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Hassan MM, Li YD, Ma MW, Teng M, Byun WS, Puvar K, Lumpkin R, Sandoval B, Rutter JC, Jin CY, Wang MY, Xu S, Schmoker AM, Cheong H, Groendyke BJ, Qi J, Fischer ES, Ebert BL, Gray NS. Exploration of the Tunability of BRD4 Degradation by DCAF16 Trans-labelling Covalent Glues. bioRxiv 2023:2023.10.07.561308. [PMID: 37873358 PMCID: PMC10592706 DOI: 10.1101/2023.10.07.561308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Small molecules that can induce protein degradation by inducing proximity between a desired target and an E3 ligase have the potential to greatly expand the number of proteins that can be manipulated pharmacologically. Current strategies for targeted protein degradation are mostly limited in their target scope to proteins with preexisting ligands. Alternate modalities such as molecular glues, as exemplified by the glutarimide class of ligands for the CUL4CRBN ligase, have been mostly discovered serendipitously. We recently reported a trans-labelling covalent glue mechanism which we named 'Template-assisted covalent modification', where an electrophile decorated small molecule binder of BRD4 was effectively delivered to a cysteine residue on an E3 ligase DCAF16 as a consequence of a BRD4-DCAF16 protein-protein interaction. Herein, we report our medicinal chemistry efforts to evaluate how various electrophilic modifications to the BRD4 binder, JQ1, affect DCAF16 trans-labeling and subsequent BRD4 degradation efficiency. We discovered a decent correlation between the ability of the electrophilic small molecule to induce ternary complex formation between BRD4 and DCAF16 with its ability to induce BRD4 degradation. Moreover, we show that a more solvent-exposed warhead presentation is optimal for DCAF16 recruitment and subsequent BRD4 degradation. Unlike the sensitivity of CUL4CRBN glue degraders to chemical modifications, the diversity of covalent attachments in this class of BRD4 glue degraders suggests a high tolerance and tunability for the BRD4-DCAF16 interaction. This offers a potential new avenue for a rational design of covalent glue degraders by introducing covalent warheads to known binders.
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Affiliation(s)
- Muhammad Murtaza Hassan
- Department of Chemical and Systems Biology, ChEM-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA
| | - Yen-Der Li
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Michelle W. Ma
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Mingxing Teng
- Center for Drug Discovery, Department of Pathology & Immunology, and Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX
| | - Woong Sub Byun
- Department of Chemical and Systems Biology, ChEM-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA
| | - Kedar Puvar
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Ryan Lumpkin
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Brittany Sandoval
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Justine C. Rutter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Cyrus Y. Jin
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Michelle Y. Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
| | - Shawn Xu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Anna M. Schmoker
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Hakyung Cheong
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | | | - Jun Qi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
| | - Eric S. Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Benjamin L. Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
- Howard Hughes Medical Institute, Boston, MA
| | - Nathanael S. Gray
- Department of Chemical and Systems Biology, ChEM-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA
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Li YD, Ma MW, Hassan MM, Hunkeler M, Teng M, Puvar K, Lumpkin R, Sandoval B, Jin CY, Ficarro SB, Wang MY, Xu S, Groendyke BJ, Sigua LH, Tavares I, Zou C, Tsai JM, Park PMC, Yoon H, Majewski FC, Marto JA, Qi J, Nowak RP, Donovan KA, Słabicki M, Gray NS, Fischer ES, Ebert BL. Template-assisted covalent modification of DCAF16 underlies activity of BRD4 molecular glue degraders. bioRxiv 2023:2023.02.14.528208. [PMID: 36824856 PMCID: PMC9949066 DOI: 10.1101/2023.02.14.528208] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Small molecules that induce protein-protein interactions to exert proximity-driven pharmacology such as targeted protein degradation are a powerful class of therapeutics1-3. Molecular glues are of particular interest given their favorable size and chemical properties and represent the only clinically approved degrader drugs4-6. The discovery and development of molecular glues for novel targets, however, remains challenging. Covalent strategies could in principle facilitate molecular glue discovery by stabilizing the neo-protein interfaces. Here, we present structural and mechanistic studies that define a trans-labeling covalent molecular glue mechanism, which we term "template-assisted covalent modification". We found that a novel series of BRD4 molecular glue degraders act by recruiting the CUL4DCAF16 ligase to the second bromodomain of BRD4 (BRD4BD2). BRD4BD2, in complex with DCAF16, serves as a structural template to facilitate covalent modification of DCAF16, which stabilizes the BRD4-degrader-DCAF16 ternary complex formation and facilitates BRD4 degradation. A 2.2 Å cryo-electron microscopy structure of the ternary complex demonstrates that DCAF16 and BRD4BD2 have pre-existing structural complementarity which optimally orients the reactive moiety of the degrader for DCAF16Cys58 covalent modification. Systematic mutagenesis of both DCAF16 and BRD4BD2 revealed that the loop conformation around BRD4His437, rather than specific side chains, is critical for stable interaction with DCAF16 and BD2 selectivity. Together our work establishes "template-assisted covalent modification" as a mechanism for covalent molecular glues, which opens a new path to proximity driven pharmacology.
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Affiliation(s)
- Yen-Der Li
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Michelle W. Ma
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Muhammad Murtaza Hassan
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford , School of Medicine, Stanford University, Stanford, CA
| | - Moritz Hunkeler
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Mingxing Teng
- Department of Pathology & Immunology, and Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX
| | - Kedar Puvar
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Ryan Lumpkin
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Brittany Sandoval
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Cyrus Y. Jin
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Scott B. Ficarro
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Blais Proteomics Center, and Center for Emergent Drug Targets, Dana-Farber Cancer Institute, Boston, MA
| | - Michelle Y. Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
| | - Shawn Xu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | | | - Logan H. Sigua
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
| | - Isidoro Tavares
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Blais Proteomics Center, and Center for Emergent Drug Targets, Dana-Farber Cancer Institute, Boston, MA
| | - Charles Zou
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Jonathan M. Tsai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA
| | - Paul M. C. Park
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Hojong Yoon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Felix C. Majewski
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford , School of Medicine, Stanford University, Stanford, CA
| | - Jarrod A. Marto
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Blais Proteomics Center, and Center for Emergent Drug Targets, Dana-Farber Cancer Institute, Boston, MA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA
| | - Jun Qi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
| | - Radosław P. Nowak
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Katherine A. Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Mikołaj Słabicki
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Nathanael S. Gray
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford , School of Medicine, Stanford University, Stanford, CA
| | - Eric S. Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Benjamin L. Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
- Howard Hughes Medical Institute, Boston, MA
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Koochaki SHJ, Słabicki M, Lumpkin R, Zou C, Belizaire R, Fischer ES, Ebert BL. A STUB1 ubiquitin ligase/CHIC2 protein complex negatively regulates the IL-3, IL-5, and GM-CSF cytokine receptor common β chain (CSF2RB) protein stability. J Biol Chem 2022; 298:102484. [PMID: 36108743 PMCID: PMC9574515 DOI: 10.1016/j.jbc.2022.102484] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 04/15/2022] [Revised: 09/01/2022] [Accepted: 09/04/2022] [Indexed: 02/02/2023] Open
Abstract
The IL-3, IL-5, and GM-CSF family of cytokines play an essential role in the growth, differentiation, and effector functions of multiple hematopoietic cell types. Receptors in this family are composed of cytokine-specific α chains and a common β chain (CSF2RB), responsible for the majority of downstream signaling. CSF2RB abundance and stability influence the magnitude of the cellular response to cytokine stimulation, but the exact mechanisms of regulation are not well understood. Here, we use genetic screens in multiple cellular contexts and cytokine conditions to identify STUB1, an E3 ubiquitin ligase, and CHIC2 as regulators of CSF2RB ubiquitination and protein stability. We demonstrate that Stub1 and Chic2 form a complex that binds Csf2rb and that genetic inactivation of either Stub1 or Chic2 leads to reduced ubiquitination of Csf2rb. The effects of Stub1 and Chic2 on Csf2rb were greatest at reduced cytokine concentrations, suggesting that Stub1/Chic2-mediated regulation of Csf2rb is a mechanism of reducing cell surface accumulation when cytokine levels are low. Our study uncovers a mechanism of CSF2RB regulation through ubiquitination and lysosomal degradation and describes a role for CHIC2 in the regulation of a cytokine receptor.
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Affiliation(s)
- Sebastian H J Koochaki
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA; Harvard-MIT MD/PhD Program, Harvard Medical School, Boston, Massachusetts, USA
| | - Mikołaj Słabicki
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Ryan Lumpkin
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Charles Zou
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Roger Belizaire
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Benjamin L Ebert
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA; Howard Hughes Medical Institute, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.
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4
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Kersalé M, Meinen CS, Perez RC, Le Hénaff M, Valla D, Lamont T, Sato OT, Dong S, Terre T, van Caspel M, Chidichimo MP, van den Berg M, Speich S, Piola AR, Campos EJD, Ansorge I, Volkov DL, Lumpkin R, Garzoli SL. Highly variable upper and abyssal overturning cells in the South Atlantic. Sci Adv 2020; 6:eaba7573. [PMID: 32821826 PMCID: PMC7406378 DOI: 10.1126/sciadv.aba7573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 06/25/2020] [Indexed: 06/11/2023]
Abstract
The Meridional Overturning Circulation (MOC) is a primary mechanism driving oceanic heat redistribution on Earth, thereby affecting Earth's climate and weather. However, the full-depth structure and variability of the MOC are still poorly understood, particularly in the South Atlantic. This study presents unique multiyear records of the oceanic volume transport of both the upper (<~3100 meters) and abyssal (>~3100 meters) overturning cells based on daily moored measurements in the South Atlantic at 34.5°S. The vertical structure of the time-mean flows is consistent with the limited historical observations. Both the upper and abyssal cells exhibit a high degree of variability relative to the temporal means at time scales, ranging from a few days to a few weeks. Observed variations in the abyssal flow appear to be largely independent of the flow in the overlying upper cell. No meaningful trends are detected in either cell.
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Affiliation(s)
- M. Kersalé
- Cooperative Institute for Marine and Atmospheric Studies, University of Miami, Miami, FL, USA
- NOAA Atlantic Oceanographic and Meteorological Laboratory, Miami, FL, USA
| | - C. S. Meinen
- NOAA Atlantic Oceanographic and Meteorological Laboratory, Miami, FL, USA
| | - R. C. Perez
- NOAA Atlantic Oceanographic and Meteorological Laboratory, Miami, FL, USA
| | - M. Le Hénaff
- Cooperative Institute for Marine and Atmospheric Studies, University of Miami, Miami, FL, USA
- NOAA Atlantic Oceanographic and Meteorological Laboratory, Miami, FL, USA
| | - D. Valla
- Servicio de Hidrografía Naval, Buenos Aires, Argentina
| | - T. Lamont
- Oceans and Coasts Research Branch, Department of Environmental Affairs, Cape Town, South Africa
- Department of Oceanography, University of Cape Town, Rondebosch 7701, South Africa
| | - O. T. Sato
- Oceanographic Institute, University of São Paulo, São Paulo, Brazil
| | - S. Dong
- NOAA Atlantic Oceanographic and Meteorological Laboratory, Miami, FL, USA
| | - T. Terre
- IFREMER, University of Brest, CNRS, IRD, Laboratoire d'Océanographie Physique et Spatiale (LOPS), IUEM, Plouzané, France
| | - M. van Caspel
- Oceanographic Institute, University of São Paulo, São Paulo, Brazil
| | - M. P. Chidichimo
- Servicio de Hidrografía Naval, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
- Instituto Franco-Argentino sobre Estudio del Clima y sus Impactos (UMI-IFAECI/CNRS-CONICET-UBA), Buenos Aires, Argentina
| | - M. van den Berg
- Oceans and Coasts Research Branch, Department of Environmental Affairs, Cape Town, South Africa
| | - S. Speich
- Laboratoire de Météorologie Dynamique–IPSL, Ecole Normale Supérieure, Paris, France
| | - A. R. Piola
- Servicio de Hidrografía Naval, Buenos Aires, Argentina
- Instituto Franco-Argentino sobre Estudio del Clima y sus Impactos (UMI-IFAECI/CNRS-CONICET-UBA), Buenos Aires, Argentina
- Universidad de Buenos Aires, Buenos Aires, Argentina
| | - E. J. D. Campos
- Oceanographic Institute, University of São Paulo, São Paulo, Brazil
- Department of Biology, Chemistry and Environmental Sciences, School of Arts and Sciences, American University of Sharjah, Sharjah, United Arab Emirates
| | - I. Ansorge
- Department of Oceanography, University of Cape Town, Rondebosch 7701, South Africa
| | - D. L. Volkov
- Cooperative Institute for Marine and Atmospheric Studies, University of Miami, Miami, FL, USA
- NOAA Atlantic Oceanographic and Meteorological Laboratory, Miami, FL, USA
| | - R. Lumpkin
- NOAA Atlantic Oceanographic and Meteorological Laboratory, Miami, FL, USA
| | - S. L. Garzoli
- Cooperative Institute for Marine and Atmospheric Studies, University of Miami, Miami, FL, USA
- NOAA Atlantic Oceanographic and Meteorological Laboratory, Miami, FL, USA
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Lumpkin R, Komives E. The Dynamic Self-regulation of Modular Cullin-Ring Ligases. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.2266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Lumpkin R, Ahmad A, Chan M, Komives E. Dynamics and Assembly of ASB-Containing E3 Ubiquitin Ligases. Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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Lumpkin R. Structure and Function of the ASB-Containing E3 Ligases. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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9
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Abstract
Amylin is a 37 amino acid hormone, co-secreted with insulin from the pancreatic beta-cell in response to nutrient stimuli. Because the human amylin analog, pramlintide, is being tested in patients with diabetes mellitus, a known risk factor for nephropathy, we examined the role of the kidney on amylin and pramlintide metabolism and action in functionally nephrectomized rats. Nephrectomy markedly altered amylin metabolism: it increased incremental area under the plasma amylin concentration curve 3.6-fold (P<0.001) and increased the elimination half-life from 17+/-1 to 26+/-2 minutes (P < 0.01) after subcutaneous injection of 100 microg amylin. Nephrectomy decreased plasma amylin clearance from 20.3+/-1.1 to 7.9+/-0.4 mL/min (P < 0.0001). Thus, at these doses in the rat, the kidney is important for metabolizing amylin and pramlintide.
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Affiliation(s)
- W Vine
- Amylin Pharmaceuticals Inc., San Diego, CA 92121, USA
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Lumpkin R. The physical suffering of Christ. J Med Assoc State Ala 1978; 47:8-10, 47. [PMID: 347018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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