1
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Leissing TM, Luh LM, Cromm PM. Structure driven compound optimization in targeted protein degradation. Drug Discov Today Technol 2020; 37:73-82. [PMID: 34895657 DOI: 10.1016/j.ddtec.2020.11.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/22/2020] [Accepted: 11/23/2020] [Indexed: 06/14/2023]
Abstract
Small molecule induced protein degradation has created tremendous excitement in drug discovery within recent years. Not being confined to target inhibition and being able to remove disease-causing protein targets via engagement and subsequent ubiquitination has provided scientists with a powerful tool to expand the druggable space. At the center of this approach sits the ternary complex formed between an E3 ubiquitin ligase, the small molecule degrader, and the target protein. A productive ternary complex is pivotal for a ubiquitin to be transferred to a surface lysine of the target protein resulting in poly-ubiquitination which enables recognition and finally degradation by the proteasome. As understanding the ternary complex means understanding the degradation process, many efforts are put into obtaining structural information of the ternary complex and getting a snapshot of the underlying conformations and molecular contacts. Locking this transient trimeric intermediate in a crystalline state has proven to be very demanding but the obtained results have tremendously improved our understanding of small molecule degraders. This review discusses target protein degradation from a structural perspective and highlights the evolution of certain degraders based on the obtained structural insights.
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Affiliation(s)
| | - Laura M Luh
- Research and Development, Pharmaceuticals, Bayer AG, 13353 Berlin, Germany
| | - Philipp M Cromm
- Research and Development, Pharmaceuticals, Bayer AG, 13353 Berlin, Germany.
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2
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Luh LM, Scheib U, Juenemann K, Wortmann L, Brands M, Cromm PM. Prey for the Proteasome: Targeted Protein Degradation-A Medicinal Chemist's Perspective. Angew Chem Int Ed Engl 2020; 59:15448-15466. [PMID: 32428344 PMCID: PMC7496094 DOI: 10.1002/anie.202004310] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Indexed: 12/12/2022]
Abstract
Targeted protein degradation (TPD), the ability to control a proteins fate by triggering its degradation in a highly selective and effective manner, has created tremendous excitement in chemical biology and drug discovery within the past decades. The TPD field is spearheaded by small molecule induced protein degradation with molecular glues and proteolysis targeting chimeras (PROTACs) paving the way to expand the druggable space and to create a new paradigm in drug discovery. However, besides the therapeutic angle of TPD a plethora of novel techniques to modulate and control protein levels have been developed. This enables chemical biologists to better understand protein function and to discover and verify new therapeutic targets. This Review gives a comprehensive overview of chemical biology techniques inducing TPD. It explains the strengths and weaknesses of these methods in the context of drug discovery and discusses their future potential from a medicinal chemist's perspective.
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Affiliation(s)
- Laura M. Luh
- Research and DevelopmentPharmaceuticalsBayer AG13353BerlinGermany
| | - Ulrike Scheib
- Research and DevelopmentPharmaceuticalsBayer AG13353BerlinGermany
| | - Katrin Juenemann
- Research and DevelopmentPharmaceuticalsBayer AG13353BerlinGermany
| | - Lars Wortmann
- Research and DevelopmentPharmaceuticalsBayer AG13353BerlinGermany
| | - Michael Brands
- Research and DevelopmentPharmaceuticalsBayer AG13353BerlinGermany
| | - Philipp M. Cromm
- Research and DevelopmentPharmaceuticalsBayer AG13353BerlinGermany
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3
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Luh LM, Scheib U, Juenemann K, Wortmann L, Brands M, Cromm PM. Beute für das Proteasom: Gezielter Proteinabbau aus medizinalchemischer Perspektive. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004310] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Laura M. Luh
- Research and Development Pharmaceuticals Bayer AG 13353 Berlin Germany
| | - Ulrike Scheib
- Research and Development Pharmaceuticals Bayer AG 13353 Berlin Germany
| | - Katrin Juenemann
- Research and Development Pharmaceuticals Bayer AG 13353 Berlin Germany
| | - Lars Wortmann
- Research and Development Pharmaceuticals Bayer AG 13353 Berlin Germany
| | - Michael Brands
- Research and Development Pharmaceuticals Bayer AG 13353 Berlin Germany
| | - Philipp M. Cromm
- Research and Development Pharmaceuticals Bayer AG 13353 Berlin Germany
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4
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Cromm PM, Adihou H, Kapoor S, Vazquez‐Chantada M, Davey P, Longmire D, Hennes E, Hofer W, Küchler P, Chiarparin E, Waldmann H, Grossmann TN. Cover Feature: Lipidated Stapled Peptides Targeting the Acyl Binding Protein UNC119 (ChemBioChem 24/2019). Chembiochem 2019. [DOI: 10.1002/cbic.201900704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Philipp M. Cromm
- Department of Chemical BiologyMax-Planck-Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Technische Universität DortmundFakultät für Chemie und Chemische Biologie Otto-Hahn-Strasse 6 44227 Dortmund Germany
- Present address: Research and DevelopmentPharmaceuticalsBayer AG Muellerstrasse 178 13353 Berlin Germany
| | - Hélène Adihou
- Department of Chemical BiologyMax-Planck-Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Early CVRM Medicinal ChemistryR&D BioPharmaceuticalsAstraZeneca Pepparedsleden 1 431 83 Mölndal Sweden
| | - Shobhna Kapoor
- Department of Chemical BiologyMax-Planck-Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Mercedes Vazquez‐Chantada
- Chemistry, Oncology R&DAstraZeneca Darwin Building 310 Cambridge Science Park Milton Road Cambridge CB4 0WG UK
| | - Paul Davey
- Chemistry, Oncology R&DAstraZeneca Darwin Building 310 Cambridge Science Park Milton Road Cambridge CB4 0WG UK
| | - David Longmire
- Chemistry, Oncology R&DAstraZeneca Darwin Building 310 Cambridge Science Park Milton Road Cambridge CB4 0WG UK
| | - Elisabeth Hennes
- Department of Chemical BiologyMax-Planck-Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Walter Hofer
- Department of Chemical BiologyMax-Planck-Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Philipp Küchler
- Department of Chemical BiologyMax-Planck-Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Elisabetta Chiarparin
- Chemistry, Oncology R&DAstraZeneca Darwin Building 310 Cambridge Science Park Milton Road Cambridge CB4 0WG UK
| | - Herbert Waldmann
- Department of Chemical BiologyMax-Planck-Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Technische Universität DortmundFakultät für Chemie und Chemische Biologie Otto-Hahn-Strasse 6 44227 Dortmund Germany
| | - Tom N. Grossmann
- Vrije Universiteit AmsterdamDepartment of Chemistry and Pharmaceutical Sciences De Boelelaan 1083 1081 HV Amsterdam The Netherlands
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5
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Cromm PM, Adihou H, Kapoor S, Vazquez-Chantada M, Davey P, Longmire D, Hennes E, Hofer W, Küchler P, Chiarparin E, Waldmann H, Grossmann TN. Lipidated Stapled Peptides Targeting the Acyl Binding Protein UNC119. Chembiochem 2019; 20:2987-2990. [PMID: 31680402 PMCID: PMC6973269 DOI: 10.1002/cbic.201900615] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Indexed: 01/09/2023]
Abstract
The acyl-binding UNC119 proteins mediate the activation and transport of various N-myristoylated proteins. In particular, UNC119a plays a crucial role in the completion of cytokinesis. Herein, we report the use of a lipidated peptide originating from the UNC119 binding partner Gnat1 as the basis for the design of lipidated, stabilized α-helical peptides that target UNC119a. By using the hydrocarbon peptide-stapling approach, cell-permeable binders of UNC119a were generated that induced the accumulation of cytokinetic and binucleated cells; this suggests UNC119a as a potential target for the inhibition of cytokinesis.
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Affiliation(s)
- Philipp M Cromm
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany.,Technische Universität Dortmund, Fakultät für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany.,Present address: Research and Development, Pharmaceuticals, Bayer AG, Muellerstrasse 178, 13353, Berlin, Germany
| | - Hélène Adihou
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany.,Early CVRM Medicinal Chemistry, R&D BioPharmaceuticals, AstraZeneca, Pepparedsleden 1, 431 83, Mölndal, Sweden
| | - Shobhna Kapoor
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany
| | - Mercedes Vazquez-Chantada
- Chemistry, Oncology R&D, AstraZeneca, Darwin Building 310, Cambridge Science Park, Milton Road, Cambridge, CB4 0WG, UK
| | - Paul Davey
- Chemistry, Oncology R&D, AstraZeneca, Darwin Building 310, Cambridge Science Park, Milton Road, Cambridge, CB4 0WG, UK
| | - David Longmire
- Chemistry, Oncology R&D, AstraZeneca, Darwin Building 310, Cambridge Science Park, Milton Road, Cambridge, CB4 0WG, UK
| | - Elisabeth Hennes
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany
| | - Walter Hofer
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany
| | - Philipp Küchler
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany
| | - Elisabetta Chiarparin
- Chemistry, Oncology R&D, AstraZeneca, Darwin Building 310, Cambridge Science Park, Milton Road, Cambridge, CB4 0WG, UK
| | - Herbert Waldmann
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany.,Technische Universität Dortmund, Fakultät für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
| | - Tom N Grossmann
- Vrije Universiteit Amsterdam, Department of Chemistry and Pharmaceutical Sciences, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
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6
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Cromm PM, Samarasinghe KTG, Hines J, Crews CM. Addressing Kinase-Independent Functions of Fak via PROTAC-Mediated Degradation. J Am Chem Soc 2018; 140:17019-17026. [DOI: 10.1021/jacs.8b08008] [Citation(s) in RCA: 153] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Philipp M. Cromm
- Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, Connecticut 06511, United States
| | - Kusal T. G. Samarasinghe
- Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, Connecticut 06511, United States
| | - John Hines
- Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, Connecticut 06511, United States
| | - Craig M. Crews
- Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, Connecticut 06511, United States
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States
- Department of Pharmacology, Yale University, New Haven, Connecticut 06511, United States
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7
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Durek T, Cromm PM, White AM, Schroeder CI, Kaas Q, Weidmann J, Ahmad Fuaad A, Cheneval O, Harvey PJ, Daly NL, Zhou Y, Dellsén A, Österlund T, Larsson N, Knerr L, Bauer U, Kessler H, Cai M, Hruby VJ, Plowright AT, Craik DJ. Development of Novel Melanocortin Receptor Agonists Based on the Cyclic Peptide Framework of Sunflower Trypsin Inhibitor-1. J Med Chem 2018; 61:3674-3684. [PMID: 29605997 DOI: 10.1021/acs.jmedchem.8b00170] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Ultrastable cyclic peptide frameworks offer great potential for drug design due to their improved bioavailability compared to their linear analogues. Using the sunflower trypsin inhibitor-1 (SFTI-1) peptide scaffold in combination with systematic N-methylation of the grafted pharmacophore led to the identification of novel subtype selective melanocortin receptor (MCR) agonists. Multiple bicyclic peptides were synthesized and tested toward their activity at MC1R and MC3-5R. Double N-methylated compound 18 showed a p Ki of 8.73 ± 0.08 ( Ki = 1.92 ± 0.34 nM) and a pEC50 of 9.13 ± 0.04 (EC50 = 0.75 ± 0.08 nM) at the human MC1R and was over 100 times more selective for MC1R. Nuclear magnetic resonance structural analysis of 18 emphasized the role of peptide bond N-methylation in shaping the conformation of the grafted pharmacophore. More broadly, this study highlights the potential of cyclic peptide scaffolds for epitope grafting in combination with N-methylation to introduce receptor subtype selectivity in the context of peptide-based drug discovery.
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Affiliation(s)
- Thomas Durek
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , QLD 4072 , Australia
| | - Philipp M Cromm
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , QLD 4072 , Australia.,Institute for Advanced Study and Center of Integrated Protein Science, Department Chemie , Technische Universität München , Lichtenbergstrasse 4 , 85747 Garching , Germany
| | - Andrew M White
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , QLD 4072 , Australia
| | - Christina I Schroeder
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , QLD 4072 , Australia
| | - Quentin Kaas
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , QLD 4072 , Australia
| | - Joachim Weidmann
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , QLD 4072 , Australia
| | - Abdullah Ahmad Fuaad
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , QLD 4072 , Australia
| | - Olivier Cheneval
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , QLD 4072 , Australia
| | - Peta J Harvey
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , QLD 4072 , Australia
| | - Norelle L Daly
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , QLD 4072 , Australia
| | - Yang Zhou
- Department of Chemistry and Biochemistry , University of Arizona , Tucson , Arizona 85721 , United States
| | - Anita Dellsén
- Mechanistic Biology & Profiling, Discovery Sciences, IMED Biotech Unit , AstraZeneca , Gothenburg 43183 Sweden
| | - Torben Österlund
- Discovery Biology, Discovery Sciences, IMED Biotech Unit , AstraZeneca , Gothenburg 43183 Sweden.,Drug Safety and Metabolism, IMED Biotech Unit , AstraZeneca , Gothenburg 43183 Sweden
| | - Niklas Larsson
- Discovery Biology, Discovery Sciences, IMED Biotech Unit , AstraZeneca , Gothenburg 43183 Sweden
| | - Laurent Knerr
- Medicinal Chemistry, Cardiovascular and Metabolic Diseases, IMED Biotech Unit , AstraZeneca , Gothenburg 43183 Sweden
| | - Udo Bauer
- Medicinal Chemistry, Cardiovascular and Metabolic Diseases, IMED Biotech Unit , AstraZeneca , Gothenburg 43183 Sweden
| | - Horst Kessler
- Institute for Advanced Study and Center of Integrated Protein Science, Department Chemie , Technische Universität München , Lichtenbergstrasse 4 , 85747 Garching , Germany
| | - Minying Cai
- Department of Chemistry and Biochemistry , University of Arizona , Tucson , Arizona 85721 , United States
| | - Victor J Hruby
- Department of Chemistry and Biochemistry , University of Arizona , Tucson , Arizona 85721 , United States
| | - Alleyn T Plowright
- Medicinal Chemistry, Cardiovascular and Metabolic Diseases, IMED Biotech Unit , AstraZeneca , Gothenburg 43183 Sweden
| | - David J Craik
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , QLD 4072 , Australia
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8
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Ottis P, Toure M, Cromm PM, Ko E, Gustafson JL, Crews CM. Assessing Different E3 Ligases for Small Molecule Induced Protein Ubiquitination and Degradation. ACS Chem Biol 2017; 12:2570-2578. [PMID: 28767222 DOI: 10.1021/acschembio.7b00485] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proteolysis targeting chimera (PROTAC) technology, the recruitment of E3 ubiquitin ligases to induce the degradation of a protein target, is rapidly impacting chemical biology, as well as modern drug development. Here, we explore the universality of this approach by evaluating different E3 ubiquitin ligases, engineered in their substrate binding domains to accept a recruiting ligand. Five out of six E3 ligases were found to be amenable to recruitment for target degradation. Taking advantage of the tight spatiotemporal control of inducing ubiquitination on a preselected target in living cells, we focused on two of the engineered E3 ligases, βTRCP and parkin, to unravel their ubiquitination characteristics in comparison with the PROTAC-recruited endogenous E3 ligases VHL and cereblon.
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Affiliation(s)
- Philipp Ottis
- Department
of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, United States
| | - Momar Toure
- Department
of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, United States
| | - Philipp M. Cromm
- Department
of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, United States
| | - Eunhwa Ko
- Department
of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, United States
| | - Jeffrey L. Gustafson
- Department
of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, United States
| | - Craig M. Crews
- Department
of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, United States
- Department
of Chemistry, Yale University, New Haven, Connecticut, United States
- Department
of Pharmacology, Yale University, New Haven, Connecticut, United States
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9
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Abstract
As the central figure of the cellular protein degradation machinery, the proteasome is critical for cell survival. Having been extensively targeted for inhibition, the constitutive proteasome has proven its role as a highly valuable drug target. However, recent advances in the protein homeostasis field suggest that additional chapters can be added to this successful story. For example, selective immunoproteasome inhibition promises high clinical efficacy for autoimmune disorders and inflammation, and proteasome inhibitors might serve as novel therapeutics for malaria or other microorganisms. Furthermore, utilizing the destructive force of the proteasome for selective degradation of essential drivers of human disorders has opened up a new and exciting area of drug discovery. Thus, the field of proteasome drug discovery still holds exciting questions to be answered and does not simply end with inhibiting the constitutive proteasome.
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Affiliation(s)
- Philipp M. Cromm
- Department
of Molecular, Cellular & Developmental Biology, Yale University, New Haven, Connecticut 06511, United States
| | - Craig M. Crews
- Department
of Molecular, Cellular & Developmental Biology, Yale University, New Haven, Connecticut 06511, United States
- Department
of Chemistry, Yale University, New Haven, Connecticut 06511, United States
- Department
of Pharmacology, Yale University, New Haven, Connecticut 06511, United States
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10
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Abstract
Traditional pharmaceutical drug discovery is almost exclusively focused on directly controlling protein activity to cure diseases. Modulators of protein activity, especially inhibitors, are developed and applied at high concentration to achieve maximal effects. Thereby, reduced bioavailability and off-target effects can hamper compound efficacy. Nucleic acid-based strategies that control protein function by affecting expression have emerged as an alternative. However, metabolic stability and broad bioavailability represent development hurdles that remain to be overcome for these approaches. More recently, utilizing the cell's own protein destruction machinery for selective degradation of essential drivers of human disorders has opened up a new and exciting area of drug discovery. Small-molecule-induced proteolysis of selected substrates offers the potential of reaching beyond the limitations of the current pharmaceutical paradigm to expand the druggable target space.
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Affiliation(s)
- Philipp M Cromm
- Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT 06511, USA.
| | - Craig M Crews
- Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT 06511, USA; Department of Chemistry, Yale University, New Haven, CT 06511, USA; Department of Pharmacology, Yale University, New Haven, CT 06511, USA.
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11
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Cromm PM, Wallraven K, Glas A, Bier D, Fürstner A, Ottmann C, Grossmann TN. Constraining an Irregular Peptide Secondary Structure through Ring-Closing Alkyne Metathesis. Chembiochem 2016; 17:1915-1919. [PMID: 27596722 PMCID: PMC5096054 DOI: 10.1002/cbic.201600362] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Indexed: 01/04/2023]
Abstract
Macrocyclization can be used to constrain peptides in their bioactive conformations, thereby supporting target affinity and bioactivity. In particular, for the targeting of challenging protein-protein interactions, macrocyclic peptides have proven to be very useful. Available approaches focus on the stabilization of α-helices, which limits their general applicability. Here we report for the first time on the use of ring-closing alkyne metathesis for the stabilization of an irregular peptide secondary structure. A small library of alkyne-crosslinked peptides provided a number of derivatives with improved target affinity relative to the linear parent peptide. In addition, we report the crystal structure of the highest-affinity derivative in a complex with its protein target 14-3-3ζ. It can be expected that the alkyne-based macrocyclization of irregular binding epitopes should give rise to new scaffolds suitable for targeting of currently intractable proteins.
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Affiliation(s)
- Philipp M Cromm
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany
- Technische Universität Dortmund, Fakultät für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
| | - Kerstin Wallraven
- VU University Amsterdam, Department of Chemistry and Pharmaceutical Sciences, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Adrian Glas
- Technische Universität Dortmund, Fakultät für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, 44227, Dortmund, Germany
| | - David Bier
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, 44227, Dortmund, Germany
- University of Eindhoven, Department of Biomedical Engineering, Institute of Complex Molecular Systems, Den Dolech 2, 5612 AZ, Eindhoven, The Netherlands
- Department of Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45141, Essen, Germany
| | - Alois Fürstner
- Technische Universität Dortmund, Fakultät für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim/Ruhr, Germany
| | - Christian Ottmann
- University of Eindhoven, Department of Biomedical Engineering, Institute of Complex Molecular Systems, Den Dolech 2, 5612 AZ, Eindhoven, The Netherlands
- Department of Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45141, Essen, Germany
| | - Tom N Grossmann
- Technische Universität Dortmund, Fakultät für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany.
- VU University Amsterdam, Department of Chemistry and Pharmaceutical Sciences, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands.
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, 44227, Dortmund, Germany.
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12
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Cromm PM, Spiegel J, Küchler P, Dietrich L, Kriegesmann J, Wendt M, Goody RS, Waldmann H, Grossmann TN. Protease-Resistant and Cell-Permeable Double-Stapled Peptides Targeting the Rab8a GTPase. ACS Chem Biol 2016; 11:2375-82. [PMID: 27336832 DOI: 10.1021/acschembio.6b00386] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Small GTPases comprise a family of highly relevant targets in chemical biology and medicinal chemistry research and have been considered "undruggable" due to the persisting lack of effective synthetic modulators and suitable binding pockets. As molecular switches, small GTPases control a multitude of pivotal cellular functions, and their dysregulation is associated with many human diseases such as various forms of cancer. Rab-GTPases represent the largest subfamily of small GTPases and are master regulators of vesicular transport interacting with various proteins via flat and extensive protein-protein interactions (PPIs). The only reported synthetic inhibitor of a PPI involving an activated Rab GTPase is the hydrocarbon stapled peptide StRIP3. However, this macrocyclic peptide shows low proteolytic stability and cell permeability. Here, we report the design of a bioavailable StRIP3 analogue that harbors two hydrophobic cross-links and exhibits increased binding affinity, combined with robust cellular uptake and extremely high proteolytic stability. Localization experiments reveal that this double-stapled peptide and its target protein Rab8a accumulate in the same cellular compartments. The reported approach offers a strategy for the implementation of biostability into conformationally constrained peptides while supporting cellular uptake and target affinity, thereby conveying drug-like properties.
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Affiliation(s)
- Philipp M. Cromm
- Department
of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany
- Technische Universität Dortmund, Fakultät
für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany
| | - Jochen Spiegel
- Department
of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany
- Technische Universität Dortmund, Fakultät
für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany
| | - Philipp Küchler
- Department
of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany
- Technische Universität Dortmund, Fakultät
für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany
| | - Laura Dietrich
- Technische Universität Dortmund, Fakultät
für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany
| | - Julia Kriegesmann
- Technische Universität Dortmund, Fakultät
für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany
- VU University Amsterdam, Department of Chemistry & Pharmaceutical Sciences, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Mathias Wendt
- Technische Universität Dortmund, Fakultät
für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany
- VU University Amsterdam, Department of Chemistry & Pharmaceutical Sciences, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Roger S. Goody
- Structural
Biochemistry, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse
11, D-44227 Dortmund, Germany
| | - Herbert Waldmann
- Department
of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany
- Technische Universität Dortmund, Fakultät
für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany
| | - Tom N. Grossmann
- Technische Universität Dortmund, Fakultät
für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany
- VU University Amsterdam, Department of Chemistry & Pharmaceutical Sciences, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
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Cromm PM, Schaubach S, Spiegel J, Fürstner A, Grossmann TN, Waldmann H. Orthogonal ring-closing alkyne and olefin metathesis for the synthesis of small GTPase-targeting bicyclic peptides. Nat Commun 2016; 7:11300. [PMID: 27075966 PMCID: PMC4834642 DOI: 10.1038/ncomms11300] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 03/11/2016] [Indexed: 02/06/2023] Open
Abstract
Bicyclic peptides are promising scaffolds for the development of inhibitors of biological targets that proved intractable by typical small molecules. So far, access to bioactive bicyclic peptide architectures is limited due to a lack of appropriate orthogonal ring-closing reactions. Here, we report chemically orthogonal ring-closing olefin (RCM) and alkyne metathesis (RCAM), which enable an efficient chemo- and regioselective synthesis of complex bicyclic peptide scaffolds with variable macrocycle geometries. We also demonstrate that the formed alkyne macrocycle can be functionalized subsequently. The orthogonal RCM/RCAM system was successfully used to evolve a monocyclic peptide inhibitor of the small GTPase Rab8 into a bicyclic ligand. This modified peptide shows the highest affinity for an activated Rab GTPase that has been reported so far. The RCM/RCAM-based formation of bicyclic peptides provides novel opportunities for the design of bioactive scaffolds suitable for the modulation of challenging protein targets. Bicyclic peptides can inhibit biological targets hard to address with small molecules. Here, the authors combine two orthogonal ring-closing reactions to produce bicyclic peptides with improved bioactivity thereby providing a strategy that can greatly improve the structural diversity of such peptides.
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Affiliation(s)
- Philipp M Cromm
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany.,Technische Universität Dortmund, Fakultät für Chemie and Chemische Biologie, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany
| | - Sebastian Schaubach
- Technische Universität Dortmund, Fakultät für Chemie and Chemische Biologie, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany.,Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim/Ruhr, Germany
| | - Jochen Spiegel
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany.,Technische Universität Dortmund, Fakultät für Chemie and Chemische Biologie, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany
| | - Alois Fürstner
- Technische Universität Dortmund, Fakultät für Chemie and Chemische Biologie, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany.,Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim/Ruhr, Germany
| | - Tom N Grossmann
- Technische Universität Dortmund, Fakultät für Chemie and Chemische Biologie, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany.,Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany.,Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Herbert Waldmann
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany.,Technische Universität Dortmund, Fakultät für Chemie and Chemische Biologie, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany
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15
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Cromm PM, Spiegel J, Grossmann TN, Waldmann H. Direct Modulation of Small GTPase Activity and Function. Angew Chem Int Ed Engl 2015; 54:13516-37. [DOI: 10.1002/anie.201504357] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Indexed: 12/19/2022]
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Abstract
Peptide-based drug discovery has experienced a significant upturn within the past decade since the introduction of chemical modifications and unnatural amino acids has allowed for overcoming some of the drawbacks associated with peptide therapeutics. Strengthened by such features, modified peptides become capable of occupying a niche that emerges between the two major classes of today's therapeutics-small molecules (<500 Da) and biologics (>5000 Da). Stabilized α-helices have proven particularly successful at impairing disease-relevant PPIs previously considered "undruggable." Among those, hydrocarbon stapled α-helical peptides have emerged as a novel class of potential peptide therapeutics. This review provides a comprehensive overview of the development and applications of hydrocarbon stapled peptides discussing the benefits and limitations of this technique.
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Affiliation(s)
- Philipp M. Cromm
- Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
- Technical University Dortmund, Department of Chemistry and Chemical Biology, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Jochen Spiegel
- Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
- Technical University Dortmund, Department of Chemistry and Chemical Biology, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Tom N. Grossmann
- Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
- Technical University Dortmund, Department of Chemistry and Chemical Biology, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Str. 15, 44227 Dortmund, Germany
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17
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Spiegel J, Cromm PM, Itzen A, Goody RS, Grossmann TN, Waldmann H. Direkte Modulation von Rab-GTPase-Effektor-Wechselwirkungen. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201308568] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Spiegel J, Cromm PM, Itzen A, Goody RS, Grossmann TN, Waldmann H. Direct targeting of Rab-GTPase-effector interactions. Angew Chem Int Ed Engl 2014; 53:2498-503. [PMID: 24481744 DOI: 10.1002/anie.201308568] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 11/26/2013] [Indexed: 11/06/2022]
Abstract
Small GTPases are molecular switches using GDP/GTP alternation to control numerous vital cellular processes. Although aberrant function and regulation of GTPases are implicated in various human diseases, direct targeting of this class of proteins has proven difficult, as GTPase signaling and regulation is mediated by extensive and shallow protein interfaces. Here we report the development of inhibitors of protein-protein interactions involving Rab proteins, a subfamily of GTPases, which are key regulators of vesicular transport. Hydrocarbon-stapled peptides were designed based on crystal structures of Rab proteins bound to their interaction partners. These modified peptides exhibit significantly increased affinities and include a stapled peptide (StRIP3) that selectively binds to activated Rab8a and inhibits a Rab8a-effector interaction in vitro.
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Affiliation(s)
- Jochen Spiegel
- Max-Planck-Institut für Molekulare Physiologie, Abteilung Chemische Biologie, Otto-Hahn-Strasse 11, 44227 Dortmund (Germany); Technische Universität Dortmund, Fakultät für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, 44227 Dortmund (Germany)
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