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Chen SY, Fiedler MK, Gronauer TF, Omelko O, von Wrisberg MK, Wang T, Schneider S, Sieber SA, Zacharias M. Unraveling the mechanism of small molecule induced activation of Staphylococcus aureus signal peptidase IB. Commun Biol 2024; 7:895. [PMID: 39043865 PMCID: PMC11266668 DOI: 10.1038/s42003-024-06575-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 07/11/2024] [Indexed: 07/25/2024] Open
Abstract
Staphylococcus aureus signal peptidase IB (SpsB) is an essential enzyme for protein secretion. While inhibition of its activity by small molecules is a well-precedented mechanism to kill bacteria, the mode of activation is however less understood. We here investigate the activation mechanism of a recently introduced activator, the antibiotic compound PK150, and demonstrate by combined experimental and Molecular Dynamics (MD) simulation studies a unique principle of enzyme stimulation. Mass spectrometric studies with an affinity-based probe of PK150 unravel the binding site of PK150 in SpsB which is used as a starting point for MD simulations. Our model shows the localization of the molecule in an allosteric pocket next to the active site which shields the catalytic dyad from excess water that destabilizes the catalytic geometry. This mechanism is validated by the placement of mutations aligning the binding pocket of PK150. While the mutants retain turnover of the SpsB substrate, no stimulation of activity is observed upon PK150 addition. Overall, our study elucidates a previously little investigated mechanism of enzyme activation and serves as a starting point for the development of future enzyme activators.
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Affiliation(s)
- Shu-Yu Chen
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 2, Zurich, 8093, Switzerland
- TUM School of Natural Sciences, Department Biosciences, Theoretical Biophysics (T38), Center for Functional Protein Assemblies (CPA), Technical University Munich (TUM), Ernst-Otto-Fischer Str. 8, Garching, 85748, Germany
| | - Michaela K Fiedler
- TUM School of Natural Sciences, Department Biosciences, Chair of Organic Chemistry II, Center for Functional Protein Assemblies (CPA), Technical University Munich (TUM), Ernst-Otto-Fischer Str. 8, Garching, 85748, Germany
| | - Thomas F Gronauer
- TUM School of Natural Sciences, Department Biosciences, Chair of Organic Chemistry II, Center for Functional Protein Assemblies (CPA), Technical University Munich (TUM), Ernst-Otto-Fischer Str. 8, Garching, 85748, Germany
| | - Olesia Omelko
- TUM School of Natural Sciences, Department Biosciences, Chair of Organic Chemistry II, Center for Functional Protein Assemblies (CPA), Technical University Munich (TUM), Ernst-Otto-Fischer Str. 8, Garching, 85748, Germany
| | - Marie-Kristin von Wrisberg
- Department of Chemistry, Ludwig-Maximilians University Munich (LMU), Butenandtstr. 5-13, Munich, 81377, Germany
| | - Tao Wang
- TUM School of Natural Sciences, Department Biosciences, Chair of Organic Chemistry II, Center for Functional Protein Assemblies (CPA), Technical University Munich (TUM), Ernst-Otto-Fischer Str. 8, Garching, 85748, Germany
| | - Sabine Schneider
- Department of Chemistry, Ludwig-Maximilians University Munich (LMU), Butenandtstr. 5-13, Munich, 81377, Germany
| | - Stephan A Sieber
- TUM School of Natural Sciences, Department Biosciences, Chair of Organic Chemistry II, Center for Functional Protein Assemblies (CPA), Technical University Munich (TUM), Ernst-Otto-Fischer Str. 8, Garching, 85748, Germany.
| | - Martin Zacharias
- TUM School of Natural Sciences, Department Biosciences, Theoretical Biophysics (T38), Center for Functional Protein Assemblies (CPA), Technical University Munich (TUM), Ernst-Otto-Fischer Str. 8, Garching, 85748, Germany.
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2
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Bardhan A, Brown W, Albright S, Tsang M, Davidson LA, Deiters A. Direct Activation of Nucleobases with Small Molecules for the Conditional Control of Antisense Function. Angew Chem Int Ed Engl 2024; 63:e202318773. [PMID: 38411401 DOI: 10.1002/anie.202318773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 02/28/2024]
Abstract
Conditionally controlled antisense oligonucleotides provide precise interrogation of gene function at different developmental stages in animal models. Only one example of small molecule-induced activation of antisense function exist. This has been restricted to cyclic caged morpholinos that, based on sequence, can have significant background activity in the absence of the trigger. Here, we provide a new approach using azido-caged nucleobases that are site-specifically introduced into antisense morpholinos. The caging group design is a simple azidomethylene (Azm) group that, despite its very small size, efficiently blocks Watson-Crick base pairing in a programmable fashion. Furthermore, it undergoes facile decaging via Staudinger reduction when exposed to a small molecule phosphine, generating the native antisense oligonucleotide under conditions compatible with biological environments. We demonstrated small molecule-induced gene knockdown in mammalian cells, zebrafish embryos, and frog embryos. We validated the general applicability of this approach by targeting three different genes.
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Affiliation(s)
- Anirban Bardhan
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Wes Brown
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Savannah Albright
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Michael Tsang
- Department of Cell Biology, Center for Integrative Organ Systems., University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Lance A Davidson
- Department of Bioengineering, Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
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3
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Wu N, Barahona M, Yaliraki SN. Allosteric communication and signal transduction in proteins. Curr Opin Struct Biol 2024; 84:102737. [PMID: 38171189 DOI: 10.1016/j.sbi.2023.102737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 01/05/2024]
Abstract
Allostery is one of the cornerstones of biological function, as it plays a fundamental role in regulating protein activity. The modelling of allostery has gradually moved from a conformation-based framework, linked to structural changes, to dynamics-based allostery, whereby the effects of ligand binding propagate via signal transduction from the allosteric site to other regions of the protein via inter-residue interactions. Characterising such allosteric signalling pathways, which do not necessarily lead to conformational changes, has been pursued experimentally and complemented by computational analysis of protein networks to detect subtle dynamic propagation paths. Considering allostery from the perspective of signal transduction broadens the understanding of allosteric mechanisms, underscores the importance of protein topology, and can provide insights into allosteric drug design.
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Affiliation(s)
- Nan Wu
- Department of Chemistry, Imperial College London, United Kingdom
| | - Mauricio Barahona
- Department of Mathematics, Imperial College London, United Kingdom. https://twitter.com/@CMPHImperial
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4
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Dow LF, Case AM, Paustian MP, Pinkerton BR, Simeon P, Trippier PC. The evolution of small molecule enzyme activators. RSC Med Chem 2023; 14:2206-2230. [PMID: 37974956 PMCID: PMC10650962 DOI: 10.1039/d3md00399j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 09/20/2023] [Indexed: 11/19/2023] Open
Abstract
There is a myriad of enzymes within the body responsible for maintaining homeostasis by providing the means to convert substrates to products as and when required. Physiological enzymes are tightly controlled by many signaling pathways and their products subsequently control other pathways. Traditionally, most drug discovery efforts focus on identifying enzyme inhibitors, due to upregulation being prevalent in many diseases and the existence of endogenous substrates that can be modified to afford inhibitor compounds. As enzyme downregulation and reduction of endogenous activators are observed in multiple diseases, the identification of small molecules with the ability to activate enzymes has recently entered the medicinal chemistry toolbox to afford chemical probes and potential therapeutics as an alternative means to intervene in diseases. In this review we highlight the progress made in the identification and advancement of non-kinase enzyme activators and their potential in treating various disease states.
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Affiliation(s)
- Louise F Dow
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center Omaha NE 68106 USA
| | - Alfie M Case
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center Omaha NE 68106 USA
| | - Megan P Paustian
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center Omaha NE 68106 USA
| | - Braeden R Pinkerton
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center Omaha NE 68106 USA
| | - Princess Simeon
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center Omaha NE 68106 USA
| | - Paul C Trippier
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center Omaha NE 68106 USA
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center Omaha NE 68106 USA
- UNMC Center for Drug Discovery, University of Nebraska Medical Center Omaha NE 68106 USA
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5
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Xie X, Yu T, Li X, Zhang N, Foster LJ, Peng C, Huang W, He G. Recent advances in targeting the "undruggable" proteins: from drug discovery to clinical trials. Signal Transduct Target Ther 2023; 8:335. [PMID: 37669923 PMCID: PMC10480221 DOI: 10.1038/s41392-023-01589-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/22/2023] [Accepted: 08/02/2023] [Indexed: 09/07/2023] Open
Abstract
Undruggable proteins are a class of proteins that are often characterized by large, complex structures or functions that are difficult to interfere with using conventional drug design strategies. Targeting such undruggable targets has been considered also a great opportunity for treatment of human diseases and has attracted substantial efforts in the field of medicine. Therefore, in this review, we focus on the recent development of drug discovery targeting "undruggable" proteins and their application in clinic. To make this review well organized, we discuss the design strategies targeting the undruggable proteins, including covalent regulation, allosteric inhibition, protein-protein/DNA interaction inhibition, targeted proteins regulation, nucleic acid-based approach, immunotherapy and others.
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Affiliation(s)
- Xin Xie
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Medical Technology and School of Pharmacy, Chengdu University of Traditional Chinese Medicine, 611137, Chengdu, China
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Tingting Yu
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Medical Technology and School of Pharmacy, Chengdu University of Traditional Chinese Medicine, 611137, Chengdu, China
| | - Xiang Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Medical Technology and School of Pharmacy, Chengdu University of Traditional Chinese Medicine, 611137, Chengdu, China
| | - Nan Zhang
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Medical Technology and School of Pharmacy, Chengdu University of Traditional Chinese Medicine, 611137, Chengdu, China
- Department of Dermatology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, 610041, Chengdu, China
| | - Leonard J Foster
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Cheng Peng
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Medical Technology and School of Pharmacy, Chengdu University of Traditional Chinese Medicine, 611137, Chengdu, China.
| | - Wei Huang
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Medical Technology and School of Pharmacy, Chengdu University of Traditional Chinese Medicine, 611137, Chengdu, China.
| | - Gu He
- Department of Dermatology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, 610041, Chengdu, China.
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6
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Sun J, Li P, Gui H, Rittié L, Lombard DB, Rietscher K, Magin TM, Xie Q, Liu L, Omary MB. Deacetylation via SIRT2 prevents keratin-mutation-associated injury and keratin aggregation. JCI Insight 2023; 8:e166314. [PMID: 37485877 PMCID: PMC10443796 DOI: 10.1172/jci.insight.166314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 06/02/2023] [Indexed: 07/25/2023] Open
Abstract
Keratin (K) and other intermediate filament (IF) protein mutations at conserved arginines disrupt keratin filaments into aggregates and cause human epidermolysis bullosa simplex (EBS; K14-R125C) or predispose to mouse liver injury (K18-R90C). The challenge for more than 70 IF-associated diseases is the lack of clinically utilized IF-targeted therapies. We used high-throughput drug screening to identify compounds that normalized mutation-triggered keratin filament disruption. Parthenolide, a plant sesquiterpene lactone, dramatically reversed keratin filament disruption and protected cells and mice expressing K18-R90C from apoptosis. K18-R90C became hyperacetylated compared with K18-WT and treatment with parthenolide normalized K18 acetylation. Parthenolide upregulated the NAD-dependent SIRT2, and increased SIRT2-keratin association. SIRT2 knockdown or pharmacologic inhibition blocked the parthenolide effect, while site-specific Lys-to-Arg mutation of keratin acetylation sites normalized K18-R90C filaments. Treatment of K18-R90C-expressing cells and mice with nicotinamide mononucleotide had a parthenolide-like protective effect. In 2 human K18 variants that associate with human fatal drug-induced liver injury, parthenolide protected K18-D89H- but not K8-K393R-induced filament disruption and cell death. Importantly, parthenolide normalized K14-R125C-mediated filament disruption in keratinocytes and inhibited dispase-triggered keratinocyte sheet fragmentation and Fas-mediated apoptosis. Therefore, keratin acetylation may provide a novel therapeutic target for some keratin-associated diseases.
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Affiliation(s)
- Jingyuan Sun
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, USA
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, PR China
| | - Pei Li
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, USA
| | - Honglian Gui
- Department of Infectious Diseases, Ruijin Hospital, Jiaotong University School of Medicine, Shanghai, PR China
| | - Laure Rittié
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - David B. Lombard
- Sylvester Comprehensive Cancer Center, and Department of Pathology & Laboratory Medicine, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Katrin Rietscher
- Division of Cell and Developmental Biology, Institute of Biology, Leipzig University, Leipzig, Germany
| | - Thomas M. Magin
- Division of Cell and Developmental Biology, Institute of Biology, Leipzig University, Leipzig, Germany
| | - Qing Xie
- Department of Infectious Diseases, Ruijin Hospital, Jiaotong University School of Medicine, Shanghai, PR China
| | - Li Liu
- Hepatology Unit and Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, PR China
| | - M. Bishr Omary
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, USA
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
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7
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Sun G, Liao J, Kurze E, Hoffmann TD, Steinchen W, McGraphery K, Habegger R, Marek L, Catici DAM, Ludwig C, Jing T, Hoffmann T, Song C, Schwab W. Apocarotenoids are allosteric effectors of a dimeric plant glycosyltransferase involved in defense and lignin formation. THE NEW PHYTOLOGIST 2023; 238:2080-2098. [PMID: 36908092 DOI: 10.1111/nph.18875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 03/02/2023] [Indexed: 05/04/2023]
Abstract
Glycosyltransferases are nature's versatile tools to tailor the functionalities of proteins, carbohydrates, lipids, and small molecules by transferring sugars. Prominent substrates are hydroxycoumarins such as scopoletin, which serve as natural plant protection agents. Similarly, C13-apocarotenoids, which are oxidative degradation products of carotenoids/xanthophylls, protect plants by repelling pests and attracting pest predators. We show that C13-apocarotenoids interact with the plant glycosyltransferase NbUGT72AY1 and induce conformational changes in the enzyme catalytic center ultimately reducing its inherent UDP-α-d-glucose glucohydrolase activity and increasing its catalytic activity for productive hydroxycoumarin substrates. By contrast, C13-apocarotenoids show no effect on the catalytic activity toward monolignol lignin precursors, which are competitive substrates. In vivo studies in tobacco plants (Nicotiana benthamiana) confirmed increased glycosylation activity upon apocarotenoid supplementation. Thus, hydroxycoumarins and apocarotenoids represent specialized damage-associated molecular patterns, as they each provide precise information about the plant compartments damaged by pathogen attack. The molecular basis for the C13-apocarotenoid-mediated interplay of two plant protective mechanisms and their function as allosteric enhancers opens up potential applications of the natural products in agriculture and pharmaceutical industry.
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Affiliation(s)
- Guangxin Sun
- Biotechnology of Natural Products, School of Life Sciences Weihenstephan, Technische Universität München, Liesel-Beckmann-Str. 1, 85354, Freising, Germany
| | - Jieren Liao
- Biotechnology of Natural Products, School of Life Sciences Weihenstephan, Technische Universität München, Liesel-Beckmann-Str. 1, 85354, Freising, Germany
| | - Elisabeth Kurze
- Biotechnology of Natural Products, School of Life Sciences Weihenstephan, Technische Universität München, Liesel-Beckmann-Str. 1, 85354, Freising, Germany
| | - Timothy D Hoffmann
- Biotechnology of Natural Products, School of Life Sciences Weihenstephan, Technische Universität München, Liesel-Beckmann-Str. 1, 85354, Freising, Germany
| | - Wieland Steinchen
- Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Philipps-University Marburg, Karl-von-Frisch-Straße 14, 35043, Marburg, Germany
| | - Kate McGraphery
- Biotechnology of Natural Products, School of Life Sciences Weihenstephan, Technische Universität München, Liesel-Beckmann-Str. 1, 85354, Freising, Germany
| | - Ruth Habegger
- Biotechnology of Natural Products, School of Life Sciences Weihenstephan, Technische Universität München, Liesel-Beckmann-Str. 1, 85354, Freising, Germany
| | - Ludwig Marek
- Biotechnology of Natural Products, School of Life Sciences Weihenstephan, Technische Universität München, Liesel-Beckmann-Str. 1, 85354, Freising, Germany
| | - Dragana A M Catici
- Center for Protein Assemblies (CPA), Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748, Garching, Germany
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), School of Life Sciences Weihenstephan, Technische Universität München, Gregor-Mendel-Str. 4, 85354, Freising, Germany
| | - Tingting Jing
- State Key Laboratory of Tea Plant Biology and Utilization, International Joint Laboratory on Tea Chemistry and Health Effects, Anhui Agricultural University, 230036, Hefei, Anhui, China
| | - Thomas Hoffmann
- Biotechnology of Natural Products, School of Life Sciences Weihenstephan, Technische Universität München, Liesel-Beckmann-Str. 1, 85354, Freising, Germany
| | - Chuankui Song
- State Key Laboratory of Tea Plant Biology and Utilization, International Joint Laboratory on Tea Chemistry and Health Effects, Anhui Agricultural University, 230036, Hefei, Anhui, China
| | - Wilfried Schwab
- Biotechnology of Natural Products, School of Life Sciences Weihenstephan, Technische Universität München, Liesel-Beckmann-Str. 1, 85354, Freising, Germany
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8
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Petri YD, Gutierrez CS, Raines RT. Chemoselective Caging of Carboxyl Groups for On-Demand Protein Activation with Small Molecules. Angew Chem Int Ed Engl 2023; 62:e202215614. [PMID: 36964973 PMCID: PMC10243506 DOI: 10.1002/anie.202215614] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 03/02/2023] [Accepted: 03/24/2023] [Indexed: 03/27/2023]
Abstract
Tools for on-demand protein activation enable impactful gain-of-function studies in biological settings. Thus far, however, proteins have been chemically caged at primarily Lys, Tyr, and Sec, typically through the genetic encoding of unnatural amino acids. Herein, we report that the preferential reactivity of diazo compounds with protonated acids can be used to expand this toolbox to solvent-accessible carboxyl groups with an elevated pKa value. As a model protein, we employed lysozyme (Lyz), which has an active-site Glu35 residue with a pKa value of 6.2. A diazo compound with a bioorthogonal self-immolative handle esterified Glu35 selectively, inactivating Lyz. The hydrolytic activity of the caged Lyz on bacterial cell walls was restored with two small-molecule triggers. The decaging was more efficient by small molecules than by esterases. This simple chemical strategy was also applied to a hemeprotein and an aspartyl protease, setting the stage for broad applicability.
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Affiliation(s)
- Yana D. Petri
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, USA
| | - Clair S. Gutierrez
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, USA
| | - Ronald T. Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, USA
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9
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Ciulla DA, Xu Z, Pezzullo JL, Dranchak P, Wang C, Giner JL, Inglese J, Callahan BP. Paracatalytic induction: Subverting specificity in hedgehog protein autoprocessing with small molecules. Methods Enzymol 2023; 685:1-41. [PMID: 37245899 PMCID: PMC10294009 DOI: 10.1016/bs.mie.2023.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Paracatalytic inducers are antagonists that shift the specificity of biological catalysts, resulting in non-native transformations. In this Chapter we describe methods to discover paracatalytic inducers of Hedgehog (Hh) protein autoprocessing. Native autoprocessing uses cholesterol as a substrate nucleophile to assist in cleaving an internal peptide bond within a precursor form of Hh. This unusual reaction is brought about by HhC, an enzymatic domain that resides within the C-terminal region of Hh precursor proteins. Recently, we reported paracatalytic inducers as a novel class of Hh autoprocessing antagonists. These small molecules bind HhC and tilt the substrate specificity away from cholesterol in favor of solvent water. The resulting cholesterol-independent autoproteolysis of the Hh precursor generates a non-native Hh side product with substantially reduced biological signaling activity. Protocols are provided for in vitro FRET-based and in-cell bioluminescence assays to discover and characterize paracatalytic inducers of Drosophila and human hedgehog protein autoprocessing, respectively.
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Affiliation(s)
- Daniel A Ciulla
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, United States.
| | - Zihan Xu
- Chemistry Department, Binghamton University, Binghamton, NY, United States
| | - John L Pezzullo
- State University of New York, College of Environmental Science and Forestry, Syracuse, NY, United States
| | - Patricia Dranchak
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, United States
| | - Chunyu Wang
- Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - José-Luis Giner
- State University of New York, College of Environmental Science and Forestry, Syracuse, NY, United States
| | - James Inglese
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, United States; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Brian P Callahan
- Chemistry Department, Binghamton University, Binghamton, NY, United States
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10
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Poirier D. Description of Chemical Synthesis, Nuclear Magnetic Resonance Characterization and Biological Activity of Estrane-Based Inhibitors/Activators of Steroidogenesis. Molecules 2023; 28:molecules28083499. [PMID: 37110733 PMCID: PMC10143840 DOI: 10.3390/molecules28083499] [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: 03/10/2023] [Revised: 04/08/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Steroid hormones play a crucial role in several aspects of human life, and steroidogenesis is the process by which hormones are produced from cholesterol using several enzymes that work in concert to obtain the appropriate levels of each hormone at the right time. Unfortunately, many diseases, such as cancer, endometriosis, and osteoporosis as examples, are caused by an increase in the production of certain hormones. For these diseases, the use of an inhibitor to block the activity of an enzyme and, in doing so, the production of a key hormone is a proven therapeutic strategy whose development continues. This account-type article focuses on seven inhibitors (compounds 1-7) and an activator (compound 8) of six enzymes involved in steroidogenesis, namely steroid sulfatase, aldo-keto reductase 1C3, types 1, 2, 3, and 12 of the 17β-hydroxysteroid dehydrogenases. For these steroid derivatives, three topics will be addressed: (1) Their chemical synthesis from the same starting material, estrone, (2) their structural characterization using nuclear magnetic resonance, and (3) their in vitro or in vivo biological activities. These bioactive molecules constitute potential therapeutic or mechanistic tools that could be used to better understand the role of certain hormones in steroidogenesis.
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Affiliation(s)
- Donald Poirier
- Laboratory of Medicinal Chemistry, Endocrinology and Nephrology Unit, CHU de Québec Research Center-Université Laval, Québec, QC G1V 4G2, Canada
- Department of Molecular Medicine, Faculty of Medicine, Université Laval, Québec, QC G1V 0A6, Canada
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11
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Molinari S, Imbriano C, Moresi V, Renzini A, Belluti S, Lozanoska-Ochser B, Gigli G, Cedola A. Histone deacetylase functions and therapeutic implications for adult skeletal muscle metabolism. Front Mol Biosci 2023; 10:1130183. [PMID: 37006625 PMCID: PMC10050567 DOI: 10.3389/fmolb.2023.1130183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 03/06/2023] [Indexed: 03/17/2023] Open
Abstract
Skeletal muscle is a highly adaptive organ that sustains continuous metabolic changes in response to different functional demands. Healthy skeletal muscle can adjust fuel utilization to the intensity of muscle activity, the availability of nutrients and the intrinsic characteristics of muscle fibers. This property is defined as metabolic flexibility. Importantly, impaired metabolic flexibility has been associated with, and likely contributes to the onset and progression of numerous pathologies, including sarcopenia and type 2 diabetes. Numerous studies involving genetic and pharmacological manipulations of histone deacetylases (HDACs) in vitro and in vivo have elucidated their multiple functions in regulating adult skeletal muscle metabolism and adaptation. Here, we briefly review HDAC classification and skeletal muscle metabolism in physiological conditions and upon metabolic stimuli. We then discuss HDAC functions in regulating skeletal muscle metabolism at baseline and following exercise. Finally, we give an overview of the literature regarding the activity of HDACs in skeletal muscle aging and their potential as therapeutic targets for the treatment of insulin resistance.
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Affiliation(s)
- Susanna Molinari
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Carol Imbriano
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Viviana Moresi
- Institute of Nanotechnology, Department of Physics, National Research Council (CNR-NANOTEC), Sapienza University of Rome, Rome, Italy
- *Correspondence: Viviana Moresi,
| | - Alessandra Renzini
- DAHFMO Unit of Histology and Medical Embryology, Sapienza University of Rome, Rome, Italy
| | - Silvia Belluti
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | | | - Giuseppe Gigli
- Institute of Nanotechnology, National Research Council (CNR-NANOTEC), Lecce, Italy
| | - Alessia Cedola
- Institute of Nanotechnology, Department of Physics, National Research Council (CNR-NANOTEC), Sapienza University of Rome, Rome, Italy
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12
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Callahan BP, Xu Z. There's more to enzyme antagonism than inhibition. Bioorg Med Chem 2023; 82:117231. [PMID: 36893527 PMCID: PMC10228466 DOI: 10.1016/j.bmc.2023.117231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/26/2023] [Accepted: 03/01/2023] [Indexed: 03/07/2023]
Abstract
A native enzyme's usual assurance in recognizing their physiological substrate(s) at the ground state and on going to the transition state can be undermined by interactions with selected small molecule antagonists, leading to the generation of abnormal products. We classify this mode of enzyme antagonism resulting in the gain-of-nonnative-function as paracatalytic induction. Enzymes bound by paracatalytic inducers exhibit new or enhanced activity toward transformations that appear aberrant or erroneous. The enzyme/ paracatalytic inducer complex may take up native substrate but then bring about a transformation that is chemically distinct from the normal reaction. Alternatively, the enzyme / paracatalytic inducer complex may exhibit abnormal ground state selectivity, preferentially interacting with and transforming a molecule outside the physiological substrate scope. Paracatalytic inducers can be cytotoxic, while in other cases they divert enzyme activity toward transformations that appear adaptive and even therapeutically useful. In this perspective, we highlight two noteworthy examples from recent literature.
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Affiliation(s)
- Brian P Callahan
- Chemistry Department, Binghamton University, Binghamton, NY 13902, United States.
| | - Zihan Xu
- Chemistry Department, Binghamton University, Binghamton, NY 13902, United States
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13
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Ge Y, Lu H, Yang B, Woo CM. Small Molecule-Activated O-GlcNAcase for Spatiotemporal Removal of O-GlcNAc in Live Cells. ACS Chem Biol 2023; 18:193-201. [PMID: 36598936 DOI: 10.1021/acschembio.2c00894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The nutrient sensor O-linked N-acetylglucosamine (O-GlcNAc) is a post-translational modification found on thousands of nucleocytoplasmic proteins. O-GlcNAc levels in cells dynamically respond to environmental cues in a temporal and spatial manner, leading to altered signal transduction and functional effects. The spatiotemporal regulation of O-GlcNAc levels would accelerate functional interrogation of O-GlcNAc and manipulation of cell behaviors for desired outcomes. Here, we report a strategy for spatiotemporal reduction of O-GlcNAc in live cells by designing an O-GlcNAcase (OGA) fused to an intein triggered by 4-hydroxytamoxifen (4-HT). After rational protein engineering and optimization, we identified an OGA-intein variant whose deglycosidase activity can be triggered in the desired subcellular compartments by 4-HT in a time- and dose-dependent manner. Finally, we demonstrated that 4-HT activation of the OGA-intein fusion can likewise potentiate inhibitory effects in breast cancer cells by virtue of the reduction of O-GlcNAc. The spatiotemporal control of O-GlcNAc through the chemically activatable OGA-intein fusion will facilitate the manipulation and functional understanding of O-GlcNAc in live cells.
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Affiliation(s)
- Yun Ge
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States.,Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen 518107, China
| | - Hailin Lu
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen 518107, China
| | - Bo Yang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Christina M Woo
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
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14
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Battisti UM, Gao C, Nilsson O, Akladios F, Lulla A, Bogucka A, Nain-Perez A, Håversen L, Kim W, Boren J, Hyvönen M, Uhlen M, Mardinoglu A, Grøtli M. Serendipitous Identification of a Covalent Activator of Liver Pyruvate Kinase. Chembiochem 2023; 24:e202200339. [PMID: 36250581 PMCID: PMC10099687 DOI: 10.1002/cbic.202200339] [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: 06/14/2022] [Revised: 10/14/2022] [Indexed: 01/05/2023]
Abstract
Enzymes are effective biological catalysts that accelerate almost all metabolic reactions in living organisms. Synthetic modulators of enzymes are useful tools for the study of enzymatic reactions and can provide starting points for the design of new drugs. Here, we report on the discovery of a class of biologically active compounds that covalently modifies lysine residues in human liver pyruvate kinase (PKL), leading to allosteric activation of the enzyme (EC50 =0.29 μM). Surprisingly, the allosteric activation control point resides on the lysine residue K282 present in the catalytic site of PKL. These findings were confirmed by structural data, MS/MS experiments, and molecular modelling studies. Altogether, our study provides a molecular basis for the activation mechanism and establishes a framework for further development of human liver pyruvate kinase covalent activators.
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Affiliation(s)
- Umberto Maria Battisti
- Department of Chemistry and Molecular Biology, University of Gothenburg, 412 96, Gothenburg, Sweden
| | - Chunxia Gao
- Department of Chemistry and Molecular Biology, University of Gothenburg, 412 96, Gothenburg, Sweden
| | - Oscar Nilsson
- Department of Chemistry and Molecular Biology, University of Gothenburg, 412 96, Gothenburg, Sweden
| | - Fady Akladios
- Department of Chemistry and Molecular Biology, University of Gothenburg, 412 96, Gothenburg, Sweden
| | - Aleksei Lulla
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Agnieszka Bogucka
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Amalyn Nain-Perez
- Department of Chemistry and Molecular Biology, University of Gothenburg, 412 96, Gothenburg, Sweden
| | - Liliana Håversen
- Department of Molecular and Clinical Medicine, University of Gothenburg and Sahlgrenska University Hospital, 413 45, Gothenburg, Sweden
| | - Woonghee Kim
- Science for Life Laboratory, KTH-Royal Institute of Technology, 171 21, Stockholm, Sweden
| | - Jan Boren
- Department of Molecular and Clinical Medicine, University of Gothenburg and Sahlgrenska University Hospital, 413 45, Gothenburg, Sweden
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Mathias Uhlen
- Science for Life Laboratory, KTH-Royal Institute of Technology, 171 21, Stockholm, Sweden
| | - Adil Mardinoglu
- Science for Life Laboratory, KTH-Royal Institute of Technology, 171 21, Stockholm, Sweden
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology, University of Gothenburg, 412 96, Gothenburg, Sweden
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15
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Zacharioudakis E, Gavathiotis E. Targeting protein conformations with small molecules to control protein complexes. Trends Biochem Sci 2022; 47:1023-1037. [PMID: 35985943 PMCID: PMC9669135 DOI: 10.1016/j.tibs.2022.07.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 06/23/2022] [Accepted: 07/11/2022] [Indexed: 12/24/2022]
Abstract
Dynamic protein complexes function in all cellular processes, from signaling to transcription, using distinct conformations that regulate their activity. Conformational switching of proteins can turn on or off their activity through protein-protein interactions, catalytic function, cellular localization, or membrane interaction. Recent advances in structural, computational, and chemical methodologies have enabled the discovery of small-molecule activators and inhibitors of conformationally dynamic proteins by using a more rational design than a serendipitous screening approach. Here, we discuss such recent examples, focusing on the mechanism of protein conformational switching and its regulation by small molecules. We emphasize the rational approaches to control protein oligomerization with small molecules that offer exciting opportunities for investigation of novel biological mechanisms and drug discovery.
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Affiliation(s)
- Emmanouil Zacharioudakis
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA; Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA; Albert Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, NY, USA; Wilf Family Cardiovascular Research Institute, Albert Einstein College of Medicine, Bronx, NY, USA; Institute for Aging Research, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Evripidis Gavathiotis
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA; Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA; Albert Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, NY, USA; Wilf Family Cardiovascular Research Institute, Albert Einstein College of Medicine, Bronx, NY, USA; Institute for Aging Research, Albert Einstein College of Medicine, Bronx, NY, USA.
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16
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Turberville A, Semple H, Davies G, Ivanov D, Holdgate GA. A perspective on the discovery of enzyme activators. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2022; 27:419-427. [PMID: 36089246 DOI: 10.1016/j.slasd.2022.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/26/2022] [Accepted: 09/06/2022] [Indexed: 12/15/2022]
Abstract
Enzyme activation remains a largely under-represented and poorly exploited area of drug discovery despite some key literature examples of the successful application of enzyme activators by various mechanisms and their importance in a wide range of therapeutic interventions. Here we describe the background nomenclature, present the current position of this field of drug discovery and discuss the challenges of hit identification for enzyme activation, as well as our perspectives on the approaches needed to overcome these challenges in early drug discovery.
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Affiliation(s)
- Antonia Turberville
- High-throughput Screening, Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, United Kingdom
| | - Hannah Semple
- High-throughput Screening, Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, United Kingdom
| | - Gareth Davies
- High-throughput Screening, Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, United Kingdom
| | - Delyan Ivanov
- High-throughput Screening, Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, United Kingdom
| | - Geoffrey A Holdgate
- High-throughput Screening, Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, United Kingdom.
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17
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Discovery of novel compounds as potent activators of Sirt3. Bioorg Med Chem 2022; 73:116999. [DOI: 10.1016/j.bmc.2022.116999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 08/14/2022] [Accepted: 09/01/2022] [Indexed: 11/18/2022]
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18
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Teng M, Young DW, Tan Z. The Pursuit of Enzyme Activation: A Snapshot of the Gold Rush. J Med Chem 2022; 65:14289-14304. [PMID: 36265019 DOI: 10.1021/acs.jmedchem.2c01291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A range of enzymes drive human physiology, and their activities are tightly regulated through numerous signaling pathways. Depending on the context, these pathways may activate or inhibit an enzyme as a way to ensure proper execution of cellular functions. From a drug discovery and development perspective, pharmacological inhibition of enzymes has been a focus of interest, as many diseases are associated with the upregulation of enzyme function. On the other hand, however, pharmacological activation of enzymes such as kinases and phosphatases has been of increasing interest. In this review, we discuss seven case studies that highlight pharmacological activation strategy, describe the binding modes and pharmacology of the activators, and comment on how this on-demand activation strategy complements the commonly pursued inhibition strategy, thus jointly enabling bidirectional modulation of specific target of interest. Going forward, we expect activators to play important roles as chemical probes and drug leads.
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Affiliation(s)
- Mingxing Teng
- Department of Pathology & Immunology, and Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Damian W Young
- Department of Pathology & Immunology, and Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Zhi Tan
- Department of Pathology & Immunology, and Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas 77030, United States
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19
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Clausse V, Fang Y, Tao D, Tagad HD, Sun H, Wang Y, Karavadhi S, Lane K, Shi ZD, Vasalatiy O, LeClair CA, Eells R, Shen M, Patnaik S, Appella E, Coussens NP, Hall MD, Appella DH. Discovery of Novel Small-Molecule Scaffolds for the Inhibition and Activation of WIP1 Phosphatase from a RapidFire Mass Spectrometry High-Throughput Screen. ACS Pharmacol Transl Sci 2022; 5:993-1006. [PMID: 36268125 PMCID: PMC9578142 DOI: 10.1021/acsptsci.2c00147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Indexed: 11/28/2022]
Abstract
Wild-type P53-induced phosphatase 1 (WIP1), also known as PPM1D or PP2Cδ, is a serine/threonine protein phosphatase induced by P53 after genotoxic stress. WIP1 inhibition has been proposed as a therapeutic strategy for P53 wild-type cancers in which it is overexpressed, but this approach would be ineffective in P53-negative cancers. Furthermore, there are several cancers with mutated P53 where WIP1 acts as a tumor suppressor. Therefore, activating WIP1 phosphatase might also be a therapeutic strategy, depending on the P53 status. To date, no specific, potent WIP1 inhibitors with appropriate pharmacokinetic properties have been reported, nor have WIP1-specific activators. Here, we report the discovery of new WIP1 modulators from a high-throughput screen (HTS) using previously described orthogonal biochemical assays suitable for identifying both inhibitors and activators. The primary HTS was performed against a library of 102 277 compounds at a single concentration using a RapidFire mass spectrometry assay. Hits were further evaluated over a range of 11 concentrations with both the RapidFire MS assay and an orthogonal fluorescence-based assay. Further biophysical, biochemical, and cell-based studies of confirmed hits revealed a WIP1 activator and two inhibitors, one competitive and one uncompetitive. These new scaffolds are prime candidates for optimization which might enable inhibitors with improved pharmacokinetics and a first-in-class WIP1 activator.
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Affiliation(s)
- Victor Clausse
- Synthetic
Bioactive Molecules Section, Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Yuhong Fang
- National
Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Dingyin Tao
- National
Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Harichandra D. Tagad
- Laboratory
of Cell Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Hongmao Sun
- National
Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Yuhong Wang
- National
Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Surendra Karavadhi
- National
Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Kelly Lane
- Chemistry
and Synthesis Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Zhen-Dan Shi
- Chemistry
and Synthesis Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Olga Vasalatiy
- Chemistry
and Synthesis Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Christopher A. LeClair
- National
Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Rebecca Eells
- Reaction
Biology Corporation, 1 Great Valley Parkway, Suite 2, Malvern, Pennsylvania 19355, United States
| | - Min Shen
- National
Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Samarjit Patnaik
- National
Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Ettore Appella
- Laboratory
of Cell Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Nathan P. Coussens
- Molecular
Pharmacology Laboratories, Applied and Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Matthew D. Hall
- National
Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Daniel H. Appella
- Synthetic
Bioactive Molecules Section, Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Bethesda, Maryland 20892, United States
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20
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Shen C, Nayak A, Neitzel LR, Yang F, Li B, Williams CH, Hong CC, Ahmed Y, Lee E, Robbins DJ. The Casein kinase 1α agonist pyrvinium attenuates Wnt-mediated CK1α degradation via interaction with the E3 ubiquitin ligase component Cereblon. J Biol Chem 2022; 298:102227. [PMID: 35780831 PMCID: PMC9352546 DOI: 10.1016/j.jbc.2022.102227] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 06/23/2022] [Accepted: 06/27/2022] [Indexed: 12/04/2022] Open
Abstract
The Cullin-RING ligase 4 E3 ubiquitin ligase component Cereblon (CRBN) is a well-established target for a class of small molecules termed immunomodulatory drugs (IMiDs). These drugs drive CRBN to modulate the degradation of a number of neosubstrates required for the growth of multiple cancers. Whereas the mechanism underlying the activation of CRBN by IMiDs is well described, the normal physiological regulation of CRBN is poorly understood. We recently showed that CRBN is activated following exposure to Wnt ligands and subsequently mediates the degradation of a subset of physiological substrates. Among the Wnt-dependent substrates of CRBN is Casein kinase 1α (CK1α), a known negative regulator of Wnt signaling. Wnt-mediated degradation of CK1α occurs via its association with CRBN at a known IMiD binding pocket. Herein, we demonstrate that a small-molecule CK1α agonist, pyrvinium, directly prevents the Wnt-dependent interaction of CRBN with CK1α, attenuating the consequent CK1α degradation. We further show that pyrvinium disrupts the ability of CRBN to interact with CK1α at the IMiD binding pocket within the CRBN-CK1α complex. Of note, this function of pyrvinium is independent of its previously reported ability to enhance CK1α kinase activity. Furthermore, we also demonstrate that pyrvinium attenuates CRBN-induced Wnt pathway activation in vivo. Collectively, these results reveal a novel dual mechanism through which pyrvinium inhibits Wnt signaling by both attenuating the CRBN-mediated destabilization of CK1α and activating CK1α kinase activity.
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Affiliation(s)
- Chen Shen
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia, USA; Molecular Oncology Program, The DeWitt Daughtry Family Department of Surgery, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Anmada Nayak
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia, USA; Molecular Oncology Program, The DeWitt Daughtry Family Department of Surgery, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Leif R Neitzel
- Department of Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Fan Yang
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia, USA; Molecular Oncology Program, The DeWitt Daughtry Family Department of Surgery, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Bin Li
- Molecular Oncology Program, The DeWitt Daughtry Family Department of Surgery, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Charles H Williams
- Department of Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Charles C Hong
- Department of Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Yashi Ahmed
- Department of Molecular and Systems Biology and the Norris Cotton Cancer Center, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Ethan Lee
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - David J Robbins
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia, USA.
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21
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Egbert M, Jones G, Collins MR, Kozakov D, Vajda S. FTMove: A Web Server for Detection and Analysis of Cryptic and Allosteric Binding Sites by Mapping Multiple Protein Structures. J Mol Biol 2022; 434:167587. [PMID: 35662465 PMCID: PMC9789685 DOI: 10.1016/j.jmb.2022.167587] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 02/25/2022] [Accepted: 04/07/2022] [Indexed: 12/27/2022]
Abstract
Protein mapping distributes many copies of different molecular probes on the surface of a target protein in order to determine binding hot spots, regions that are highly preferable for ligand binding. While mapping of X-ray structures by the FTMap server is inherently static, this limitation can be overcome by the simultaneous analysis of multiple structures of the protein. FTMove is an automated web server that implements this approach. From the input of a target protein, by PDB code, the server identifies all structures of the protein available in the PDB, runs mapping on them, and combines the results to form binding hot spots and binding sites. The user may also upload their own protein structures, bypassing the PDB search for similar structures. Output of the server consists of the consensus binding sites and the individual mapping results for each structure - including the number of probes located in each binding site, for each structure. This level of detail allows the users to investigate how the strength of a binding site relates to the protein conformation, other binding sites, and the presence of ligands or mutations. In addition, the structures are clustered on the basis of their binding properties. The use of FTMove is demonstrated by application to 22 proteins with known allosteric binding sites; the orthosteric and allosteric binding sites were identified in all but one case, and the sites were typically ranked among the top five. The FTMove server is publicly available at https://ftmove.bu.edu.
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Affiliation(s)
- Megan Egbert
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - George Jones
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Matthew R Collins
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Dima Kozakov
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Sandor Vajda
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Department of Chemistry, Boston University, Boston, MA 02215, USA.
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22
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Integration of Adenylate Kinase 1 with Its Peptide Conformational Imprint. Int J Mol Sci 2022; 23:ijms23126521. [PMID: 35742970 PMCID: PMC9223553 DOI: 10.3390/ijms23126521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/09/2022] [Accepted: 06/09/2022] [Indexed: 02/01/2023] Open
Abstract
In the present study, molecularly imprinted polymers (MIPs) were used as a tool to grasp a targeted α-helix or β-sheet of protein. During the fabrication of the hinge-mediated MIPs, elegant cavities took shape in a special solvent on quartz crystal microbalance (QCM) chips. The cavities, which were complementary to the protein secondary structure, acted as a peptide conformational imprint (PCI) for adenylate kinase 1 (AK1). We established a promising strategy to examine the binding affinities of human AK1 in conformational dynamics using the peptide-imprinting method. Moreover, when bound to AK1, PCIs are able to gain stability and tend to maintain higher catalytic activities than free AK1. Such designed fixations not only act on hinges as accelerators; some are also inhibitors. One example of PCI inhibition of AK1 catalytic activity takes place when PCI integrates with an AK19-23 β-sheet. In addition, conformation ties, a general MIP method derived from random-coil AK1133-144 in buffer/acetonitrile, are also inhibitors. The inhibition may be due to the need for this peptide to execute conformational transition during catalysis.
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23
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Henning NJ, Boike L, Spradlin JN, Ward CC, Liu G, Zhang E, Belcher BP, Brittain SM, Hesse MJ, Dovala D, McGregor LM, Valdez Misiolek R, Plasschaert LW, Rowlands DJ, Wang F, Frank AO, Fuller D, Estes AR, Randal KL, Panidapu A, McKenna JM, Tallarico JA, Schirle M, Nomura DK. Deubiquitinase-targeting chimeras for targeted protein stabilization. Nat Chem Biol 2022; 18:412-421. [PMID: 35210618 PMCID: PMC10125259 DOI: 10.1038/s41589-022-00971-2] [Citation(s) in RCA: 106] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 01/09/2022] [Indexed: 12/12/2022]
Abstract
Many diseases are driven by proteins that are aberrantly ubiquitinated and degraded. These diseases would be therapeutically benefited by targeted protein stabilization (TPS). Here we present deubiquitinase-targeting chimeras (DUBTACs), heterobifunctional small molecules consisting of a deubiquitinase recruiter linked to a protein-targeting ligand, to stabilize the levels of specific proteins degraded in a ubiquitin-dependent manner. Using chemoproteomic approaches, we discovered the covalent ligand EN523 that targets a non-catalytic allosteric cysteine C23 in the K48-ubiquitin-specific deubiquitinase OTUB1. We showed that a DUBTAC consisting of our EN523 OTUB1 recruiter linked to lumacaftor, a drug used to treat cystic fibrosis that binds ΔF508-cystic fibrosis transmembrane conductance regulator (CFTR), robustly stabilized ΔF508-CFTR protein levels, leading to improved chloride channel conductance in human cystic fibrosis bronchial epithelial cells. We also demonstrated stabilization of the tumor suppressor kinase WEE1 in hepatoma cells. Our study showcases covalent chemoproteomic approaches to develop new induced proximity-based therapeutic modalities and introduces the DUBTAC platform for TPS.
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Affiliation(s)
- Nathaniel J Henning
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Lydia Boike
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Jessica N Spradlin
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Carl C Ward
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Gang Liu
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Erika Zhang
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Bridget P Belcher
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Scott M Brittain
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Matthew J Hesse
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Dustin Dovala
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Lynn M McGregor
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | | | | | - Feng Wang
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Andreas O Frank
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Daniel Fuller
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Abigail R Estes
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Katelyn L Randal
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Anoohya Panidapu
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Jeffrey M McKenna
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - John A Tallarico
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Markus Schirle
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Daniel K Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA.
- Innovative Genomics Institute, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA, USA.
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24
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Chow CFW, Guo X, Asthana P, Zhang S, Wong SKK, Fallah S, Che S, Gurung S, Wang Z, Lee KB, Ge X, Yuan S, Xu H, Ip JPK, Jiang Z, Zhai L, Wu J, Zhang Y, Mahato AK, Saarma M, Lin CY, Kwan HY, Huang T, Lyu A, Zhou Z, Bian ZX, Wong HLX. Body weight regulation via MT1-MMP-mediated cleavage of GFRAL. Nat Metab 2022; 4:203-212. [PMID: 35177851 DOI: 10.1038/s42255-022-00529-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 01/07/2022] [Indexed: 12/24/2022]
Abstract
GDNF-family receptor a-like (GFRAL) has been identified as the cognate receptor of growth/differentiation factor 15 (GDF15/MIC-1), considered a key signaling axis in energy homeostasis and body weight regulation. Currently, little is known about the physiological regulation of the GDF15-GFRAL signaling pathway. Here we show that membrane-bound matrix metalloproteinase 14 (MT1-MMP/MMP14) is an endogenous negative regulator of GFRAL in the context of obesity. Overnutrition-induced obesity increased MT1-MMP activation, which proteolytically inactivated GFRAL to suppress GDF15-GFRAL signaling, thus modulating the anorectic effects of the GDF15-GFRAL axis in vivo. Genetic ablation of MT1-MMP specifically in GFRAL+ neurons restored GFRAL expression, resulting in reduced weight gain, along with decreased food intake in obese mice. Conversely, depletion of GFRAL abolished the anti-obesity effects of MT1-MMP inhibition. MT1-MMP inhibition also potentiated GDF15 activity specifically in obese phenotypes. Our findings identify a negative regulator of GFRAL for the control of non-homeostatic body weight regulation, provide mechanistic insights into the regulation of GDF15 sensitivity, highlight negative regulators of the GDF15-GFRAL pathway as a therapeutic avenue against obesity and identify MT1-MMP as a promising target.
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Affiliation(s)
- Chi Fung Willis Chow
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
- Center for Systems Biology Dresden, Max Planck Institute for Molecular Cell and Biology, Dresden, Germany
| | - Xuanming Guo
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Pallavi Asthana
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Shuo Zhang
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| | - Sheung Kin Ken Wong
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| | - Samane Fallah
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Sijia Che
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Susma Gurung
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Zening Wang
- Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Ki Baek Lee
- Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Xin Ge
- Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Shiyang Yuan
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Haoyu Xu
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Jacque Pak Kan Ip
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Zhixin Jiang
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| | - Lixiang Zhai
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Jiayan Wu
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Yijing Zhang
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Arun Kumar Mahato
- Institute of Biotechnology-HILIFE, University of Helsinki, Helsinki, Finland
| | - Mart Saarma
- Institute of Biotechnology-HILIFE, University of Helsinki, Helsinki, Finland
| | - Cheng Yuan Lin
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
- Centre for Chinese Herbal Medicine Drug Development Limited, Hong Kong Baptist University, Hong Kong SAR, China
| | - Hiu Yee Kwan
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Tao Huang
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Aiping Lyu
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Zhongjun Zhou
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| | - Zhao-Xiang Bian
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Centre for Chinese Herbal Medicine Drug Development Limited, Hong Kong Baptist University, Hong Kong SAR, China.
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25
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Querfurth H, Marshall J, Parang K, Rioult-Pedotti MS, Tiwari R, Kwon B, Reisinger S, Lee HK. A PDK-1 allosteric agonist neutralizes insulin signaling derangements and beta-amyloid toxicity in neuronal cells and in vitro. PLoS One 2022; 17:e0261696. [PMID: 35061720 PMCID: PMC8782417 DOI: 10.1371/journal.pone.0261696] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 12/08/2021] [Indexed: 01/09/2023] Open
Abstract
The Alzheimer's brain is affected by multiple pathophysiological processes, which include a unique, organ-specific form of insulin resistance that begins early in its course. An additional complexity arises from the four-fold risk of Alzheimer's Disease (AD) in type 2 diabetics, however there is no definitive proof of causation. Several strategies to improve brain insulin signaling have been proposed and some have been clinically tested. We report findings on a small allosteric molecule that reverses several indices of insulin insensitivity in both cell culture and in vitro models of AD that emphasize the intracellular accumulation of β-amyloid (Aβi). PS48, a chlorophenyl pentenoic acid, is an allosteric activator of PDK-1, which is an Akt-kinase in the insulin/PI3K pathway. PS48 was active at 10 nM to 1 μM in restoring normal insulin-dependent Akt activation and in mitigating Aβi peptide toxicity. Synaptic plasticity (LTP) in prefrontal cortical slices from normal rat exposed to Aβ oligomers also benefited from PS48. During these experiments, neither overstimulation of PI3K/Akt signaling nor toxic effects on cells was observed. Another neurotoxicity model producing insulin insensitivity, utilizing palmitic acid, also responded to PS48 treatment, thus validating the target and indicating that its therapeutic potential may extend outside of β-amyloid reliance. The described in vitro and cell based-in vitro coupled enzymatic assay systems proved suitable platforms to screen a preliminary library of new analogs.
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Affiliation(s)
- Henry Querfurth
- Department of Neurology, Tufts Medical Center, Boston, MA, United States of America
| | - John Marshall
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI, United States of America
| | - Keykavous Parang
- Center for Targeted Drug Delivery, Chapman University, School of Pharmacology, Irvine, CA United States of America
| | - Mengia S. Rioult-Pedotti
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI, United States of America
- Department of Neurology, Clinical Neurorehabilitation, University of Zurich, Zurich, Switzerland
| | - Rakesh Tiwari
- Center for Targeted Drug Delivery, Chapman University, School of Pharmacology, Irvine, CA United States of America
| | - Bumsup Kwon
- Department of Neurology, Rhode Island Hospital, Providence, RI, United States of America
| | | | - Han-Kyu Lee
- Department of Neurology, Tufts Medical Center, Boston, MA, United States of America
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Schoger E, Lelek S, Panáková D, Zelarayán LC. Tailoring Cardiac Synthetic Transcriptional Modulation Towards Precision Medicine. Front Cardiovasc Med 2022; 8:783072. [PMID: 35097003 PMCID: PMC8795974 DOI: 10.3389/fcvm.2021.783072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 12/07/2021] [Indexed: 11/13/2022] Open
Abstract
Molecular and genetic differences between individual cells within tissues underlie cellular heterogeneities defining organ physiology and function in homeostasis as well as in disease states. Transcriptional control of endogenous gene expression has been intensively studied for decades. Thanks to a fast-developing field of single cell genomics, we are facing an unprecedented leap in information available pertaining organ biology offering a comprehensive overview. The single-cell technologies that arose aided in resolving the precise cellular composition of many organ systems in the past years. Importantly, when applied to diseased tissues, the novel approaches have been immensely improving our understanding of the underlying pathophysiology of common human diseases. With this information, precise prediction of regulatory elements controlling gene expression upon perturbations in a given cell type or a specific context will be realistic. Simultaneously, the technological advances in CRISPR-mediated regulation of gene transcription as well as their application in the context of epigenome modulation, have opened up novel avenues for targeted therapy and personalized medicine. Here, we discuss the fast-paced advancements during the recent years and the applications thereof in the context of cardiac biology and common cardiac disease. The combination of single cell technologies and the deep knowledge of fundamental biology of the diseased heart together with the CRISPR-mediated modulation of gene regulatory networks will be instrumental in tailoring the right strategies for personalized and precision medicine in the near future. In this review, we provide a brief overview of how single cell transcriptomics has advanced our knowledge and paved the way for emerging CRISPR/Cas9-technologies in clinical applications in cardiac biomedicine.
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Affiliation(s)
- Eric Schoger
- Institute of Pharmacology and Toxicology, University Medical Center Goettingen, Goettingen, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Goettingen, Goettingen, Germany
- Cluster of Excellence “Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells”, University of Goettingen, Goettingen, Germany
| | - Sara Lelek
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
| | - Daniela Panáková
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
- Daniela Panáková
| | - Laura Cecilia Zelarayán
- Institute of Pharmacology and Toxicology, University Medical Center Goettingen, Goettingen, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Goettingen, Goettingen, Germany
- Cluster of Excellence “Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells”, University of Goettingen, Goettingen, Germany
- *Correspondence: Laura Cecilia Zelarayán
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Triveri A, Sanchez-Martin C, Torielli L, Serapian SA, Marchetti F, D'Acerno G, Pirota V, Castelli M, Moroni E, Ferraro M, Quadrelli P, Rasola A, Colombo G. Protein allostery and ligand design: Computational design meets experiments to discover novel chemical probes. J Mol Biol 2022; 434:167468. [DOI: 10.1016/j.jmb.2022.167468] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/18/2022] [Accepted: 01/21/2022] [Indexed: 10/19/2022]
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Jayaraman S, Kocot J, Esfahani SH, Wangler NJ, Uyar A, Mechref Y, Trippier PC, Abbruscato TJ, Dickson A, Aihara H, Ostrov DA, Karamyan VT. Identification and Characterization of Two Structurally Related Dipeptides that Enhance Catalytic Efficiency of Neurolysin. J Pharmacol Exp Ther 2021; 379:191-202. [PMID: 34389655 PMCID: PMC8626779 DOI: 10.1124/jpet.121.000840] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 08/10/2021] [Indexed: 11/22/2022] Open
Abstract
Neurolysin (Nln) is a recently recognized endogenous mechanism functioning to preserve the brain from ischemic injury. To further understand the pathophysiological function of this peptidase in stroke and other neurologic disorders, the present study was designed to identify small molecule activators of Nln. Using a computational approach, the structure of Nln was explored, which was followed by docking and in silico screening of ∼140,000 molecules from the National Cancer Institute Developmental Therapeutics Program database. Top ranking compounds were evaluated in an Nln enzymatic assay, and two hit histidine-dipeptides were further studied in detail. The identified dipeptides enhanced the rate of synthetic substrate hydrolysis by recombinant (human and rat) and mouse brain-purified Nln in a concentration-dependent manner (micromolar A50 and Amax ≥ 300%) but had negligible effect on activity of closely related peptidases. Both dipeptides also enhanced hydrolysis of Nln endogenous substrates neurotensin, angiotensin I, and bradykinin and increased efficiency of the synthetic substrate hydrolysis (Vmax/Km ratio) in a concentration-dependent manner. The dipeptides and competitive inhibitor dynorphin A (1-13) did not affect each other's affinity for Nln, suggesting differing nature of their respective binding sites. Lastly, drug affinity responsive target stability (DARTS) and differential scanning fluorimetry (DSF) assays confirmed concentration-dependent interaction of Nln with the activator molecule. This is the first study demonstrating that Nln activity can be enhanced by small molecules, although the peptidic nature and low potency of the activators limit their application. The identified dipeptides provide a chemical scaffold to develop high-potency, drug-like molecules as research tools and potential drug leads. SIGNIFICANCE STATEMENT: This study describes discovery of two molecules that selectively enhance activity of peptidase Nln-a newly recognized cerebroprotective mechanism in the poststroke brain. The identified molecules will serve as a chemical scaffold for development of drug-like molecules to further study Nln and may become lead structures for a new class of drugs. In addition, our conceptual and methodological framework and research findings might be used for other peptidases and enzymes, the activation of which bears therapeutic potential.
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Affiliation(s)
- Srinidhi Jayaraman
- Department of Pharmaceutical Sciences (S.J., J.K., S.H.E., N.J.W., T.J.A., V.T.K.) and Center for Blood Brain Barrier Research (T.J.A., V.T.K.), School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan (A.U., A.D.); Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas (Y.M.); Department of Pharmaceutical Sciences, College of Pharmacy and Center for Drug Discovery, University of Nebraska Medical Center, Omaha, Nebraska (P.C.T.); Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota (H.A.); and Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida (D.A.O.)
| | - Joanna Kocot
- Department of Pharmaceutical Sciences (S.J., J.K., S.H.E., N.J.W., T.J.A., V.T.K.) and Center for Blood Brain Barrier Research (T.J.A., V.T.K.), School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan (A.U., A.D.); Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas (Y.M.); Department of Pharmaceutical Sciences, College of Pharmacy and Center for Drug Discovery, University of Nebraska Medical Center, Omaha, Nebraska (P.C.T.); Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota (H.A.); and Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida (D.A.O.)
| | - Shiva Hadi Esfahani
- Department of Pharmaceutical Sciences (S.J., J.K., S.H.E., N.J.W., T.J.A., V.T.K.) and Center for Blood Brain Barrier Research (T.J.A., V.T.K.), School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan (A.U., A.D.); Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas (Y.M.); Department of Pharmaceutical Sciences, College of Pharmacy and Center for Drug Discovery, University of Nebraska Medical Center, Omaha, Nebraska (P.C.T.); Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota (H.A.); and Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida (D.A.O.)
| | - Naomi J Wangler
- Department of Pharmaceutical Sciences (S.J., J.K., S.H.E., N.J.W., T.J.A., V.T.K.) and Center for Blood Brain Barrier Research (T.J.A., V.T.K.), School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan (A.U., A.D.); Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas (Y.M.); Department of Pharmaceutical Sciences, College of Pharmacy and Center for Drug Discovery, University of Nebraska Medical Center, Omaha, Nebraska (P.C.T.); Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota (H.A.); and Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida (D.A.O.)
| | - Arzu Uyar
- Department of Pharmaceutical Sciences (S.J., J.K., S.H.E., N.J.W., T.J.A., V.T.K.) and Center for Blood Brain Barrier Research (T.J.A., V.T.K.), School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan (A.U., A.D.); Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas (Y.M.); Department of Pharmaceutical Sciences, College of Pharmacy and Center for Drug Discovery, University of Nebraska Medical Center, Omaha, Nebraska (P.C.T.); Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota (H.A.); and Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida (D.A.O.)
| | - Yehia Mechref
- Department of Pharmaceutical Sciences (S.J., J.K., S.H.E., N.J.W., T.J.A., V.T.K.) and Center for Blood Brain Barrier Research (T.J.A., V.T.K.), School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan (A.U., A.D.); Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas (Y.M.); Department of Pharmaceutical Sciences, College of Pharmacy and Center for Drug Discovery, University of Nebraska Medical Center, Omaha, Nebraska (P.C.T.); Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota (H.A.); and Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida (D.A.O.)
| | - Paul C Trippier
- Department of Pharmaceutical Sciences (S.J., J.K., S.H.E., N.J.W., T.J.A., V.T.K.) and Center for Blood Brain Barrier Research (T.J.A., V.T.K.), School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan (A.U., A.D.); Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas (Y.M.); Department of Pharmaceutical Sciences, College of Pharmacy and Center for Drug Discovery, University of Nebraska Medical Center, Omaha, Nebraska (P.C.T.); Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota (H.A.); and Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida (D.A.O.)
| | - Thomas J Abbruscato
- Department of Pharmaceutical Sciences (S.J., J.K., S.H.E., N.J.W., T.J.A., V.T.K.) and Center for Blood Brain Barrier Research (T.J.A., V.T.K.), School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan (A.U., A.D.); Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas (Y.M.); Department of Pharmaceutical Sciences, College of Pharmacy and Center for Drug Discovery, University of Nebraska Medical Center, Omaha, Nebraska (P.C.T.); Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota (H.A.); and Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida (D.A.O.)
| | - Alex Dickson
- Department of Pharmaceutical Sciences (S.J., J.K., S.H.E., N.J.W., T.J.A., V.T.K.) and Center for Blood Brain Barrier Research (T.J.A., V.T.K.), School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan (A.U., A.D.); Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas (Y.M.); Department of Pharmaceutical Sciences, College of Pharmacy and Center for Drug Discovery, University of Nebraska Medical Center, Omaha, Nebraska (P.C.T.); Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota (H.A.); and Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida (D.A.O.)
| | - Hideki Aihara
- Department of Pharmaceutical Sciences (S.J., J.K., S.H.E., N.J.W., T.J.A., V.T.K.) and Center for Blood Brain Barrier Research (T.J.A., V.T.K.), School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan (A.U., A.D.); Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas (Y.M.); Department of Pharmaceutical Sciences, College of Pharmacy and Center for Drug Discovery, University of Nebraska Medical Center, Omaha, Nebraska (P.C.T.); Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota (H.A.); and Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida (D.A.O.)
| | - David A Ostrov
- Department of Pharmaceutical Sciences (S.J., J.K., S.H.E., N.J.W., T.J.A., V.T.K.) and Center for Blood Brain Barrier Research (T.J.A., V.T.K.), School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan (A.U., A.D.); Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas (Y.M.); Department of Pharmaceutical Sciences, College of Pharmacy and Center for Drug Discovery, University of Nebraska Medical Center, Omaha, Nebraska (P.C.T.); Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota (H.A.); and Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida (D.A.O.)
| | - Vardan T Karamyan
- Department of Pharmaceutical Sciences (S.J., J.K., S.H.E., N.J.W., T.J.A., V.T.K.) and Center for Blood Brain Barrier Research (T.J.A., V.T.K.), School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan (A.U., A.D.); Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas (Y.M.); Department of Pharmaceutical Sciences, College of Pharmacy and Center for Drug Discovery, University of Nebraska Medical Center, Omaha, Nebraska (P.C.T.); Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota (H.A.); and Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida (D.A.O.)
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Abstract
INTRODUCTION Undruggable targets refer to clinically meaningful therapeutic targets that are 'difficult to drug' or 'yet to be drugged' via traditional approaches. Featuring characteristics of lacking defined ligand-binding pockets, non-catalytic protein-protein interaction functional modes and less-investigated 3D structures, these undruggable targets have been targeted with novel therapeutic entities developed with the progress of unconventional drug discovery approaches, such as targeted degradation molecules and display technologies. AREA COVERED This review first presents the concept of 'undruggable' exemplified by RAS and other targets. Next, detailed strategies are illustrated in two aspects: innovation of therapeutic entities and development of unconventional drug discovery technologies. Finally, case studies covering typical undruggable targets (Bcl-2, p53, and RAS) are depicted to further demonstrate the feasibility of the strategies and entities above. EXPERT OPINION Targeting the undruggable expands the scope of therapeutically reachable targets. Consequently, it represents the drug discovery frontier. Biomedical studies are capable of dissecting disease mechanisms, thus broadening the list of undruggable targets. Encouraged by the recent approval of the KRAS inhibitor Sotorasib, we believe that merging multiple discovery approaches and exploiting various novel therapeutic entities would pave the way for dealing with more 'undruggable' targets in the future.
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Affiliation(s)
- Gong Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, P. R. China
| | - Juan Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, P. R. China
| | - Yuting Gao
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, P. R. China
| | - Yangfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, P. R. China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, P. R. China.,Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
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Li W, Liu J, Shao L, Mao L, Wang M. DNAzyme-Catalyzed Cellular Oxidative Stress Amplification for Pro-protein Activation in Living Cells. Chembiochem 2021; 22:2608-2613. [PMID: 34155741 DOI: 10.1002/cbic.202100225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/16/2021] [Indexed: 11/10/2022]
Abstract
The conditional control of protein function in response to the physiological change of cells is of great interest for studying protein function in biological settings and developing protein therapeutics. We report herein that catalase (CAT) DNAzyme can potentiate the generation of reactive oxygen species (ROS) in living cells by knocking down catalase expression, which could further activate a reactive oxygen species (ROS)-responsive pro-protein, RNase A-NBC, in situ. Using an optimized lipid nanoparticle delivery system to simultaneously introduce CAT DNAzyme and RNase A-NBC into cells, we show that the pro-protein, RNase A-NBC, could be activated in a significantly enhanced manner to prohibit tumor cell growth in different types of cancer cells. We believe the methodology of regulating pro-protein activity using DNAzyme biocatalysis to differentiate intracellular environment could further be extended to other functional proteins, and even fundamental investigations in living systems to develop pro-protein therapeutics.
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Affiliation(s)
- Wenting Li
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun North First Street 2, 100190, Beijing, P. R. China
- University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing, 100049, P. R. China
| | - Ji Liu
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun North First Street 2, 100190, Beijing, P. R. China
- University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing, 100049, P. R. China
| | - Leihou Shao
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun North First Street 2, 100190, Beijing, P. R. China
- Beijing Key Laboratory of Organic Materials Testing Technology and Quality Evaluation, Beijing Center for Physical and Chemical Analysis, Beijing, 100089, P. R. China
| | - Lanqun Mao
- College of Chemistry, Beijing Normal University, No.19, Xinjiekouwai Street, Haidian District, Beijing, 100875, P. R. China
| | - Ming Wang
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun North First Street 2, 100190, Beijing, P. R. China
- University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing, 100049, P. R. China
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31
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Molecular insights on ABL kinase activation using tree-based machine learning models and molecular docking. Mol Divers 2021; 25:1301-1314. [PMID: 34191245 PMCID: PMC8241884 DOI: 10.1007/s11030-021-10261-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/18/2021] [Indexed: 12/14/2022]
Abstract
Abelson kinase (c-Abl) is a non-receptor tyrosine kinase involved in several biological processes essential for cell differentiation, migration, proliferation, and survival. This enzyme's activation might be an alternative strategy for treating diseases such as neutropenia induced by chemotherapy, prostate, and breast cancer. Recently, a series of compounds that promote the activation of c-Abl has been identified, opening a promising ground for c-Abl drug development. Structure-based drug design (SBDD) and ligand-based drug design (LBDD) methodologies have significantly impacted recent drug development initiatives. Here, we combined SBDD and LBDD approaches to characterize critical chemical properties and interactions of identified c-Abl's activators. We used molecular docking simulations combined with tree-based machine learning models—decision tree, AdaBoost, and random forest to understand the c-Abl activators' structural features required for binding to myristoyl pocket, and consequently, to promote enzyme and cellular activation. We obtained predictive and robust models with Matthews correlation coefficient values higher than 0.4 for all endpoints and identified characteristics that led to constructing a structure–activity relationship model (SAR).
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32
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Abstract
Proteome-wide profiling of protein phosphorylation has been widely used to reveal the underlying mechanism of diverse cellular signaling events. Yet, characterizing subcellular phosphoproteome with high spatial-temporal resolution has remained challenging. Herein, we developed a subcellular-specific uncaging-assisted biotinylation and mapping of phosphoproteome (SubMAPP) strategy to monitor the phosphorylation dynamics of subcellular proteome in living cells and animals. Our method capitalizes on the genetically encoded bioorthogonal decaging strategy, which enables the rapid activation of subcellular localized proximity labeling biotin ligase through either light illumination or small-molecule triggers. By further adopting an integrated orthogonal pull-down strategy with quantitative mass spectrometry, SubMAPP allowed for the investigation of subcellular phosphoproteome dynamics, revealing the altered phosphorylation patterns of endoplasmic reticulum (ER) luminal proteins under ER stress. Finally, we further expanded the scope of the SubMAPP strategy to primary neuron culture and living mice.
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33
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Mashima T, Rosier BJHM, Oohora K, de Greef TFA, Hayashi T, Brunsveld L. Dynamic Protease Activation on a Multimeric Synthetic Protein Scaffold via Adaptable DNA-Based Recruitment Domains. Angew Chem Int Ed Engl 2021; 60:11262-11266. [PMID: 33725379 PMCID: PMC8252739 DOI: 10.1002/anie.202102160] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Indexed: 12/21/2022]
Abstract
Hexameric hemoprotein (HTHP) is employed as a scaffold protein for the supramolecular assembly and activation of the apoptotic signalling enzyme caspase‐9, using short DNA elements as modular recruitment domains. Caspase‐9 assembly and activation on the HTHP platform due to enhanced proximity is followed by combinatorial inhibition at high scaffold concentrations. The DNA recruitment domains allow for reversible switching of the caspase‐9 assembly and activity state using short modulatory DNA strands. Tuning of the recruitment domain affinity allows for generating kinetically trapped active enzyme complexes, as well as for dynamic repositioning of caspases over scaffold populations and inhibition using monovalent sink platforms. The conceptual combination of a highly structured multivalent protein platform with modular DNA recruitment domains provides emergent biomimicry properties with advanced levels of control over protein assembly.
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Affiliation(s)
- Tsuyoshi Mashima
- Institute for Complex Molecular Systems and, Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600, MB, Eindhoven, The Netherlands
| | - Bas J H M Rosier
- Institute for Complex Molecular Systems and, Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600, MB, Eindhoven, The Netherlands
| | - Koji Oohora
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita 565-0871, Osaka, Japan
| | - Tom F A de Greef
- Institute for Complex Molecular Systems and, Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600, MB, Eindhoven, The Netherlands.,Computational Biology group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Takashi Hayashi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita 565-0871, Osaka, Japan
| | - Luc Brunsveld
- Institute for Complex Molecular Systems and, Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600, MB, Eindhoven, The Netherlands
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34
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Mashima T, Rosier BJHM, Oohora K, Greef TFA, Hayashi T, Brunsveld L. Dynamic Protease Activation on a Multimeric Synthetic Protein Scaffold via Adaptable DNA‐Based Recruitment Domains. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Tsuyoshi Mashima
- Institute for Complex Molecular Systems and Laboratory of Chemical Biology Department of Biomedical Engineering Eindhoven University of Technology P.O. Box 513, 5600 MB Eindhoven The Netherlands
| | - Bas J. H. M. Rosier
- Institute for Complex Molecular Systems and Laboratory of Chemical Biology Department of Biomedical Engineering Eindhoven University of Technology P.O. Box 513, 5600 MB Eindhoven The Netherlands
| | - Koji Oohora
- Department of Applied Chemistry Graduate School of Engineering Osaka University Suita 565–0871 Osaka Japan
| | - Tom F. A. Greef
- Institute for Complex Molecular Systems and Laboratory of Chemical Biology Department of Biomedical Engineering Eindhoven University of Technology P.O. Box 513, 5600 MB Eindhoven The Netherlands
- Computational Biology group Department of Biomedical Engineering Eindhoven University of Technology Eindhoven The Netherlands
| | - Takashi Hayashi
- Department of Applied Chemistry Graduate School of Engineering Osaka University Suita 565–0871 Osaka Japan
| | - Luc Brunsveld
- Institute for Complex Molecular Systems and Laboratory of Chemical Biology Department of Biomedical Engineering Eindhoven University of Technology P.O. Box 513, 5600 MB Eindhoven The Netherlands
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35
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Marchetti F, Moroni E, Pandini A, Colombo G. Machine Learning Prediction of Allosteric Drug Activity from Molecular Dynamics. J Phys Chem Lett 2021; 12:3724-3732. [PMID: 33843228 PMCID: PMC8154828 DOI: 10.1021/acs.jpclett.1c00045] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 04/05/2021] [Indexed: 05/13/2023]
Abstract
Allosteric drugs have been attracting increasing interest over the past few years. In this context, it is common practice to use high-throughput screening for the discovery of non-natural allosteric drugs. While the discovery stage is supported by a growing amount of biological information and increasing computing power, major challenges still remain in selecting allosteric ligands and predicting their effect on the target protein's function. Indeed, allosteric compounds can act both as inhibitors and activators of biological responses. Computational approaches to the problem have focused on variations on the theme of molecular docking coupled to molecular dynamics with the aim of recovering information on the (long-range) modulation typical of allosteric proteins.
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Affiliation(s)
- Filippo Marchetti
- Department
of Chemistry, Università Degli Studi
di Pavia, Viale Taramelli 12, 27100 Pavia, Italy
- Università
Degli Studi di Milano, Via C. Golgi, 19, I-20133 Milan, Italy
| | - Elisabetta Moroni
- Istituto
di Scienze e Tecnologie Chimiche, Via Mario Bianco 9, 20131 Milano, Italy
| | | | - Giorgio Colombo
- Department
of Chemistry, Università Degli Studi
di Pavia, Viale Taramelli 12, 27100 Pavia, Italy
- Istituto
di Scienze e Tecnologie Chimiche, Via Mario Bianco 9, 20131 Milano, Italy
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36
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Jiang L, Yuan C, Huang M. A general strategy to inhibit serine protease by targeting its autolysis loop. FASEB J 2021; 35:e21259. [DOI: 10.1096/fj.202002139rr] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 11/20/2020] [Accepted: 11/25/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Longguang Jiang
- College of Chemistry Fuzhou University Fuzhou P.R. China
- Fujian Key Laboratory of Marine Enzyme Engineering Fuzhou University Fuzhou P.R. China
| | - Cai Yuan
- College of Biological Science and Engineering Fuzhou University Fuzhou P.R. China
| | - Mingdong Huang
- College of Chemistry Fuzhou University Fuzhou P.R. China
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37
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Du S, Liew SS, Zhang CW, Du W, Lang W, Yao CCY, Li L, Ge J, Yao SQ. Cell-Permeant Bioadaptors for Cytosolic Delivery of Native Antibodies: A "Mix-and-Go" Approach. ACS CENTRAL SCIENCE 2020; 6:2362-2376. [PMID: 33376798 PMCID: PMC7760483 DOI: 10.1021/acscentsci.0c01379] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Indexed: 05/05/2023]
Abstract
Antibodies are powerful tools that may potentially find wide applications in live-cell bioimaging, disease diagnostics, and therapeutics. Their practical applications have however remained limited thus far, owing to their inability to cross the cell membrane. Existing approaches for cytosolic delivery of functional antibodies are available, but they are constantly plagued by the need for chemical/genetic modifications, low delivery efficiency, and severe endolysosomal trapping. Consequently, it is of paramount importance to develop new strategies capable of highly efficient cytosolic delivery of native antibodies with immediate bioavailability. Herein, we report a modification-free, convenient "mix-and-go" strategy for the cytosolic delivery of native antibodies to different live mammalian cells efficiently, with minimal endolysosomal trapping and immediate bioavailability. By simply mixing a cell-permeant bioadaptor (derived from protein A or TRIM21) with a commercially available off-the-shelf antibody, the resulting noncovalent complex could be immediately used for intracellular delivery of native antibodies needed in subsequent cytosolic target engagement. The versatility of this approach was successfully illustrated in a number of applications, including antibody-based, live-cell imaging of the endogenous protein glutathionylation to detect oxidative cell stress, antibody-based activation of endogenous caspase-3, and inhibition of endogenous PTP1B activity, and finally TRIM21-mediated endogenous protein degradation for potential targeted therapy. Our results thus indicate this newly developed, "mix-and-go" antibody delivery method should have broad applications in chemical biology and future drug discovery.
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Affiliation(s)
- Shubo Du
- Department
of Chemistry, National University of Singapore, Singapore 117543, Singapore
| | - Si Si Liew
- Department
of Chemistry, National University of Singapore, Singapore 117543, Singapore
| | - Cheng-wu Zhang
- Department
of Chemistry, National University of Singapore, Singapore 117543, Singapore
| | - Wei Du
- Department
of Chemistry, National University of Singapore, Singapore 117543, Singapore
- Shaanxi
Institute of Flexible Electronics (SIFE) & Xi’an Key Laboratory
of Biomedical Materials & Engineering, Northwestern Polytechnical University (NPU), Xi’an 710072, China
| | - Wenjie Lang
- Key
Laboratory of Bioorganic Synthesis of Zhejiang Province, College of
Biotechnology and Bioengineering, Zhejiang
University of Technology, Hangzhou 310014, China
| | - Cassandra C. Y. Yao
- Department
of Chemistry, National University of Singapore, Singapore 117543, Singapore
| | - Lin Li
- Shaanxi
Institute of Flexible Electronics (SIFE) & Xi’an Key Laboratory
of Biomedical Materials & Engineering, Northwestern Polytechnical University (NPU), Xi’an 710072, China
| | - Jingyan Ge
- Key
Laboratory of Bioorganic Synthesis of Zhejiang Province, College of
Biotechnology and Bioengineering, Zhejiang
University of Technology, Hangzhou 310014, China
| | - Shao Q. Yao
- Department
of Chemistry, National University of Singapore, Singapore 117543, Singapore
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38
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Porte K, Riberaud M, Châtre R, Audisio D, Papot S, Taran F. Bioorthogonal Reactions in Animals. Chembiochem 2020; 22:100-113. [PMID: 32935888 DOI: 10.1002/cbic.202000525] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/15/2020] [Indexed: 01/04/2023]
Abstract
The advent of bioorthogonal chemistry has led to the development of powerful chemical tools that enable increasingly ambitious applications. In particular, these tools have made it possible to achieve what is considered to be the holy grail of many researchers involved in chemical biology: to perform unnatural chemical reactions within living organisms. In this minireview, we present an update of bioorthogonal reactions that have been carried out in animals for various applications. We outline the advances made in the understanding of fundamental biological processes, and the development of innovative imaging and therapeutic strategies using bioorthogonal chemistry.
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Affiliation(s)
- Karine Porte
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SCBM, 91191, Gif-sur-Yvette, France
| | - Maxime Riberaud
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SCBM, 91191, Gif-sur-Yvette, France
| | - Rémi Châtre
- Université de Poitiers, UMR-CNRS 7285, Institut de Chimie des Milieux et des Matériaux de Poitiers (IC2MP), 86022, Poitiers, France) E-mail
| | - Davide Audisio
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SCBM, 91191, Gif-sur-Yvette, France
| | - Sébastien Papot
- Université de Poitiers, UMR-CNRS 7285, Institut de Chimie des Milieux et des Matériaux de Poitiers (IC2MP), 86022, Poitiers, France) E-mail
| | - Frédéric Taran
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SCBM, 91191, Gif-sur-Yvette, France
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39
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How to make an undruggable enzyme druggable: lessons from ras proteins. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020. [PMID: 32951811 DOI: 10.1016/bs.apcsb.2020.05.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Significant advances have been made toward discovering allosteric inhibitors for challenging drug targets such as the Ras family of membrane-associated signaling proteins. Malfunction of Ras proteins due to somatic mutations is associated with up to a quarter of all human cancers. Computational techniques have played critical roles in identifying and characterizing allosteric ligand-binding sites on these proteins, and to screen ligand libraries against those sites. These efforts, combined with a wide range of biophysical, structural, biochemical and cell biological experiments, are beginning to yield promising inhibitors to treat malignancies associated with mutated Ras proteins. In this chapter, we discuss some of these developments and how the lessons learned from Ras might be applied to similar other challenging drug targets.
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40
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Serapian SA, Colombo G. Designing Molecular Spanners to Throw in the Protein Networks. Chemistry 2020; 26:4656-4670. [DOI: 10.1002/chem.201904523] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/18/2019] [Indexed: 12/18/2022]
Affiliation(s)
- Stefano A. Serapian
- Department of ChemistryUniversity of Pavia Via Taramelli 12 27100 Pavia Italy
| | - Giorgio Colombo
- Department of ChemistryUniversity of Pavia Via Taramelli 12, 27 100 Pavia Italy
- SCITEC-CNR Via Mario Bianco 9 20131 Milano Italy
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41
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Rivoire O. Parsimonious evolutionary scenario for the origin of allostery and coevolution patterns in proteins. Phys Rev E 2020; 100:032411. [PMID: 31640027 DOI: 10.1103/physreve.100.032411] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Indexed: 12/16/2022]
Abstract
Proteins display generic properties that are challenging to explain by direct selection, notably allostery, the capacity to be regulated through long-range effects, and evolvability, the capacity to adapt to new selective pressures. An evolutionary scenario is proposed where proteins acquire these two features indirectly as a by-product of their selection for a more fundamental property, exquisite discrimination, the capacity to bind discriminatively very similar ligands. Achieving this task is shown to typically require proteins to undergo a conformational change. We argue that physical and evolutionary constraints impel this change to be controlled by a group of sites extending from the binding site. Proteins can thus acquire a latent potential for allosteric regulation and evolutionary adaptation because of long-range effects that initially arise as evolutionary spandrels. This scenario accounts for the groups of conserved and coevolving residues observed in multiple sequence alignments. However, we propose that most pairs of coevolving and contacting residues inferred from such alignments have a different origin, related to thermal stability. A physical model is presented that illustrates this evolutionary scenario and its implications. The scenario can be implemented in experiments of protein evolution to directly test its predictions.
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Affiliation(s)
- Olivier Rivoire
- Center for Interdisciplinary Research in Biology, Collège de France, Centre National de la Recherche Scientifique, INSERM, PSL Research University, 75005 Paris, France
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42
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Smith CJ, Wagner AG, Stagnitta RT, Xu Z, Pezzullo JL, Giner JL, Xie J, Covey DF, Wang C, Callahan BP. Subverting Hedgehog Protein Autoprocessing by Chemical Induction of Paracatalysis. Biochemistry 2020; 59:736-741. [PMID: 32013401 PMCID: PMC7031038 DOI: 10.1021/acs.biochem.0c00013] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Hedgehog proteins, a family of vital cell signaling factors, are expressed in precursor form, which requires specialized autoprocessing, called cholesterolysis, for full biological activity. Cholesterolysis occurs in cis through the action of the precursor's C-terminal enzymatic domain, HhC. In this work, we describe HhC activator compounds (HACs), a novel class of noncovalent modulators that induce autoprocessing infidelity, diminishing native cholesterolysis in favor of precursor autoproteolysis, an otherwise minor and apparently nonphysiological side reaction. HAC-induced autoproteolysis generates hedgehog protein that is cholesterol free and hence signaling deficient. The most effective HAC has an AC50 of 9 μM, accelerates HhC autoproteolytic activity by 225-fold, and functions in the presence and absence of cholesterol, the native substrate. HACs join a rare class of "antagonists" that suppress native enzymatic activity by subverting mechanistic fidelity.
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Affiliation(s)
- Carl J Smith
- Department of Chemistry , Binghamton University, State University of New York , 4400 Vestal Parkway East , Binghamton , New York 13902 , United States
| | - Andrew G Wagner
- Department of Chemistry , Binghamton University, State University of New York , 4400 Vestal Parkway East , Binghamton , New York 13902 , United States
| | - Robert T Stagnitta
- Department of Chemistry , Binghamton University, State University of New York , 4400 Vestal Parkway East , Binghamton , New York 13902 , United States
| | - Zihan Xu
- Department of Chemistry , Binghamton University, State University of New York , 4400 Vestal Parkway East , Binghamton , New York 13902 , United States
| | - John L Pezzullo
- Department of Chemistry , State University of New York College of Environmental Science and Forestry , Syracuse , New York 13210 , United States
| | - José-Luis Giner
- Department of Chemistry , State University of New York College of Environmental Science and Forestry , Syracuse , New York 13210 , United States
| | - Jian Xie
- Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies , Rensselaer Polytechnic Institute , 110 8th Street , Troy , New York 12180 , United States
| | - Douglas F Covey
- Department of Developmental Biology , Taylor Family Institute for Innovative Psychiatric Research , 660 South Euclid Avenue , St. Louis , Missouri 63110 , United States
| | - Chunyu Wang
- Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies , Rensselaer Polytechnic Institute , 110 8th Street , Troy , New York 12180 , United States
| | - Brian P Callahan
- Department of Chemistry , Binghamton University, State University of New York , 4400 Vestal Parkway East , Binghamton , New York 13902 , United States
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43
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Gomes P, Viana SD, Nunes S, Rolo AP, Palmeira CM, Reis F. The yin and yang faces of the mitochondrial deacetylase sirtuin 3 in age-related disorders. Ageing Res Rev 2020; 57:100983. [PMID: 31740222 DOI: 10.1016/j.arr.2019.100983] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 10/08/2019] [Accepted: 11/14/2019] [Indexed: 02/07/2023]
Abstract
Aging, the most important risk factor for many of the chronic diseases affecting Western society, is associated with a decline in mitochondrial function and dynamics. Sirtuin 3 (SIRT3) is a mitochondrial deacetylase that has emerged as a key regulator of fundamental processes which are frequently dysregulated in aging and related disorders. This review highlights recent advances and controversies regarding the yin and yang functions of SIRT3 in metabolic, cardiovascular and neurodegenerative diseases, as well as the use of SIRT3 modulators as a therapeutic strategy against those disorders. Although most studies point to a protective role upon SIRT3 activation, there are conflicting findings that need a better elucidation. The discovery of novel SIRT3 modulators with higher selectivity together with the assessment of the relative importance of different SIRT3 enzymatic activities and the relevance of crosstalk between distinct sirtuin isoforms will be pivotal to validate SIRT3 as a useful drug target for the prevention and treatment of age-related diseases.
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Affiliation(s)
- Pedro Gomes
- Institute of Pharmacology & Experimental Therapeutics, Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, Portugal; CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Portugal; CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Portugal; Department of Biomedicine, Faculty of Medicine, University of Porto, Portugal; CINTESIS - Center for Health Technology and Services Research, University of Porto, Portugal
| | - Sofia D Viana
- Institute of Pharmacology & Experimental Therapeutics, Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, Portugal; CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Portugal; Polytechnic Institute of Coimbra, ESTESC-Coimbra Health School, Pharmacy, Coimbra, Portugal
| | - Sara Nunes
- Institute of Pharmacology & Experimental Therapeutics, Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, Portugal; CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Portugal
| | - Anabela P Rolo
- CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Portugal; CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Portugal; Department of Life Sciences, University of Coimbra, Portugal
| | - Carlos M Palmeira
- CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Portugal; CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Portugal; Department of Life Sciences, University of Coimbra, Portugal
| | - Flávio Reis
- Institute of Pharmacology & Experimental Therapeutics, Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, Portugal; CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Portugal.
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44
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Vukomanovic D, Jia Z, Nakatsu K, Smith GN, Ozolinš TRS. Riboflavin and pyrroloquinoline quinone generate carbon monoxide in the presence of tissue microsomes or recombinant human cytochrome P-450 oxidoreductase: implications for possible roles in gasotransmission. Can J Physiol Pharmacol 2019; 98:336-342. [PMID: 31825651 DOI: 10.1139/cjpp-2019-0376] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Carbon monoxide (CO), an endogenously produced gasotransmitter, regulates inflammation and vascular tone, suggesting that delivery of CO may be therapeutically useful for pathologies like preeclampsia where CO insufficiency is implicated. Our strategy is to identify chemicals that increase the activity of endogenous CO-producing enzymes, including cytochrome P-450 oxidoreductase (CPR). Realizing that both riboflavin and pyrroloquinoline quinone (PQQ) are relatively nontoxic, even at high doses, and that they share chemical properties with toxic CO activators that we previously identified, our goal was to determine whether riboflavin or PQQ could stimulate CO production. Riboflavin and PQQ were incubated in sealed vessels with rat and human tissue extracts and CO generation was measured with headspace-gas chromatography. Riboflavin and PQQ increased CO production ∼60% in rat spleen microsomes. In rat brain microsomes, riboflavin and PQQ increased respective CO production approximately fourfold and twofold compared to baseline. CO production by human placenta microsomes increased fourfold with riboflavin and fivefold with PQQ. In the presence of recombinant human CPR, CO production was threefold greater with PQQ than with riboflavin. These observations demonstrate for the first time that riboflavin and PQQ facilitate tissue-specific CO production with significant contributions from CPR. We propose a novel biochemical role for these nutrients in gastransmission.
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Affiliation(s)
- Dragic Vukomanovic
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada.,Department of Obstetrics and Gynaecology, Kingston General Hospital, Kingston, ON K7L 3N6, Canada
| | - Zongchao Jia
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Kanji Nakatsu
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Graeme N Smith
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada.,Department of Obstetrics and Gynaecology, Kingston General Hospital, Kingston, ON K7L 3N6, Canada
| | - Terence R S Ozolinš
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
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45
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Shen C, Li B, Astudillo L, Deutscher MP, Cobb MH, Capobianco AJ, Lee E, Robbins DJ. The CK1α Activator Pyrvinium Enhances the Catalytic Efficiency ( kcat/ Km) of CK1α. Biochemistry 2019; 58:5102-5106. [PMID: 31820934 DOI: 10.1021/acs.biochem.9b00891] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The serine/threonine protein kinase casein kinase 1α (CK1α) functions as a negative regulator of Wnt signaling, phosphorylating β-catenin at serine 45 (P-S45) to initiate its eventual ubiquitin-mediated degradation. We previously showed that the repurposed, FDA-approved anthelminthic drug pyrvinium potently inhibits Wnt signaling in vitro and in vivo. Moreover, we proposed that pyrvinium's Wnt inhibitory activity was the result of its function as an activator of CK1α. An understanding of the mechanism by which pyrvinium activates CK1α is important because pyrvinium was given an orphan drug designation by the FDA to treat familial adenomatous polyposis, a precancerous condition driven by constitutive Wnt signaling. In the current study, we show that pyrvinium stimulates the phosphorylation of S45 β-catenin, a known CK1α substrate, in a cell-based assay, and does so in a dose- and time-dependent manner. Alternative splicing of CK1α results in four forms of the protein with distinct biological properties. We evaluated these splice products and identified the CK1α splice variant, CK1αS, as the form that exhibits the most robust response to pyrvinium in cells. Kinetic studies indicate that pyrvinium also stimulates the kinase activity of purified, recombinant CK1αS in vitro, increasing its catalytic efficiency (kcat/Km) toward substrates. These studies provide strong and clear mechanistic evidence that pyrvinium enhances CK1α kinase activity.
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Affiliation(s)
- Chen Shen
- Molecular Oncology Program, The DeWitt Daughtry Family Department of Surgery, Miller School of Medicine , University of Miami , Miami , Florida 33136 , United States.,The Sheila and David Fuente Graduate Program in Cancer Biology, Miller School of Medicine , University of Miami , Miami , Florida 33136 , United States
| | - Bin Li
- Molecular Oncology Program, The DeWitt Daughtry Family Department of Surgery, Miller School of Medicine , University of Miami , Miami , Florida 33136 , United States
| | - Luisana Astudillo
- Molecular Oncology Program, The DeWitt Daughtry Family Department of Surgery, Miller School of Medicine , University of Miami , Miami , Florida 33136 , United States
| | - Murray P Deutscher
- Department of Biochemistry and Molecular Biology, Miller School of Medicine , University of Miami , Miami , Florida 33136 , United States
| | - Melanie H Cobb
- Department of Pharmacology , University of Texas Southwestern Medical Center , Dallas , Texas 75390 , United States
| | - Anthony J Capobianco
- Molecular Oncology Program, The DeWitt Daughtry Family Department of Surgery, Miller School of Medicine , University of Miami , Miami , Florida 33136 , United States.,Sylvester Cancer Center, Miller School of Medicine , University of Miami , Miami , Florida 33136 , United States
| | - Ethan Lee
- Department of Cell and Developmental Biology , Vanderbilt University , Nashville , Tennessee 37232 , United States
| | - David J Robbins
- Molecular Oncology Program, The DeWitt Daughtry Family Department of Surgery, Miller School of Medicine , University of Miami , Miami , Florida 33136 , United States.,Sylvester Cancer Center, Miller School of Medicine , University of Miami , Miami , Florida 33136 , United States.,Department of Biochemistry and Molecular Biology, Miller School of Medicine , University of Miami , Miami , Florida 33136 , United States
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46
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Baráth E, Mejía E. Ein Fest der Wissenschaft inmitten der Natur: Die 54. Bürgenstock‐Konferenz. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201906781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Eszter Baráth
- Department ChemieZentralforschungsinstitut für KatalyseTechnische Universität München Lichtenbergstraße 4 85748 Garching Deutschland
| | - Esteban Mejía
- Leibniz-Institut für Katalyse (LIKAT) Albert-Einstein-Straße 29a 18059 Rostock Deutschland
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47
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Baráth E, Mejía E. A Celebration of Science amidst Nature: The 54th Bürgenstock Conference. Angew Chem Int Ed Engl 2019; 58:17107-17113. [PMID: 31441577 DOI: 10.1002/anie.201906781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Indexed: 11/11/2022]
Affiliation(s)
- Eszter Baráth
- Department of Chemistry and Catalysis Research Center, Technische Universität München, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Esteban Mejía
- Leibniz Institute for Catalysis (LIKAT), Albert-Einstein-Straße 29a, 18059, Rostock, Germany
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48
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Abduljaleel Z. Comprehensive structure-function analysis of causative variants in retinal pigment epithelium specific 65 kDa protein associated Leber Congenital Amaurosis. Noncoding RNA Res 2019; 4:121-127. [PMID: 32072079 PMCID: PMC7012777 DOI: 10.1016/j.ncrna.2019.11.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 11/07/2019] [Accepted: 11/08/2019] [Indexed: 12/23/2022] Open
Abstract
A recent study published to screen RPE65 in 187 families with Leber Congenital Amaurosis (LCA) by Zilin Zhong in 2019. There are seven novel variants were identified in RPE65, which was associated with LCA, but among only five were missense mutations [(c.124C > T, p.(Leu42Phe), c.149T > C, p. (Phe50Ser), c.340A > C, p.(Asn114His), c.425A > G, p.(Asp142Gly) and c.1399C > G, p.(Pro467Ala)] in the Chinese population and potentially facilitates its clinical implementation. Further in-continuation of this study to the target of five novel missense mutations were the analysis of both structural and functional impact by the molecular dynamics and simulation. The result of five missense mutations might in critical structural alterations of RPE65 protein, disrupt its membrane association or rescue the activity of enzyme due to thermodynamics stability, and for this reason impair its isomerohydrolase activity, resulting in retinal dystrophy. These observations suggest that the reduced protein stability and altered subcellular localization of RPE65 might signify a mechanism for these mutations to lead to vision loss in LCA patients.
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Affiliation(s)
- Zainularifeen Abduljaleel
- Department of Medical Genetics, Umm Al-Qura University, P.O. Box 715, Makkah, 21955, Saudi Arabia.,Science and Technology Unit, Umm Al Qura University, P.O. Box 715, Makkah, 21955, Saudi Arabia.,Bircham International University, Av. Sierra, 2, 28691, Villanueva de La Cañada, Madrid, Spain
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49
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Plaman BA, Chan WC, Bishop AC. Chemical activation of divergent protein tyrosine phosphatase domains with cyanine-based biarsenicals. Sci Rep 2019; 9:16148. [PMID: 31695052 PMCID: PMC6834593 DOI: 10.1038/s41598-019-52002-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 10/11/2019] [Indexed: 12/28/2022] Open
Abstract
Strategies for the direct chemical activation of specific signaling proteins could provide powerful tools for interrogating cellular signal transduction. However, targeted protein activation is chemically challenging, and few broadly applicable activation strategies for signaling enzymes have been developed. Here we report that classical protein tyrosine phosphatase (PTP) domains from multiple subfamilies can be systematically sensitized to target-specific activation by the cyanine-based biarsenical compounds AsCy3 and AsCy5. Engineering of the activatable PTPs (actPTPs) is achieved by the introduction of three cysteine residues within a conserved loop of the PTP domain, and the positions of the sensitizing mutations are readily identifiable from primary sequence alignments. In the current study we have generated and characterized actPTP domains from three different subfamilies of both receptor and non-receptor PTPs. Biarsenical-induced stimulation of the actPTPs is rapid and dose-dependent, and is operative with both purified enzymes and complex proteomic mixtures. Our results suggest that a substantial fraction of the classical PTP family will be compatible with the act-engineering approach, which provides a novel chemical-biological tool for the control of PTP activity and the study of PTP function.
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Affiliation(s)
- Bailey A Plaman
- Amherst College, Department of Chemistry, Amherst, Massachusetts, 01002, USA
| | - Wai Cheung Chan
- Amherst College, Department of Chemistry, Amherst, Massachusetts, 01002, USA.,Dana-Farber Cancer Institute, Department of Cancer Biology, Boston, MA, 02215, USA
| | - Anthony C Bishop
- Amherst College, Department of Chemistry, Amherst, Massachusetts, 01002, USA.
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50
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Clausse V, Tao D, Debnath S, Fang Y, Tagad HD, Wang Y, Sun H, LeClair CA, Mazur SJ, Lane K, Shi ZD, Vasalatiy O, Eells R, Baker LK, Henderson MJ, Webb MR, Shen M, Hall MD, Appella E, Appella DH, Coussens NP. Physiologically relevant orthogonal assays for the discovery of small-molecule modulators of WIP1 phosphatase in high-throughput screens. J Biol Chem 2019; 294:17654-17668. [PMID: 31481464 PMCID: PMC6873202 DOI: 10.1074/jbc.ra119.010201] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/30/2019] [Indexed: 01/07/2023] Open
Abstract
WT P53-Induced Phosphatase 1 (WIP1) is a member of the magnesium-dependent serine/threonine protein phosphatase (PPM) family and is induced by P53 in response to DNA damage. In several human cancers, the WIP1 protein is overexpressed, which is generally associated with a worse prognosis. Although WIP1 is an attractive therapeutic target, no potent, selective, and bioactive small-molecule modulator with favorable pharmacokinetics has been reported. Phosphatase enzymes are among the most challenging targets for small molecules because of the difficulty of achieving both modulator selectivity and bioavailability. Another major obstacle has been the availability of robust and physiologically relevant phosphatase assays that are suitable for high-throughput screening. Here, we describe orthogonal biochemical WIP1 activity assays that utilize phosphopeptides from native WIP1 substrates. We optimized an MS assay to quantify the enzymatically dephosphorylated peptide reaction product in a 384-well format. Additionally, a red-shifted fluorescence assay was optimized in a 1,536-well format to enable real-time WIP1 activity measurements through the detection of the orthogonal reaction product, Pi. We validated these two optimized assays by quantitative high-throughput screening against the National Center for Advancing Translational Sciences (NCATS) Pharmaceutical Collection and used secondary assays to confirm and evaluate inhibitors identified in the primary screen. Five inhibitors were further tested with an orthogonal WIP1 activity assay and surface plasmon resonance binding studies. Our results validate the application of miniaturized physiologically relevant and orthogonal WIP1 activity assays to discover small-molecule modulators from high-throughput screens.
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Affiliation(s)
- Victor Clausse
- Synthetic Bioactive Molecules Section, Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Bethesda, Maryland 20892
| | - Dingyin Tao
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Subrata Debnath
- Laboratory of Cell Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Yuhong Fang
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Harichandra D Tagad
- Laboratory of Cell Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Yuhong Wang
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Hongmao Sun
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Christopher A LeClair
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Sharlyn J Mazur
- Laboratory of Cell Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Kelly Lane
- Imaging Probe Development Center, NHLBI, National Institutes of Health, Rockville, Maryland 20850
| | - Zhen-Dan Shi
- Imaging Probe Development Center, NHLBI, National Institutes of Health, Rockville, Maryland 20850
| | - Olga Vasalatiy
- Imaging Probe Development Center, NHLBI, National Institutes of Health, Rockville, Maryland 20850
| | - Rebecca Eells
- Reaction Biology Corporation, 1 Great Valley Parkway, Suite 2, Malvern, Pennsylvania 19355
| | - Lynn K Baker
- Reaction Biology Corporation, 1 Great Valley Parkway, Suite 2, Malvern, Pennsylvania 19355
| | - Mark J Henderson
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Martin R Webb
- Francis Crick Institute, 1 Midland Road, London NW1 AT, United Kingdom
| | - Min Shen
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Matthew D Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Ettore Appella
- Laboratory of Cell Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Daniel H Appella
- Synthetic Bioactive Molecules Section, Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Bethesda, Maryland 20892
| | - Nathan P Coussens
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
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