1
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Duong-Ly KC, Kuo YM, Johnson MC, Cote JM, Kollman JM, Soboloff J, Rall GF, Andrews AJ, Peterson JR. T cell activation triggers reversible inosine-5'-monophosphate dehydrogenase assembly. J Cell Sci 2018; 131:jcs.223289. [PMID: 30154209 DOI: 10.1242/jcs.223289] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 08/06/2018] [Indexed: 12/17/2022] Open
Abstract
T cell-mediated adaptive immunity requires naïve, unstimulated T cells to transition from a quiescent metabolic state into a highly proliferative state upon T cell receptor engagement. This complex process depends on transcriptional changes mediated by Ca2+-dependent NFAT signaling, mTOR-mediated signaling and increased activity of the guanine nucleotide biosynthetic inosine-5'-monophosphate (IMP) dehydrogenase 1 and 2 enzymes (IMPDH1 and IMPDH2, hereafter IMPDH). Inhibitors of these pathways serve as potent immunosuppressants. Unexpectedly, we discovered that all three pathways converge to promote the assembly of IMPDH protein into micron-scale macromolecular filamentous structures in response to T cell activation. Assembly is post-transcriptionally controlled by mTOR and the Ca2+ influx regulator STIM1. Furthermore, IMPDH assembly and catalytic activity were negatively regulated by guanine nucleotide levels, suggesting a negative feedback loop that limits biosynthesis of guanine nucleotides. Filamentous IMPDH may be more resistant to this inhibition, facilitating accumulation of the higher GTP levels required for T cell proliferation.
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Affiliation(s)
- Krisna C Duong-Ly
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Yin-Ming Kuo
- Cancer Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Matthew C Johnson
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Joy M Cote
- Cancer Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Justin M Kollman
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Jonathan Soboloff
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, PA 19140, USA
| | - Glenn F Rall
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Andrew J Andrews
- Cancer Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Jeffrey R Peterson
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
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2
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Anthony SA, Burrell AL, Johnson MC, Duong-Ly KC, Kuo YM, Simonet JC, Michener P, Andrews A, Kollman JM, Peterson JR. Reconstituted IMPDH polymers accommodate both catalytically active and inactive conformations. Mol Biol Cell 2017; 28:mbc.E17-04-0263. [PMID: 28794265 PMCID: PMC5620369 DOI: 10.1091/mbc.e17-04-0263] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 08/02/2017] [Accepted: 08/04/2017] [Indexed: 01/01/2023] Open
Abstract
Several metabolic enzymes undergo reversible polymerization into macromolecular assemblies. The function of these assemblies is often unclear but in some cases they regulate enzyme activity and metabolic homeostasis. The guanine nucleotide biosynthetic enzyme inosine monophosphate dehydrogenase (IMPDH) forms octamers that polymerize into helical chains. In mammalian cells, IMPDH filaments can associate into micron-length assemblies. Polymerization and enzyme activity are regulated in part by binding of purine nucleotides to an allosteric regulatory domain. ATP promotes octamer polymerization, whereas GTP promotes a compact, inactive conformation whose ability to polymerize is unknown. Also unclear is whether polymerization directly alters IMPDH catalytic activity. To address this, we identified point mutants of human IMPDH2 that either prevent or promote polymerization. Unexpectedly, we found that polymerized and non-assembled forms of recombinant IMPDH have comparable catalytic activity, substrate affinity, and GTP sensitivity and validated this finding in cells. Electron microscopy revealed that substrates and allosteric nucleotides shift the equilibrium between active and inactive conformations in both the octamer and the filament. Unlike other metabolic filaments, which selectively stabilize active or inactive conformations, recombinant IMPDH filaments accommodate multiple states. These conformational states are finely tuned by substrate availability and purine balance, while polymerization may allow cooperative transitions between states.
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Affiliation(s)
- Sajitha A Anthony
- Cancer Biology Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111
| | - Anika L Burrell
- Department of Biochemistry, University of Washington, 1959 NE Pacific Street, Box 357350, Seattle, WA 98195
| | - Matthew C Johnson
- Department of Biochemistry, University of Washington, 1959 NE Pacific Street, Box 357350, Seattle, WA 98195
| | - Krisna C Duong-Ly
- Cancer Biology Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111
| | - Yin-Ming Kuo
- Cancer Biology Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111
| | - Jacqueline C Simonet
- Cancer Biology Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111
| | - Peter Michener
- Department of Biochemistry & Molecular Biology, Drexel University College of Medicine, 245 N. 15th Street, Philadelphia, PA 19102
| | - Andrew Andrews
- Cancer Biology Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111
| | - Justin M Kollman
- Department of Biochemistry, University of Washington, 1959 NE Pacific Street, Box 357350, Seattle, WA 98195
| | - Jeffrey R Peterson
- Cancer Biology Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111
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3
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Abstract
Aberrant kinase signaling has been implicated in a number of diseases. While kinases have become attractive drug targets, only a small fraction of human protein kinases have validated inhibitors. Screening of libraries of compounds against a kinase or kinases of interest is routinely performed during kinase inhibitor development to identify promising scaffolds for a particular target and to identify kinase targets for compounds of interest. Screening of more focused compound libraries may also be conducted in the later stages of inhibitor development to improve potency and optimize selectivity. The dot blot kinase assay is a robust, high-throughput kinase assay that can be used to screen a number of small-molecule compounds against one kinase of interest or several kinases. Here, a protocol for a dot blot kinase assay used for measuring insulin receptor kinase activity is presented. This protocol can be readily adapted for use with other protein kinases.
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Affiliation(s)
- Krisna C Duong-Ly
- Cancer Biology Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, USA
| | - Jeffrey R Peterson
- Cancer Biology Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, USA.
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4
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Saotome K, Duong-Ly KC, Howard KP. Influenza A M2 protein conformation depends on choice of model membrane. Biopolymers 2016; 104:405-11. [PMID: 25652904 DOI: 10.1002/bip.22617] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [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: 12/15/2014] [Revised: 01/17/2015] [Accepted: 01/24/2015] [Indexed: 11/08/2022]
Abstract
While crystal and NMR structures exist of the influenza A M2 protein, there is disagreement between models. Depending on the requirements of the technique employed, M2 has been studied in a range of membrane mimetics including detergent micelles and membrane bilayers differing in lipid composition. The use of different model membranes complicates the integration of results from published studies necessary for an overall understanding of the M2 protein. Here we show using site-directed spin-label EPR spectroscopy (SDSL-EPR) that the conformations of M2 peptides in membrane bilayers are clearly influenced by the lipid composition of the bilayers. Altering the bilayer thickness or the lateral pressure profile within the bilayer membrane changes the M2 conformation observed. The multiple M2 peptide conformations observed here, and in other published studies, optimistically may be considered conformations that are sampled by the protein at various stages during influenza infectivity. However, care should be taken that the heterogeneity observed in published structures is not simply an artifact of the choice of the model membrane.
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Affiliation(s)
- Kei Saotome
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA 19081
| | - Krisna C Duong-Ly
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA 19081
| | - Kathleen P Howard
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA 19081
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5
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Duong-Ly KC, Devarajan K, Liang S, Horiuchi KY, Wang Y, Ma H, Peterson JR. Kinase Inhibitor Profiling Reveals Unexpected Opportunities to Inhibit Disease-Associated Mutant Kinases. Cell Rep 2016; 14:772-781. [PMID: 26776524 DOI: 10.1016/j.celrep.2015.12.080] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 10/30/2015] [Accepted: 12/16/2015] [Indexed: 01/01/2023] Open
Abstract
Small-molecule kinase inhibitors have typically been designed to inhibit wild-type kinases rather than the mutant forms that frequently arise in diseases such as cancer. Mutations can have serious clinical implications by increasing kinase catalytic activity or conferring therapeutic resistance. To identify opportunities to repurpose inhibitors against disease-associated mutant kinases, we conducted a large-scale functional screen of 183 known kinase inhibitors against 76 recombinant mutant kinases. The results revealed lead compounds with activity against clinically important mutant kinases, including ALK, LRRK2, RET, and EGFR, as well as unexpected opportunities for repurposing FDA-approved kinase inhibitors as leads for additional indications. Furthermore, using T674I PDGFRα as an example, we show how single-dose screening data can provide predictive structure-activity data to guide subsequent inhibitor optimization. This study provides a resource for the development of inhibitors against numerous disease-associated mutant kinases and illustrates the potential of unbiased profiling as an approach to compound-centric inhibitor development.
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Affiliation(s)
- Krisna C Duong-Ly
- Program in Cancer Biology, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
| | - Karthik Devarajan
- Department of Biostatistics and Bioinformatics, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
| | - Shuguang Liang
- Reaction Biology Corporation, 1 Great Valley Parkway, Suite 2, Malvern, PA 19355, USA
| | - Kurumi Y Horiuchi
- Reaction Biology Corporation, 1 Great Valley Parkway, Suite 2, Malvern, PA 19355, USA
| | - Yuren Wang
- Reaction Biology Corporation, 1 Great Valley Parkway, Suite 2, Malvern, PA 19355, USA
| | - Haiching Ma
- Reaction Biology Corporation, 1 Great Valley Parkway, Suite 2, Malvern, PA 19355, USA
| | - Jeffrey R Peterson
- Program in Cancer Biology, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA.
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6
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Duong-Ly KC, Devarajan K, Liang S, Horiuchi K, Wang Y, Ma H, Peterson JR. Abstract 3649: Broad profiling reveals opportunities for selective inhibition of disease-associated mutant kinases. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-3649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Small molecule kinase inhibitors are promising therapeutic agents in a number of diseases, most notably cancer. However, mutations in kinases, both intrinsic and acquired, can drastically alter inhibitor sensitivity. To identify inhibitors of disease-associated mutant kinases, we conducted an unbiased functional screen of 182 small molecule kinase inhibitors against 76 mutated recombinant kinases arising from 21 cognate wild-type kinases. The results revealed novel lead compounds that were exquisitely selective for mutant kinases, including several that exhibited preferred inhibition of mutant kinases over their cognate wild-type kinases. This study provides a resource for the development of novel small molecule inhibitors against disease-associated mutant kinases and illustrates the potential of unbiased large-scale profiling as an approach to compound-centric kinase inhibitor discovery.
Citation Format: Krisna C. Duong-Ly, Karthik Devarajan, Shuguang Liang, Kurumi Horiuchi, Yuren Wang, Haiching Ma, Jeffrey R. Peterson. Broad profiling reveals opportunities for selective inhibition of disease-associated mutant kinases. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3649. doi:10.1158/1538-7445.AM2015-3649
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Affiliation(s)
| | | | | | | | - Yuren Wang
- 2Reaction Biology Corporation, Malvern, PA
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7
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Abstract
Expression of fusion proteins such as MBP fusions can be used as a way to improve the solubility of the expressed protein in E. coli (Fox and Waugh, 2003; Nallamsetty et al., 2005; Nallamsetty and Waugh, 2006) and as a way to introduce an affinity purification tag. The protocol that follows was designed by the authors as a first step in the purification of a recombinant protein fused with MBP, using fast protein liquid chromatography (FPLC). Cells should have been thawed, resuspended in binding buffer, and lysed by sonication or microfluidization before mixing with the amylose resin or loading on the column. Slight modifications to this protocol may be made to accommodate both the protein of interest and the availability of equipment.
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Affiliation(s)
- Krisna C Duong-Ly
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 N. Wolfe St., 603 WBSB, Baltimore, MD 21205, USA
| | - Sandra B Gabelli
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 N. Wolfe St., 603 WBSB, Baltimore, MD 21205, USA.
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8
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Vijayan RSK, He P, Modi V, Duong-Ly KC, Ma H, Peterson JR, Dunbrack RL, Levy RM. Conformational analysis of the DFG-out kinase motif and biochemical profiling of structurally validated type II inhibitors. J Med Chem 2014; 58:466-79. [PMID: 25478866 PMCID: PMC4326797 DOI: 10.1021/jm501603h] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
![]()
Structural
coverage of the human kinome has been steadily increasing
over time. The structures provide valuable insights into the molecular
basis of kinase function and also provide a foundation for understanding
the mechanisms of kinase inhibitors. There are a large number of kinase
structures in the PDB for which the Asp and Phe of the DFG motif on
the activation loop swap positions, resulting in the formation of
a new allosteric pocket. We refer to these structures as “classical
DFG-out” conformations in order to distinguish them from conformations
that have also been referred to as DFG-out in the literature but that
do not have a fully formed allosteric pocket. We have completed a
structural analysis of almost 200 small molecule inhibitors bound
to classical DFG-out conformations; we find that they are recognized
by both type I and type II inhibitors. In contrast, we find that nonclassical
DFG-out conformations strongly select against type II inhibitors because
these structures have not formed a large enough allosteric pocket
to accommodate this type of binding mode. In the course of this study
we discovered that the number of structurally validated type II inhibitors
that can be found in the PDB and that are also represented in publicly
available biochemical profiling studies of kinase inhibitors is very
small. We have obtained new profiling results for several additional
structurally validated type II inhibitors identified through our conformational
analysis. Although the available profiling data for type II inhibitors
is still much smaller than for type I inhibitors, a comparison of
the two data sets supports the conclusion that type II inhibitors
are more selective than type I. We comment on the possible contribution
of the DFG-in to DFG-out conformational reorganization to the selectivity.
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Affiliation(s)
- R S K Vijayan
- Center for Biophysics & Computational Biology and Institute for Computational Molecular Science, Temple University , Philadelphia, Pennsylvania 19122, United States
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9
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Gabelli SB, Echeverria I, Alexander M, Duong-Ly KC, Chaves-Moreira D, Brower ET, Vogelstein B, Amzel LM. Activation of PI3Kα by physiological effectors and by oncogenic mutations: structural and dynamic effects. Biophys Rev 2014; 6:89-95. [PMID: 25309634 PMCID: PMC4192660 DOI: 10.1007/s12551-013-0131-1] [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] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 12/03/2013] [Indexed: 12/12/2022] Open
Abstract
PI3Kα, a heterodimeric lipid kinase, catalyzes the conversion of phosphoinositide-4,5-bisphosphate (PIP2) to phosphoinositide-3,4,5-trisphosphate (PIP3), a lipid that recruits to the plasma membrane proteins that regulate signaling cascades that control key cellular processes such as cell proliferation, carbohydrate metabolism, cell motility, and apoptosis. PI3Kα is composed of two subunits, p110α and p85, that are activated by binding to phosphorylated receptor tyrosine kinases (RTKs) or their substrates. The gene coding for p110α, PIK3CA, has been found to be mutated in a large number of tumors; these mutations result in increased PI3Kα kinase activity. The structure of the complex of p110α with a fragment of p85 containing the nSH2 and the iSH2 domains has provided valuable information about the mechanisms underlying the physiological activation of PI3Kα and its pathological activation by oncogenic mutations. This review discusses information derived from x-ray diffraction and theoretical calculations regarding the structural and dynamic effects of mutations in four highly mutated regions of PI3K p110α, as well as the proposed mechanisms by which these mutations increase kinase activity. During the physiological activation of PI3Kα, the phosphorylated tyrosine of RTKs binds to the nSH2 domain of p85, dislodging an inhibitory interaction between the p85 nSH2 and a loop of the helical domain of p110α. Several of the oncogenic mutations in p110α activate the enzyme by weakening this autoinhibitory interaction. These effects involve structural changes as well as changes in the dynamics of the enzyme. One of the most common p110α mutations, H1047R, activates PI3Kα by a different mechanism: it increases the interaction of the enzyme with the membrane, maximizing the access of the PI3Kα to its substrate PIP2, a membrane lipid.
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Affiliation(s)
- Sandra B. Gabelli
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Departments of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Departments of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Ignacia Echeverria
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Megan Alexander
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Krisna C. Duong-Ly
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Daniele Chaves-Moreira
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Evan T. Brower
- Ludwig Center for Cancer Genetics and Therapeutics and Howard Hughes Medical Institute at the Hopkins-Kimmel Cancer Center, University School of Medicine, Baltimore, MD 21231 USA
| | - B. Vogelstein
- Ludwig Center for Cancer Genetics and Therapeutics and Howard Hughes Medical Institute at the Hopkins-Kimmel Cancer Center, University School of Medicine, Baltimore, MD 21231 USA
| | - L. Mario Amzel
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
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10
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11
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Abstract
One of the most daunting problems for biochemists is the expression of recombinant proteins. Often, the host organism differs from the organism from which the gene coding for the protein of interest was derived. This article provides guidelines to determine whether or not protein expression is a problem, describes possible reasons for low protein expression, and covers several possible solutions. A protocol for measuring protein expression during E. coli cell growth and after induction is given. The reader should note that low protein expression is a complex problem that often stems from a variety of factors. Combinations of the solutions presented in this article may be required to solve a problem of protein expression. A brief overview of host cell expression systems is given, but the article primarily focuses on expression in E. coli as this is the most commonly used host organism. Some of the methods discussed here, however, may be applied to other expression systems.
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Affiliation(s)
- Krisna C Duong-Ly
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sandra B Gabelli
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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12
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Duong-Ly KC, Anastassiadis T, Deacon SW, Lafontant A, Ma H, Devarajan K, Dunbrack RL, Wu J, Peterson JR. Abstract A291: A highly selective dual insulin receptor (IR)/insulin-like growth factor 1 receptor (IGF-1R) inhibitor derived from an ERK inhibitor. Mol Cancer Ther 2013. [DOI: 10.1158/1535-7163.targ-13-a291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Dual inhibitors of the closely related receptor tyrosine kinases insulin-like growth factor 1 receptor (IGF-1R) and insulin receptor (IR) are promising therapeutic agents in cancer. Here we report an unusually selective class of dual inhibitors of IGF-1R and IR identified in a parallel screen of known kinase inhibitors against a panel of 300 human protein kinases. Biochemical and structural studies indicate that this class achieves its high selectivity by binding to the ATP-binding pocket of inactive, unphosphorylated IGF-1R/IR and stabilizing the activation loop in a native-like inactive conformation. One member of this compound family was originally reported as an inhibitor of the serine/threonine kinase ERK, a kinase that is distinct in the structure of its unphosphorylated/inactive form from IR/IGF-1R. Remarkably, this compound binds to the ATP-binding pocket of ERK in an entirely different conformation to that of IGF-1R/IR, explaining the potency against these two structurally distinct kinase families. These findings suggest a novel approach to polypharmacology in which two or more unrelated kinases are inhibited by a single compound that targets different conformations of each target kinase.
Citation Information: Mol Cancer Ther 2013;12(11 Suppl):A291.
Citation Format: Krisna C. Duong-Ly, Theonie Anastassiadis, Sean W. Deacon, Alec Lafontant, Haiching Ma, Karthik Devarajan, Roland L. Dunbrack, Jinhua Wu, Jeffrey R. Peterson. A highly selective dual insulin receptor (IR)/insulin-like growth factor 1 receptor (IGF-1R) inhibitor derived from an ERK inhibitor. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr A291.
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Affiliation(s)
| | | | | | | | | | | | | | - Jinhua Wu
- 1Fox Chase Cancer Center, Philadelphia, PA
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13
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Anastassiadis T, Duong-Ly KC, Deacon SW, Lafontant A, Ma H, Devarajan K, Dunbrack RL, Wu J, Peterson JR. A highly selective dual insulin receptor (IR)/insulin-like growth factor 1 receptor (IGF-1R) inhibitor derived from an extracellular signal-regulated kinase (ERK) inhibitor. J Biol Chem 2013; 288:28068-77. [PMID: 23935097 PMCID: PMC3784719 DOI: 10.1074/jbc.m113.505032] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [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: 01/07/2023] Open
Abstract
Dual inhibitors of the closely related receptor tyrosine kinases insulin-like growth factor 1 receptor (IGF-1R) and insulin receptor (IR) are promising therapeutic agents in cancer. Here, we report an unusually selective class of dual inhibitors of IGF-1R and IR identified in a parallel screen of known kinase inhibitors against a panel of 300 human protein kinases. Biochemical and structural studies indicate that this class achieves its high selectivity by binding to the ATP-binding pocket of inactive, unphosphorylated IGF-1R/IR and stabilizing the activation loop in a native-like inactive conformation. One member of this compound family was originally reported as an inhibitor of the serine/threonine kinase ERK, a kinase that is distinct in the structure of its unphosphorylated/inactive form from IR/IGF-1R. Remarkably, this compound binds to the ATP-binding pocket of ERK in an entirely different conformation to that of IGF-1R/IR, explaining the potency against these two structurally distinct kinase families. These findings suggest a novel approach to polypharmacology in which two or more unrelated kinases are inhibited by a single compound that targets different conformations of each target kinase.
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Affiliation(s)
- Theonie Anastassiadis
- From the Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111
| | - Krisna C. Duong-Ly
- From the Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111
| | - Sean W. Deacon
- Reaction Biology Corporation, Malvern, Pennsylvania 19355
| | - Alec Lafontant
- the Developmental Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, and
| | - Haiching Ma
- Reaction Biology Corporation, Malvern, Pennsylvania 19355
| | - Karthik Devarajan
- the Department of Biostatistics and Bioinformatics, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111
| | - Roland L. Dunbrack
- the Developmental Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, and
| | - Jinhua Wu
- the Developmental Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, and
| | - Jeffrey R. Peterson
- From the Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, , To whom correspondence should be addressed: Fox Chase Cancer Center, 333 Cottman Ave., Rm. P3165, Philadelphia, PA 19111. Tel.: 215-728-3568; Fax: 215-728-3574; E-mail:
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14
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Abstract
Protein and lipid kinases play key regulatory roles in a number of biological processes. Unsurprisingly, activating mutations in kinases have been linked to a number of disorders and diseases, most notably cancers. Thus, kinases have emerged as promising clinical targets. There are more than 500 human protein kinases and about 20 lipid kinases. Most protein kinases share a highly conserved domain, the eukaryotic protein kinase (ePK) domain, which contains the ATP and substrate-binding sites. Many inhibitors in clinical use bind to the highly conserved ATP binding site. For this reason, many kinase inhibitors are not exclusively selective for their intended targets. Furthermore, despite the current interest in kinase inhibitors, very few kinases implicated in disease have validated inhibitors. This unit describes the human kinome, ePK structure, and types of kinase inhibitors, focusing on methods to identify potent and selective kinase inhibitors.
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Affiliation(s)
- Krisna C Duong-Ly
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
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15
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Duong-Ly KC, Woo HN, Dunn CA, Xu W, Babič A, Bessman MJ, Amzel LM, Gabelli SB. A UDP-X diphosphatase from Streptococcus pneumoniae hydrolyzes precursors of peptidoglycan biosynthesis. PLoS One 2013; 8:e64241. [PMID: 23691178 PMCID: PMC3655063 DOI: 10.1371/journal.pone.0064241] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Accepted: 03/29/2013] [Indexed: 01/09/2023] Open
Abstract
The gene for a Nudix enzyme (SP_1669) was found to code for a UDP-X diphosphatase. The SP_1669 gene is localized among genes encoding proteins that participate in cell division in Streptococcus pneumoniae. One of these genes, MurF, encodes an enzyme that catalyzes the last step of the Mur pathway of peptidoglycan biosynthesis. Mur pathway substrates are all derived from UDP-glucosamine and all are potential Nudix substrates. We showed that UDP-X diphosphatase can hydrolyze the Mur pathway substrates UDP-N-acetylmuramic acid and UDP-N-acetylmuramoyl-L-alanine. The 1.39 Å resolution crystal structure of this enzyme shows that it folds as an asymmetric homodimer with two distinct active sites, each containing elements of the conserved Nudix box sequence. In addition to its Nudix catalytic activity, the enzyme has a 3'5' RNA exonuclease activity. We propose that the structural asymmetry in UDP-X diphosphatase facilitates the recognition of these two distinct classes of substrates, Nudix substrates and RNA. UDP-X diphosphatase is a prototype of a new family of Nudix enzymes with unique structural characteristics: two monomers, each consisting of an N-terminal helix bundle domain and a C-terminal Nudix domain, form an asymmetric dimer with two distinct active sites. These enzymes function to hydrolyze bacterial cell wall precursors and degrade RNA.
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Affiliation(s)
- Krisna C. Duong-Ly
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Hyun Nyun Woo
- Department of Biology and McCollum-Pratt Institute, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Christopher A. Dunn
- Department of Biology and McCollum-Pratt Institute, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - WenLian Xu
- Department of Biology and McCollum-Pratt Institute, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Andrej Babič
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Maurice J. Bessman
- Department of Biology and McCollum-Pratt Institute, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - L. Mario Amzel
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- * E-mail: (LMA); (SBG)
| | - Sandra B. Gabelli
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- * E-mail: (LMA); (SBG)
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16
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Duong-Ly KC, Gabelli SB, Xu W, Dunn CA, Schoeffield AJ, Bessman MJ, Amzel LM. The Nudix hydrolase CDP-chase, a CDP-choline pyrophosphatase, is an asymmetric dimer with two distinct enzymatic activities. J Bacteriol 2011; 193:3175-85. [PMID: 21531795 PMCID: PMC3133267 DOI: 10.1128/jb.00089-11] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [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: 01/18/2011] [Accepted: 04/22/2011] [Indexed: 11/20/2022] Open
Abstract
A Nudix enzyme from Bacillus cereus (NCBI RefSeq accession no. NP_831800) catalyzes the hydrolysis of CDP-choline to produce CMP and phosphocholine. Here, we show that in addition, the enzyme has a 3'→5' RNA exonuclease activity. The structure of the free enzyme, determined to a 1.8-Å resolution, shows that the enzyme is an asymmetric dimer. Each monomer consists of two domains, an N-terminal helical domain and a C-terminal Nudix domain. The N-terminal domain is placed relative to the C-terminal domain such as to result in an overall asymmetric arrangement with two distinct catalytic sites: one with an "enclosed" Nudix pyrophosphatase site and the other with a more open, less-defined cavity. Residues that may be important for determining the asymmetry are conserved among a group of uncharacterized Nudix enzymes from Gram-positive bacteria. Our data support a model where CDP-choline hydrolysis is catalyzed by the enclosed Nudix site and RNA exonuclease activity is catalyzed by the open site. CDP-Chase is the first identified member of a novel Nudix family in which structural asymmetry has a profound effect on the recognition of substrates.
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Affiliation(s)
- Krisna C. Duong-Ly
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Sandra B. Gabelli
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - WenLian Xu
- Department of Biology and McCollum-Pratt Institute, Johns Hopkins University, Baltimore, Maryland 21218
| | - Christopher A. Dunn
- Department of Biology and McCollum-Pratt Institute, Johns Hopkins University, Baltimore, Maryland 21218
| | | | - Maurice J. Bessman
- Department of Biology and McCollum-Pratt Institute, Johns Hopkins University, Baltimore, Maryland 21218
| | - L. Mario Amzel
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
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17
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Duong-Ly KC, Gabelli SB, Xu W, Dunn CA, Bessman MJ, Amzel LM. CDP-Chase, a CDP-Choline Pyrophosphatase, is a Member of a Novel Nudix Family in Gram-Positive Bacteria. Biophys J 2011. [DOI: 10.1016/j.bpj.2010.12.1402] [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: 11/24/2022] Open
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18
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Gabelli SB, Duong-Ly KC, Brower ET, Amzel LM. Capitalizing on tumor genotyping: towards the design of mutation specific inhibitors of phosphoinsitide-3-kinase. ACTA ACUST UNITED AC 2010; 51:273-9. [PMID: 21035489 DOI: 10.1016/j.advenzreg.2010.09.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2010] [Accepted: 09/27/2010] [Indexed: 10/18/2022]
Abstract
PI3Ks catalyze the phosphorylation of the inositol hydroxyls of phosphoinositide membrane components. The changes in phosphorylation of the inositides recruit proteins to the plasma membrane that initiate important signaling cascades. PI3Kα, one of the class IA PI3Ks, is highly mutated in cancers. All mutations analyzed result in an increase in enzymatic activity. The structures of this enzyme determined by X-ray diffraction, provide a framework for analyzing the possible structural effect of these mutations and their effect on the enzymatic activity. Many of the mutations occur at domain interfaces where they can affect domain interactions and relieve the inhibition of the wild-type enzyme by the nSH2 domain of p85. This mechanism is analogous to the mechanism of physiological activation by activated tyrosine-kinase receptors in which the phosphorylated tyrosine of the receptor (or their substrates) dislodges the nSH2 from its inhibitory position in the complex by competing with its binding to a loop in the helical domain. Other mutations in the kinase domain can directly affect the conformation of the catalytic site. One mutation, His1047Arg, uses a completely different mechanism: it changes the conformation of the C-terminal loop in such a way that it increases the interaction of the enzyme with the membrane, granting increased access to the phosphoinositide substrates. Taking advantage of the reliance of some cancers on the increased activity of mutated PI3Kα, will require the development of isoform-specific, mutant-specific inhibitors. The structural, biochemical and physiological data that are becoming available for PI3Ks are an important first step in this direction.
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Affiliation(s)
- Sandra B Gabelli
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Abstract
The M2 protein from influenza A virus is a 97-amino-acid protein with a single transmembrane helix that forms proton-selective channels essential to virus function. The hydrophobic transmembrane domain of the M2 protein (M2TM) contains a sequence motif that mediates the formation of functional tetramers in membrane environments. A variety of structural models have previously been proposed which differ in the degree of helix tilt, with proposed tilts ranging from approximately 15 degrees to 38 degrees . An important issue for understanding the structure of M2TM is the role of peptide-lipid interactions in the stabilization of the lipid bilayer bound tetramer. Here, we labeled the N terminus of M2TM with a nitroxide and studied the tetramer reconstituted into lipid bilayers of different thicknesses using EPR spectroscopy. Analyses of spectral changes provide evidence that the lipid bilayer does influence the conformation. The structural plasticity displayed by M2TM in response to membrane composition may be indicative of functional requirements for conformational change. The various structural models for M2TM proposed to date--each defined by a different set of criteria and in a different environment--might provide snapshots of the distinct conformational states sampled by the protein.
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Affiliation(s)
- Krisna C Duong-Ly
- Department of Chemistry, Swarthmore College, Swarthmore, PA 19081, USA
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