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Kim SS, Alves MJ, Gygli P, Otero J, Lindert S. Identification of Novel Cyclin A2 Binding Site and Nanomolar Inhibitors of Cyclin A2-CDK2 Complex. Curr Comput Aided Drug Des 2021; 17:57-68. [PMID: 31889491 DOI: 10.2174/1573409916666191231113055] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 11/25/2019] [Accepted: 12/09/2019] [Indexed: 01/10/2023]
Abstract
BACKGROUND Given the diverse roles of cyclin A2 both in cell cycle regulation and in DNA damage response, identifying small molecule regulators of cyclin A2 activity carries significant potential to regulate diverse cellular processes in both ageing/neurodegeneration and in cancer. OBJECTIVE Based on cyclin A2's recently discovered role in DNA repair, we hypothesized that small molecule inhibitors that were predicted to bind to both cyclin A2 and CDK2 will be useful as a radiosensitizer of cancer cells. In this study, we used structure-based drug discovery to find inhibitors that target both cyclin A2 and CDK2. METHODS Molecular dynamics simulations were used to generate diverse binding pocket conformations for application of the relaxed complex scheme. We then used structure-based virtual screening to find potential dual cyclin A2 and CDK2 inhibitors. Based on a consensus score of docked poses from Glide and AutoDock Vina, we identified about 40 promising hit compounds, where all PAINS scaffolds were removed from consideration. A biochemical luminescence assay of cyclin A2-CDK2 function was used for experimental verification. RESULTS Four lead inhibitors of cyclin A2-CDK2 complex have been identified using a relaxed complex scheme virtual screen have been verified in a biochemical luminescence assay of cyclin A2- CDK2 function. Two of the four lead inhibitors had inhibitory concentrations in the nanomolar range. CONCLUSION The four cyclin A2-CDK2 complex inhibitors are the first reported inhibitors that were specifically designed not to target the cyclin A2-CDK2 protein-protein interface. Overall, our results highlight the potential of combined advanced computational tools and biochemical verification to discover novel binding scaffolds.
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Affiliation(s)
- Stephanie S Kim
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, 43210, United States
| | - Michele J Alves
- Departments of Neuroscience, Pathology and Neuropathology, Ohio State University, Columbus, OH, 43210, United States
| | - Patrick Gygli
- Departments of Neuroscience, Pathology and Neuropathology, Ohio State University, Columbus, OH, 43210, United States
| | - Jose Otero
- Departments of Neuroscience, Pathology and Neuropathology, Ohio State University, Columbus, OH, 43210, United States
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, 43210, United States
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2
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Timón-Gómez A, Bartley-Dier EL, Fontanesi F, Barrientos A. HIGD-Driven Regulation of Cytochrome c Oxidase Biogenesis and Function. Cells 2020; 9:cells9122620. [PMID: 33291261 PMCID: PMC7762129 DOI: 10.3390/cells9122620] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/02/2020] [Accepted: 12/04/2020] [Indexed: 12/24/2022] Open
Abstract
The biogenesis and function of eukaryotic cytochrome c oxidase or mitochondrial respiratory chain complex IV (CIV) undergo several levels of regulation to adapt to changing environmental conditions. Adaptation to hypoxia and oxidative stress involves CIV subunit isoform switch, changes in phosphorylation status, and modulation of CIV assembly and enzymatic activity by interacting factors. The latter include the Hypoxia Inducible Gene Domain (HIGD) family yeast respiratory supercomplex factors 1 and 2 (Rcf1 and Rcf2) and two mammalian homologs of Rcf1, the proteins HIGD1A and HIGD2A. Whereas Rcf1 and Rcf2 are expressed constitutively, expression of HIGD1A and HIGD2A is induced under stress conditions, such as hypoxia and/or low glucose levels. In both systems, the HIGD proteins localize in the mitochondrial inner membrane and play a role in the biogenesis of CIV as a free unit or as part as respiratory supercomplexes. Notably, they remain bound to assembled CIV and, by modulating its activity, regulate cellular respiration. Here, we will describe the current knowledge regarding the specific and overlapping roles of the several HIGD proteins in physiological and stress conditions.
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Affiliation(s)
- Alba Timón-Gómez
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, USA;
| | - Emma L. Bartley-Dier
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA; (E.L.B.-D.); (F.F.)
| | - Flavia Fontanesi
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA; (E.L.B.-D.); (F.F.)
| | - Antoni Barrientos
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, USA;
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA; (E.L.B.-D.); (F.F.)
- Correspondence:
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3
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Functional Stability of the Human Kappa Opioid Receptor Reconstituted in Nanodiscs Revealed by a Time-Resolved Scintillation Proximity Assay. PLoS One 2016; 11:e0150658. [PMID: 27035823 PMCID: PMC4817975 DOI: 10.1371/journal.pone.0150658] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 02/16/2016] [Indexed: 11/19/2022] Open
Abstract
Long-term functional stability of isolated membrane proteins is crucial for many in vitro applications used to elucidate molecular mechanisms, and used for drug screening platforms in modern pharmaceutical industry. Compared to soluble proteins, the understanding at the molecular level of membrane proteins remains a challenge. This is partly due to the difficulty to isolate and simultaneously maintain their structural and functional stability, because of their hydrophobic nature. Here we show, how scintillation proximity assay can be used to analyze time-resolved high-affinity ligand binding to membrane proteins solubilized in various environments. The assay was used to establish conditions that preserved the biological function of isolated human kappa opioid receptor. In detergent solution the receptor lost high-affinity ligand binding to a radiolabelled ligand within minutes at room temperature. After reconstitution in Nanodiscs made of phospholipid bilayer the half-life of high-affinity ligand binding to the majority of receptors increased 70-fold compared to detergent solubilized receptors—a level of stability that is appropriate for further downstream applications. Time-resolved scintillation proximity assay has the potential to screen numerous conditions in parallel to obtain high levels of stable and active membrane proteins, which are intrinsically unstable in detergent solution, and with minimum material consumption.
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4
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Li Q, Duan MJ, Li SS, Zhang YL, Qiao P, Bian LJ. Recognition and binding of voltage-dependent anion channel-1 with ATP and NADH by spectroscopic analysis and molecular docking. RSC Adv 2016. [DOI: 10.1039/c5ra27694b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Recognition and binding of voltage-dependent anion channel-1 with ATP and NADH by spectroscopic analysis and molecular docking.
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Affiliation(s)
- Q. Li
- College of Life Science
- Northwest University
- Xi'an 710069
- China
| | - M. J. Duan
- College of Life Science
- Northwest University
- Xi'an 710069
- China
| | - S. S. Li
- College of Life Science
- Northwest University
- Xi'an 710069
- China
| | - Y. L. Zhang
- College of Life Science
- Northwest University
- Xi'an 710069
- China
| | - P. Qiao
- College of Life Science
- Northwest University
- Xi'an 710069
- China
| | - L. J. Bian
- College of Life Science
- Northwest University
- Xi'an 710069
- China
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5
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Bartolowits M, Davisson VJ. Considerations of Protein Subpockets in Fragment-Based Drug Design. Chem Biol Drug Des 2015; 87:5-20. [PMID: 26307335 DOI: 10.1111/cbdd.12631] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
While the fragment-based drug design approach continues to gain importance, gaps in the tools and methods available in the identification and accurate utilization of protein subpockets have limited the scope. The importance of these features of small molecule-protein recognition is highlighted with several examples. A generalized solution for the identification of subpockets and corresponding chemical fragments remains elusive, but there are numerous advancements in methods that can be used in combination to address subpockets. Finally, additional examples of approaches that consider the relative importance of small-molecule co-dependence of protein conformations are highlighted to emphasize an increased significance of subpockets, especially at protein interfaces.
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Affiliation(s)
- Matthew Bartolowits
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Dr., West Lafayette, IN, 47907, USA
| | - V Jo Davisson
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Dr., West Lafayette, IN, 47907, USA
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Abstract
The large-scale production of recombinant G protein-coupled receptors (GPCRs) is one of the major bottlenecks that hamper functional and structural studies of this important class of integral membrane proteins. Heterologous overexpression of GPCRs often results in low yields of active protein, usually due to a combination of several factors, such as low expression levels, protein insolubility, host cell toxicity, and the need to use harsh and often denaturing detergents (e.g., SDS, LDAO, OG, and DDM, among others) to extract the recombinant receptor from the host cell membrane. Many of these problematic issues are inherently linked to cell-based expression systems and can therefore be circumvented by the use of cell-free systems. In this unit, we provide a range of protocols for the production of GPCRs in a cell-free expression system. Using this system, we typically obtain GPCR expression levels of ∼1 mg per ml of reaction mixture in the continuous-exchange configuration. Although the protocols in this unit have been optimized for the cell-free expression of GPCRs, they should provide a good starting point for the production of other classes of membrane proteins, such as ion channels, aquaporins, carrier proteins, membrane-bound enzymes, and even large molecular complexes.
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Affiliation(s)
- Kenneth Segers
- VIB Center for the Biology of Disease, Flanders Institute for Biotechnology (VIB), Leuven, Belgium.,Structural Biology Group, Biologics Research Europe, Janssen Research & Development, Beerse, Belgium
| | - Stefan Masure
- Structural Biology Group, Biologics Research Europe, Janssen Research & Development, Beerse, Belgium
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Henrich E, Hein C, Dötsch V, Bernhard F. Membrane protein production in Escherichia coli cell-free lysates. FEBS Lett 2015; 589:1713-22. [PMID: 25937121 DOI: 10.1016/j.febslet.2015.04.045] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 04/17/2015] [Accepted: 04/21/2015] [Indexed: 01/01/2023]
Abstract
Cell-free protein production has become a core technology in the rapidly spreading field of synthetic biology. In particular the synthesis of membrane proteins, highly problematic proteins in conventional cellular production systems, is an ideal application for cell-free expression. A large variety of artificial as well as natural environments for the optimal co-translational folding and stabilization of membrane proteins can rationally be designed. The high success rate of cell-free membrane protein production allows to focus on individually selected targets and to modulate their functional and structural properties with appropriate supplements. The efficiency and robustness of lysates from Escherichia coli strains allow a wide diversity of applications and we summarize current strategies for the successful production of high quality membrane protein samples.
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Affiliation(s)
- Erik Henrich
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt-am-Main, Germany
| | - Christopher Hein
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt-am-Main, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt-am-Main, Germany
| | - Frank Bernhard
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt-am-Main, Germany.
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8
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Ameri K, Maltepe E. HIGD1A-mediated dormancy and tumor survival. Mol Cell Oncol 2015; 2:e1030537. [PMID: 27308509 DOI: 10.1080/23723556.2015.1030537] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 03/10/2015] [Accepted: 03/11/2015] [Indexed: 12/24/2022]
Abstract
Solid tumors contain regions of anoxia that are also glucose deprived. How cancer cells survive such extreme conditions remains unclear. Here, we discuss our recent findings that regulation of hypoxia inducible gene domain family member 1 A (HIGD1A) via epigenetic mechanisms during glucose starvation modulates oxygen consumption and reactive oxygen species production to enable tumor cell survival through the activation of dormancy mechanisms.
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Affiliation(s)
- Kurosh Ameri
- Department of Pediatrics; University of California, San Francisco ; San Francisco, CA, USA
| | - Emin Maltepe
- Department of Pediatrics; University of California, San Francisco; San Francisco, CA, USA; Department of Biomedical Sciences; University of California, San Francisco; San Francisco, CA, USA; Department of Developmental and Stem Cell Biology; University of California, San Francisco; San Francisco, CA, USA
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9
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Ameri K, Jahangiri A, Rajah AM, Tormos KV, Nagarajan R, Pekmezci M, Nguyen V, Wheeler ML, Murphy MP, Sanders TA, Jeffrey SS, Yeghiazarians Y, Rinaudo PF, Costello JF, Aghi MK, Maltepe E. HIGD1A Regulates Oxygen Consumption, ROS Production, and AMPK Activity during Glucose Deprivation to Modulate Cell Survival and Tumor Growth. Cell Rep 2015; 10:891-899. [PMID: 25683712 DOI: 10.1016/j.celrep.2015.01.020] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 10/27/2014] [Accepted: 01/09/2015] [Indexed: 02/07/2023] Open
Abstract
Hypoxia-inducible gene domain family member 1A (HIGD1A) is a survival factor induced by hypoxia-inducible factor 1 (HIF-1). HIF-1 regulates many responses to oxygen deprivation, but viable cells within hypoxic perinecrotic solid tumor regions frequently lack HIF-1α. HIGD1A is induced in these HIF-deficient extreme environments and interacts with the mitochondrial electron transport chain to repress oxygen consumption, enhance AMPK activity, and lower cellular ROS levels. Importantly, HIGD1A decreases tumor growth but promotes tumor cell survival in vivo. The human Higd1a gene is located on chromosome 3p22.1, where many tumor suppressor genes reside. Consistent with this, the Higd1a gene promoter is differentially methylated in human cancers, preventing its hypoxic induction. However, when hypoxic tumor cells are confronted with glucose deprivation, DNA methyltransferase activity is inhibited, enabling HIGD1A expression, metabolic adaptation, and possible dormancy induction. Our findings therefore reveal important new roles for this family of mitochondrial proteins in cancer biology.
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Affiliation(s)
- Kurosh Ameri
- Department of Pediatrics/Biomedical Sciences, University of California San Francisco, San Francisco, CA 94143, USA
| | - Arman Jahangiri
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94143, USA
| | - Anthony M Rajah
- Department of Pediatrics/Biomedical Sciences, University of California San Francisco, San Francisco, CA 94143, USA
| | - Kathryn V Tormos
- Department of Pediatrics/Biomedical Sciences, University of California San Francisco, San Francisco, CA 94143, USA
| | - Ravi Nagarajan
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94143, USA
| | - Melike Pekmezci
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Vien Nguyen
- Department of Biomedical Sciences, University of California San Francisco, San Francisco, CA 94143, USA
| | - Matthew L Wheeler
- Department of Microbiology/Immunology, University of California San Francisco, San Francisco, CA 94143, USA
| | | | - Timothy A Sanders
- Department of Pediatrics/Biomedical Sciences, University of California San Francisco, San Francisco, CA 94143, USA
| | - Stefanie S Jeffrey
- Department of Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yerem Yeghiazarians
- Department of Medicine/CVRI/Eli and Edythe Broad Center for Regeneration Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Paolo F Rinaudo
- Department of Obstetrics, Gynecology/Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA
| | - Joseph F Costello
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94143, USA
| | - Manish K Aghi
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94143, USA
| | - Emin Maltepe
- Department of Pediatrics/Biomedical Sciences, University of California San Francisco, San Francisco, CA 94143, USA.
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10
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Gupta A, Iyer BR, Chaturvedi D, Maurya SR, Mahalakshmi R. Thermodynamic, structural and functional properties of membrane protein inclusion bodies are analogous to purified counterparts: case study from bacteria and humans. RSC Adv 2015. [DOI: 10.1039/c4ra11207e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Purification-free transmembrane protein inclusion body preparations for rapid and cost-effective biophysical, functional and structural studies.
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Affiliation(s)
- Ankit Gupta
- Molecular Biophysics Laboratory
- Department of Biological Sciences
- Indian Institute of Science Education and Research
- Bhopal
- India
| | - Bharat Ramasubramanian Iyer
- Molecular Biophysics Laboratory
- Department of Biological Sciences
- Indian Institute of Science Education and Research
- Bhopal
- India
| | - Deepti Chaturvedi
- Molecular Biophysics Laboratory
- Department of Biological Sciences
- Indian Institute of Science Education and Research
- Bhopal
- India
| | - Svetlana Rajkumar Maurya
- Molecular Biophysics Laboratory
- Department of Biological Sciences
- Indian Institute of Science Education and Research
- Bhopal
- India
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory
- Department of Biological Sciences
- Indian Institute of Science Education and Research
- Bhopal
- India
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11
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Stagljar I. Editorial for ''advances in OMICs-based disciplines". Biochem Biophys Res Commun 2014; 445:681-682. [PMID: 24691180 DOI: 10.1016/j.bbrc.2014.03.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Affiliation(s)
- Igor Stagljar
- Donnelly Centre, Department of Molecular Genetics, Department of Biochemistry, University of Toronto, 160 College Street, Room 1204, Toronto, Ontario M5S 3E1, Canada.
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