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Castellani B, Eleuteri M, Di Bona S, Cruciani G, Desantis J, Goracci L. VHL-Modified PROteolysis TArgeting Chimeras (PROTACs) as a Strategy to Evade Metabolic Degradation in In Vitro Applications. J Med Chem 2023; 66:13148-13171. [PMID: 37699425 DOI: 10.1021/acs.jmedchem.3c01144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
PROteolysis TArgeting Chimeras (PROTACs) are tripartite molecules consisting of a linker connecting a ligand for a protein of interest to an E3 ligase recruiter, whose rationale relies on proteasome-based protein degradation. PROTACs have expanded as a therapeutic strategy to open new avenues for unmet medical needs. Leveraging our expertise, we undertook a series of in vitro experiments aimed at elucidating PROTAC metabolism. In particular, we focused on PROTACs recruiting the von Hippel-Lindau (VHL) E3 ligase. After high-resolution mass spectrometry measurements, a characteristic metabolite with mass reduction of 200 units was detected and successively confirmed as a product deriving from the cleavage of the VHL ligand moiety. Subsequently, we identified hepatic and extrahepatic prolyl endopeptidases as the main putative metabolic enzymes involved. Finally, we designed and synthesized analogs of the VHL ligands that we further exploited for the synthesis of novel VHL-directed PROTACs with an improved metabolic stability in in vitro applications.
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Affiliation(s)
| | - Michela Eleuteri
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia 06123, Italy
| | | | - Gabriele Cruciani
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia 06123, Italy
| | - Jenny Desantis
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia 06123, Italy
| | - Laura Goracci
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia 06123, Italy
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Smolobochkin AV, Turmanov RA, Abdullaeva DS, Gazizov AS, Voronina JK, Appazov NO, Buzyurova DN, Burilov AR, Pudovik MA. 2‐(Het)aryl‐
N
‐phosphorylpyrrolidines via Cyclization of Phosphorus Acid Amides: A Regioselective Approach. ChemistrySelect 2020. [DOI: 10.1002/slct.202003353] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Andrey V. Smolobochkin
- Arbuzov Institute of Organic and Physical Chemistry FRC Kazan Scientific Center Russian Academy of Sciences, 4 20088 Arbuzova str., 8 Kazan Russian Federation
| | - Rakhymzhan A. Turmanov
- Arbuzov Institute of Organic and Physical Chemistry FRC Kazan Scientific Center Russian Academy of Sciences, 4 20088 Arbuzova str., 8 Kazan Russian Federation
- Kazan National Research Technological University 420015 Karl Marx str., 68 Kazan Russian Federation
| | | | - Almir S. Gazizov
- Arbuzov Institute of Organic and Physical Chemistry FRC Kazan Scientific Center Russian Academy of Sciences, 4 20088 Arbuzova str., 8 Kazan Russian Federation
| | - Julia K. Voronina
- N.S. Kurnakov Institute of General and Inorganic Chemistry, RAS 31 Leninsky Av. 119991 Moscow Russian Federation
- G.V. Plekhanov Russian University of Economics 36 Stremyanny Per. Moscow 117997 Russian Federation
| | - Nurbol O. Appazov
- Korkyt Ata Kyzylorda State University 120014 Aiteke bike str., 29A Kyzylorda, Republic of Kazakhstan
| | - Daina N. Buzyurova
- Arbuzov Institute of Organic and Physical Chemistry FRC Kazan Scientific Center Russian Academy of Sciences, 4 20088 Arbuzova str., 8 Kazan Russian Federation
| | - Alexander R. Burilov
- Arbuzov Institute of Organic and Physical Chemistry FRC Kazan Scientific Center Russian Academy of Sciences, 4 20088 Arbuzova str., 8 Kazan Russian Federation
| | - Michail A. Pudovik
- Arbuzov Institute of Organic and Physical Chemistry FRC Kazan Scientific Center Russian Academy of Sciences, 4 20088 Arbuzova str., 8 Kazan Russian Federation
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3
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Smolobochkin AV, Turmanov RA, Gazizov AS, Voloshina AD, Voronina JK, Sapunova AS, Burilov AR, Pudovik MA. One-pot imination / Arbuzov reaction of 4-aminobutanal derivatives: Synthesis of 2-phosphorylpyrrolidines and evaluation of anticancer activity. Tetrahedron 2020. [DOI: 10.1016/j.tet.2020.131369] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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4
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Smolobochkin AV, Turmanov RA, Gazizov AS, Kuznetsova EA, Burilov AR, Pudovik MA. Reaction of N-(4,4-Diethoxybutyl)phosphamides with Chloro(diphenyl)phosphine. Synthesis of 2-(Diphenylphosphoryl)pyrrolidines. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2020. [DOI: 10.1134/s107042802006024x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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5
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Bagautdinova RK, Vagapova LI, Smolobochkin AV, Gazizov AS, Burilov AR, Pudovik MA, Voloshina AD. Synthesis of 1-(2-aminoethylsulfonyl)-2-phosphorylpyrrolidines via consecutive Arbuzov and aza-Michael reactions and their antitumor activity. MENDELEEV COMMUNICATIONS 2019. [DOI: 10.1016/j.mencom.2019.11.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Smolobochkin AV, Turmanov RA, Gazizov AS, Appazov NO, Burilov AR, Pudovik MA. Synthesis of 2-(Diphenylphosphoryl)pyrrolidine-1-carboxamides Based on the Reaction of 1-(4,4-Diethoxybutyl)ureas with Diphenyl Chlorophosphine. RUSS J GEN CHEM+ 2019. [DOI: 10.1134/s1070363219100244] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Schulz-Fincke AC, Tikhomirov AS, Braune A, Girbl T, Gilberg E, Bajorath J, Blaut M, Nourshargh S, Gütschow M. Design of an Activity-Based Probe for Human Neutrophil Elastase: Implementation of the Lossen Rearrangement To Induce Förster Resonance Energy Transfers. Biochemistry 2018; 57:742-752. [PMID: 29286643 DOI: 10.1021/acs.biochem.7b00906] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Human neutrophil elastase is an important regulator of the immune response and plays a role in host defense mechanisms and further physiological processes. The uncontrolled activity of this serine protease may cause severe tissue alterations and impair inflammatory states. The design of an activity-based probe for human neutrophil elastase reported herein relies on a sulfonyloxyphthalimide moiety as a new type of warhead that is linker-connected to a coumarin fluorophore. The inhibitory potency of the activity-based probe was assessed against several serine and cysteine proteases, and the selectivity for human neutrophil elastase (Ki = 6.85 nM) was determined. The adequate fluorescent tag of the probe allowed for the in-gel fluorescence detection of human neutrophil elastase in the low nanomolar range. The coumarin moiety and the anthranilic acid function of the probe, produced in the course of a Lossen rearrangement, were part of two different Förster resonance energy transfers.
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Affiliation(s)
- Anna-Christina Schulz-Fincke
- Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn , An der Immenburg 4, 53121 Bonn, Germany
| | - Alexander S Tikhomirov
- Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn , An der Immenburg 4, 53121 Bonn, Germany.,Gause Institute of New Antibiotics , 11 Bolshaya Pirogovskaya Street, Moscow 119021, Russia
| | - Annett Braune
- Department of Gastrointestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke , Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
| | - Tamara Girbl
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London , Charterhouse Square, London EC1M 6BQ, U.K
| | - Erik Gilberg
- Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn , An der Immenburg 4, 53121 Bonn, Germany.,Department of Life Science Informatics, B-IT, LIMES Program Unit of Chemical Biology and Medicinal Chemistry, University of Bonn , Dahlmannstrasse 2, 53113 Bonn, Germany
| | - Jürgen Bajorath
- Department of Life Science Informatics, B-IT, LIMES Program Unit of Chemical Biology and Medicinal Chemistry, University of Bonn , Dahlmannstrasse 2, 53113 Bonn, Germany
| | - Michael Blaut
- Department of Gastrointestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke , Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
| | - Sussan Nourshargh
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London , Charterhouse Square, London EC1M 6BQ, U.K
| | - Michael Gütschow
- Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn , An der Immenburg 4, 53121 Bonn, Germany
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Häußler D, Schulz-Fincke AC, Beckmann AM, Keils A, Gilberg E, Mangold M, Bajorath J, Stirnberg M, Steinmetzer T, Gütschow M. A Fluorescent-Labeled Phosphono Bisbenzguanidine As an Activity-Based Probe for Matriptase. Chemistry 2017; 23:5205-5209. [DOI: 10.1002/chem.201700319] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Revised: 02/24/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Daniela Häußler
- Pharmaceutical Institute, Pharmaceutical Chemistry I; University of Bonn; An der Immenburg 4 53121 Bonn Germany
| | | | - Anna-Madeleine Beckmann
- Pharmaceutical Institute, Pharmaceutical Chemistry I; University of Bonn; An der Immenburg 4 53121 Bonn Germany
| | - Aline Keils
- Institute of Pharmaceutical Chemistry; Philipps University of Marburg; Marbacher Weg 6 35032 Marburg Germany
| | - Erik Gilberg
- Pharmaceutical Institute, Pharmaceutical Chemistry I; University of Bonn; An der Immenburg 4 53121 Bonn Germany
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry; University of Bonn; Dahlmannstr. 2 53113 Bonn Germany
| | - Martin Mangold
- Pharmaceutical Institute, Pharmaceutical Chemistry I; University of Bonn; An der Immenburg 4 53121 Bonn Germany
| | - Jürgen Bajorath
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry; University of Bonn; Dahlmannstr. 2 53113 Bonn Germany
| | - Marit Stirnberg
- Pharmaceutical Institute, Pharmaceutical Chemistry I; University of Bonn; An der Immenburg 4 53121 Bonn Germany
| | - Torsten Steinmetzer
- Institute of Pharmaceutical Chemistry; Philipps University of Marburg; Marbacher Weg 6 35032 Marburg Germany
| | - Michael Gütschow
- Pharmaceutical Institute, Pharmaceutical Chemistry I; University of Bonn; An der Immenburg 4 53121 Bonn Germany
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9
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Häußler D, Mangold M, Furtmann N, Braune A, Blaut M, Bajorath J, Stirnberg M, Gütschow M. Phosphono Bisbenzguanidines as Irreversible Dipeptidomimetic Inhibitors and Activity-Based Probes of Matriptase-2. Chemistry 2016; 22:8525-35. [DOI: 10.1002/chem.201600206] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Indexed: 12/15/2022]
Affiliation(s)
- Daniela Häußler
- Pharmaceutical Institute; Pharmaceutical Chemistry I; University of Bonn; An der Immenburg 4 53121 Bonn Germany
| | - Martin Mangold
- Pharmaceutical Institute; Pharmaceutical Chemistry I; University of Bonn; An der Immenburg 4 53121 Bonn Germany
| | - Norbert Furtmann
- Pharmaceutical Institute; Pharmaceutical Chemistry I; University of Bonn; An der Immenburg 4 53121 Bonn Germany
- Department of Life Science Informatics, B-IT; LIMES Program Unit Chemical Biology and Medicinal Chemistry; University of Bonn; Dahlmannstrasse 2 53113 Bonn Germany
| | - Annett Braune
- Department of Gastrointestinal Microbiology; German Institute of Human Nutrition Potsdam-Rehbruecke; Arthur-Scheunert-Allee 114-116 14558 Nuthetal Germany
| | - Michael Blaut
- Department of Gastrointestinal Microbiology; German Institute of Human Nutrition Potsdam-Rehbruecke; Arthur-Scheunert-Allee 114-116 14558 Nuthetal Germany
| | - Jürgen Bajorath
- Department of Life Science Informatics, B-IT; LIMES Program Unit Chemical Biology and Medicinal Chemistry; University of Bonn; Dahlmannstrasse 2 53113 Bonn Germany
| | - Marit Stirnberg
- Pharmaceutical Institute; Pharmaceutical Chemistry I; University of Bonn; An der Immenburg 4 53121 Bonn Germany
| | - Michael Gütschow
- Pharmaceutical Institute; Pharmaceutical Chemistry I; University of Bonn; An der Immenburg 4 53121 Bonn Germany
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10
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Lennicke C, Rahn J, Heimer N, Lichtenfels R, Wessjohann LA, Seliger B. Redox proteomics: Methods for the identification and enrichment of redox-modified proteins and their applications. Proteomics 2015; 16:197-213. [PMID: 26508685 DOI: 10.1002/pmic.201500268] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 09/14/2015] [Accepted: 10/15/2015] [Indexed: 01/24/2023]
Abstract
PTMs are defined as covalent additions to functional groups of amino acid residues in proteins like phosphorylation, glycosylation, S-nitrosylation, acetylation, methylation, lipidation, SUMOylation as well as oxidation. Oxidation of proteins has been characterized as a double-edged sword. While oxidative modifications, in particular of cysteine residues, are widely involved in the regulation of cellular homeostasis, oxidative stress resulting in the oxidation of biomolecules along with the disruption of their biological functions can be associated with the development of diseases, such as cancer, diabetes, and neurodegenerative diseases, respectively. This is also the case for advanced glycation end products, which result from chemical reactions of keto compounds such as oxidized sugars with proteins. The role of oxidative modifications under physiological and pathophysiological conditions remains largely unknown. Recently, novel technologies have been established that allow the enrichment, identification, and characterization of specific oxidative PTMs (oxPTMs). This is essential to develop strategies to prevent and treat diseases that are associated with oxidative stress. Therefore this review will focus on (i) the methods and technologies, which are currently applied for the detection, identification, and quantification of oxPTMs including the design of high throughput approaches and (ii) the analyses of oxPTMs related to physiological and pathological conditions.
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Affiliation(s)
- Claudia Lennicke
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Jette Rahn
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Nadine Heimer
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Rudolf Lichtenfels
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | | | - Barbara Seliger
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
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11
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Häußler D, Scheidt T, Stirnberg M, Steinmetzer T, Gütschow M. A Bisbenzamidine Phosphonate as a Janus-faced Inhibitor for Trypsin-like Serine Proteases. ChemMedChem 2015; 10:1641-6. [PMID: 26306030 DOI: 10.1002/cmdc.201500319] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Indexed: 12/19/2022]
Abstract
A hybrid approach was applied for the design of an inhibitor of trypsin-like serine proteases. Compound 16 [(R,R)- and (R,S)-diphenyl (4-(1-(4-amidinobenzylamino)-1-oxo-3-phenylpropan-2-ylcarbamoyl)phenylamino)(4-amidinophenyl)methylphosphonate hydrochloride], prepared in a convergent synthetic procedure, possesses a phosphonate warhead prone to react with the active site serine residue in a covalent, irreversible manner. Each of the two benzamidine moieties of 16 can potentially be accommodated in the S1 pocket of the target enzyme, but only the benzamidine close to the phosphonate group would then promote an irreversible interaction. The Janus-faced inhibitor 16 was evaluated against several serine proteases and caused a pronounced inactivation of human thrombin with a second-order rate constant (kinac /Ki) of 59 500 M(-1) s(-1). With human matriptase, 16 showed preference for a reversible mode of inhibition (IC50 =2.6 μM) as indicated by linear progress curves and enzyme reactivation.
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Affiliation(s)
- Daniela Häußler
- Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, 53121 Bonn (Germany)
| | - Tamara Scheidt
- Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, 53121 Bonn (Germany)
| | - Marit Stirnberg
- Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, 53121 Bonn (Germany)
| | - Torsten Steinmetzer
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35032 Marburg (Germany)
| | - Michael Gütschow
- Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, 53121 Bonn (Germany).
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12
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Mertens MD, Schmitz J, Horn M, Furtmann N, Bajorath J, Mareš M, Gütschow M. A coumarin-labeled vinyl sulfone as tripeptidomimetic activity-based probe for cysteine cathepsins. Chembiochem 2014; 15:955-9. [PMID: 24648212 DOI: 10.1002/cbic.201300806] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Indexed: 12/15/2022]
Abstract
A coumarin-tetrahydroquinoline hydride 8 was synthesized as a chemical tool for fluorescent labeling. The rigidified tricyclic coumarin structure was chosen for its suitable fluorescence properties. The connection of 8 with a vinyl sulfone building block was accomplished by convergent synthesis thereby leading to the coumarin-based, tripeptidomimetic activity-based probe 10, containing a Gly-Phe-Gly motif. Probe 10 was evaluated as inactivator of the therapeutically relevant human cysteine cathepsins S, L, K, and B: it showed particularly strong inactivation of cathepsin S. The detection of recombinant and native cathepsin S was demonstrated by applying 10 to in-gel fluorescence imaging.
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Affiliation(s)
- Matthias D Mertens
- Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, 53121 Bonn (Germany)
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Martell J, Weerapana E. Applications of copper-catalyzed click chemistry in activity-based protein profiling. Molecules 2014; 19:1378-93. [PMID: 24473203 PMCID: PMC6270908 DOI: 10.3390/molecules19021378] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 01/09/2014] [Accepted: 01/17/2014] [Indexed: 12/24/2022] Open
Abstract
Activity-based protein profiling (ABPP) is a chemical proteomic technique that enables the interrogation of protein activity directly within complex proteomes. Given the dominant role of posttranslational modifications in regulating protein function in vivo, ABPP provides a direct readout of activity that is not attained through traditional proteomic methods. ABPP relies on the design of covalent binding probes that either target a specific enzyme or a class of enzymes with related function. These covalent warheads are coupled to either fluorophores or biotin groups for visualization and enrichment of these active proteins. The advent of bioorthogonal chemistries, in particular, the copper (I)-catalyzed azide-alkyne cycloaddition (CuAAC), has benefitted the field of ABPP by achieving the following: (1) replacing bulky reporter groups with smaller alkyne or azide groups to promote cell permeability; (2) adding modularity to the system such that a single probe can be diversified with a variety of reporter groups without the need to develop new synthetic routes; and (3) enabling the conjugation of complex linkers to facilitate quantitative proteomic analyses. Here, we summarize recent examples of CuAAC in ABPP that serve to illustrate the contribution of bioorthogonal chemistry to advancing discoveries in this field.
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Affiliation(s)
- Julianne Martell
- Department of Chemistry, Boston College, Chestnut Hill, MA 02467, USA.
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Van der Veken P, Fülöp V, Rea D, Gerard M, Van Elzen R, Joossens J, Cheng JD, Baekelandt V, De Meester I, Lambeir AM, Augustyns K. P2-substituted N-acylprolylpyrrolidine inhibitors of prolyl oligopeptidase: biochemical evaluation, binding mode determination, and assessment in a cellular model of synucleinopathy. J Med Chem 2012; 55:9856-67. [PMID: 23121075 DOI: 10.1021/jm301060g] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
We have investigated the effect of regiospecifically introducing substituents in the P2 part of the typical dipeptide derived basic structure of PREP inhibitors. This hitherto unexplored modification type can be used to improve target affinity, selectivity, and physicochemical parameters in drug discovery programs focusing on PREP inhibitors. Biochemical evaluation of the produced inhibitors identified several substituent types that significantly increase target affinity, thereby reducing the need for an electrophilic "warhead" functionality. Pronounced PREP specificity within the group of Clan SC proteases was generally observed. Omission of the P1 electrophilic function did not affect the overall binding mode of three representative compounds, as studied by X-ray crystallography, while the P2 substituents were demonstrated to be accommodated in a cavity of PREP that, to date, has not been probed by inhibitors. Finally, we report on results of selected inhibitors in a SH-SY5Y cellular model of synucleinopathy and demonstrate a significant antiaggregation effect on α-synuclein.
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Affiliation(s)
- Pieter Van der Veken
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium.
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16
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Serim S, Haedke U, Verhelst SHL. Activity-based probes for the study of proteases: recent advances and developments. ChemMedChem 2012; 7:1146-59. [PMID: 22431376 DOI: 10.1002/cmdc.201200057] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Revised: 02/28/2012] [Indexed: 11/11/2022]
Abstract
Proteases are important targets for the treatment of human disease. Several protease inhibitors have failed in clinical trials due to a lack of in vivo specificity, indicating the need for studies of protease function and inhibition in complex, disease-related models. The tight post-translational regulation of protease activity complicates protease analysis by traditional proteomics methods. Activity-based protein profiling is a powerful technique that can resolve this issue. It uses small-molecule tools-activity-based probes-to label and analyze active enzymes in lysates, cells, and whole animals. Over the last twelve years, a wide variety of protease activity-based probes have been developed. These synthetic efforts have enabled techniques ranging from real-time in vivo imaging of protease activity to high-throughput screening of uncharacterized proteases. This Review introduces the general principles of activity-based protein profiling and describes the recent advancements in probe design and analysis techniques, which have increased the knowledge of protease biology and will aid future protease drug discovery.
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Affiliation(s)
- Sevnur Serim
- Center for Integrated Protein Science Munich (CIPS(M)), Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
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17
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Arizpe A, Sayago FJ, Jiménez AI, Ordóñez M, Cativiela C. Synthesis of Phosphoproline Derivatives with an Octahydroisoindole Structure. European J Org Chem 2011. [DOI: 10.1002/ejoc.201101014] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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18
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Sieńczyk M, Podgórski D, Błażejewska A, Kulbacka J, Saczko J, Oleksyszyn J. Phosphonic pseudopeptides as human neutrophil elastase inhibitors—a combinatorial approach. Bioorg Med Chem 2011; 19:1277-84. [DOI: 10.1016/j.bmc.2010.12.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2010] [Revised: 12/02/2010] [Accepted: 12/04/2010] [Indexed: 10/18/2022]
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Sabidó E, Tarragó T, Giralt E. Towards the identification of unknown neuropeptide precursor-processing enzymes: Design and synthesis of a new family of dipeptidyl phosphonate activity probes for substrate-based protease identification. Bioorg Med Chem 2010; 18:8350-5. [DOI: 10.1016/j.bmc.2010.09.066] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2010] [Revised: 09/19/2010] [Accepted: 09/24/2010] [Indexed: 10/19/2022]
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Heal WP, Dang THT, Tate EW. Activity-based probes: discovering new biology and new drug targets. Chem Soc Rev 2010; 40:246-57. [PMID: 20886146 DOI: 10.1039/c0cs00004c] [Citation(s) in RCA: 141] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The development and application of chemical technologies enabling direct analysis of enzyme activity in living systems has undergone explosive growth in recent years. Activity-based protein profiling (ABPP) is a key constituent of this broad field, and is among the most powerful and mature chemical proteomic technologies. This tutorial review introduces the essential features of ABPP and the design and application of activity-based probes (ABPs) from drug target elucidation and in vivo visualisation of enzyme activity to comprehensive profiling of the catalytic content of living systems, and the discovery of new biological pathways.
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Affiliation(s)
- William P Heal
- Department of Chemistry, South Kensington Campus, Imperial College, London, SW7 2AZ, UK
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