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Yamniuk AP, Newitt JA, Doyle ML, Arisaka F, Giannetti AM, Hensley P, Myszka DG, Schwarz FP, Thomson JA, Eisenstein E. Development of a Model Protein Interaction Pair as a Benchmarking Tool for the Quantitative Analysis of 2-Site Protein-Protein Interactions. J Biomol Tech 2015; 26:125-41. [PMID: 26543437 DOI: 10.7171/jbt.15-2604-001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
A significant challenge in the molecular interaction field is to accurately determine the stoichiometry and stepwise binding affinity constants for macromolecules having >1 binding site. The mission of the Molecular Interactions Research Group (MIRG) of the Association of Biomolecular Resource Facilities (ABRF) is to show how biophysical technologies are used to quantitatively characterize molecular interactions, and to educate the ABRF members and scientific community on the utility and limitations of core technologies [such as biosensor, microcalorimetry, or analytic ultracentrifugation (AUC)]. In the present work, the MIRG has developed a robust model protein interaction pair consisting of a bivalent variant of the Bacillus amyloliquefaciens extracellular RNase barnase and a variant of its natural monovalent intracellular inhibitor protein barstar. It is demonstrated that this system can serve as a benchmarking tool for the quantitative analysis of 2-site protein-protein interactions. The protein interaction pair enables determination of precise binding constants for the barstar protein binding to 2 distinct sites on the bivalent barnase binding partner (termed binase), where the 2 binding sites were engineered to possess affinities that differed by 2 orders of magnitude. Multiple MIRG laboratories characterized the interaction using isothermal titration calorimetry (ITC), AUC, and surface plasmon resonance (SPR) methods to evaluate the feasibility of the system as a benchmarking model. Although general agreement was seen for the binding constants measured using solution-based ITC and AUC approaches, weaker affinity was seen for surface-based method SPR, with protein immobilization likely affecting affinity. An analysis of the results from multiple MIRG laboratories suggests that the bivalent barnase-barstar system is a suitable model for benchmarking new approaches for the quantitative characterization of complex biomolecular interactions.
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Affiliation(s)
- Aaron P Yamniuk
- 1 Bristol-Myers Squibb, Princeton, New Jersey 08540, USA; 2 Tokyo Institute of Technology, Yokohama 226-8503, Japan; 3 Google[x], Google Life Sciences, Mountain View, California 94043, USA; 4 SystaMedic, Incorporated, Groton, Connecticut 06340, USA; 5 Biosensor Tools LLC, Salt Lake City, Utah 84103, USA; 6 National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA; 7 Polaris Pharmaceuticals, Incorporated, San Diego, California 92121, USA; and 8 Institute for Bioscience and Biotechnology Research, Fischell Department of Bioengineering, University of Maryland, Rockville, Maryland 20850, USA
| | - John A Newitt
- 1 Bristol-Myers Squibb, Princeton, New Jersey 08540, USA; 2 Tokyo Institute of Technology, Yokohama 226-8503, Japan; 3 Google[x], Google Life Sciences, Mountain View, California 94043, USA; 4 SystaMedic, Incorporated, Groton, Connecticut 06340, USA; 5 Biosensor Tools LLC, Salt Lake City, Utah 84103, USA; 6 National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA; 7 Polaris Pharmaceuticals, Incorporated, San Diego, California 92121, USA; and 8 Institute for Bioscience and Biotechnology Research, Fischell Department of Bioengineering, University of Maryland, Rockville, Maryland 20850, USA
| | - Michael L Doyle
- 1 Bristol-Myers Squibb, Princeton, New Jersey 08540, USA; 2 Tokyo Institute of Technology, Yokohama 226-8503, Japan; 3 Google[x], Google Life Sciences, Mountain View, California 94043, USA; 4 SystaMedic, Incorporated, Groton, Connecticut 06340, USA; 5 Biosensor Tools LLC, Salt Lake City, Utah 84103, USA; 6 National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA; 7 Polaris Pharmaceuticals, Incorporated, San Diego, California 92121, USA; and 8 Institute for Bioscience and Biotechnology Research, Fischell Department of Bioengineering, University of Maryland, Rockville, Maryland 20850, USA
| | - Fumio Arisaka
- 1 Bristol-Myers Squibb, Princeton, New Jersey 08540, USA; 2 Tokyo Institute of Technology, Yokohama 226-8503, Japan; 3 Google[x], Google Life Sciences, Mountain View, California 94043, USA; 4 SystaMedic, Incorporated, Groton, Connecticut 06340, USA; 5 Biosensor Tools LLC, Salt Lake City, Utah 84103, USA; 6 National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA; 7 Polaris Pharmaceuticals, Incorporated, San Diego, California 92121, USA; and 8 Institute for Bioscience and Biotechnology Research, Fischell Department of Bioengineering, University of Maryland, Rockville, Maryland 20850, USA
| | - Anthony M Giannetti
- 1 Bristol-Myers Squibb, Princeton, New Jersey 08540, USA; 2 Tokyo Institute of Technology, Yokohama 226-8503, Japan; 3 Google[x], Google Life Sciences, Mountain View, California 94043, USA; 4 SystaMedic, Incorporated, Groton, Connecticut 06340, USA; 5 Biosensor Tools LLC, Salt Lake City, Utah 84103, USA; 6 National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA; 7 Polaris Pharmaceuticals, Incorporated, San Diego, California 92121, USA; and 8 Institute for Bioscience and Biotechnology Research, Fischell Department of Bioengineering, University of Maryland, Rockville, Maryland 20850, USA
| | - Preston Hensley
- 1 Bristol-Myers Squibb, Princeton, New Jersey 08540, USA; 2 Tokyo Institute of Technology, Yokohama 226-8503, Japan; 3 Google[x], Google Life Sciences, Mountain View, California 94043, USA; 4 SystaMedic, Incorporated, Groton, Connecticut 06340, USA; 5 Biosensor Tools LLC, Salt Lake City, Utah 84103, USA; 6 National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA; 7 Polaris Pharmaceuticals, Incorporated, San Diego, California 92121, USA; and 8 Institute for Bioscience and Biotechnology Research, Fischell Department of Bioengineering, University of Maryland, Rockville, Maryland 20850, USA
| | - David G Myszka
- 1 Bristol-Myers Squibb, Princeton, New Jersey 08540, USA; 2 Tokyo Institute of Technology, Yokohama 226-8503, Japan; 3 Google[x], Google Life Sciences, Mountain View, California 94043, USA; 4 SystaMedic, Incorporated, Groton, Connecticut 06340, USA; 5 Biosensor Tools LLC, Salt Lake City, Utah 84103, USA; 6 National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA; 7 Polaris Pharmaceuticals, Incorporated, San Diego, California 92121, USA; and 8 Institute for Bioscience and Biotechnology Research, Fischell Department of Bioengineering, University of Maryland, Rockville, Maryland 20850, USA
| | - Fred P Schwarz
- 1 Bristol-Myers Squibb, Princeton, New Jersey 08540, USA; 2 Tokyo Institute of Technology, Yokohama 226-8503, Japan; 3 Google[x], Google Life Sciences, Mountain View, California 94043, USA; 4 SystaMedic, Incorporated, Groton, Connecticut 06340, USA; 5 Biosensor Tools LLC, Salt Lake City, Utah 84103, USA; 6 National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA; 7 Polaris Pharmaceuticals, Incorporated, San Diego, California 92121, USA; and 8 Institute for Bioscience and Biotechnology Research, Fischell Department of Bioengineering, University of Maryland, Rockville, Maryland 20850, USA
| | - James A Thomson
- 1 Bristol-Myers Squibb, Princeton, New Jersey 08540, USA; 2 Tokyo Institute of Technology, Yokohama 226-8503, Japan; 3 Google[x], Google Life Sciences, Mountain View, California 94043, USA; 4 SystaMedic, Incorporated, Groton, Connecticut 06340, USA; 5 Biosensor Tools LLC, Salt Lake City, Utah 84103, USA; 6 National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA; 7 Polaris Pharmaceuticals, Incorporated, San Diego, California 92121, USA; and 8 Institute for Bioscience and Biotechnology Research, Fischell Department of Bioengineering, University of Maryland, Rockville, Maryland 20850, USA
| | - Edward Eisenstein
- 1 Bristol-Myers Squibb, Princeton, New Jersey 08540, USA; 2 Tokyo Institute of Technology, Yokohama 226-8503, Japan; 3 Google[x], Google Life Sciences, Mountain View, California 94043, USA; 4 SystaMedic, Incorporated, Groton, Connecticut 06340, USA; 5 Biosensor Tools LLC, Salt Lake City, Utah 84103, USA; 6 National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA; 7 Polaris Pharmaceuticals, Incorporated, San Diego, California 92121, USA; and 8 Institute for Bioscience and Biotechnology Research, Fischell Department of Bioengineering, University of Maryland, Rockville, Maryland 20850, USA
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2
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Gobbi A, Giannetti AM, Chen H, Lee ML. Atom-Atom-Path similarity and Sphere Exclusion clustering: tools for prioritizing fragment hits. J Cheminform 2015; 7:11. [PMID: 25866564 PMCID: PMC4392110 DOI: 10.1186/s13321-015-0056-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [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] [Received: 11/21/2014] [Accepted: 02/09/2015] [Indexed: 11/10/2022] Open
Abstract
Background After performing a fragment based screen the resulting hits need to be prioritized for follow-up structure elucidation and chemistry. This paper describes a new similarity metric, Atom-Atom-Path (AAP) similarity that is used in conjunction with the Directed Sphere Exclusion (DISE) clustering method to effectively organize and prioritize the fragment hits. The AAP similarity rewards common substructures and recognizes minimal structure differences. The DISE method is order-dependent and can be used to enrich fragments with properties of interest in the first clusters. Results The merit of the software is demonstrated by its application to the MAP4K4 fragment screening hits using ligand efficiency (LE) as quality measure. The first clusters contain the hits with the highest LE. The clustering results can be easily visualized in a LE-over-clusters scatterplot with points colored by the members’ similarity to the corresponding cluster seed. The scatterplot enables the extraction of preliminary SAR. Conclusions The detailed structure differentiation of the AAP similarity metric is ideal for fragment-sized molecules. The order-dependent nature of the DISE clustering method results in clusters ordered by a property of interest to the teams. The combination of both allows for efficient prioritization of fragment hit for follow-ups. AAP similarity computation and DISE clustering visualization. ![]()
Electronic supplementary material The online version of this article (doi:10.1186/s13321-015-0056-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alberto Gobbi
- Small Molecule Discovery, Discovery Chemistry, Genentech, 1 DNA Way, 94080 South San Francisco, CA USA
| | - Anthony M Giannetti
- Small Molecule Discovery, Biochemical and Cellular Pharmacology, Genentech, 1 DNA Way, 94080 South San Francisco, CA USA
| | - Huifen Chen
- Small Molecule Discovery, Discovery Chemistry, Genentech, 1 DNA Way, 94080 South San Francisco, CA USA
| | - Man-Ling Lee
- Small Molecule Discovery, Discovery Chemistry, Genentech, 1 DNA Way, 94080 South San Francisco, CA USA
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3
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Giannetti AM, Gilbert HN, Huddler DP, Reiter M, Strande C, Pitts KE, Bravo BJ. CHAPTER 2. Getting the Most Value from Your Screens: Advances in Hardware, Software, and Methodologies to Enhance Surface Plasmon Resonance Based Fragment Screening and Hit-to-Lead Support. Fragment-Based Drug Discovery 2015. [DOI: 10.1039/9781782620938-00019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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4
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Wang L, Stanley M, Boggs JW, Crawford TD, Bravo BJ, Giannetti AM, Harris SF, Magnuson SR, Nonomiya J, Schmidt S, Wu P, Ye W, Gould SE, Murray LJ, Ndubaku CO, Chen H. Fragment-based identification and optimization of a class of potent pyrrolo[2,1-f][1,2,4]triazine MAP4K4 inhibitors. Bioorg Med Chem Lett 2014; 24:4546-4552. [PMID: 25139565 DOI: 10.1016/j.bmcl.2014.07.071] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [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] [Received: 06/26/2014] [Revised: 07/24/2014] [Accepted: 07/28/2014] [Indexed: 01/27/2023]
Abstract
MAP4K4 has been shown to regulate key cellular processes that are tied to disease pathogenesis. In an effort to generate small molecule MAP4K4 inhibitors, a fragment-based screen was carried out and a pyrrolotriazine fragment with excellent ligand efficiency was identified. Further modification of this fragment guided by X-ray crystal structures and molecular modeling led to the discovery of a series of promising compounds with good structural diversity and physicochemical properties. These compounds exhibited single digit nanomolar potency and compounds 35 and 44 achieved good in vivo exposure.
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Affiliation(s)
- Lan Wang
- Department of Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Mark Stanley
- Department of Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Jason W Boggs
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Terry D Crawford
- Department of Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Brandon J Bravo
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Anthony M Giannetti
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Seth F Harris
- Department of Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Steven R Magnuson
- Department of Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Jim Nonomiya
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Stephen Schmidt
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Ping Wu
- Department of Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Weilan Ye
- Department of Molecular Oncology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Stephen E Gould
- Department of Molecular Oncology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Lesley J Murray
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Chudi O Ndubaku
- Department of Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States.
| | - Huifen Chen
- Department of Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States.
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5
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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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6
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Dragovich PS, Fauber BP, Boggs J, Chen J, Corson LB, Ding CZ, Eigenbrot C, Ge H, Giannetti AM, Hunsaker T, Labadie S, Li C, Liu Y, Liu Y, Ma S, Malek S, Peterson D, Pitts KE, Purkey HE, Robarge K, Salphati L, Sideris S, Ultsch M, VanderPorten E, Wang J, Wei B, Xu Q, Yen I, Yue Q, Zhang H, Zhang X, Zhou A. Identification of substituted 3-hydroxy-2-mercaptocyclohex-2-enones as potent inhibitors of human lactate dehydrogenase. Bioorg Med Chem Lett 2014; 24:3764-71. [DOI: 10.1016/j.bmcl.2014.06.076] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Revised: 06/23/2014] [Accepted: 06/25/2014] [Indexed: 02/08/2023]
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7
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Crawford TD, Ndubaku CO, Chen H, Boggs JW, Bravo BJ, Delatorre K, Giannetti AM, Gould SE, Harris SF, Magnuson SR, McNamara E, Murray LJ, Nonomiya J, Sambrone A, Schmidt S, Smyczek T, Stanley M, Vitorino P, Wang L, West K, Wu P, Ye W. Discovery of selective 4-Amino-pyridopyrimidine inhibitors of MAP4K4 using fragment-based lead identification and optimization. J Med Chem 2014; 57:3484-93. [PMID: 24673130 DOI: 10.1021/jm500155b] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4) is a serine/threonine kinase implicated in the regulation of many biological processes. A fragment-based lead discovery approach was used to generate potent and selective MAP4K4 inhibitors. The fragment hit pursued in this article had excellent ligand efficiency (LE), an important attribute for subsequent successful optimization into drug-like lead compounds. The optimization efforts eventually led us to focus on the pyridopyrimidine series, from which 6-(2-fluoropyridin-4-yl)pyrido[3,2-d]pyrimidin-4-amine (29) was identified. This compound had low nanomolar potency, excellent kinase selectivity, and good in vivo exposure, and demonstrated in vivo pharmacodynamic effects in a human tumor xenograft model.
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Affiliation(s)
- Terry D Crawford
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
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8
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Giannetti AM, Zheng X, Skelton NJ, Wang W, Bravo BJ, Bair KW, Baumeister T, Cheng E, Crocker L, Feng Y, Gunzner-Toste J, Ho YC, Hua R, Liederer BM, Liu Y, Ma X, O'Brien T, Oeh J, Sampath D, Shen Y, Wang C, Wang L, Wu H, Xiao Y, Yuen PW, Zak M, Zhao G, Zhao Q, Dragovich PS. Fragment-based identification of amides derived from trans-2-(pyridin-3-yl)cyclopropanecarboxylic acid as potent inhibitors of human nicotinamide phosphoribosyltransferase (NAMPT). J Med Chem 2014; 57:770-92. [PMID: 24405419 DOI: 10.1021/jm4015108] [Citation(s) in RCA: 26] [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] [Indexed: 01/17/2023]
Abstract
Potent, trans-2-(pyridin-3-yl)cyclopropanecarboxamide-containing inhibitors of the human nicotinamide phosphoribosyltransferase (NAMPT) enzyme were identified using fragment-based screening and structure-based design techniques. Multiple crystal structures were obtained of initial fragment leads, and this structural information was utilized to improve the biochemical and cell-based potency of the associated molecules. Many of the optimized compounds exhibited nanomolar antiproliferative activities against human tumor lines in in vitro cell culture experiments. In a key example, a fragment lead (13, KD = 51 μM) was elaborated into a potent NAMPT inhibitor (39, NAMPT IC50 = 0.0051 μM, A2780 cell culture IC50 = 0.000 49 μM) which demonstrated encouraging in vivo efficacy in an HT-1080 mouse xenograft tumor model.
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Affiliation(s)
- Anthony M Giannetti
- Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States
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9
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Murray J, Giannetti AM, Steffek M, Gibbons P, Hearn BR, Cohen F, Tam C, Pozniak C, Bravo B, Lewcock J, Jaishankar P, Ly CQ, Zhao X, Tang Y, Chugha P, Arkin MR, Flygare J, Renslo AR. Inside Cover: Tailoring Small Molecules for an Allosteric Site on Procaspase-6 (ChemMedChem 1/2014). ChemMedChem 2013. [DOI: 10.1002/cmdc.201390058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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10
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Dragovich PS, Zhao G, Baumeister T, Bravo B, Giannetti AM, Ho YC, Hua R, Li G, Liang X, Ma X, O'Brien T, Oh A, Skelton NJ, Wang C, Wang W, Wang Y, Xiao Y, Yuen PW, Zak M, Zhao Q, Zheng X. Fragment-based design of 3-aminopyridine-derived amides as potent inhibitors of human nicotinamide phosphoribosyltransferase (NAMPT). Bioorg Med Chem Lett 2013; 24:954-62. [PMID: 24433859 DOI: 10.1016/j.bmcl.2013.12.062] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [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: 10/17/2013] [Revised: 12/12/2013] [Accepted: 12/16/2013] [Indexed: 01/26/2023]
Abstract
The fragment-based identification of two novel and potent biochemical inhibitors of the nicotinamide phosphoribosyltransferase (NAMPT) enzyme is described. These compounds (51 and 63) incorporate an amide moiety derived from 3-aminopyridine, and are thus structurally distinct from other known anti-NAMPT agents. Each exhibits potent inhibition of NAMPT biochemical activity (IC50=19 and 15 nM, respectively) as well as robust antiproliferative properties in A2780 cell culture experiments (IC50=121 and 99 nM, respectively). However, additional biological studies indicate that only inhibitor 51 exerts its A2780 cell culture effects via a NAMPT-mediated mechanism. The crystal structures of both 51 and 63 in complex with NAMPT are also independently described.
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Affiliation(s)
| | - Guiling Zhao
- Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Timm Baumeister
- Forma Therapeutics, Inc., 500 Arsenal Street, Watertown, MA 02472, USA
| | - Brandon Bravo
- Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | | | - Yen-Ching Ho
- Forma Therapeutics, Inc., 500 Arsenal Street, Watertown, MA 02472, USA
| | - Rongbao Hua
- Pharmaron Beijing, Co. Ltd., 6 Taihe Road, BDA, Beijing 100176, PR China
| | - Guangkun Li
- Pharmaron Beijing, Co. Ltd., 6 Taihe Road, BDA, Beijing 100176, PR China
| | - Xiaorong Liang
- Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Xiaolei Ma
- Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Thomas O'Brien
- Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Angela Oh
- Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | | | - Chengcheng Wang
- Crown Bioscience, Science & Technology Innovation Park, No.6 Beijing West Road, Taicang City, Jiangsu Province, PR China
| | - Weiru Wang
- Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Yunli Wang
- Pharmaron Beijing, Co. Ltd., 6 Taihe Road, BDA, Beijing 100176, PR China
| | - Yang Xiao
- Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Po-wai Yuen
- Pharmaron Beijing, Co. Ltd., 6 Taihe Road, BDA, Beijing 100176, PR China
| | - Mark Zak
- Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Qiang Zhao
- Crown Bioscience, Science & Technology Innovation Park, No.6 Beijing West Road, Taicang City, Jiangsu Province, PR China
| | - Xiaozhang Zheng
- Forma Therapeutics, Inc., 500 Arsenal Street, Watertown, MA 02472, USA
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11
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Murray J, Giannetti AM, Steffek M, Gibbons P, Hearn BR, Cohen F, Tam C, Pozniak C, Bravo B, Lewcock J, Jaishankar P, Ly CQ, Zhao X, Tang Y, Chugha P, Arkin MR, Flygare J, Renslo AR. Tailoring small molecules for an allosteric site on procaspase-6. ChemMedChem 2013; 9:73-7, 2. [PMID: 24259468 DOI: 10.1002/cmdc.201300424] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Indexed: 12/20/2022]
Abstract
Although they represent attractive therapeutic targets, caspases have so far proven recalcitrant to the development of drugs targeting the active site. Allosteric modulation of caspase activity is an alternate strategy that potentially avoids the need for anionic and electrophilic functionality present in most active-site inhibitors. Caspase-6 has been implicated in neurodegenerative disease, including Huntington's and Alzheimer's diseases. Herein we describe a fragment-based lead discovery effort focused on caspase-6 in its active and zymogen forms. Fragments were identified for procaspase-6 using surface plasmon resonance methods and subsequently shown by X-ray crystallography to bind a putative allosteric site at the dimer interface. A fragment-merging strategy was employed to produce nanomolar-affinity ligands that contact residues in the L2 loop at the dimer interface, significantly stabilizing procaspase-6. Because rearrangement of the L2 loop is required for caspase-6 activation, our results suggest a strategy for the allosteric control of caspase activation with drug-like small molecules.
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Affiliation(s)
- Jeremy Murray
- Departments of Structural Biology, Biochemical Pharmacology, Neuroscience, and Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080 (USA).
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12
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Fauber BP, Dragovich PS, Chen J, Corson LB, Ding CZ, Eigenbrot C, Giannetti AM, Hunsaker T, Labadie S, Liu Y, Liu Y, Malek S, Peterson D, Pitts K, Sideris S, Ultsch M, VanderPorten E, Wang J, Wei B, Yen I, Yue Q. Identification of 2-amino-5-aryl-pyrazines as inhibitors of human lactate dehydrogenase. Bioorg Med Chem Lett 2013; 23:5533-9. [PMID: 24012183 DOI: 10.1016/j.bmcl.2013.08.060] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [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: 07/09/2013] [Revised: 08/09/2013] [Accepted: 08/13/2013] [Indexed: 12/18/2022]
Abstract
A 2-amino-5-aryl-pyrazine was identified as an inhibitor of human lactate dehydrogenase A (LDHA) via a biochemical screening campaign. Biochemical and biophysical experiments demonstrated that the compound specifically interacted with human LDHA. Structural variation of the screening hit resulted in improvements in LDHA biochemical inhibition and pharmacokinetic properties. A crystal structure of an improved compound bound to human LDHA was also obtained and it explained many of the observed structure-activity relationships.
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13
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Talamas FX, Ao-Ieong G, Brameld KA, Chin E, de Vicente J, Dunn JP, Ghate M, Giannetti AM, Harris SF, Labadie SS, Leveque V, Li J, Lui AST, McCaleb KL, Nájera I, Schoenfeld RC, Wang B, Wong A. De novo fragment design: a medicinal chemistry approach to fragment-based lead generation. J Med Chem 2013; 56:3115-9. [PMID: 23509929 DOI: 10.1021/jm4002605] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The use of fragments with low binding affinity for their targets as starting points has received much attention recently. Screening of fragment libraries has been the most common method to find attractive starting points. Herein, we describe a unique, alternative approach to generating fragment leads. A binding model was developed and a set of guidelines were then selected to use this model to design fragments, enabling our discovery of a novel fragment with high LE.
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Affiliation(s)
- Francisco X Talamas
- Hoffmann-La Roche Inc, Pharma Research & Early Development, 340 Kingsland Street, Nutley, New Jersey 07110, United States.
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14
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Heise CE, Murray J, Augustyn KE, Bravo B, Chugha P, Cohen F, Giannetti AM, Gibbons P, Hannoush RN, Hearn BR, Jaishankar P, Ly CQ, Shah K, Stanger K, Steffek M, Tang Y, Zhao X, Lewcock JW, Renslo AR, Flygare J, Arkin MR. Mechanistic and structural understanding of uncompetitive inhibitors of caspase-6. PLoS One 2012; 7:e50864. [PMID: 23227217 PMCID: PMC3515450 DOI: 10.1371/journal.pone.0050864] [Citation(s) in RCA: 28] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 10/25/2012] [Indexed: 01/13/2023] Open
Abstract
Inhibition of caspase-6 is a potential therapeutic strategy for some neurodegenerative diseases, but it has been difficult to develop selective inhibitors against caspases. We report the discovery and characterization of a potent inhibitor of caspase-6 that acts by an uncompetitive binding mode that is an unprecedented mechanism of inhibition against this target class. Biochemical assays demonstrate that, while exquisitely selective for caspase-6 over caspase-3 and -7, the compound's inhibitory activity is also dependent on the amino acid sequence and P1' character of the peptide substrate. The crystal structure of the ternary complex of caspase-6, substrate-mimetic and an 11 nM inhibitor reveals the molecular basis of inhibition. The general strategy to develop uncompetitive inhibitors together with the unique mechanism described herein provides a rationale for engineering caspase selectivity.
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Affiliation(s)
- Christopher E. Heise
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., South San Francisco, California, United States of America
| | - Jeremy Murray
- Department of Structural Biology, Genentech, Inc., South San Francisco, California, United States of America
| | - Katherine E. Augustyn
- Small Molecule Discovery Center, University of California San Francisco, San Francisco, California, United States of America
| | - Brandon Bravo
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., South San Francisco, California, United States of America
| | - Preeti Chugha
- Small Molecule Discovery Center, University of California San Francisco, San Francisco, California, United States of America
| | - Frederick Cohen
- Department of Discovery Chemistry, Genentech, Inc., South San Francisco, California, United States of America
| | - Anthony M. Giannetti
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., South San Francisco, California, United States of America
| | - Paul Gibbons
- Department of Discovery Chemistry, Genentech, Inc., South San Francisco, California, United States of America
| | - Rami N. Hannoush
- Department of Early Discovery Biochemistry, Genentech, Inc., South San Francisco, California, United States of America
| | - Brian R. Hearn
- Small Molecule Discovery Center, University of California San Francisco, San Francisco, California, United States of America
| | - Priyadarshini Jaishankar
- Small Molecule Discovery Center, University of California San Francisco, San Francisco, California, United States of America
| | - Cuong Q. Ly
- Department of Discovery Chemistry, Genentech, Inc., South San Francisco, California, United States of America
| | - Kinjalkumar Shah
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., South San Francisco, California, United States of America
| | - Karen Stanger
- Department of Early Discovery Biochemistry, Genentech, Inc., South San Francisco, California, United States of America
| | - Micah Steffek
- Department of Structural Biology, Genentech, Inc., South San Francisco, California, United States of America
| | - Yinyan Tang
- Small Molecule Discovery Center, University of California San Francisco, San Francisco, California, United States of America
| | - Xianrui Zhao
- Department of Discovery Chemistry, Genentech, Inc., South San Francisco, California, United States of America
| | - Joseph W. Lewcock
- Department of Neuroscience, Genentech, Inc., South San Francisco, California, United States of America
| | - Adam R. Renslo
- Small Molecule Discovery Center, University of California San Francisco, San Francisco, California, United States of America
| | - John Flygare
- Department of Discovery Chemistry, Genentech, Inc., South San Francisco, California, United States of America
| | - Michelle R. Arkin
- Small Molecule Discovery Center, University of California San Francisco, San Francisco, California, United States of America
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15
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Giannetti AM, Wong H, Dijkgraaf GJP, Dueber EC, Ortwine DF, Bravo BJ, Gould SE, Plise EG, Lum BL, Malhi V, Graham RA. Identification, Characterization, and Implications of Species-Dependent Plasma Protein Binding for the Oral Hedgehog Pathway Inhibitor Vismodegib (GDC-0449). J Med Chem 2011; 54:2592-601. [DOI: 10.1021/jm1008924] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
| | - Harvey Wong
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | | | - Erin C. Dueber
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Daniel F. Ortwine
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Brandon J. Bravo
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Stephen E. Gould
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Emile G. Plise
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Bert L. Lum
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Vikram Malhi
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Richard A. Graham
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
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16
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17
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Hang JQ, Yang Y, Harris SF, Leveque V, Whittington HJ, Rajyaguru S, Ao-Ieong G, McCown MF, Wong A, Giannetti AM, Le Pogam S, Talamás F, Cammack N, Nájera I, Klumpp K. Slow binding inhibition and mechanism of resistance of non-nucleoside polymerase inhibitors of hepatitis C virus. J Biol Chem 2009; 284:15517-29. [PMID: 19246450 PMCID: PMC2708848 DOI: 10.1074/jbc.m808889200] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2008] [Revised: 01/20/2009] [Indexed: 01/03/2023] Open
Abstract
The binding affinity of four palm and thumb site representative non-nucleoside inhibitors (NNIs) of HCV polymerase NS5B to wild-type and resistant NS5B polymerase proteins was determined, and the influence of RNA binding on NNI binding affinity was investigated. NNIs with high binding affinity potently inhibited HCV RNA polymerase activity and replicon replication. Among the compounds tested, HCV-796 showed slow binding kinetics to NS5B. The binding affinity of HCV-796 to NS5B increased 27-fold over a 3-h incubation period with an equilibrium Kd of 71 +/- 2 nm. Slow binding kinetics of HCV-796 was driven by slow dissociation from NS5B with a k(off) of 4.9 +/- 0.5 x 10(-4) s(-1). NS5B bound a long, 378-nucleotide HCV RNA oligonucleotide with high affinity (Kd = 6.9 +/- 0.3 nm), whereas the binding affinity was significantly lower for a short, 21-nucleotide RNA (Kd = 155.1 +/- 16.2 nm). The formation of the NS5B-HCV RNA complex did not affect the slow binding kinetics profile and only slightly reduced NS5B binding affinity of HCV-796. The magnitude of reduction of NNI binding affinity for the NS5B proteins with various resistance mutations in the palm and thumb binding sites correlated well with resistance -fold shifts in NS5B polymerase activity and replicon assays. Co-crystal structures of NS5B-Con1 and NS5B-BK with HCV-796 revealed a deep hydrophobic binding pocket at the palm region of NS5B. HCV-796 interaction with the induced binding pocket on NS5B is consistent with slow binding kinetics and loss of binding affinity with mutations at amino acid position 316.
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Affiliation(s)
- Julie Qi Hang
- From Roche Palo Alto LLC, Palo Alto, California 94304
| | - Yanli Yang
- From Roche Palo Alto LLC, Palo Alto, California 94304
| | | | | | | | | | | | | | - April Wong
- From Roche Palo Alto LLC, Palo Alto, California 94304
| | | | | | | | - Nick Cammack
- From Roche Palo Alto LLC, Palo Alto, California 94304
| | - Isabel Nájera
- From Roche Palo Alto LLC, Palo Alto, California 94304
| | - Klaus Klumpp
- From Roche Palo Alto LLC, Palo Alto, California 94304
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18
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Rich RL, Papalia GA, Flynn PJ, Furneisen J, Quinn J, Klein JS, Katsamba PS, Waddell MB, Scott M, Thompson J, Berlier J, Corry S, Baltzinger M, Zeder-Lutz G, Schoenemann A, Clabbers A, Wieckowski S, Murphy MM, Page P, Ryan TE, Duffner J, Ganguly T, Corbin J, Gautam S, Anderluh G, Bavdek A, Reichmann D, Yadav SP, Hommema E, Pol E, Drake A, Klakamp S, Chapman T, Kernaghan D, Miller K, Schuman J, Lindquist K, Herlihy K, Murphy MB, Bohnsack R, Andrien B, Brandani P, Terwey D, Millican R, Darling RJ, Wang L, Carter Q, Dotzlaf J, Lopez-Sagaseta J, Campbell I, Torreri P, Hoos S, England P, Liu Y, Abdiche Y, Malashock D, Pinkerton A, Wong M, Lafer E, Hinck C, Thompson K, Primo CD, Joyce A, Brooks J, Torta F, Bagge Hagel AB, Krarup J, Pass J, Ferreira M, Shikov S, Mikolajczyk M, Abe Y, Barbato G, Giannetti AM, Krishnamoorthy G, Beusink B, Satpaev D, Tsang T, Fang E, Partridge J, Brohawn S, Horn J, Pritsch O, Obal G, Nilapwar S, Busby B, Gutierrez-Sanchez G, Gupta RD, Canepa S, Witte K, Nikolovska-Coleska Z, Cho YH, D'Agata R, Schlick K, Calvert R, Munoz EM, Hernaiz MJ, Bravman T, Dines M, Yang MH, Puskas A, Boni E, Li J, Wear M, Grinberg A, Baardsnes J, Dolezal O, Gainey M, Anderson H, Peng J, Lewis M, Spies P, Trinh Q, Bibikov S, Raymond J, Yousef M, Chandrasekaran V, Feng Y, Emerick A, Mundodo S, Guimaraes R, McGirr K, Li YJ, Hughes H, Mantz H, Skrabana R, Witmer M, Ballard J, Martin L, Skladal P, Korza G, Laird-Offringa I, Lee CS, Khadir A, Podlaski F, Neuner P, Rothacker J, Rafique A, Dankbar N, Kainz P, Gedig E, Vuyisich M, Boozer C, Ly N, Toews M, Uren A, Kalyuzhniy O, Lewis K, Chomey E, Pak BJ, Myszka DG. A global benchmark study using affinity-based biosensors. Anal Biochem 2008; 386:194-216. [PMID: 19133223 DOI: 10.1016/j.ab.2008.11.021] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2008] [Revised: 11/04/2008] [Accepted: 11/12/2008] [Indexed: 01/29/2023]
Abstract
To explore the variability in biosensor studies, 150 participants from 20 countries were given the same protein samples and asked to determine kinetic rate constants for the interaction. We chose a protein system that was amenable to analysis using different biosensor platforms as well as by users of different expertise levels. The two proteins (a 50-kDa Fab and a 60-kDa glutathione S-transferase [GST] antigen) form a relatively high-affinity complex, so participants needed to optimize several experimental parameters, including ligand immobilization and regeneration conditions as well as analyte concentrations and injection/dissociation times. Although most participants collected binding responses that could be fit to yield kinetic parameters, the quality of a few data sets could have been improved by optimizing the assay design. Once these outliers were removed, the average reported affinity across the remaining panel of participants was 620 pM with a standard deviation of 980 pM. These results demonstrate that when this biosensor assay was designed and executed appropriately, the reported rate constants were consistent, and independent of which protein was immobilized and which biosensor was used.
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Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, School of Medicine, University of Utah, Salt Lake City, UT 84132, USA
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19
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Tsang E, Giannetti AM, Shaw D, Dinh M, Tse JKY, Gandhi S, Ho H, Wang S, Papp E, Bradshaw JM. Molecular mechanism of the Syk activation switch. J Biol Chem 2008; 283:32650-9. [PMID: 18818202 DOI: 10.1074/jbc.m806340200] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Many immune signaling pathways require activation of the Syk tyrosine kinase to link ligation of surface receptors to changes in gene expression. Despite the central role of Syk in these pathways, the Syk activation process remains poorly understood. In this work we quantitatively characterized the molecular mechanism of Syk activation in vitro using a real time fluorescence kinase assay, mutagenesis, and other biochemical techniques. We found that dephosphorylated full-length Syk demonstrates a low initial rate of substrate phosphorylation that increases during the kinase reaction due to autophosphorylation. The initial rate of Syk activity was strongly increased by either pre-autophosphorylation or binding of phosphorylated immune tyrosine activation motif peptides, and each of these factors independently fully activated Syk. Deletion mutagenesis was used to identify regions of Syk important for regulation, and residues 340-356 of the SH2 kinase linker region were identified to be important for suppression of activity before activation. Comparison of the activation processes of Syk and Zap-70 revealed that Syk is more readily activated by autophosphorylation than Zap-70, although both kinases are rapidly activated by Src family kinases. We also studied Syk activity in B cell lysates and found endogenous Syk is also activated by phosphorylation and immune tyrosine activation motif binding. Together these experiments show that Syk functions as an "OR-gate" type of molecular switch. This mechanism of switch-like activation helps explain how Syk is both rapidly activated after receptor binding but also sustains activity over time to facilitate longer term changes in gene expression.
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Affiliation(s)
- Emily Tsang
- Department of Inflammation Discovery, Roche Palo Alto LLC, Palo Alto, California 94304, USA
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20
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Sweeney ZK, Acharya S, Briggs A, Dunn JP, Elworthy TR, Fretland J, Giannetti AM, Heilek G, Li Y, Kaiser AC, Martin M, Saito YD, Smith M, Suh JM, Swallow S, Wu J, Hang JQ, Zhou AS, Klumpp K. Discovery of triazolinone non-nucleoside inhibitors of HIV reverse transcriptase. Bioorg Med Chem Lett 2008; 18:4348-51. [DOI: 10.1016/j.bmcl.2008.06.080] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2008] [Revised: 06/20/2008] [Accepted: 06/24/2008] [Indexed: 11/27/2022]
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21
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Giannetti AM, Halbrooks PJ, Mason AB, Vogt TM, Enns CA, Björkman PJ. The molecular mechanism for receptor-stimulated iron release from the plasma iron transport protein transferrin. Structure 2008; 13:1613-23. [PMID: 16271884 DOI: 10.1016/j.str.2005.07.016] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [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: 06/14/2005] [Revised: 07/19/2005] [Accepted: 07/23/2005] [Indexed: 01/08/2023]
Abstract
Human transferrin receptor 1 (TfR) binds iron-loaded transferrin (Fe-Tf) and transports it to acidic endosomes where iron is released in a TfR-facilitated process. Consistent with our hypothesis that TfR binding stimulates iron release from Fe-Tf at acidic pH by stabilizing the apo-Tf conformation, a TfR mutant (W641A/F760A-TfR) that binds Fe-Tf, but not apo-Tf, cannot stimulate iron release from Fe-Tf, and less iron is released from Fe-Tf inside cells expressing W641A/F760A-TfR than cells expressing wild-type TfR (wtTfR). Electron paramagnetic resonance spectroscopy shows that binding at acidic pH to wtTfR, but not W641A/F760A-TfR, changes the Tf iron binding site > or =30 A from the TfR W641/F760 patch. Mutation of Tf histidine residues predicted to interact with the W641/F760 patch eliminates TfR-dependent acceleration of iron release. Identification of TfR and Tf residues critical for TfR-facilitated iron release, yet distant from a Tf iron binding site, demonstrates that TfR transmits long-range conformational changes and stabilizes the conformation of apo-Tf to accelerate iron release from Fe-Tf.
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Affiliation(s)
- Anthony M Giannetti
- Division of Biology 114-96, California Institute of Technology, Pasadena, California 91125, USA
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22
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Schmidt PJ, Toran PT, Giannetti AM, Bjorkman PJ, Andrews NC. The transferrin receptor modulates Hfe-dependent regulation of hepcidin expression. Cell Metab 2008; 7:205-14. [PMID: 18316026 PMCID: PMC2292811 DOI: 10.1016/j.cmet.2007.11.016] [Citation(s) in RCA: 226] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2007] [Revised: 11/10/2007] [Accepted: 11/30/2007] [Indexed: 12/21/2022]
Abstract
Hemochromatosis is caused by mutations in HFE, a protein that competes with transferrin (TF) for binding to transferrin receptor 1 (TFR1). We developed mutant mouse strains to gain insight into the role of the Hfe/Tfr1 complex in regulating iron homeostasis. We introduced mutations into a ubiquitously expressed Tfr1 transgene or the endogenous Tfr1 locus to promote or prevent the Hfe/Tfr1 interaction. Under conditions favoring a constitutive Hfe/Tfr1 interaction, mice developed iron overload attributable to inappropriately low expression of the hormone hepcidin. In contrast, mice carrying a mutation that interferes with the Hfe/Tfr1 interaction developed iron deficiency associated with inappropriately high hepcidin expression. High-level expression of a liver-specific Hfe transgene in Hfe-/- mice was also associated with increased hepcidin production and iron deficiency. Together, these models suggest that Hfe induces hepcidin expression when it is not in complex with Tfr1.
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Affiliation(s)
- Paul J Schmidt
- Division of Hematology/Oncology, Children's Hospital Boston, Boston, MA 02115, USA
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23
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Giannetti AM, Koch BD, Browner MF. Surface plasmon resonance based assay for the detection and characterization of promiscuous inhibitors. J Med Chem 2008; 51:574-80. [PMID: 18181566 DOI: 10.1021/jm700952v] [Citation(s) in RCA: 139] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Promiscuous binders achieve enzyme inhibition using a nonspecific aggregation-type binding mechanism to proteins. These compounds are a source of false-positive hits in biochemical inhibition assays and should be removed from screening hit lists because they are not good candidates to initiate medicinal chemistry programs. We introduce a robust approach to identify these molecules early in the lead generation process using real time surface plasmon resonance based biosensors to observe the behavior of the binding interactions between promiscuous compounds and proteins. Furthermore, the time resolution of the assay reveals a number of distinct mechanisms that promiscuous compounds employ to inhibit enzyme function and indicate that the type of mechanism can vary depending on the protein target. A classification scheme for these compounds is presented that can be used to rapidly characterize the hits from high-throughput screens and eliminate compounds with a nonspecific mechanism of inhibition.
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24
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Tse JKY, Giannetti AM, Bradshaw JM. Thermodynamics of calmodulin trapping by Ca2+/calmodulin-dependent protein kinase II: subpicomolar Kd determined using competition titration calorimetry. Biochemistry 2007; 46:4017-27. [PMID: 17352496 DOI: 10.1021/bi700013y] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [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
Calmodulin (CaM) trapping by Ca2+/calmodulin-dependent protein kinase II (CaMKII) is a phenomenon whereby the affinity of CaM for CaMKII increases >1000-fold following CaMKII autophosphorylation. The molecular basis of this effect is not entirely understood. Binding of CaM to the phosphorylated and the unphosphorylated states of CaMKII is well mimicked by the interaction of CaM with two different length peptides taken from the CaM-binding region of CaMKII, peptides we refer to as the long and intermediate peptides. To better understand the conformational change accompanying CaM trapping, we have used isothermal titration calorimetry (ITC) to compare the binding thermodynamics of CaM to these peptides as well as to a shorter CaMKII-based peptide. Calorimetric analysis revealed that the enthalpy, rather than the entropy, distinguished binding of these three peptides. Furthermore, the heat capacity change was found to be similar for the long and intermediate peptides but smaller in magnitude for the short peptide. Direct titration of CaM with peptide provided the Kd value for the short peptide (Kd = 5.9 +/- 2.4 microM), but a novel, two-phased competitive binding strategy was necessary to ascertain the affinities of the intermediate (Kd = 0.17 +/- 0.06 nM) and long (Kd = 0.07 +/- 0.04 pM) peptides. To our knowledge, the Kd for the long peptide is the most potent measured to date using ITC. Together, the findings reported here support a model whereby the final conformational change accompanying CaM trapping buries little additional surface area but does involve formation of new hydrogen bonds and van der Waals contacts that contribute to formation of the high-affinity, CaM-trapped state.
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Affiliation(s)
- Joyce K Y Tse
- Department of Biochemical Pharmacology, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304, USA
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25
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Papalia GA, Leavitt S, Bynum MA, Katsamba PS, Wilton R, Qiu H, Steukers M, Wang S, Bindu L, Phogat S, Giannetti AM, Ryan TE, Pudlak VA, Matusiewicz K, Michelson KM, Nowakowski A, Pham-Baginski A, Brooks J, Tieman BC, Bruce BD, Vaughn M, Baksh M, Cho YH, Wit MD, Smets A, Vandersmissen J, Michiels L, Myszka DG. Comparative analysis of 10 small molecules binding to carbonic anhydrase II by different investigators using Biacore technology. Anal Biochem 2006; 359:94-105. [PMID: 17007806 DOI: 10.1016/j.ab.2006.08.021] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.6] [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: 07/20/2006] [Revised: 08/18/2006] [Accepted: 08/22/2006] [Indexed: 02/02/2023]
Abstract
In this benchmark study, 26 investigators were asked to characterize the kinetics and affinities of 10 sulfonamide inhibitors binding to the enzyme carbonic anhydrase II using Biacore optical biosensors. A majority of the participants collected data that could be fit to a 1:1 interaction model, but a subset of the data sets obtained from some instruments were of poor quality. The experimental errors in the k(a), k(d), and K(D) parameters determined for each of the compounds averaged 34, 24, and 37%, respectively. As expected, the greatest variation in the reported constants was observed for compounds with exceptionally weak affinity and/or fast association rates. The binding constants determined using the biosensor correlated well with solution-based titration calorimetry measurements. The results of this study provide insight into the challenges, as well as the level of experimental variation, that one would expect to observe when using Biacore technology for small molecule analyses.
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Affiliation(s)
- Giuseppe A Papalia
- Center for Biomolecular Interaction Analysis, School of Medicine, University of Utah, Salt Lake City, UT 84132, USA
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26
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Byrne SL, Leverence R, Klein JS, Giannetti AM, Smith VC, MacGillivray RTA, Kaltashov IA, Mason AB. Effect of glycosylation on the function of a soluble, recombinant form of the transferrin receptor. Biochemistry 2006; 45:6663-73. [PMID: 16716077 DOI: 10.1021/bi0600695] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [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] [Indexed: 11/29/2022]
Abstract
Production of the soluble portion of the transferrin receptor (sTFR) by baby hamster kidney (BHK) cells is described, and the effect of glycosylation on the biological function of sTFR is evaluated for the first time. The sTFR (residues 121-760) has three N-linked glycosylation sites (Asn251, Asn317, and Asn727). Although fully glycosylated sTFR is secreted into the tissue culture medium ( approximately 40 mg/L), no nonglycosylated sTFR could be produced, suggesting that carbohydrate is critical to the folding, stability, and/or secretion of the receptor. Mutants in which glycosylation at positions 251 and 727 (N251D and N727D) is eliminated are well expressed, whereas production of the N317D mutant is poor. Analysis by electrospray ionization mass spectrometry confirms dimerization of the sTFR and the absence of the carbohydrate at the single site in each mutant. The effect of glycosylation on binding to diferric human transferrin (Fe(2) hTF), an authentic monoferric hTF with iron in the C-lobe (designated Fe(C) hTF), and a mutant (designated Mut-Fe(C) hTF that features a 30-fold slower iron release rate) was determined by surface plasmon resonance; a small ( approximately 20%) but consistent difference is noted for the binding of Fe(C) hTF and the Mut-Fe(C) hTF to the sTFR N317D mutant. The rate of iron release from Fe(C) hTF and Mut-Fe(C) hTF in complex with the sTFR and the sTFR mutants at pH 5.6 reveals that only the N317D mutant has a significant effect. The carbohydrate at position 317 lies close to a region of the TFR previously shown to interact with hTF.
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Affiliation(s)
- Shaina L Byrne
- Department of Biochemistry, University of Vermont College of Medicine, Burlington, Vermont 05405-0068, USA
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27
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Le Pogam S, Kang H, Harris SF, Leveque V, Giannetti AM, Ali S, Jiang WR, Rajyaguru S, Tavares G, Oshiro C, Hendricks T, Klumpp K, Symons J, Browner MF, Cammack N, Nájera I. Selection and characterization of replicon variants dually resistant to thumb- and palm-binding nonnucleoside polymerase inhibitors of the hepatitis C virus. J Virol 2006; 80:6146-54. [PMID: 16731953 PMCID: PMC1472602 DOI: 10.1128/jvi.02628-05] [Citation(s) in RCA: 116] [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: 01/07/2023] Open
Abstract
Multiple nonnucleoside inhibitor binding sites have been identified within the hepatitis C virus (HCV) polymerase, including in the palm and thumb domains. After a single treatment with a thumb site inhibitor (thiophene-2-carboxylic acid NNI-1), resistant HCV replicon variants emerged that contained mutations at residues Leu419, Met423, and Ile482 in the polymerase thumb domain. Binding studies using wild-type (WT) and mutant enzymes and structure-based modeling showed that the mechanism of resistance is through the reduced binding of the inhibitor to the mutant enzymes. Combined treatment with a thumb- and a palm-binding polymerase inhibitor had a dramatic impact on the number of replicon colonies able to replicate in the presence of both inhibitors. A more exact characterization through molecular cloning showed that 97.7% of replicons contained amino acid substitutions that conferred resistance to either of the inhibitors. Of those, 65% contained simultaneously multiple amino acid substitutions that conferred resistance to both inhibitors. Double-mutant replicons Met414Leu and Met423Thr were predominantly selected, which showed reduced replication capacity compared to the WT replicon. These findings demonstrate the selection of replicon variants dually resistant to two NS5B polymerase inhibitors binding to different sites of the enzyme. Additionally, these findings provide initial insights into the in vitro mutational threshold of the HCV NS5B polymerase and the potential impact of viral fitness on the selection of multiple-resistant mutants.
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28
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Byrne SL, Leverence R, Kaltashov IA, Klein JS, Giannetti AM, Smith VC, MacGillivray RT, Mason AB. Expression and characterization of soluble transferrin receptor in BHK cells: effect of mutations at the three asparagine glycosylation sites. FASEB J 2006. [DOI: 10.1096/fasebj.20.4.a112-b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Shaina L Byrne
- BiochemistryUniversity of Vermont89 Beaumont AveBurlingtonVT05405
| | - Rachael Leverence
- ChemistryUniversity of Massachusetts at AmherstLGRT A‐701AmherstMA01003
| | - Igor A Kaltashov
- Biochemistry and Molecular BiophysicsCalifornia Institute of TechnologyPasadenaCA91125
| | - Joshua S Klein
- Biochemistry and Molecular BiophysicsCalifornia Institute of TechnologyPasadenaCA91125
| | - Anthony M Giannetti
- Biochemistry and Molecular BiophysicsCalifornia Institute of TechnologyPasadenaCA91125
| | - Valerie C Smith
- Biochemistry and Molecular BiologyUniversity of British ColumbiaBlood CenterVancouverBritish ColumbiaV6T 1Z3Canada
| | - Ross T.A MacGillivray
- Biochemistry and Molecular BiologyUniversity of British ColumbiaBlood CenterVancouverBritish ColumbiaV6T 1Z3Canada
| | - Anne B Mason
- BiochemistryUniversity of Vermont89 Beaumont AveBurlingtonVT05405
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29
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Halbrooks PJ, Giannetti AM, Klein JS, Björkman PJ, Larouche JR, Smith VC, MacGillivray RTA, Everse SJ, Mason AB. Composition of pH-sensitive triad in C-lobe of human serum transferrin. Comparison to sequences of ovotransferrin and lactoferrin provides insight into functional differences in iron release. Biochemistry 2006; 44:15451-60. [PMID: 16300393 DOI: 10.1021/bi0518693] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [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] [Indexed: 11/29/2022]
Abstract
The transferrins (TF) are a family of bilobal glycoproteins that tightly bind ferric iron. Each of the homologous N- and C-lobes contains a single iron-binding site situated in a deep cleft. Human serum transferrin (hTF) serves as the iron transport protein in the blood; circulating transferrin binds to receptors on the cell surface, and the complex is internalized by endocytosis. Within the cell, a reduction in pH leads to iron release from hTF in a receptor-dependent process resulting in a large conformational change in each lobe. In the hTF N-lobe, two critical lysines facilitate this pH-dependent conformational change allowing entry of a chelator to capture the iron. In the C-lobe, the lysine pair is replaced by a triad of residues: Lys534, Arg632, and Asp634. Previous studies show that mutation of any of these triad residues to alanine results in significant retardation of iron release at both pH 7.4 and pH 5.6. In the present work, the role of the three residues is probed further by conversion to the residues observed at the equivalent positions in ovotransferrin (Q-K-L) and human lactoferrin (K-N-N) as well as a triad with an interchanged lysine and arginine (K534R/R632K). As expected, all of the constructs bind iron and associate with the receptor with nearly the same K(D) as the wild-type monoferric hTF control. However, interesting differences in the effect of the substitutions on the iron release rate in the presence and absence of the receptor at pH 5.6 are observed. Additionally, titration with KCl indicates that position 632 must have a positively charged residue to elicit a robust rate acceleration as a function of increasing salt. On the basis of these observations, a model for iron release from the hTF C-lobe is proposed. These studies provide insight into the importance of charge and geometry of the amino acids at these positions as a partial explanation for differences in behavior of individual TF family members, human serum transferrin, ovotransferrin, and lactoferrin. The studies collectively highlight important features common to both the N- and C-lobes of TF and the critical role of the receptor in iron release.
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Affiliation(s)
- Peter J Halbrooks
- Department of Biochemistry, University of Vermont, College of Medicine, Burlington, Vermont 05405, USA
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30
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Abstract
Transferrin receptor (TfR) is a dimeric cell surface protein that binds both the serum iron transport protein transferrin (Fe-Tf) and HFE, the protein mutated in patients with the iron overload disorder hereditary hemochromatosis. HFE and Fe-Tf can bind simultaneously to TfR to form a ternary complex, but HFE binding to TfR lowers the apparent affinity of the Fe-Tf/TfR interaction. This apparent affinity reduction could result from direct competition between HFE and Fe-Tf for their overlapping binding sites on each TfR polypeptide chain, from negative cooperativity, or from a combination of both. To explore the mechanism of the affinity reduction, we constructed a heterodimeric TfR that contains mutations such that one TfR chain binds only HFE and the other binds only Fe-Tf. Binding studies using a heterodimeric form of soluble TfR demonstrate that TfR does not exhibit cooperativity in heterotropic ligand binding, suggesting that some or all of the effects of HFE on iron homeostasis result from competition with Fe-Tf for TfR binding. Experiments using transfected cell lines demonstrate a physiological role for this competition in altering HFE trafficking patterns.
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Affiliation(s)
- Anthony M Giannetti
- Graduate Option in Biochemistry and Molecular Biophysics, California Institute of Technology, Pasadena, CA 91125, USA
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31
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Abstract
Transferrin receptor 1 (TfR) plays a critical role in cellular iron import for most higher organisms. Cell surface TfR binds to circulating iron-loaded transferrin (Fe-Tf) and transports it to acidic endosomes, where low pH promotes iron to dissociate from transferrin (Tf) in a TfR-assisted process. The iron-free form of Tf (apo-Tf) remains bound to TfR and is recycled to the cell surface, where the complex dissociates upon exposure to the slightly basic pH of the blood. Fe-Tf competes for binding to TfR with HFE, the protein mutated in the iron-overload disease hereditary hemochromatosis. We used a quantitative surface plasmon resonance assay to determine the binding affinities of an extensive set of site-directed TfR mutants to HFE and Fe-Tf at pH 7.4 and to apo-Tf at pH 6.3. These results confirm the previous finding that Fe-Tf and HFE compete for the receptor by binding to an overlapping site on the TfR helical domain. Spatially distant mutations in the TfR protease-like domain affect binding of Fe-Tf, but not iron-loaded Tf C-lobe, apo-Tf, or HFE, and mutations at the edge of the TfR helical domain affect binding of apo-Tf, but not Fe-Tf or HFE. The binding data presented here reveal the binding footprints on TfR for Fe-Tf and apo-Tf. These data support a model in which the Tf C-lobe contacts the TfR helical domain and the Tf N-lobe contacts the base of the TfR protease-like domain. The differential effects of some TfR mutations on binding to Fe-Tf and apo-Tf suggest differences in the contact points between TfR and the two forms of Tf that could be caused by pH-dependent conformational changes in Tf, TfR, or both. From these data, we propose a structure-based model for the mechanism of TfR-assisted iron release from Fe-Tf. Differences in the contact points between the transferrin receptor and the two forms of transferrin (with or without iron) are consistent with pH-dependent conformational changes in transferrin, its receptor, or both
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Affiliation(s)
- Anthony M Giannetti
- 1Graduate Option in Biochemistry and Molecular Biophysics, California Institute of TechnologyPasadena, CaliforniaUnited States of America
| | - Peter M Snow
- 2Caltech Protein Expression Center, Division of Biology California Institute of TechnologyPasadena, CaliforniaUnited States of America
| | - Olga Zak
- 3Department of Physiology and Biophysics, Albert Einstein College of MedicineBronx, New YorkUnited States of America
| | - Pamela J Björkman
- 4Division of Biology and Howard Hughes Medical Institute, California Institute of TechnologyPasadena, CaliforniaUnited States of America
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Abstract
Cellular iron uptake in most tissues occurs via endocytosis of diferric transferrin (Tf) bound to the transferrin receptor (TfR). Recently, a second transferrin receptor, transferrin receptor 2 (TfR2), has been identified and shown to play a critical role in iron metabolism. TfR2 is capable of Tf-mediated iron uptake and mutations in this gene result in a rare form of hereditary hemochromatosis unrelated to the hereditary hemochromatosis protein, HFE. Unlike TfR, TfR2 expression is not controlled by cellular iron concentrations and little information is currently available regarding the role of TfR2 in cellular iron homeostasis. To investigate the relationship between TfR and TfR2, we performed a series of in vivo and in vitro experiments using antibodies generated to each receptor. Western blots demonstrate that TfR2 protein is expressed strongest in erythroid/myeloid cell lines. Metabolic labeling studies indicate that TfR2 protein levels are approximately 20-fold lower than TfR in these cells. TfR and TfR2 have similar cellular localizations in K562 cells and coimmunoprecipitate to only a very limited extent. Western analysis of the receptors under nonreducing conditions reveals that they can form heterodimers.
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Affiliation(s)
- Todd M Vogt
- Department of Cell and Developmental Biology, Oregon Health and Science University, Portland OR 97201-3098, USA
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33
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West AP, Giannetti AM, Herr AB, Bennett MJ, Nangiana JS, Pierce JR, Weiner LP, Snow PM, Bjorkman PJ. Mutational analysis of the transferrin receptor reveals overlapping HFE and transferrin binding sites. J Mol Biol 2001; 313:385-97. [PMID: 11800564 DOI: 10.1006/jmbi.2001.5048] [Citation(s) in RCA: 103] [Impact Index Per Article: 4.5] [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] [Indexed: 01/12/2023]
Abstract
The transferrin receptor (TfR) binds two proteins critical for iron metabolism: transferrin (Tf) and HFE, the protein mutated in hereditary hemochromatosis. Previous results demonstrated that Tf and HFE compete for binding to TfR, suggesting that Tf and HFE bind to the same or an overlapping site on TfR. TfR is a homodimer that binds one Tf per polypeptide chain (2:2, TfR/Tf stoichiometry), whereas both 2:1 and 2:2 TfR/HFE stoichiometries have been observed. In order to more fully characterize the interaction between HFE and TfR, we determined the binding stoichiometry using equilibrium gel-filtration and analytical ultracentrifugation. Both techniques indicate that a 2:2 TfR/HFE complex can form at submicromolar concentrations in solution, consistent with the hypothesis that HFE competes for Tf binding to TfR by blocking the Tf binding site rather than by exerting an allosteric effect. To determine whether the Tf and HFE binding sites on TfR overlap, residues at the HFE binding site on TfR were identified from the 2.8 A resolution HFE-TfR co-crystal structure, then mutated and tested for their effects on HFE and Tf binding. The binding affinities of soluble TfR mutants for HFE and Tf were determined using a surface plasmon resonance assay. Substitutions of five TfR residues at the HFE binding site (L619A, R629A, Y643A, G647A and F650Q) resulted in significant reductions in Tf binding affinity. The findings that both HFE and Tf form 2:2 complexes with TfR and that mutations at the HFE binding site affect Tf binding support a model in which HFE and Tf compete for overlapping binding sites on TfR.
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Affiliation(s)
- A P West
- Division of Biology 156-29 , California Institute of Technology, Pasadena, CA 91125, USA
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34
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Giannetti AM, Lindwall G, Chau MF, Radeke MJ, Feinstein SC, Kohlstaedt LA. Fibers of tau fragments, but not full length tau, exhibit a cross beta-structure: implications for the formation of paired helical filaments. Protein Sci 2000; 9:2427-35. [PMID: 11206064 PMCID: PMC2144525 DOI: 10.1110/ps.9.12.2427] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [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] [Indexed: 10/21/2022]
Abstract
We have used X-ray fiber diffraction to probe the structure of fibers of tau and tau fragments. Fibers of fragments from the microtubule binding domain had a cross beta-structure that closely resembles that reported both for neurofibrillary tangles found in Alzheimer's disease brain and for fibrous lesions from other protein folding diseases. In contrast, fibers of full-length tau had a different, more complex structure. Despite major differences at the molecular level, all fiber types exhibited very similar morphology by electron microscopy. These results have a number of implications for understanding the etiology of Alzheimer's and other tauopathic diseases. The morphology of the peptide fibers suggests that the region in tau corresponding to the peptides plays a critical role in the nucleation of fiber assembly. The dramatically different structure of the full length tau fibers suggests that some region in tau has enough inherent structure to interfere with the formation of cross beta-fibers. Additionally, the similar appearance by electron microscopy of fibrils with varying molecular structure suggests that different molecular arrangements may exist in other samples of fibers formed from tau.
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Affiliation(s)
- A M Giannetti
- Program in Biochemistry, California Institute of Technology, University of California, Santa Barbara 93106, USA
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