describe the structure-based design of IAP antagonists with high affinities and selectivity (>2000-fold) for c-IAP1 over XIAP and their functional characterization as activators of apoptosis in tumor cells. Although capable of inducing cell death and preventing clonogenic survival, c-IAP-selective antagonists are significantly less potent in promoting apoptosis when compared to pan-selective compounds. However, both pan-IAP- and c-IAP-selective antagonists stimulate c-IAP1 and c-IAP2 degradation and activation of NF-kappaB pathways with comparable potencies. Therefore, although compounds that specifically target c-IAP1 and c-IAP2 are capable of inducing apoptosis, antagonism of the c-IAP proteins and XIAP is required for efficient induction of cancer cell death by IAP antagonists.
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Affiliation(s)
- Chudi Ndubaku
- Departments of Medicinal Chemistry and Protein Engineering, Genentech, Inc., South San Francisco, California 94080
| | - Eugene Varfolomeev
- Departments of Medicinal Chemistry and Protein Engineering, Genentech, Inc., South San Francisco, California 94080
| | - Lan Wang
- Departments of Medicinal Chemistry and Protein Engineering, Genentech, Inc., South San Francisco, California 94080
| | - Kerry Zobel
- Departments of Medicinal Chemistry and Protein Engineering, Genentech, Inc., South San Francisco, California 94080
| | - Kevin Lau
- Departments of Medicinal Chemistry and Protein Engineering, Genentech, Inc., South San Francisco, California 94080
| | - Linda O. Elliott
- Departments of Medicinal Chemistry and Protein Engineering, Genentech, Inc., South San Francisco, California 94080
| | - Brigitte Maurer
- Departments of Medicinal Chemistry and Protein Engineering, Genentech, Inc., South San Francisco, California 94080
| | - Anna V. Fedorova
- Departments of Medicinal Chemistry and Protein Engineering, Genentech, Inc., South San Francisco, California 94080
| | - Jasmin N. Dynek
- Departments of Medicinal Chemistry and Protein Engineering, Genentech, Inc., South San Francisco, California 94080
| | - Michael Koehler
- Departments of Medicinal Chemistry and Protein Engineering, Genentech, Inc., South San Francisco, California 94080
| | - Sarah G. Hymowitz
- Departments of Medicinal Chemistry and Protein Engineering, Genentech, Inc., South San Francisco, California 94080
| | - Vickie Tsui
- Departments of Medicinal Chemistry and Protein Engineering, Genentech, Inc., South San Francisco, California 94080
| | - Kurt Deshayes
- Departments of Medicinal Chemistry and Protein Engineering, Genentech, Inc., South San Francisco, California 94080
| | - Wayne J. Fairbrother
- Departments of Medicinal Chemistry and Protein Engineering, Genentech, Inc., South San Francisco, California 94080
| | - John A. Flygare
- Departments of Medicinal Chemistry and Protein Engineering, Genentech, Inc., South San Francisco, California 94080
| | - Domagoj Vucic
- Departments of Medicinal Chemistry and Protein Engineering, Genentech, Inc., South San Francisco, California 94080
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31
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Bosanac I, Maun HR, Scales SJ, Wen X, Lingel A, Bazan JF, de Sauvage FJ, Hymowitz SG, Lazarus RA. The structure of SHH in complex with HHIP reveals a recognition role for the Shh pseudo active site in signaling. Nat Struct Mol Biol 2009; 16:691-7. [PMID: 19561609 DOI: 10.1038/nsmb.1632] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2009] [Accepted: 06/04/2009] [Indexed: 12/26/2022]
Abstract
Hedgehog (Hh) signaling is crucial for many aspects of embryonic development, whereas dysregulation of this pathway is associated with several types of cancer. Hedgehog-interacting protein (Hhip) is a surface receptor antagonist that is equipotent against all three mammalian Hh homologs. The crystal structures of human HHIP alone and bound to Sonic hedgehog (SHH) now reveal that HHIP is comprised of two EGF domains and a six-bladed beta-propeller domain. In the complex structure, a critical loop from HHIP binds the pseudo active site groove of SHH and directly coordinates its Zn2+ cation. Notably, sequence comparisons of this SHH binding loop with the Hh receptor Patched (Ptc1) ectodomains and HHIP- and PTC1-peptide binding studies suggest a 'patch for Patched' at the Shh pseudo active site; thus, we propose a role for Hhip as a structural decoy receptor for vertebrate Hh.
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Affiliation(s)
- Ivan Bosanac
- Department of Structural Biology, Genentech, Inc., South San Francisco, California, USA
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32
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Newton K, Matsumoto ML, Wertz IE, Kirkpatrick DS, Lill JR, Tan J, Dugger D, Gordon N, Sidhu SS, Fellouse FA, Komuves L, French DM, Ferrando RE, Lam C, Compaan D, Yu C, Bosanac I, Hymowitz SG, Kelley RF, Dixit VM. Ubiquitin Chain Editing Revealed by Polyubiquitin Linkage-Specific Antibodies. Cell 2008; 134:668-78. [DOI: 10.1016/j.cell.2008.07.039] [Citation(s) in RCA: 402] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2008] [Revised: 06/26/2008] [Accepted: 07/29/2008] [Indexed: 10/21/2022]
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33
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Seshasayee D, Lee WP, Zhou M, Shu J, Suto E, Zhang J, Diehl L, Austin CD, Meng YG, Tan M, Bullens SL, Seeber S, Fuentes ME, Labrijn AF, Graus YMF, Miller LA, Schelegle ES, Hyde DM, Wu LC, Hymowitz SG, Martin F. In vivo blockade of OX40 ligand inhibits thymic stromal lymphopoietin driven atopic inflammation. J Clin Invest 2008; 117:3868-78. [PMID: 18060034 DOI: 10.1172/jci33559] [Citation(s) in RCA: 171] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2007] [Accepted: 09/26/2007] [Indexed: 01/26/2023] Open
Abstract
Thymic stromal lymphopoietin (TSLP) potently induces deregulation of Th2 responses, a hallmark feature of allergic inflammatory diseases such as asthma, atopic dermatitis, and allergic rhinitis. However, direct downstream in vivo mediators in the TSLP-induced atopic immune cascade have not been identified. In our current study, we have shown that OX40 ligand (OX40L) is a critical in vivo mediator of TSLP-mediated Th2 responses. Treating mice with OX40L-blocking antibodies substantially inhibited immune responses induced by TSLP in the lung and skin, including Th2 inflammatory cell infiltration, cytokine secretion, and IgE production. OX40L-blocking antibodies also inhibited antigen-driven Th2 inflammation in mouse and nonhuman primate models of asthma. This treatment resulted in both blockade of the OX40-OX40L receptor-ligand interaction and depletion of OX40L-positive cells. The use of a blocking, OX40L-specific mAb thus presents a promising strategy for the treatment of allergic diseases associated with pathologic Th2 immune responses.
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Affiliation(s)
- Dhaya Seshasayee
- Department of Immunology, Genentech Inc., South San Francisco, California 94080, USA
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Abstract
Survivin is a member of the IAP (inhibitor of apoptosis) protein family, defined in part by the presence of a zinc-binding baculoviral inhibitory repeat (BIR) domain. Most BIR domains bind short sequences beginning with alanine, and in this manner, they recognize and block the action of key targets in apoptotic pathways. However, Survivin binds only very weakly to typical IAP ligands. Unique features of Survivin are the long C-terminal helix following the BIR domain and a short segment (linking the helix and BIR domains) that mediates Survivin homodimerization. Despite this detailed knowledge of the structure of Survivin itself, there is a current lack of understanding about how Survivin recognizes cellular binding partners, and consequently, many questions about Survivin function remain unanswered. We determined two co-crystal structures of Survivin and a minimal binding fragment from the chromosomal passenger protein Borealin, a well validated functional interactor. The interaction between Survivin and Borealin involves extensive packing between the long C-terminal helix of Survivin and a long Borealin helix. Surprisingly, an additional important interaction occurs between the Survivin homodimerization interface and a short segment of Borealin. This segment both structurally mimics and displaces one Survivin monomer. The relevance of this unexpected interaction was tested by mutagenesis of two key Borealin residues. Mutant Borealin introduced into HeLa cells failed to localize properly during mitosis and also caused mislocalization of other chromosomal passenger proteins. This suggests that the mutant is dominant-negative and confirms the functional importance of the interaction surface identified in the crystal structures.
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Affiliation(s)
- Eric Bourhis
- Department of Protein Engineering, Genentech, Incorporated, South San Francisco, California 94080, USA
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35
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Wagner KW, Punnoose EA, Januario T, Lawrence DA, Pitti RM, Lancaster K, Lee D, von Goetz M, Yee SF, Totpal K, Huw L, Katta V, Cavet G, Hymowitz SG, Amler L, Ashkenazi A. Death-receptor O-glycosylation controls tumor-cell sensitivity to the proapoptotic ligand Apo2L/TRAIL. Nat Med 2007; 13:1070-7. [PMID: 17767167 DOI: 10.1038/nm1627] [Citation(s) in RCA: 447] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2007] [Accepted: 07/11/2007] [Indexed: 01/10/2023]
Abstract
Apo2L/TRAIL stimulates cancer cell death through the proapoptotic receptors DR4 and DR5, but the determinants of tumor susceptibility to this ligand are not fully defined. mRNA expression of the peptidyl O-glycosyltransferase GALNT14 correlated with Apo2L/TRAIL sensitivity in pancreatic carcinoma, non-small-cell lung carcinoma and melanoma cell lines, and up to 30% of samples from various human malignancies showed GALNT14 overexpression. RNA interference of GALNT14 reduced cellular Apo2L/TRAIL sensitivity, whereas overexpression increased responsiveness. Biochemical analysis of DR5 identified several ectodomain O-(N-acetyl galactosamine-galactose-sialic acid) structures. Sequence comparison predicted conserved extracellular DR4 and DR5 O-glycosylation sites; progressive mutation of the DR5 sites attenuated apoptotic signaling. O-glycosylation promoted ligand-stimulated clustering of DR4 and DR5, which mediated recruitment and activation of the apoptosis-initiating protease caspase-8. These results uncover a new link between death-receptor O-glycosylation and apoptotic signaling, providing potential predictive biomarkers for Apo2L/TRAIL-based cancer therapy.
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Affiliation(s)
- Klaus W Wagner
- Department of Molecular Diagnostics, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, USA
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36
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Lee CV, Hymowitz SG, Wallweber HJ, Gordon NC, Billeci KL, Tsai SP, Compaan DM, Yin J, Gong Q, Kelley RF, DeForge LE, Martin F, Starovasnik MA, Fuh G. Synthetic anti-BR3 antibodies that mimic BAFF binding and target both human and murine B cells. Blood 2006; 108:3103-11. [PMID: 16840730 DOI: 10.1182/blood-2006-03-011031] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Abstract
BR3, which is expressed on all mature B cells, is a specific receptor for the B-cell survival and maturation factor BAFF (B-cell–activating factor belonging to the tumor necrosis factor [TNF] family). In order to investigate the consequences of targeting BR3 in murine models and to assess the potential of BR3 antibodies as human therapeutics, synthetic antibody phage libraries were employed to identify BAFF-blocking antibodies cross-reactive to murine and human BR3, which share 52% identity in their extracellular domains. We found an antibody, CB1, which exhibits μM affinity for murine BR3 and very weak affinity for the human receptor. CB3s, an affinity-matured variant of CB1, has sub-nM affinity for BR3 from both species. Alanine scanning and crystallographic structural analysis of the CB3s/BR3 complex reveal that CB3s mimics BAFF by interacting with a similar region of the BR3 surface. Despite this similarity in binding epitopes, CB1 variants antagonize BAFF-dependent human B-cell proliferation in vitro and are effective at reducing murine B-cell populations in vivo, showing significant promise as therapeutics for human B-cell–mediated diseases.
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Affiliation(s)
- Chingwei V Lee
- Department of Protein Engineering, Genentech Inc, 1 DNA Way, South San Francisco, CA 94080, USA
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37
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Compaan DM, Hymowitz SG. The crystal structure of the costimulatory OX40-OX40L complex. Structure 2006; 14:1321-30. [PMID: 16905106 DOI: 10.1016/j.str.2006.06.015] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2006] [Revised: 06/22/2006] [Accepted: 06/24/2006] [Indexed: 01/06/2023]
Abstract
OX40 is a T cell costimulator activated by OX40L. Blockade of the OX40L-OX40 interaction has ameliorative effects in animal models of T cell pathologies. In order to better understand the interaction between OX40 and OX40L, we have determined the crystal structure of murine OX40L and of the human OX40-OX40L complex at 1.45 and 2.4 A, respectively. These structures show that OX40L is an unusually small member of the tumor necrosis factor superfamily (TNFSF). The arrangement of the OX40L protomers forming the functional trimer is atypical and differs from that of other members by a 15 degrees rotation of each protomer with respect to the trimer axis, resulting in an open assembly. Site-directed changes of the interfacial residues of OX40L suggest this interface lacks a single "hot spot" and that instead, binding energy is dispersed over at least two distinct areas. These structures demonstrate the structural plasticity of TNFSF members and their interactions with receptors.
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Affiliation(s)
- Deanne M Compaan
- Department of Protein Engineering, Genentech, Incorporated, 1 DNA Way, South San Francisco, California 94080, USA
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38
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Eimon PM, Kratz E, Varfolomeev E, Hymowitz SG, Stern H, Zha J, Ashkenazi A. Delineation of the cell-extrinsic apoptosis pathway in the zebrafish. Cell Death Differ 2006; 13:1619-30. [PMID: 16888647 DOI: 10.1038/sj.cdd.4402015] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
The mammalian extrinsic apoptosis pathway is triggered by Fas ligand (FasL) and Apo2 ligand/tumor necrosis factor (TNF)-related apoptosis-inducing ligand (Apo2L/TRAIL). Ligand binding to cognate receptors activates initiator caspases directly in a death-inducing signaling complex. In Drosophila, TNF ligand binding activates initiator caspases indirectly, through JNK. We characterized the extrinsic pathway in zebrafish to determine how it operates in a nonmammalian vertebrate. We identified homologs of FasL and Apo2L/TRAIL, their receptors, and other components of the cell death machinery. Studies with three Apo2L/TRAIL homologs demonstrated that they bind the receptors zHDR (previously linked to hematopoiesis) and ovarian TNFR (zOTR). Ectopic expression of these ligands during embryogenesis induced apoptosis in erythroblasts and notochord cells. Inhibition of zHDR, zOTR, the adaptor zFADD, or caspase-8-like proteases blocked ligand-induced apoptosis, as did antiapoptotic Bcl-2 family members. Thus, the extrinsic apoptosis pathway in zebrafish closely resembles its mammalian counterpart and cooperates with the intrinsic pathway to trigger tissue-specific apoptosis during embryogenesis in response to ectopic Apo2L/TRAIL expression.
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Affiliation(s)
- P M Eimon
- Department of Molecular Oncology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
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Li B, Russell SJ, Compaan DM, Totpal K, Marsters SA, Ashkenazi A, Cochran AG, Hymowitz SG, Sidhu SS. Activation of the proapoptotic death receptor DR5 by oligomeric peptide and antibody agonists. J Mol Biol 2006; 361:522-36. [PMID: 16859704 DOI: 10.1016/j.jmb.2006.06.042] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2006] [Revised: 06/11/2006] [Accepted: 06/16/2006] [Indexed: 01/10/2023]
Abstract
The cell-extrinsic apoptotic pathway triggers programmed cell death in response to certain ligands that bind to cell-surface death receptors. Apoptosis is essential for normal development and homeostasis in metazoans, and furthermore, selective activation of the cell-extrinsic pathway in tumor cells holds considerable promise for cancer therapy. We used phage display to identify peptides and synthetic antibodies that specifically bind to the human proapoptotic death receptor DR5. Despite great differences in overall size and structure, the DR5-binding peptides and antibodies shared a tripeptide motif, which was conserved within a disulfide-constrained loop of the peptides and the third complementarity determining region of the antibody heavy chains. The X-ray crystal structure of an antibody in complex with DR5 revealed that the tripeptide motif is buried at the core of the interface, confirming its central role in antigen recognition. We found that certain peptides and antibodies exhibited potent proapoptotic activity against DR5-expressing SK-MES-1 lung carcinoma cells. These phage-derived ligands may be useful for elucidating DR5 activation at the molecular level and for creating synthetic agonists of proapoptotic death receptors.
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Affiliation(s)
- Bing Li
- Department of Protein Engineering, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
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40
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41
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Abstract
Five CD28-like proteins exert positive or negative effects on immune cells. Only four of these five receptors interact with members of the B7 family. The exception is BTLA (B and T lymphocyte attenuator), which instead interacts with the tumor necrosis factor receptor superfamily member HVEM (herpes virus entry mediator). To better understand this interaction, we determined the 2.8-A crystal structure of the BTLA-HVEM complex. This structure shows that BTLA binds the N-terminal cysteine-rich domain of HVEM and employs a unique binding surface compared with other CD28-like receptors. Moreover, the structure shows that BTLA recognizes the same surface on HVEM as gD (herpes virus glycoprotein D) and utilizes a similar binding motif. Light scattering analysis demonstrates that the extracellular domain of BTLA is monomeric and that BTLA and HVEM form a 1:1 complex. Alanine-scanning mutagenesis of HVEM was used to further define critical binding residues. Finally, BTLA adopts an immunoglobulin I-set fold. Despite structural similarities to other CD28-like members, BTLA represents a unique co-receptor.
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MESH Headings
- Amino Acid Motifs
- Amino Acid Sequence
- Binding Sites
- Crystallography, X-Ray
- Humans
- In Vitro Techniques
- Light
- Lymphocytes/immunology
- Models, Molecular
- Molecular Mimicry
- Molecular Sequence Data
- Multiprotein Complexes/chemistry
- Mutagenesis, Insertional
- Protein Structure, Tertiary
- Receptors, Immunologic/chemistry
- Receptors, Immunologic/genetics
- Receptors, Immunologic/physiology
- Receptors, Tumor Necrosis Factor/chemistry
- Receptors, Tumor Necrosis Factor/genetics
- Receptors, Tumor Necrosis Factor/physiology
- Receptors, Tumor Necrosis Factor, Member 14
- Receptors, Virus/chemistry
- Receptors, Virus/genetics
- Receptors, Virus/physiology
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Scattering, Radiation
- Sequence Homology, Amino Acid
- Viral Envelope Proteins/chemistry
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Affiliation(s)
- Deanne M Compaan
- Department of Protein Engineering, Genentech, Inc., S. San Francisco, California 94080, USA
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42
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Fellouse FA, Li B, Compaan DM, Peden AA, Hymowitz SG, Sidhu SS. Molecular recognition by a binary code. J Mol Biol 2005; 348:1153-62. [PMID: 15854651 DOI: 10.1016/j.jmb.2005.03.041] [Citation(s) in RCA: 157] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2004] [Revised: 03/10/2005] [Accepted: 03/14/2005] [Indexed: 11/16/2022]
Abstract
Functional antibodies were obtained from a library of antigen-binding sites generated by a binary code restricted to tyrosine and serine. An antibody raised against human vascular endothelial growth factor recognized the antigen with high affinity (K(D)=60 nM) and high specificity in cell-based assays. The crystal structure of another antigen binding fragment in complex with its antigen (human death receptor DR5) revealed the structural basis for this minimalist mode of molecular recognition. Natural antigen-binding sites are enriched for tyrosine and serine, and we show that these amino acid residues are intrinsically well suited for molecular recognition. Furthermore, these results demonstrate that molecular recognition can evolve from even the simplest chemical diversity.
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Affiliation(s)
- Frederic A Fellouse
- Department of Protein Engineering, Genentech Inc, 1 DNA Way, South San Francisco, CA 94080, USA
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43
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Hymowitz SG, Patel DR, Wallweber HJA, Runyon S, Yan M, Yin J, Shriver SK, Gordon NC, Pan B, Skelton NJ, Kelley RF, Starovasnik MA. Structures of APRIL-Receptor Complexes. J Biol Chem 2005; 280:7218-27. [PMID: 15542592 DOI: 10.1074/jbc.m411714200] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
TACI is a member of the tumor necrosis factor receptor superfamily and serves as a key regulator of B cell function. TACI binds two ligands, APRIL and BAFF, with high affinity and contains two cysteine-rich domains (CRDs) in its extracellular region; in contrast, BCMA and BR3, the other known high affinity receptors for APRIL and BAFF, respectively, contain only a single or partial CRD. However, another form of TACI exists wherein the N-terminal CRD is removed by alternative splicing. We find that this shorter form is capable of ligand-induced cell signaling and that the second CRD alone (TACI_d2) contains full affinity for both ligands. Furthermore, we report the solution structure and alanine-scanning mutagenesis of TACI_d2 along with co-crystal structures of APRIL.TACI_d2 and APRIL.BCMA complexes that together reveal the mechanism by which TACI engages high affinity ligand binding through a single CRD, and we highlight sources of ligand-receptor specificity within the APRIL/BAFF system.
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Affiliation(s)
- Sarah G Hymowitz
- Department of Protein Engineering, Molecular Oncology, Medicinal Chemistry, and Immunology, Genentech, Inc., South San Francisco, California 94080, USA
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44
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Kelley RF, Totpal K, Lindstrom SH, Mathieu M, Billeci K, Deforge L, Pai R, Hymowitz SG, Ashkenazi A. Receptor-selective Mutants of Apoptosis-inducing Ligand 2/Tumor Necrosis Factor-related Apoptosis-inducing Ligand Reveal a Greater Contribution of Death Receptor (DR) 5 than DR4 to Apoptosis Signaling. J Biol Chem 2005; 280:2205-12. [PMID: 15520016 DOI: 10.1074/jbc.m410660200] [Citation(s) in RCA: 207] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Apoptosis-inducing ligand 2 (Apo2L), also called tumor necrosis factor-related apoptosis-inducing ligand (TRAIL), triggers programmed cell death in various types of cancer cells but not in most normal cells. Apo2L/TRAIL is a homotrimeric protein that interacts with five receptors: death receptor 4 (DR4) and DR5 mediate apoptosis activation, whereas decoy receptor 1 (DcR1), DcR2, and osteoprotegerin counteract this function. Many cancer cell lines express both DR4 and DR5, and each of these receptors can initiate apoptosis independently of the other. However, the relative contribution of DR4 and DR5 to ligand-induced apoptosis is unknown. To investigate this question, we generated death receptor-selective Apo2L/TRAIL variants using a novel approach that enables phage display of mutated trimeric proteins. Selective binding to DR4 or DR5 was achieved with three to six-ligand amino acid substitutions. The DR4-selective Apo2L/TRAIL variants examined in this study showed a markedly reduced ability to trigger apoptosis, whereas the DR5-selective variants had minimally decreased or slightly increased apoptosis-inducing activity. These results suggest that DR5 may contribute more than DR4 to Apo2L/TRAIL-induced apoptosis in cancer cells that express both death receptors.
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Affiliation(s)
- Robert F Kelley
- Department of Protein Engineering, Genentech, Inc., South San Francisco, California 94080, USA.
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45
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Wallweber HJA, Compaan DM, Starovasnik MA, Hymowitz SG. The Crystal Structure of A Proliferation-inducing Ligand, APRIL. J Mol Biol 2004; 343:283-90. [PMID: 15451660 DOI: 10.1016/j.jmb.2004.08.040] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2004] [Revised: 07/28/2004] [Accepted: 08/09/2004] [Indexed: 11/19/2022]
Abstract
A proliferation-inducing ligand (APRIL) is a TNF-like cytokine that stimulates tumor cell growth. Within the TNF ligand superfamily, APRIL is most similar to B-cell activation factor (BAFF) with which it shares 30% sequence identity. APRIL binds the receptors B-cell maturation antigen (BCMA) and TACI with high affinity; both of these receptors have also been shown to bind BAFF, although BCMA has significantly higher affinity for APRIL than BAFF. Determination of the crystal structure of APRIL from three crystallization conditions at resolutions of 1.8-2.4A over a pH range from 5.0 to 8.5 reveals a compact trimeric ligand with a backbone fold very similar to that of BAFF (1.1A RMSD over 122 structurally equivalent Calpha atoms), with the exception of differences in the AA' and DE loop regions. Whereas BAFF has been shown to form 20-trimer assemblies under certain conditions, the molecular determinants required for BAFF-like assemblies are absent in the APRIL structure. No crystal packing suggestive of the formation of higher-order assemblies is seen in any of the crystal forms nor does the structure vary significantly between pH 5.0 and 8.5. Modeling of the APRIL-BCMA complex shows the resulting interface is in agreement with mutagenesis data.
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Affiliation(s)
- Heidi J A Wallweber
- Department of Protein Engineering, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
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46
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Hymowitz SG, Compaan DM, Yan M, Wallweber HJA, Dixit VM, Starovasnik MA, de Vos AM. The crystal structures of EDA-A1 and EDA-A2: splice variants with distinct receptor specificity. Structure 2004; 11:1513-20. [PMID: 14656435 DOI: 10.1016/j.str.2003.11.009] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
EDA is a tumor necrosis factor family member involved in ectodermal development. Splice variants EDA-A1 and EDA-A2 differ only by the presence of Glu 308 and Val 309 in the expected receptor binding region of EDA-A1 but not EDA-A2. This two amino acid difference functions as a switch controlling receptor specificity. EDA-A1 binds only to EDAR, while EDA-A2 is specific for XEDAR. In order to understand the structural basis of this switch, we determined the X-ray crystal structures of the TNF domain of both EDA-A1 and EDA-A2 at 2.3 A and 2.2 A, respectively. While the backbone conformation around the splice difference is similar in both isoforms, the conformation of the following loop, the surface charge, and the shape of the expected receptor binding site differ significantly.
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Affiliation(s)
- Sarah G Hymowitz
- Department of Protein Engineering, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
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47
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Gordon NC, Pan B, Hymowitz SG, Yin J, Kelley RF, Cochran AG, Yan M, Dixit VM, Fairbrother WJ, Starovasnik MA. BAFF/BLyS receptor 3 comprises a minimal TNF receptor-like module that encodes a highly focused ligand-binding site. Biochemistry 2003; 42:5977-83. [PMID: 12755599 DOI: 10.1021/bi034017g] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BAFF/BLyS, a member of the tumor necrosis family (TNF) superfamily of ligands, is a crucial survival factor for B cells. BAFF binds three receptors, TACI, BCMA, and BR3, with signaling through BR3 being essential for promoting B cell function. Typical TNF receptor (TNFR) family members bind their cognate ligands through interactions with two cysteine-rich domains (CRDs). However, the extracellular domain (ECD) of BR3 consists of only a partial CRD, with cysteine spacing distinct from other modules described previously. Herein, we report the solution structure of the BR3 ECD. A core region of only 19 residues adopts a stable structure in solution. The BR3 fold is analogous to the first half of a canonical TNFR CRD but is stabilized by an additional noncanonical disulfide bond. BAFF-binding determinants were identified by shotgun alanine-scanning mutagenesis of the BR3 ECD expressed on phage. Several of the key BAFF-binding residues are presented from a beta-turn that we have shown previously to be sufficient for ligand binding when transferred to a structured beta-hairpin scaffold [Kayagaki, N., Yan, M., Seshasayee, D., Wang, H., Lee, W., French, D. M., Grewal, I. S., Cochran, A. G., Gordon, N. C., Yin, J., Starovasnik, M. A, and Dixit, V. M. (2002) Immunity 10, 515-524]. Outside of the turn, mutagenesis identifies additional hydrophobic contacts that enhance the BAFF-BR3 interaction. The crystal structure of the minimal hairpin peptide, bhpBR3, in complex with BAFF reveals intimate packing of the six-residue BR3 turn into a cavity on the ligand surface. Thus, BR3 binds BAFF through a highly focused interaction site, unprecedented in the TNFR family.
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Affiliation(s)
- Nathaniel C Gordon
- Department of Protein Engineering, Genentech, Inc., One DNA Way, South San Francisco, California 94080, USA
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48
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Hymowitz SG, Filvaroff EH, Yin J, Lee J, Cai L, Risser P, Maruoka M, Mao W, Foster J, Kelley RF, Pan G, Gurney AL, de Vos AM, Starovasnik MA. IL-17s adopt a cystine knot fold: structure and activity of a novel cytokine, IL-17F, and implications for receptor binding. EMBO J 2001; 20:5332-41. [PMID: 11574464 PMCID: PMC125646 DOI: 10.1093/emboj/20.19.5332] [Citation(s) in RCA: 407] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The proinflammatory cytokine interleukin 17 (IL-17) is the founding member of a family of secreted proteins that elicit potent cellular responses. We report a novel human IL-17 homolog, IL-17F, and show that it is expressed by activated T cells, can stimulate production of other cytokines such as IL-6, IL-8 and granulocyte colony-stimulating factor, and can regulate cartilage matrix turnover. Unexpectedly, the crystal structure of IL-17F reveals that IL-17 family members adopt a monomer fold typical of cystine knot growth factors, despite lacking the disulfide responsible for defining the canonical "knot" structure. IL-17F dimerizes in a parallel manner like neurotrophins, and features an unusually large cavity on its surface. Remarkably, this cavity is located in precisely the same position where nerve growth factor binds its high affinity receptor, TrkA, suggesting further parallels between IL-17s and neurotrophins with respect to receptor recognition.
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Affiliation(s)
| | - Ellen H. Filvaroff
- Departments of Protein Engineering,
Molecular Oncology and Molecular Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA Corresponding author e-mail:
| | | | - James Lee
- Departments of Protein Engineering,
Molecular Oncology and Molecular Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA Corresponding author e-mail:
| | - Liping Cai
- Departments of Protein Engineering,
Molecular Oncology and Molecular Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA Corresponding author e-mail:
| | - Philip Risser
- Departments of Protein Engineering,
Molecular Oncology and Molecular Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA Corresponding author e-mail:
| | - Miko Maruoka
- Departments of Protein Engineering,
Molecular Oncology and Molecular Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA Corresponding author e-mail:
| | - Weiguang Mao
- Departments of Protein Engineering,
Molecular Oncology and Molecular Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA Corresponding author e-mail:
| | - Jessica Foster
- Departments of Protein Engineering,
Molecular Oncology and Molecular Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA Corresponding author e-mail:
| | | | - Guohua Pan
- Departments of Protein Engineering,
Molecular Oncology and Molecular Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA Corresponding author e-mail:
| | - Austin L. Gurney
- Departments of Protein Engineering,
Molecular Oncology and Molecular Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA Corresponding author e-mail:
| | | | - Melissa A. Starovasnik
- Departments of Protein Engineering,
Molecular Oncology and Molecular Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA Corresponding author e-mail:
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49
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Yan M, Wang LC, Hymowitz SG, Schilbach S, Lee J, Goddard A, de Vos AM, Gao WQ, Dixit VM. Two-amino acid molecular switch in an epithelial morphogen that regulates binding to two distinct receptors. Science 2000; 290:523-7. [PMID: 11039935 DOI: 10.1126/science.290.5491.523] [Citation(s) in RCA: 224] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Ectodysplasin, a member of the tumor necrosis factor family, is encoded by the anhidrotic ectodermal dysplasia (EDA) gene. Mutations in EDA give rise to a clinical syndrome characterized by loss of hair, sweat glands, and teeth. EDA-A1 and EDA-A2 are two isoforms of ectodysplasin that differ only by an insertion of two amino acids. This insertion functions to determine receptor binding specificity, such that EDA-A1 binds only the receptor EDAR, whereas EDA-A2 binds only the related, but distinct, X-linked ectodysplasin-A2 receptor (XEDAR). In situ binding and organ culture studies indicate that EDA-A1 and EDA-A2 are differentially expressed and play a role in epidermal morphogenesis.
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Affiliation(s)
- M Yan
- Department of Molecular Oncology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
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50
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Hymowitz SG, O'Connell MP, Ultsch MH, Hurst A, Totpal K, Ashkenazi A, de Vos AM, Kelley RF. A unique zinc-binding site revealed by a high-resolution X-ray structure of homotrimeric Apo2L/TRAIL. Biochemistry 2000; 39:633-40. [PMID: 10651627 DOI: 10.1021/bi992242l] [Citation(s) in RCA: 196] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Apoptosis-inducing ligand 2 (Apo2L, also called TRAIL), a member of the tumor necrosis factor (TNF) family, induces apoptosis in a variety of human tumor cell lines but not in normal cells [Wiley, S. R., Schooley, K., Smolak, P. J., Din, W. S., Huang, C.-P., Nicholl, J. K., Sutherland, G. R., Smith, T. D., Rauch, C., Smith, C. A., and Goodwin, R. G. (1995) Immunity 3, 673-682; Pitti, R. M., Marsters, S. A., Ruppert, S., Donahue, C. J., Moore, A., and Ashkenazi, A. (1996) J. Biol. Chem. 271, 12687-12690]. Here we describe the structure of Apo2L at 1.3 A resolution and use alanine-scanning mutagenesis to map the receptor contact regions. The structure reveals a homotrimeric protein that resembles TNF with receptor-binding epitopes at the interface between monomers. A zinc ion is buried at the trimer interface, coordinated by the single cysteine residue of each monomer. The zinc ion is required for maintaining the native structure and stability and, hence, the biological activity of Apo2L. This is the first example of metal-dependent oligomerization and function of a cytokine.
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Affiliation(s)
- S G Hymowitz
- Department of Protein Engineering, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, USA
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