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Shanker AK, Bhanu D, Alluri A, Gupta S. Whole-genome sequence analysis and homology modelling of the main protease and non-structural protein 3 of SARS-CoV-2 reveal an aza-peptide and a lead inhibitor with possible antiviral properties. NEW J CHEM 2020. [DOI: 10.1039/d0nj00974a] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
SARS-CoV-2 3CLpro shows homology in binding to an aza-peptide epoxide (APE) known for the irreversible inhibition of main peptidase in SARS-CoV.
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Affiliation(s)
- Arun K. Shanker
- ICAR – Central Research Institute for Dryland Agriculture, Santoshnagar
- Hyderabad – 500059
- India
| | - Divya Bhanu
- ICAR – Central Research Institute for Dryland Agriculture, Santoshnagar
- Hyderabad – 500059
- India
- Centre for Plant Molecular Biology
- Osmania University
| | - Anjani Alluri
- Advanced Post Graduate Centre
- Acharya N. G. Ranga Agricultural University
- Guntur
- India
| | - Samriddhi Gupta
- Department of Biochemistry
- School of Life Sciences
- University of Hyderabad
- India
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Boselli M, Lee BH, Robert J, Prado MA, Min SW, Cheng C, Silva MC, Seong C, Elsasser S, Hatle KM, Gahman TC, Gygi SP, Haggarty SJ, Gan L, King RW, Finley D. An inhibitor of the proteasomal deubiquitinating enzyme USP14 induces tau elimination in cultured neurons. J Biol Chem 2017; 292:19209-19225. [PMID: 28972160 DOI: 10.1074/jbc.m117.815126] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Indexed: 11/06/2022] Open
Abstract
The ubiquitin-proteasome system (UPS) is responsible for most selective protein degradation in eukaryotes and regulates numerous cellular processes, including cell cycle control and protein quality control. A component of this system, the deubiquitinating enzyme USP14, associates with the proteasome where it can rescue substrates from degradation by removal of the ubiquitin tag. We previously found that a small-molecule inhibitor of USP14, known as IU1, can increase the rate of degradation of a subset of proteasome substrates. We report here the synthesis and characterization of 87 variants of IU1, which resulted in the identification of a 10-fold more potent USP14 inhibitor that retains specificity for USP14. The capacity of this compound, IU1-47, to enhance protein degradation in cells was tested using as a reporter the microtubule-associated protein tau, which has been implicated in many neurodegenerative diseases. Using primary neuronal cultures, IU1-47 was found to accelerate the rate of degradation of wild-type tau, the pathological tau mutants P301L and P301S, and the A152T tau variant. We also report that a specific residue in tau, lysine 174, is critical for the IU1-47-mediated tau degradation by the proteasome. Finally, we show that IU1-47 stimulates autophagic flux in primary neurons. In summary, these findings provide a powerful research tool for investigating the complex biology of USP14.
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Affiliation(s)
- Monica Boselli
- From the Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Byung-Hoon Lee
- From the Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115.,the Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, 42988 Daegu, Korea
| | - Jessica Robert
- From the Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Miguel A Prado
- From the Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Sang-Won Min
- the Department of Neurology, Gladstone Institute of Neurological Diseases, University of California, San Francisco, California 94158
| | - Chialin Cheng
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114
| | - M Catarina Silva
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114
| | - Changhyun Seong
- From the Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115.,Regeneron Pharmaceuticals, Tarrytown, New York 10591, and
| | - Suzanne Elsasser
- From the Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Ketki M Hatle
- From the Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Timothy C Gahman
- Small Molecule Discovery Program, Ludwig Institute for Cancer Research, La Jolla, California 92093
| | - Steven P Gygi
- From the Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Stephen J Haggarty
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114
| | - Li Gan
- the Department of Neurology, Gladstone Institute of Neurological Diseases, University of California, San Francisco, California 94158
| | - Randall W King
- From the Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115,
| | - Daniel Finley
- From the Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115,
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Khairallah A, Farag AA, Johar D, Bernstein L. Endocrine Imbalance Associated With Proteome Changes in Diabetes. J Cell Biochem 2017; 118:3569-3576. [PMID: 28419534 DOI: 10.1002/jcb.26071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 04/14/2017] [Indexed: 11/06/2022]
Abstract
The dynamics of cellular metabolism involves rapid interactions between proteins and nucleic acids, proteins and proteins, and signaling. These involve the interactions with respect to the sulfur bond, noncovalent electrostatic interactions, protein structure stabilization and protein-ligand binding, weak electrostatic interactions in proteins, oxygen radicals that initiate a change in conformation and a chain of events. We review a development in molecular medicine that is a very promising work in progress. We also review the current and future research methods involving mitochondria. Long-term effects of diabetes include glycation of proteins, for example, glycohemoglobin (HbA1c), increased risk of cardiovascular diseases, atherosclerosis, retinopathy, nephropathy, and neurological dysfunctions. Tissues are exposed to significant quantities of highly reactive chemical species including nitric oxide • NO and reactive oxygen species ROS over months to years, to an extent generated by mitochondrial activities. The reactions of • NO can be broadly discussed with reference to three main processes which control their fate in biological systems: (1) diffusion and intra-cellular consumption; (2) autooxidation to form nitrous anhydride N2 O3 ; and (3) reaction with superoxide O2• - to form peroxynitrite ONOO-. Reactive nitrogen species produced by macrophages and neutrophils in the interstitial space, with emphasis on • NO, N2 O3 , ONOO-, and nitrogen dioxide radicals • NO2 generate protein and DNA damage. Serum thiol (-SH) groups act as an important extracellular scavenger of peroxides and are therefore helpful in protecting the surrounding tissues. The events described here are a homeostatic endocrine imbalance that is associated with proteostasis. The advances we have seen in untangling this web of interactions are sure to continue at a breathtaking pace. J. Cell. Biochem. 118: 3569-3576, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Ahmed Khairallah
- Pharmacology Department, Medical Research Division, National Research Center, Dokki, Cairo, Egypt
| | | | - Dina Johar
- Faculty of Women for Arts, Sciences and Education, Department of Biochemistry and Nutrition, Ain Shams University, Heliopolis, Cairo, Egypt.,Rady College of Medicine, Max Rady Faculty of Health Sciences, Department of Physiology and Pathophysiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Larry Bernstein
- Triplex Consulting, 54 Firethorn Lane, Northampton, Massachusetts
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Abdul Rehman SA, Kristariyanto YA, Choi SY, Nkosi PJ, Weidlich S, Labib K, Hofmann K, Kulathu Y. MINDY-1 Is a Member of an Evolutionarily Conserved and Structurally Distinct New Family of Deubiquitinating Enzymes. Mol Cell 2016; 63:146-55. [PMID: 27292798 PMCID: PMC4942677 DOI: 10.1016/j.molcel.2016.05.009] [Citation(s) in RCA: 254] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 04/15/2016] [Accepted: 05/05/2016] [Indexed: 12/22/2022]
Abstract
Deubiquitinating enzymes (DUBs) remove ubiquitin (Ub) from Ub-conjugated substrates to regulate the functional outcome of ubiquitylation. Here we report the discovery of a new family of DUBs, which we have named MINDY (motif interacting with Ub-containing novel DUB family). Found in all eukaryotes, MINDY-family DUBs are highly selective at cleaving K48-linked polyUb, a signal that targets proteins for degradation. We identify the catalytic activity to be encoded within a previously unannotated domain, the crystal structure of which reveals a distinct protein fold with no homology to any of the known DUBs. The crystal structure of MINDY-1 (also known as FAM63A) in complex with propargylated Ub reveals conformational changes that realign the active site for catalysis. MINDY-1 prefers cleaving long polyUb chains and works by trimming chains from the distal end. Collectively, our results reveal a new family of DUBs that may have specialized roles in regulating proteostasis.
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Affiliation(s)
- Syed Arif Abdul Rehman
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Yosua Adi Kristariyanto
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Soo-Youn Choi
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Pedro Junior Nkosi
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Simone Weidlich
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Karim Labib
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Kay Hofmann
- Institute for Genetics, University of Cologne, Zülpicher Straße 47a, 50674 Cologne, Germany
| | - Yogesh Kulathu
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
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Baranczak A, Kelly JW. A current pharmacologic agent versus the promise of next generation therapeutics to ameliorate protein misfolding and/or aggregation diseases. Curr Opin Chem Biol 2016; 32:10-21. [PMID: 26859714 DOI: 10.1016/j.cbpa.2016.01.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 01/14/2016] [Accepted: 01/14/2016] [Indexed: 12/18/2022]
Abstract
The list of protein aggregation-associated degenerative diseases is long and growing, while the portfolio of disease-modifying strategies is very small. In this review and perspective, we assess what has worked to slow the progression of an aggregation-associated degenerative disease, covering the underlying mechanism of pharmacologic action and what we have learned about the etiology of the transthyretin amyloid diseases and likely amyloidoses in general. Next, we introduce emerging therapies that should apply more generally to protein misfolding and/or aggregation diseases, approaches that rely on adapting the protein homeostasis or proteostasis network for disease amelioration.
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Affiliation(s)
- Aleksandra Baranczak
- Department of Chemistry and The Skaggs Institute for Chemical Biology, La Jolla, CA 92037, USA; Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Jeffery W Kelly
- Department of Chemistry and The Skaggs Institute for Chemical Biology, La Jolla, CA 92037, USA; Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.
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Moarefi I. Protein Complex Production from the Drug Discovery Standpoint. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 896:3-13. [DOI: 10.1007/978-3-319-27216-0_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Wu S, Yu L. Targeting cullin-RING ligases for cancer treatment: rationales, advances and therapeutic implications. Cytotechnology 2015; 68:1-8. [PMID: 25899169 DOI: 10.1007/s10616-015-9870-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 03/26/2015] [Indexed: 02/02/2023] Open
Abstract
New therapeutic intervention strategies for the treatment of human malignancies are always desired. Approval of bortezomib as a front-line treatment for multiple myeloma highlighted the significance of ubiquitin-proteasome system (UPS) as a promising therapeutic target. However, due to the broad impact of proteasome inhibition, deleterious side effects have been reported with bortezomib treatment. Cullin RING ligases (CRLs)-mediated ubiquitin conjugation process is responsible for the ubiquitin conjugation of 20 % cellular proteins that are designated for degradation through the UPS, most of them are critical proteins involved in cell cycle progression, signaling transduction and apoptosis. Studies have depicted the upstream NEDDylation pathway that controls the CRL activity by regulating the conjugation of an ubiquitin-like-protein NEDD8 to the cullin protein in the complex. A specific pharmaceutical inhibitor of NEDD8 activating enzyme (NAE; E1) MLN4924 was recently developed and has been promoted to Phase I clinical trials for the treatment of several human malignancies. This article summarizes the most recent understanding about the process of NEDD8 conjugation, its relevance for cancer therapy and molecular mechanisms responsible for the potent anti-tumor activity of MLN4924.
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Affiliation(s)
- Shuju Wu
- School of Life Science and Technology, Harbin Normal University, Harbin, 150025, People's Republic of China.
| | - Lijie Yu
- School of Life Science and Technology, Harbin Normal University, Harbin, 150025, People's Republic of China
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