1
|
Ortiz Zacarías NV, Röth S, Broekhuis JD, van der Es D, Moreau K, Heitman LH. Inducing Receptor Degradation as a Novel Approach to Target CC Chemokine Receptor 2 (CCR2). Int J Mol Sci 2024; 25:8984. [PMID: 39201670 PMCID: PMC11354370 DOI: 10.3390/ijms25168984] [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: 07/18/2024] [Revised: 08/10/2024] [Accepted: 08/15/2024] [Indexed: 09/03/2024] Open
Abstract
CC chemokine receptor 2 (CCR2) has been linked to many inflammatory and immune diseases, making it a relevant drug target. Yet, all CCR2 antagonists developed so far have failed in clinical trials; thus, novel strategies are needed to target this receptor. Targeted protein degradation represents a novel approach to inhibit protein function by hijacking the cellular degradation machinery, such as the proteasome, to degrade the protein of interest. Here, we aimed to determine the amenability of CCR2 to chemically induced degradation by using a CCR2 fusion protein containing a HaloTag7 and HiBiT tag (CCR2-HaloTag-HiBiT). After characterization of the CCR2 construct, we used luminescence-based assays and immunofluorescence to quantify CCR2 levels, as well as a label-free, phenotypic assay to investigate the functional effect of CCR2 degradation. Treatment with HaloPROTAC3, which selectively degrades HaloTag fusion proteins, led to concentration- and time-dependent degradation of CCR2-HaloTag-HiBiT. HaloPROTAC3 induced degradation via the proteasome, as degradation was fully blocked with proteasomal inhibitors. Finally, functional assays showed that degradation of CCR2-HaloTag-HiBiT leads to a reduced functional response after agonist stimulation. Overall, our results indicate that CCR2 is amenable to targeted degradation, paving the way for the future development of CCR2 chemical degraders.
Collapse
Affiliation(s)
- Natalia V. Ortiz Zacarías
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, 2333 CC Leiden, The Netherlands; (J.D.B.); (D.v.d.E.); (L.H.H.)
| | - Sascha Röth
- Safety Innovation and PROTAC Safety, Clinical Pharmacology & Safety Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, UK; (S.R.); (K.M.)
| | - Jeremy D. Broekhuis
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, 2333 CC Leiden, The Netherlands; (J.D.B.); (D.v.d.E.); (L.H.H.)
- Oncode Institute, 2333 CC Leiden, The Netherlands
| | - Daan van der Es
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, 2333 CC Leiden, The Netherlands; (J.D.B.); (D.v.d.E.); (L.H.H.)
| | - Kevin Moreau
- Safety Innovation and PROTAC Safety, Clinical Pharmacology & Safety Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, UK; (S.R.); (K.M.)
| | - Laura H. Heitman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, 2333 CC Leiden, The Netherlands; (J.D.B.); (D.v.d.E.); (L.H.H.)
- Oncode Institute, 2333 CC Leiden, The Netherlands
| |
Collapse
|
2
|
Diehl CJ, Salerno A, Ciulli A. Ternary Complex-Templated Dynamic Combinatorial Chemistry for the Selection and Identification of Homo-PROTACs. Angew Chem Int Ed Engl 2024; 63:e202319456. [PMID: 38626385 DOI: 10.1002/anie.202319456] [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: 12/16/2023] [Revised: 04/08/2024] [Accepted: 04/15/2024] [Indexed: 04/18/2024]
Abstract
Dynamic combinatorial chemistry (DCC) leverages a reversible reaction to generate compound libraries from constituting building blocks under thermodynamic control. The position of this equilibrium can be biased by addition of a target macromolecule towards enrichment of bound ligands. While DCC has been applied to select ligands for a single target protein, its application to identifying chimeric molecules inducing proximity between two proteins is unprecedented. In this proof-of-concept study, we develop a DCC approach to select bifunctional proteolysis targeting chimeras (PROTACs) based on their ability to stabilize the ternary complex. We focus on VHL-targeting Homo-PROTACs as model system, and show that the formation of a VHL2 : Homo-PROTAC ternary complex reversibly assembled using thiol-disulfide exchange chemistry leads to amplification of potent VHL Homo-PROTACs with degradation activities which correlated well with their biophysical ability to dimerize VHL. Ternary complex templated dynamic combinatorial libraries allowed identification of novel Homo-PROTAC degraders. We anticipate future applications of ternary-complex directed DCC to early PROTAC screenings and expansion to other proximity-inducing modalities beyond PROTACs.
Collapse
Affiliation(s)
- Claudia J Diehl
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, DD1 5JJ, Dundee, Scotland, U.K
| | - Alessandra Salerno
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, DD1 5JJ, Dundee, Scotland, U.K
| | - Alessio Ciulli
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, DD1 5JJ, Dundee, Scotland, U.K
| |
Collapse
|
3
|
Bouvier C, Lawrence R, Cavallo F, Xolalpa W, Jordan A, Hjerpe R, Rodriguez MS. Breaking Bad Proteins-Discovery Approaches and the Road to Clinic for Degraders. Cells 2024; 13:578. [PMID: 38607017 PMCID: PMC11011670 DOI: 10.3390/cells13070578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 03/12/2024] [Accepted: 03/18/2024] [Indexed: 04/13/2024] Open
Abstract
Proteolysis-targeting chimeras (PROTACs) describe compounds that bind to and induce degradation of a target by simultaneously binding to a ubiquitin ligase. More generally referred to as bifunctional degraders, PROTACs have led the way in the field of targeted protein degradation (TPD), with several compounds currently undergoing clinical testing. Alongside bifunctional degraders, single-moiety compounds, or molecular glue degraders (MGDs), are increasingly being considered as a viable approach for development of therapeutics, driven by advances in rational discovery approaches. This review focuses on drug discovery with respect to bifunctional and molecular glue degraders within the ubiquitin proteasome system, including analysis of mechanistic concepts and discovery approaches, with an overview of current clinical and pre-clinical degrader status in oncology, neurodegenerative and inflammatory disease.
Collapse
Affiliation(s)
- Corentin Bouvier
- Laboratoire de Chimie de Coordination LCC-UPR 8241-CNRS, 31077 Toulouse, France; (C.B.); (M.S.R.)
| | - Rachel Lawrence
- Sygnature Discovery, Bio City, Pennyfoot St., Nottingham NG1 1GR, UK (F.C.); (A.J.)
| | - Francesca Cavallo
- Sygnature Discovery, Bio City, Pennyfoot St., Nottingham NG1 1GR, UK (F.C.); (A.J.)
| | - Wendy Xolalpa
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62209, Morelos, Mexico;
| | - Allan Jordan
- Sygnature Discovery, Bio City, Pennyfoot St., Nottingham NG1 1GR, UK (F.C.); (A.J.)
| | - Roland Hjerpe
- Sygnature Discovery, Bio City, Pennyfoot St., Nottingham NG1 1GR, UK (F.C.); (A.J.)
| | - Manuel S. Rodriguez
- Laboratoire de Chimie de Coordination LCC-UPR 8241-CNRS, 31077 Toulouse, France; (C.B.); (M.S.R.)
- Pharmadev, UMR 152, Université de Toulouse, IRD, UT3, 31400 Toulouse, France
- B Molecular, Centre Pierre Potier, Canceropôle, 31106 Toulouse, France
| |
Collapse
|
4
|
Plesniak MP, Taylor EK, Eisele F, Kourra CMK, Michaelides IN, Oram A, Wernevik J, Valencia ZS, Rowbottom H, Mann N, Fredlund L, Pivnytska V, Novén A, Pirmoradian M, Lundbäck T, Storer RI, Pettersson M, De Donatis GM, Rehnström M. Rapid PROTAC Discovery Platform: Nanomole-Scale Array Synthesis and Direct Screening of Reaction Mixtures. ACS Med Chem Lett 2023; 14:1882-1890. [PMID: 38116431 PMCID: PMC10726452 DOI: 10.1021/acsmedchemlett.3c00314] [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: 07/31/2023] [Revised: 10/21/2023] [Accepted: 10/24/2023] [Indexed: 12/21/2023] Open
Abstract
Precise length, shape, and linker attachment points are all integral components to designing efficacious proteolysis targeting chimeras (PROTACs). Due to the synthetic complexity of these heterobifunctional degraders and the difficulty of computational modeling to aid PROTAC design, the exploration of structure-activity relationships remains mostly empirical, which requires a significant investment of time and resources. To facilitate rapid hit finding, we developed capabilities for PROTAC parallel synthesis and purification by harnessing an array of preformed E3-ligand-linker intermediates. In the next iteration of this approach, we developed a rapid, nanomole-scale PROTAC synthesis methodology using amide coupling that enables direct screening of nonpurified reaction mixtures in cell-based degradation assays, as well as logD and EPSA measurements. This approach greatly expands and accelerates PROTAC SAR exploration (5 days instead of several weeks) as well as avoids laborious and solvent-demanding purification of the reaction mixtures, thus making it an economical and more sustainable methodology for PROTAC hit finding.
Collapse
Affiliation(s)
- Mateusz P. Plesniak
- Medicinal
Chemistry, Research and Early Development, Cardiovascular, Renal and
Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg 431 83, Sweden
| | - Emilia K. Taylor
- Medicinal
Chemistry, Research and Early Development, Cardiovascular, Renal and
Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg 431 83, Sweden
| | - Frederik Eisele
- Mechanistic
& Structural Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg 431 83, Sweden
| | | | - Iacovos N. Michaelides
- Fragment
Based Lead Generation, Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, U.K.
| | - Alice Oram
- iLAB,
Compound Synthesis & Management, Discovery Sciences, R&D, AstraZeneca, Gothenburg 431 83, Sweden
| | - Johan Wernevik
- Mechanistic
& Structural Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg 431 83, Sweden
| | | | - Hannah Rowbottom
- Mechanistic
& Structural Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg 431 83, Sweden
| | - Nadia Mann
- Mechanistic
& Structural Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg 431 83, Sweden
| | - Linda Fredlund
- Mechanistic
& Structural Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg 431 83, Sweden
| | - Valentyna Pivnytska
- Mechanistic
& Structural Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg 431 83, Sweden
| | - Anna Novén
- Mechanistic
& Structural Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg 431 83, Sweden
| | - Mohammad Pirmoradian
- Mechanistic
& Structural Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg 431 83, Sweden
| | - Thomas Lundbäck
- Mechanistic
& Structural Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg 431 83, Sweden
| | - R. Ian Storer
- Hit
Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, U.K.
| | - Mariell Pettersson
- Medicinal
Chemistry, Research and Early Development, Cardiovascular, Renal and
Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg 431 83, Sweden
| | - Gian M. De Donatis
- Cellular
Assay Development, Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, U.K.
| | - Marie Rehnström
- Cell
Culture Sciences & Banking, Discovery Biology, Discovery Sciences,
R&D, AstraZeneca, Gothenburg 431 83, Sweden
| |
Collapse
|
5
|
Ciulli A, O'Connor S, Chung CW, Hartung IV, Testa A, Daniels DL, Heitman LH. The 17 th EFMC Short Course on Medicinal Chemistry on Small Molecule Protein Degraders. ChemMedChem 2023; 18:e202300464. [PMID: 37817354 DOI: 10.1002/cmdc.202300464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 09/10/2023] [Indexed: 10/12/2023]
Abstract
The 17th EFMC Short Course on Medicinal Chemistry took place April 23-26, 2023 in Oegstgeest, near Leiden in the Netherlands. It covered for the first time the exciting topic of Targeted Protein Degradation (full title: Small Molecule Protein Degraders: A New Opportunity for Drug Design and Development). The course was oversubscribed, with 35 attendees and 6 instructors mainly from Europe but also from the US and South Africa, and representing both industry and academia. This report summarizes the successful event, key lectures given and topics discussed.
Collapse
Affiliation(s)
- Alessio Ciulli
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee, DD1 5JJ Scotland, UK
| | - Suzanne O'Connor
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee, DD1 5JJ Scotland, UK
| | | | - Ingo V Hartung
- Merck Healthcare KGaA, Frankfurter Straße 250, 64293, Darmstadt, Germany
| | - Andrea Testa
- Amphista Therapeutics Ltd., Cori Building, Granta Park, Great Abington, Cambridge, CB21 6GQ, UK
| | - Danette L Daniels
- Foghorn Therapeutics, 500 Technology Square, Cambridge, MA 02139, USA
| | - Laura H Heitman
- Oncode Institute & Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), P. O. Box 9502, 2300RA, Leiden, The Netherlands
| |
Collapse
|
6
|
Hartung IV, Rudolph J, Mader MM, Mulder MPC, Workman P. Expanding Chemical Probe Space: Quality Criteria for Covalent and Degrader Probes. J Med Chem 2023; 66:9297-9312. [PMID: 37403870 PMCID: PMC10388296 DOI: 10.1021/acs.jmedchem.3c00550] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Indexed: 07/06/2023]
Abstract
Within druggable target space, new small-molecule modalities, particularly covalent inhibitors and targeted degraders, have expanded the repertoire of medicinal chemists. Molecules with such modes of action have a large potential not only as drugs but also as chemical probes. Criteria have previously been established to describe the potency, selectivity, and properties of small-molecule probes that are qualified to enable the interrogation and validation of drug targets. These definitions have been tailored to reversibly acting modulators but fall short in their applicability to other modalities. While initial guidelines have been proposed, we delineate here a full set of criteria for the characterization of covalent, irreversible inhibitors as well as heterobifunctional degraders ("proteolysis-targeting chimeras", or PROTACs) and molecular glue degraders. We propose modified potency and selectivity criteria compared to those for reversible inhibitors. We discuss their relevance and highlight examples of suitable probe and pathfinder compounds.
Collapse
Affiliation(s)
- Ingo V. Hartung
- Medicinal
Chemistry, Global Research & Development, Merck Healthcare KGaA, 64293 Darmstadt, Germany
| | - Joachim Rudolph
- Discovery
Chemistry, Genentech, South San Francisco, California 94080, United States
| | - Mary M. Mader
- Molecular
Innovation, Indiana Biosciences Research
Institute, Indianapolis, Indiana 64202, United States
| | - Monique P. C. Mulder
- Department
of Cell and Chemical Biology, Leiden University
Medical Center, 2333 ZA Leiden, The Netherlands
| | - Paul Workman
- Centre
for Cancer Drug Discovery, The Institute
of Cancer Research, London, Sutton SM2 5NG, United Kingdom
- Chemical
Probes Portal, https://www.chemicalprobes.org/
| |
Collapse
|
7
|
Wurz RP, Rui H, Dellamaggiore K, Ghimire-Rijal S, Choi K, Smither K, Amegadzie A, Chen N, Li X, Banerjee A, Chen Q, Mohl D, Vaish A. Affinity and cooperativity modulate ternary complex formation to drive targeted protein degradation. Nat Commun 2023; 14:4177. [PMID: 37443112 PMCID: PMC10344917 DOI: 10.1038/s41467-023-39904-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
Targeted protein degradation via "hijacking" of the ubiquitin-proteasome system using proteolysis targeting chimeras (PROTACs) has evolved into a novel therapeutic modality. The design of PROTACs is challenging; multiple steps involved in PROTAC-induced degradation make it difficult to establish coherent structure-activity relationships. Herein, we characterize PROTAC-mediated ternary complex formation and degradation by employing von Hippel-Lindau protein (VHL) recruiting PROTACs for two different target proteins, SMARCA2 and BRD4. Ternary-complex attributes and degradation activity parameters are evaluated by varying components of the PROTAC's architecture. Ternary complex binding affinity and cooperativity correlates well with degradation potency and initial rates of degradation. Additionally, we develop a ternary-complex structure modeling workflow to calculate the total buried surface area at the interface, which is in agreement with the measured ternary complex binding affinity. Our findings establish a predictive framework to guide the design of potent degraders.
Collapse
Affiliation(s)
- Ryan P Wurz
- Amgen Research, Amgen Inc., Thousand Oaks, CA, USA
| | - Huan Rui
- Amgen Research, Amgen Inc., Thousand Oaks, CA, USA
| | | | | | - Kaylee Choi
- Amgen Research, Amgen Inc., South San Francisco, CA, USA
| | - Kate Smither
- Amgen Research, Amgen Inc., Thousand Oaks, CA, USA
| | | | - Ning Chen
- Amgen Research, Amgen Inc., Thousand Oaks, CA, USA
| | - Xiaofen Li
- Amgen Research, Amgen Inc., Thousand Oaks, CA, USA
| | | | - Qing Chen
- Amgen Research, Amgen Inc., Thousand Oaks, CA, USA
| | - Dane Mohl
- Amgen Research, Amgen Inc., Thousand Oaks, CA, USA.
| | - Amit Vaish
- Amgen Research, Amgen Inc., Thousand Oaks, CA, USA.
| |
Collapse
|
8
|
Apprato G, Ermondi G, Caron G. The Quest for Oral PROTAC drugs: Evaluating the Weaknesses of the Screening Pipeline. ACS Med Chem Lett 2023; 14:879-883. [PMID: 37465314 PMCID: PMC10351046 DOI: 10.1021/acsmedchemlett.3c00231] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 06/16/2023] [Indexed: 07/20/2023] Open
Abstract
A targeted bibliographic search exposed the deficiencies within existing PROTAC preclinical pipelines, including missing, poor-quality data and technical limitations in the experimental assays. Several recommendations are proposed to improve the efficiency of preclinical platforms for PROTACs.
Collapse
|
9
|
Terra MF, García-Arévalo M, Avelino TM, Degaki KY, de Carvalho M, Torres FR, Saito A, Figueira ACM. Obesity-Linked PPARγ Ser273 Phosphorylation Promotes Beneficial Effects on the Liver, despite Reduced Insulin Sensitivity in Mice. Biomolecules 2023; 13:biom13040632. [PMID: 37189379 DOI: 10.3390/biom13040632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 03/21/2023] [Accepted: 03/22/2023] [Indexed: 04/03/2023] Open
Abstract
Since the removal of thiazolidinediones (TZDs) from the market, researchers have been exploring alternative anti-diabetic drugs that target PPARγ without causing adverse effects while promoting insulin sensitization by blocking serine 273 phosphorylation (Ser273 or S273). Nonetheless, the underlying mechanisms of the relationship between insulin resistance and S273 phosphorylation are still largely unknown, except for the involvement of growth differentiation factor (GDF3) regulation in the process. To further investigate potential pathways, we generated a whole organism knockin mouse line with a single S273A mutation (KI) that blocks the occurrence of its phosphorylation. Our observations of KI mice on different diets and feeding schedules revealed that they were hyperglycemic, hypoinsulinemic, presented more body fat at weaning, and presented an altered plasma and hepatic lipid profile, distinctive liver morphology and gene expression. These results suggest that total blockage of S273 phosphorylation may have unforeseen effects that, in addition to promoting insulin sensitivity, could lead to metabolic disturbances, particularly in the liver. Therefore, our findings demonstrate both the beneficial and detrimental effects of PPAR S273 phosphorylation and suggest selective modulation of this post translational modification is a viable strategy to treat type 2 diabetes.
Collapse
|
10
|
Lu LD, Salvino JM. The In-Cell Western immunofluorescence assay to monitor PROTAC mediated protein degradation. Methods Enzymol 2023; 681:115-153. [PMID: 36764754 DOI: 10.1016/bs.mie.2022.08.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The In-Cell Western plate-based immunofluorescence assay is a useful methodology for monitoring protein levels and provides a facile moderate through-put method for PROTAC and degrader optimization. The method is compared to other reported assays used for PROTAC development. The advantages of this method are the greater through-put compared to Western blots due to its plate-based method and the ease to transfer between cells lines. Adherent cell lines are preferred, although suspension cells can be used following recommended modifications and precautions to the protocol. This method requires a high-quality antibody that recognizes the protein epitope in its cellular context, and in general provides data similar to Western blots with higher assay through-put.
Collapse
Affiliation(s)
- Lily D Lu
- Molecular Screening and Protein Expression Facility, The Wistar Institute, Philadelphia, PA, United States
| | - Joseph M Salvino
- Molecular Screening and Protein Expression Facility, The Wistar Institute, Philadelphia, PA, United States; Medicinal Chemistry, The Wistar Institute, Philadelphia, PA, United States; Program in Molecular and Cellular Oncogenesis, The Wistar Institute, Philadelphia, PA, United States.
| |
Collapse
|
11
|
Crummy EK, Caine EA, Mikheil D, Corona C, Riching KM, Hosfield C, Urh M. Monitoring PROTAC interactions in biochemical assays using Lumit immunoassays. Methods Enzymol 2023; 681:81-113. [PMID: 36764765 DOI: 10.1016/bs.mie.2022.08.055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The discovery of new PROTAC molecules is dependent on robust and high-throughput assays to measure PROTAC-protein interactions and ternary complex formation. Here we present the optimization and execution of Lumit Immunoassays to measure PROTAC binding and ternary complex formation in a biochemical format. We demonstrate how Lumit can be used to rank order affinities of small molecules and PROTACs to BRD4(BD1, BD2) and how to measure PROTAC-mediated ternary complex formation of BRD4(BD1, BD2) and E3 Ligase VHL. Results from both biochemical assays correlate with live and lytic cell assays, indicating that Lumit Immunoassays can be used as a high-throughput compatible screening methodology to test new small molecules.
Collapse
Affiliation(s)
| | | | | | - Cesear Corona
- Promega Biosciences Incorporated, San Luis Obispo, CA, United States
| | | | | | - Marjeta Urh
- Promega Corporation, Madison, WI, United States
| |
Collapse
|
12
|
Apprato G, D’Agostini G, Rossetti P, Ermondi G, Caron G. In Silico Tools to Extract the Drug Design Information Content of Degradation Data: The Case of PROTACs Targeting the Androgen Receptor. Molecules 2023; 28:molecules28031206. [PMID: 36770875 PMCID: PMC9919651 DOI: 10.3390/molecules28031206] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/19/2023] [Accepted: 01/24/2023] [Indexed: 01/28/2023] Open
Abstract
Proteolysis-Targeting Chimeras (PROTACs) have recently emerged as a promising technology in the drug discovery landscape. Large interest in the degradation of the androgen receptor (AR) as a new anti-prostatic cancer strategy has resulted in several papers focusing on PROTACs against AR. This study explores the potential of a few in silico tools to extract drug design information from AR degradation data in the format often reported in the literature. After setting up a dataset of 92 PROTACs with consistent AR degradation values, we employed the Bemis-Murcko method for their classification. The resulting clusters were not informative in terms of structure-degradation relationship. Subsequently, we performed Degradation Cliff analysis and identified some key aspects conferring a positive contribution to activity, as well as some methodological limits when applying this approach to PROTACs. Linker structure degradation relationships were also investigated. Then, we built and characterized ternary complexes to validate previous results. Finally, we implemented machine learning classification models and showed that AR degradation for VHL-based but not CRBN-based PROTACs can be predicted from simple permeability-related 2D molecular descriptors.
Collapse
|
13
|
Fuchs O. Targeting cereblon in hematologic malignancies. Blood Rev 2023; 57:100994. [PMID: 35933246 DOI: 10.1016/j.blre.2022.100994] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 01/28/2023]
Abstract
The protein cereblon (CRBN) is a substrate receptor of the cullin 4-really interesting new gene (RING) E3 ubiquitin ligase complex CRL4CRBN. Targeting CRBN mediates selective protein ubiquitination and subsequent degradation via the proteasome. This review describes novel thalidomide analogs, immunomodulatory drugs, also known as CRBN E3 ubiquitin ligase modulators or molecular glues (avadomide, iberdomide, CC-885, CC-90009, BTX-1188, CC-92480, CC-99282, CFT7455, and CC-91633), and CRBN-based proteolysis targeting chimeras (PROTACs) with increased efficacy and potent activity for application in hematologic malignancies. Both types of CRBN-binding drugs, molecular glues, and PROTACs stimulate the interaction between CRBN and its neosubstrates, recruiting target disease-promoting proteins and the E3 ubiquitin ligase CRL4CRBN. Proteins that are traditionally difficult to target (transcription factors and oncoproteins) can be polyubiquitinated and degraded in this way. The competition of CRBN neosubstrates with endogenous CRBN-interacting proteins and the pharmacology and rational combination therapies of and mechanisms of resistance to CRL4CRBN modulators or CRBN-based PROTACs are described.
Collapse
Affiliation(s)
- Ota Fuchs
- Institute of Hematology and Blood Transfusion, U Nemocnice 1, 12800 Praha 2, Czech Republic.
| |
Collapse
|
14
|
Yu X, Wang J. Quantitative measurement of PROTAC intracellular accumulation. Methods Enzymol 2022; 681:189-214. [PMID: 36764757 PMCID: PMC11102804 DOI: 10.1016/bs.mie.2022.11.001] [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: 12/23/2022]
Abstract
In recent years, Proteolysis Targeting Chimera (PROTAC) technology has emerged as one of the most promising approaches to remove disease-associated proteins by utilizing cells' own destruction machinery. To achieve successful degradation of a protein of interest (POI), the heterobifunctional PROTAC molecules must penetrate into the cells first, followed by target engagement and formation of the POI-PROTAC-E3 ligase complex. Based on this understanding, the assessment of cell permeability and in cell target engagement are of great importance to evaluate the efficacy of PROTAC candidates. PROTAC molecules can be classified as non-covalent and covalent, and covalent PROTACs can be further divided into irreversible and reversible covalent. Here, we present a high-throughput assay to prioritize different types of BTK PROTACs by measuring their intracellular accumulation quantitatively, using kinase binding assays and the NanoBRET target engagement platform.
Collapse
Affiliation(s)
- Xin Yu
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, United States
| | - Jin Wang
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, United States.
| |
Collapse
|
15
|
Liu M, Martyn AP, Quinn RJ. Natural product-based PROteolysis TArgeting Chimeras (PROTACs). Nat Prod Rep 2022; 39:2292-2307. [PMID: 36196977 DOI: 10.1039/d2np00038e] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Covering: upto 2022Natural products have an embedded recognition of protein surfaces. They possess this property as they are produced by biosynthetic enzymes and are substrates for one or more enzymes in the biosynthetic pathway. The inherent advantages, compared to synthetic compound libraries, is this ligand-protein binding which is, in many cases, a function of the 3-dimensional properties. Protein degradation is a recent novel therapeutic approach with several compounds now in the clinic. This review highlights the potential of PROteolysis TArgeting Chimeras (PROTACs) in the area of natural products. The approach will complement existing approaches such as the direct use of a bioactive natural product or its analogues, pharmacophore development and drug-antibody conjugates. The chemical synthesis and challenges of using natural product-based PROTACs are summarised. The review also highlights methods to detect the ternary complexes necessary for PROTAC mechanism of action.
Collapse
Affiliation(s)
- Miaomiao Liu
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Queensland, Australia.
| | - Alexander P Martyn
- Cancer and Ageing Research Program (CARP), Centre for Genomics and Personalised Health (CGPH), Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Ronald J Quinn
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Queensland, Australia.
| |
Collapse
|
16
|
PROTACs: Current Trends in Protein Degradation by Proteolysis-Targeting Chimeras. BioDrugs 2022; 36:609-623. [PMID: 36098871 DOI: 10.1007/s40259-022-00551-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/08/2022] [Indexed: 11/02/2022]
Abstract
In the recent past, proteolysis-targeting chimera (PROTAC) technology has received enormous attention for its ability to overcome the limitations of protein inhibitors and its capability to target undruggable proteins. The PROTAC molecule consists of three components, a ubiquitin E3 ligase ligand, a linker, and a target protein ligand. The application of this technology is rapidly gaining momentum, especially in cancer therapy. In this review, we first look at the history of degraders, followed by a section on the ubiquitin proteasome system (UPS) and E3 ligases used in PROTAC development. PROTACs are dependent on the UPS for degradation of target proteins. We further discuss the scope and design of degraders and mitigation strategies for overcoming the hook effect seen with degraders. As PROTACs do not follow Lipinski's 'Rule of 5', these molecules face drug metabolism and pharmacokinetic challenges. A detailed section on absorption, distribution, metabolism, and excretion of degraders is provided wherein we discuss methodologies and strategies to surmount the challenges faced by these molecules. For understanding PROTAC-mediated degradation, the characterization and measurement of protein levels in cells is important. Currently used techniques and recent advancements in assessment tools for degraders are discussed. Furthermore, we examine the challenges and emerging technologies that need to be focused on in order to competently develop potent degraders. Many companies are working in this area of emerging new modality and a few PROTACs have already entered clinical trials; the details of the trials are included in this review.
Collapse
|
17
|
Riching KM, Caine EA, Urh M, Daniels DL. The importance of cellular degradation kinetics for understanding mechanisms in targeted protein degradation. Chem Soc Rev 2022; 51:6210-6221. [PMID: 35792307 DOI: 10.1039/d2cs00339b] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Targeted protein degradation has exploded over the past several years due to preclinical and early clinical therapeutic success of numerous compounds, and the emergence of new degradation modalities, which has broadened the definition of what a degrader is. The most characterized and well-studied small molecule degraders are molecular glues and proteolysis targeting chimeras (PROTACs). These degraders induce a ternary complex between a target protein, degrader, and E3 ligase component, resulting in ubiquitination and subsequent degradation of the target protein via the ubiquitin proteasomal system (UPS). This event-driven process requires success at all steps through a complex cascade of events. As more systems, degraders, and targets are tested, it has become increasingly clear that achieving degradation is only the first critical milestone in a degrader development program. Rather highly efficacious degraders require a combination of multiple optimized parameters: rapid degradation, high potency, high maximal degradation (Dmax), and sustained loss of target without re-dosing. Success to meet these more rigorous goals depends upon the ability to characterize and understand the dynamic cellular degradation profiles and relate them to the underlying mechanism for any given target treated with a specific concentration of degrader. From this starting point, optimization and fine tuning of multiple kinetic parameters such as how fast degradation occurs (the rate), how much of the target is degraded (the extent), and how long the target remains degraded (the duration) can be performed. In this review we explore the diversity of cellular kinetic degradation profiles which can arise after molecular glue and PROTAC treatment and the potential implications of these varying responses. As the overall degradation kinetics are a sum of individual mechanistic steps, each with their own kinetic contributions, we discuss the ways in which changes at any one of these steps could potentially influence the resultant kinetic degradation profiles. Looking forward, we address the importance in characterizing the kinetics of target protein loss in the early stages of degrader design and how this will enable more rapid discovery of therapeutic agents to elicit desired phenotypic outcomes.
Collapse
Affiliation(s)
- Kristin M Riching
- Promega Corporation, 5430 East Cheryl Drive, Madison, WI, 53711, USA.
| | - Elizabeth A Caine
- Promega Corporation, 5430 East Cheryl Drive, Madison, WI, 53711, USA.
| | - Marjeta Urh
- Promega Corporation, 5430 East Cheryl Drive, Madison, WI, 53711, USA.
| | - Danette L Daniels
- Promega Corporation, 5430 East Cheryl Drive, Madison, WI, 53711, USA.
| |
Collapse
|
18
|
Hendrick CE, Jorgensen JR, Chaudhry C, Strambeanu II, Brazeau JF, Schiffer J, Shi Z, Venable JD, Wolkenberg SE. Direct-to-Biology Accelerates PROTAC Synthesis and the Evaluation of Linker Effects on Permeability and Degradation. ACS Med Chem Lett 2022; 13:1182-1190. [PMID: 35859867 PMCID: PMC9290060 DOI: 10.1021/acsmedchemlett.2c00124] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
A platform to accelerate optimization of proteolysis targeting chimeras (PROTACs) has been developed using a direct-to-biology (D2B) approach with a focus on linker effects. A large number of linker analogs-with varying length, polarity, and rigidity-were rapidly prepared and characterized in four cell-based assays by streamlining time-consuming steps in synthesis and purification. The expansive dataset informs on linker structure-activity relationships (SAR) for in-cell E3 ligase target engagement, degradation, permeability, and cell toxicity. Unexpected aspects of linker SAR was discovered, consistent with literature reports on "linkerology", and the method dramatically speeds up empirical optimization. Physicochemical property trends emerged, and the platform has the potential to rapidly expand training sets for more complex prediction models. In-depth validation studies were carried out and confirm the D2B platform is a valuable tool to accelerate PROTAC design-make-test cycles.
Collapse
Affiliation(s)
- Charles E. Hendrick
- Discovery
Chemistry, Therapeutics Discovery, Janssen
Research & Development, LLC,Welsh & McKean Roads, Spring House, Pennsylvania 19477, United States
| | - Jeff R. Jorgensen
- Discovery
Technology and Molecular Pharmacology, Therapeutics Discovery, Janssen Research & Development, LLC, Welsh & McKean Roads, Spring House, Pennsylvania 19477, United States
| | - Charu Chaudhry
- Discovery
Technology and Molecular Pharmacology, Therapeutics Discovery, Janssen Research & Development, LLC, Welsh & McKean Roads, Spring House, Pennsylvania 19477, United States
| | - Iulia I. Strambeanu
- Discovery
Chemistry, Therapeutics Discovery, Janssen
Research & Development, LLC,Welsh & McKean Roads, Spring House, Pennsylvania 19477, United States
| | - Jean-Francois Brazeau
- Discovery
Chemistry, Therapeutics Discovery, Janssen
Research & Development, LLC, 3210 Merryfield Row, La Jolla, California 92121, United States
| | - Jamie Schiffer
- Computational
Chemistry, Therapeutics Discovery, Janssen
Research & Development, LLC, 3210 Merryfield Row, La Jolla, California 92121, United States
| | - Zhicai Shi
- Discovery
Chemistry, Therapeutics Discovery, Janssen
Research & Development, LLC,Welsh & McKean Roads, Spring House, Pennsylvania 19477, United States
| | - Jennifer D. Venable
- Discovery
Chemistry, Therapeutics Discovery, Janssen
Research & Development, LLC, 3210 Merryfield Row, La Jolla, California 92121, United States
| | - Scott E. Wolkenberg
- Discovery
Chemistry, Therapeutics Discovery, Janssen
Research & Development, LLC,Welsh & McKean Roads, Spring House, Pennsylvania 19477, United States
| |
Collapse
|
19
|
Krutzek F, Kopka K, Stadlbauer S. Development of Radiotracers for Imaging of the PD-1/PD-L1 Axis. Pharmaceuticals (Basel) 2022; 15:ph15060747. [PMID: 35745666 PMCID: PMC9228425 DOI: 10.3390/ph15060747] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/08/2022] [Accepted: 06/09/2022] [Indexed: 11/24/2022] Open
Abstract
Immune checkpoint inhibitor (ICI) therapy has emerged as a major treatment option for a variety of cancers. Among the immune checkpoints addressed, the programmed death receptor 1 (PD-1) and its ligand PD-L1 are the key targets for an ICI. PD-L1 has especially been proven to be a reproducible biomarker allowing for therapy decisions and monitoring therapy success. However, the expression of PD-L1 is not only heterogeneous among and within tumor lesions, but the expression is very dynamic and changes over time. Immunohistochemistry, which is the standard diagnostic tool, can only inadequately address these challenges. On the other hand, molecular imaging techniques such as positron emission tomography (PET) and single-photon emission computed tomography (SPECT) provide the advantage of a whole-body scan and therefore fully address the issue of the heterogeneous expression of checkpoints over time. Here, we provide an overview of existing PET, SPECT, and optical imaging (OI) (radio)tracers for the imaging of the upregulation levels of PD-1 and PD-L1. We summarize the preclinical and clinical data of the different molecule classes of radiotracers and discuss their respective advantages and disadvantages. At the end, we show possible future directions for developing new radiotracers for the imaging of PD-1/PD-L1 status in cancer patients.
Collapse
Affiliation(s)
- Fabian Krutzek
- Department of Translational TME Ligands, Institute of Radiopharmaceutical Cancer Research, Helmholtz Center Dresden-Rossendorf, 01328 Dresden, Germany; (F.K.); (K.K.)
| | - Klaus Kopka
- Department of Translational TME Ligands, Institute of Radiopharmaceutical Cancer Research, Helmholtz Center Dresden-Rossendorf, 01328 Dresden, Germany; (F.K.); (K.K.)
- School of Science, Faculty of Chemistry and Food Chemistry, Technical University Dresden, 01069 Dresden, Germany
- German Cancer Consortium (DKTK), Partner Site Dresden, 01307 Dresden, Germany
- National Center for Tumor Diseases (NCT), Partner Site Dresden, University Cancer Cancer (UCC), 01307 Dresden, Germany
| | - Sven Stadlbauer
- Department of Translational TME Ligands, Institute of Radiopharmaceutical Cancer Research, Helmholtz Center Dresden-Rossendorf, 01328 Dresden, Germany; (F.K.); (K.K.)
- Correspondence:
| |
Collapse
|
20
|
Pagar RR, Musale SR, Pawar G, Kulkarni D, Giram PS. Comprehensive Review on the Degradation Chemistry and Toxicity Studies of Functional Materials. ACS Biomater Sci Eng 2022; 8:2161-2195. [PMID: 35522605 DOI: 10.1021/acsbiomaterials.1c01304] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
In recent decades there has been growing interest of material chemists in the successful development of functional materials for drug delivery, tissue engineering, imaging, diagnosis, theranostic, and other biomedical applications with advanced nanotechnology tools. The efficacy and safety of functional materials are determined by their pharmacological, toxicological, and immunogenic effects. It is essential to consider all degradation pathways of functional materials and to assess plausible intermediates and final products for quality control. This review provides a brief insight into chemical degradation mechanisms of functional materials like oxidation, photodegradation, and physical and enzymatic degradation. The intermediates and products of degradation were confirmed with analytical methods such as proton nuclear magnetic resonance (1H NMR), gel permeation chromatography (GPC), UV-vis spectroscopy (UV-vis), infrared spectroscopy (IR), differential scanning calorimetry (DSC), mass spectroscopy, and other sophisticated analytical methods. These analytical methods are also used for regulatory, quality control, and stability purposes in industry. The assessment of degradation is important to predetermine the behavior of functional materials in specific storage conditions and can be relevant to their behavior during in vivo applications. Another important aspect is the evaluation of the toxicity of functional materials. Toxicity can be accessed with various methods using in vitro, in vivo, ex vivo, and in silico models. In vitro cell culture methods are used to determine mitochondrial damage, reactive oxygen species, stress responses, and cellular toxicity. In vitro cellular toxicity can be measured by MTT assay, LDH leakage assay, and hemolysis. In vivo studies are performed using various animal models involving zebrafish, rodents (mice and rats), and nonhuman primates. Ex vivo studies are also used for efficacy and toxicity determinations of functional materials like ex vivo potency assay and precision-cut liver slice (PCLS) models. The in silico tools with computational simulations like quantitative structure-activity relationships (QSAR), pharmacokinetics (PK) and pharmacodynamics (PD), dose and time response, and quantitative cationic-activity relationships ((Q)CARs) are used for prediction of the toxicity of functional materials. In this review, we studied the principle methods used for degradation studies, different degradation pathways, and mechanisms of functional material degradation with prototype examples. We discuss toxicity assessments with different toxicity approaches used for estimation of the safety and efficacy of functional materials.
Collapse
Affiliation(s)
- Roshani R Pagar
- Department of Pharmaceutics, Dr. D.Y. Patil Institute of Pharmaceutical Sciences and Research, Pimpri, Pune, Maharashtra 411018, India
| | - Shubham R Musale
- Department of Pharmaceutics, Dr. D.Y. Patil Institute of Pharmaceutical Sciences and Research, Pimpri, Pune, Maharashtra 411018, India
| | - Ganesh Pawar
- Department of Pharmacology, Dr. D.Y. Patil Institute of Pharmaceutical Sciences and Research, Pimpri, Pune, Maharashtra 411018, India
| | - Deepak Kulkarni
- Srinath College of Pharmacy, Bajajnagar, Aurangabad, Maharashtra 431136, India
| | - Prabhanjan S Giram
- Department of Pharmaceutics, Dr. D.Y. Patil Institute of Pharmaceutical Sciences and Research, Pimpri, Pune, Maharashtra 411018, India.,Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
| |
Collapse
|
21
|
Ulasov AV, Rosenkranz AA, Georgiev GP, Sobolev AS. Nrf2/Keap1/ARE signaling: Towards specific regulation. Life Sci 2022; 291:120111. [PMID: 34732330 PMCID: PMC8557391 DOI: 10.1016/j.lfs.2021.120111] [Citation(s) in RCA: 174] [Impact Index Per Article: 87.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/22/2021] [Accepted: 10/27/2021] [Indexed: 02/06/2023]
Abstract
The Nrf2 transcription factor governs the expression of hundreds genes involved in cell defense against oxidative stress, the hallmark of numerous diseases such as neurodegenerative, cardiovascular, some viral pathologies, diabetes and others. The main route for Nrf2 activity regulation is via interactions with the Keap1 protein. Under the normoxia the Keap1 binds the Nrf2 and targets it to the proteasomal degradation, while the Keap1 is regenerated. Upon oxidative stress the interactions between Nrf2 and Keap1 are interrupted and the Nrf2 activates the transcription of the protective genes. Currently, the Nrf2 system activation is considered as a powerful cytoprotective strategy for treatment of different pathologies, which pathogenesis relies on oxidative stress including viral diseases of pivotal importance such as COVID-19. The implementation of this strategy is accomplished mainly through the inactivation of the Keap1 "guardian" function. Two approaches are now developing: the Keap1 modification via electrophilic agents, which leads to the Nrf2 release, and direct interruption of the Nrf2:Keap1 protein-protein interactions (PPI). Because of theirs chemical structure, the Nrf2 electrophilic inducers could non-specifically interact with others cellular proteins leading to undesired effects. Whereas the non-electrophilic inhibitors of the Nrf2:Keap1 PPI could be more specific, thereby widening the therapeutic window.
Collapse
Affiliation(s)
- Alexey V Ulasov
- Department of Molecular Genetics of Intracellular Transport, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia.
| | - Andrey A Rosenkranz
- Department of Molecular Genetics of Intracellular Transport, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia; Faculty of Biology, Moscow State University, 1-12 Leninskiye Gory St., 119234 Moscow, Russia
| | - Georgii P Georgiev
- Department of Molecular Genetics of Intracellular Transport, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia
| | - Alexander S Sobolev
- Department of Molecular Genetics of Intracellular Transport, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia; Faculty of Biology, Moscow State University, 1-12 Leninskiye Gory St., 119234 Moscow, Russia
| |
Collapse
|
22
|
Frere GA, de Araujo ED, Gunning PT. Emerging mechanisms of targeted protein degradation by molecular glues. Methods Cell Biol 2022; 169:1-26. [DOI: 10.1016/bs.mcb.2022.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
23
|
Trivalent PROTACs enhance protein degradation via combined avidity and cooperativity. Nat Chem Biol 2021; 17:1157-1167. [PMID: 34675414 PMCID: PMC7611906 DOI: 10.1038/s41589-021-00878-4] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 08/10/2021] [Indexed: 01/01/2023]
Abstract
Bivalent proteolysis-targeting chimeras (PROTACs) drive protein degradation by simultaneously binding a target protein and an E3 ligase and forming a productive ternary complex. We hypothesized that increasing binding valency within a PROTAC could enhance degradation. Here, we designed trivalent PROTACs consisting of a bivalent bromo and extra terminal (BET) inhibitor and an E3 ligand tethered via a branched linker. We identified von Hippel-Lindau (VHL)-based SIM1 as a low picomolar BET degrader with preference for bromodomain containing 2 (BRD2). Compared to bivalent PROTACs, SIM1 showed more sustained and higher degradation efficacy, which led to more potent anticancer activity. Mechanistically, SIM1 simultaneously engages with high avidity both BET bromodomains in a cis intramolecular fashion and forms a 1:1:1 ternary complex with VHL, exhibiting positive cooperativity and high cellular stability with prolonged residence time. Collectively, our data along with favorable in vivo pharmacokinetics demonstrate that augmenting the binding valency of proximity-induced modalities can be an enabling strategy for advancing functional outcomes.
Collapse
|
24
|
Dale B, Cheng M, Park KS, Kaniskan HÜ, Xiong Y, Jin J. Advancing targeted protein degradation for cancer therapy. Nat Rev Cancer 2021; 21:638-654. [PMID: 34131295 PMCID: PMC8463487 DOI: 10.1038/s41568-021-00365-x] [Citation(s) in RCA: 274] [Impact Index Per Article: 91.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/23/2021] [Indexed: 02/05/2023]
Abstract
The human proteome contains approximately 20,000 proteins, and it is estimated that more than 600 of them are functionally important for various types of cancers, including nearly 400 non-enzyme proteins that are challenging to target by traditional occupancy-driven pharmacology. Recent advances in the development of small-molecule degraders, including molecular glues and heterobifunctional degraders such as proteolysis-targeting chimeras (PROTACs), have made it possible to target many proteins that were previously considered undruggable. In particular, PROTACs form a ternary complex with a hijacked E3 ubiquitin ligase and a target protein, leading to polyubiquitination and degradation of the target protein. The broad applicability of this approach is facilitated by the flexibility of individual E3 ligases to recognize different substrates. The vast majority of the approximately 600 human E3 ligases have not been explored, thus presenting enormous opportunities to develop degraders that target oncoproteins with tissue, tumour and subcellular selectivity. In this Review, we first discuss the molecular basis of targeted protein degradation. We then offer a comprehensive account of the most promising degraders in development as cancer therapies to date. Lastly, we provide an overview of opportunities and challenges in this exciting field.
Collapse
Affiliation(s)
- Brandon Dale
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Meng Cheng
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kwang-Su Park
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - H Ümit Kaniskan
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yue Xiong
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Cullgen Inc., San Diego, CA, USA.
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| |
Collapse
|
25
|
Márquez-Cantudo L, Ramos A, Coderch C, de Pascual-Teresa B. Proteasomal Degradation of Zn-Dependent Hdacs: The E3-Ligases Implicated and the Designed Protacs That Enable Degradation. Molecules 2021; 26:molecules26185606. [PMID: 34577077 PMCID: PMC8467390 DOI: 10.3390/molecules26185606] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 12/21/2022] Open
Abstract
Protein degradation by the Ubiquitin-Proteasome System is one of the main mechanisms of the regulation of cellular proteostasis, and the E3 ligases are the key effectors for the protein recognition and degradation. Many E3 ligases have key roles in cell cycle regulation, acting as checkpoints and checkpoint regulators. One of the many important proteins involved in the regulation of the cell cycle are the members of the Histone Deacetylase (HDAC) family. The importance of zinc dependent HDACs in the regulation of chromatin packing and, therefore, gene expression, has made them targets for the design and synthesis of HDAC inhibitors. However, achieving potency and selectivity has proven to be a challenge due to the homology between the zinc dependent HDACs. PROteolysis TArgeting Chimaera (PROTAC) design has been demonstrated to be a useful strategy to inhibit and selectively degrade protein targets. In this review, we attempt to summarize the E3 ligases that naturally ubiquitinate HDACs, analyze their structure, and list the known ligands that can bind to these E3 ligases and be used for PROTAC design, as well as the already described HDAC-targeted PROTACs.
Collapse
|
26
|
Rodriguez-Rivera FP, Levi SM. Unifying Catalysis Framework to Dissect Proteasomal Degradation Paradigms. ACS CENTRAL SCIENCE 2021; 7:1117-1125. [PMID: 34345664 PMCID: PMC8323112 DOI: 10.1021/acscentsci.1c00389] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Indexed: 06/13/2023]
Abstract
Diverging from traditional target inhibition, proteasomal protein degradation approaches have emerged as novel therapeutic modalities that embody distinct pharmacological profiles and can access previously undrugged targets. Small molecule degraders have the potential to catalytically destroy target proteins at substoichiometric concentrations, thus lowering administered doses and extending pharmacological effects. With this mechanistic premise, research efforts have advanced the development of small molecule degraders that benefit from stable and increased affinity ternary complexes. However, a holistic framework that evaluates different degradation modes from a catalytic perspective, including focusing on kinetically favored degradation mechanisms, is lacking. In this Outlook, we introduce the concept of an induced cooperativity spectrum as a unifying framework to mechanistically understand catalytic degradation profiles. This framework is bolstered by key examples of published molecular degraders extending from molecular glues to bivalent degraders. Critically, we discuss remaining challenges and future opportunities in drug discovery to rationally design and phenotypically screen for efficient degraders.
Collapse
Affiliation(s)
- Frances P. Rodriguez-Rivera
- Discovery
Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Samuel M. Levi
- Pfizer
Worldwide Research and Development, Pfizer,
Inc., 1 Portland Street, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
27
|
Cresser-Brown JO, Marsh GP, Maple HJ. Reviewing the toolbox for degrader development in oncology. Curr Opin Pharmacol 2021; 59:43-51. [PMID: 34058637 DOI: 10.1016/j.coph.2021.04.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 04/22/2021] [Accepted: 04/26/2021] [Indexed: 12/29/2022]
Abstract
The field of targeted protein degradation encompasses a growing number of modalities that achieve potent and selective knockdown of target proteins at the post-translational level. Among the most clinically advanced are bifunctional small-molecule degraders, also referred to as PROteolysis Targeting Chimeras, Degronimids, SNIPERs, or uSMITEs. Although applicable to many disease indications, oncology stands to be the first to benefit from this promising therapeutic approach, with the first investigational new drugs (INDs) filed in 2019 and a proliferation of research specifically focused on harnessing degraders for cancer treatment. In this review, we consider the toolbox of guidelines, reagents, and technologies that has evolved alongside the field to support degrader research and development.
Collapse
Affiliation(s)
- Joel O Cresser-Brown
- Bio-Techne (Tocris), The Watkins Building, Atlantic Road, Avonmouth, Bristol, UK
| | - Graham P Marsh
- Bio-Techne (Tocris), The Watkins Building, Atlantic Road, Avonmouth, Bristol, UK
| | - Hannah J Maple
- Bio-Techne (Tocris), The Watkins Building, Atlantic Road, Avonmouth, Bristol, UK.
| |
Collapse
|
28
|
Abstract
Targeted protein degradation is a broad and expanding field aimed at the modulation of protein homeostasis. A focus of this field has been directed toward molecules that hijack the ubiquitin proteasome system with heterobifunctional ligands that recruit a target protein to an E3 ligase to facilitate polyubiquitination and subsequent degradation by the 26S proteasome. Despite the success of these chimeras toward a number of clinically relevant targets, the ultimate breadth and scope of this approach remains uncertain. Here we highlight recent advances in assays and tools available to evaluate targeted protein degradation, including and beyond the study of E3-targeted chimeric ligands. We note several challenges associated with degrader development and discuss various approaches to expanding the protein homeostasis toolbox.
Collapse
|
29
|
Cecchini C, Pannilunghi S, Tardy S, Scapozza L. From Conception to Development: Investigating PROTACs Features for Improved Cell Permeability and Successful Protein Degradation. Front Chem 2021; 9:672267. [PMID: 33959589 PMCID: PMC8093871 DOI: 10.3389/fchem.2021.672267] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 03/22/2021] [Indexed: 01/16/2023] Open
Abstract
Proteolysis Targeting Chimeras (PROTACs) are heterobifunctional degraders that specifically eliminate targeted proteins by hijacking the ubiquitin-proteasome system (UPS). This modality has emerged as an orthogonal approach to the use of small-molecule inhibitors for knocking down classic targets and disease-related proteins classified, until now, as "undruggable." In early 2019, the first targeted protein degraders reached the clinic, drawing attention to PROTACs as one of the most appealing technology in the drug discovery landscape. Despite these promising results, PROTACs are often affected by poor cellular permeability due to their high molecular weight (MW) and large exposed polar surface area (PSA). Herein, we report a comprehensive record of PROTAC design, pharmacology and thermodynamic challenges and solutions, as well as some of the available strategies to enhance cellular uptake, including suggestions of promising biological tools for the in vitro evaluation of PROTACs permeability toward successful protein degradation.
Collapse
Affiliation(s)
- Carlotta Cecchini
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Pharmaceutical Biochemistry/Chemistry, Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
| | - Sara Pannilunghi
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Pharmaceutical Biochemistry/Chemistry, Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
| | - Sébastien Tardy
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Pharmaceutical Biochemistry/Chemistry, Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
| | - Leonardo Scapozza
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Pharmaceutical Biochemistry/Chemistry, Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
| |
Collapse
|
30
|
Ermondi G, Garcia-Jimenez D, Caron G. PROTACs and Building Blocks: The 2D Chemical Space in Very Early Drug Discovery. Molecules 2021; 26:672. [PMID: 33525371 PMCID: PMC7865272 DOI: 10.3390/molecules26030672] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 12/11/2022] Open
Abstract
Targeted protein degradation by PROTACs has emerged as a new modality for the knockdown of a range of proteins, and, more recently, it has become increasingly clear that the PROTAC chemical space requires characterization through a pool of ad hoc physicochemical descriptors. In this study, a new database named PROTAC-DB that provides extensive information about PROTACs and building blocks was used to obtain the 2D chemical structures of about 1600 PROTACs, 60 E3 ligands, 800 linkers, and 202 warheads. For every structure, we calculated a pool of seven 2D descriptors carefully identified as informative for large and flexible structures. For comparison purposes, the same procedure was applied to a dataset of about 50 bRo5 approved drugs reported in the literature. Correlation matrices, PCAs, box plots, and other graphical tools were used to define and understand the chemical space covered by PROTACs and building blocks in relation to other compounds. Results show that linkers have different properties than E3 ligands and warheads. Polar descriptors additivity is not respected when passing from building blocks to degraders. Moreover, a very preliminary analysis based on three PROTACs with high, intermediate, and low permeability showed how the most permeable compounds seem to occupy a region closer to bRo5 drugs and, thus, exhibit different properties than impermeable compounds. Finally, a second database, PROTACpedia, was used to discuss the relevance of physicochemical descriptors on degradation activity.
Collapse
Affiliation(s)
| | | | - Giulia Caron
- Molecular Biotechnology and Health Sciences Department, University of Torino, Via Quarello, 15, 10135 Torino, Italy; (G.E.); (D.G.-J.)
| |
Collapse
|
31
|
Vasta JD, Corona CR, Robers MB. A High-Throughput Method to Prioritize PROTAC Intracellular Target Engagement and Cell Permeability Using NanoBRET. Methods Mol Biol 2021; 2365:265-282. [PMID: 34432249 DOI: 10.1007/978-1-0716-1665-9_14] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Target engagement and cell permeation are important parameters that may limit the efficacy of proteolysis-targeting chimeras (PROTACs). Here, we present an approach that facilitates both the quantitation of PROTAC binding affinity for an E3 ligase of interest, as well as the assessment of relative intracellular availability. We present a panel of E3 ligase target engagement assays based upon the NanoBRET Target Engagement platform. Querying E3 ligase engagement under live-cell and permeabilized-cell conditions allow calculation of an availability index that can be used to rank order the intracellular availability of PROTACs. Here we present examples where the cellular availability of PROTACs and their monovalent precursors are prioritized using NanoBRET assays for CRBN or VHL E3 ligases.
Collapse
|
32
|
Kinetic Detection of E3:PROTAC:Target Ternary Complexes Using NanoBRET Technology in Live Cells. Methods Mol Biol 2021; 2365:151-171. [PMID: 34432243 DOI: 10.1007/978-1-0716-1665-9_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Heterobifunctional small-molecule degraders known as Proteolysis Targeting Chimeras (PROTACs) serve as a chemical bridge bringing into direct association a target protein with an active E3 ligase complex, called the ternary complex, to facilitate targeted protein degradation. This ternary complex formation is the first key mechanistic step in a cascade of events that results in ubiquitination and subsequent degradation of the target protein via the ubiquitin-proteasome pathway. The ternary complex, however, is a nonnative cellular complex; therefore, PROTAC compound design has many challenges to overcome to ensure successful formation, including achieving structural and electrostatic favorability among target and ligase. Due to these challenges, finding successful PROTACs typically requires testing of extensive libraries of heterobifunctional compounds with varying linkers and E3 handles. As PROTAC ternary complex formation is also critically dependent on cellular context, live cell assays and technologies for rapid and robust screening are highly enabling for triaging of early stage compounds. Here, we present cellular assays utilizing NanoBRET technology for the study of ternary complexes, showing examples with two most popular PROTAC E3 ligase components, VHL (von Hippel-Lindau disease tumor suppressor) and CRBN (Cereblon). These assays can be run in either endpoint or real-time kinetic formats, are compatible with high-throughput workflows, and provide insight into how altering the PROTAC chemical composition affects the formation and stability of the ternary complex in live cells.
Collapse
|
33
|
Caine EA, Mahan SD, Johnson RL, Nieman AN, Lam N, Warren CR, Riching KM, Urh M, Daniels DL. Targeted Protein Degradation Phenotypic Studies Using HaloTag CRISPR/Cas9 Endogenous Tagging Coupled with HaloPROTAC3. ACTA ACUST UNITED AC 2020; 91:e81. [PMID: 33332748 PMCID: PMC7818660 DOI: 10.1002/cpph.81] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
To assess the role of a protein, protein loss phenotypic studies can be used, most commonly through mutagenesis RNAi or CRISPR knockout. Such studies have been critical for the understanding of protein function and the identification of putative therapeutic targets for numerous human disease states. However, these methodological approaches present challenges because they are not easily reversible, and if an essential gene is targeted, an associated loss of cell viability can potentially hinder further studies. Here we present a reversible and conditional live‐cell knockout strategy that is applicable to numerous proteins. This modular protein‐tagging approach regulates target loss at the protein, rather than the genomic, level through the use of HaloPROTAC3, which specifically degrades HaloTag fusion proteins via recruitment of the VHL E3 ligase component. To enable HaloTag‐mediated degradation of endogenous proteins, we provide protocols for HaloTag genomic insertion at the protein N or C terminus via CRISPR/Cas9 and use of HaloTag fluorescent ligands to enrich edited cells via Fluorescence‐Activated Cell Sorting (FACS). Using these approaches, endogenous HaloTag fusion proteins present in various subcellular locations can be degraded by HaloPROTAC3. As detecting the degradation of endogenous targets is challenging, the 11‐amino‐acid peptide tag HiBiT is added to the HaloTag fusion to allows the sensitive luminescence detection of HaloTag fusion levels without the use of antibodies. Lastly, we demonstrate, through comparison of HaloPROTAC3 degradation with that of another fusion tag PROTAC, dTAG‐13, that HaloPROTAC3 has a faster degradation rate and similar extent of degradation. © 2020 The Authors. Basic Protocol 1: CRISPR/Cas9 insertion of HaloTag or HiBiT‐HaloTag Basic Protocol 2: HaloPROTAC3 degradation of endogenous HaloTag fusions
Collapse
Affiliation(s)
| | | | | | | | - Ngan Lam
- Promega Corporation, Madison, Wisconsin
| | - Curtis R Warren
- Boehringer Ingelheim Pharmaceuticals, Ridgefield, Connecticut
| | | | | | | |
Collapse
|
34
|
Affiliation(s)
- Jie Li
- School of Medicine Huaqiao University Quanzhou 362021 P. R. China
| | - Jieqing Liu
- School of Medicine Huaqiao University Quanzhou 362021 P. R. China
| |
Collapse
|
35
|
Zaidman D, Prilusky J, London N. PRosettaC: Rosetta Based Modeling of PROTAC Mediated Ternary Complexes. J Chem Inf Model 2020; 60:4894-4903. [PMID: 32976709 PMCID: PMC7592117 DOI: 10.1021/acs.jcim.0c00589] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Indexed: 12/22/2022]
Abstract
Proteolysis-targeting chimeras (PROTACs), which induce degradation by recruitment of an E3 ligase to a target protein, are gaining much interest as a new pharmacological modality. However, designing PROTACs is challenging. Formation of a ternary complex between the protein target, the PROTAC, and the recruited E3 ligase is considered paramount for successful degradation. A structural model of this ternary complex could in principle inform rational PROTAC design. Unfortunately, only a handful of structures are available for such complexes, necessitating tools for their modeling. We developed a combined protocol for the modeling of a ternary complex induced by a given PROTAC. Our protocol alternates between sampling of the protein-protein interaction space and the PROTAC molecule conformational space. Application of this protocol-PRosettaC-to a benchmark of known PROTAC ternary complexes results in near-native predictions, with often atomic accuracy prediction of the protein chains, as well as the PROTAC binding moieties. It allowed the modeling of a CRBN/BTK complex that recapitulated experimental results for a series of PROTACs. PRosettaC generated models may be used to design PROTACs for new targets, as well as improve PROTACs for existing targets, potentially cutting down time and synthesis efforts. To enable wide access to this protocol, we have made it available through a web server (https://prosettac.weizmann.ac.il/).
Collapse
Affiliation(s)
- Daniel Zaidman
- Department
of Organic Chemistry, The Weizmann Institute
of Science, 76100, Rehovot, Israel
| | - Jaime Prilusky
- Life
Sciences Core Facilities, Weizmann Institute
of Science, 76100, Rehovot, Israel
| | - Nir London
- Department
of Organic Chemistry, The Weizmann Institute
of Science, 76100, Rehovot, Israel
| |
Collapse
|
36
|
Drummond ML, Henry A, Li H, Williams CI. Improved Accuracy for Modeling PROTAC-Mediated Ternary Complex Formation and Targeted Protein Degradation via New In Silico Methodologies. J Chem Inf Model 2020; 60:5234-5254. [PMID: 32969649 DOI: 10.1021/acs.jcim.0c00897] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Extending upon our previous publication [Drummond, M.; J. Chem. Inf. Model. 2019, 59, 1634-1644], two additional computational methods are presented to model PROTAC-mediated ternary complex structures, which are then used to predict the efficacy of any accompanying protein degradation. Method 4B, an extension to one of our previous approaches, incorporates a clustering procedure uniquely suited for considering ternary complexes. Method 4B yields the highest proportion to date of crystal-like poses in modeled ternary complex ensembles, nearing 100% in two cases and always giving a hit rate of at least 10%. Techniques to further improve this performance for particularly troublesome cases are suggested and validated. This demonstrated ability to reliably reproduce known crystallographic ternary complex structures is further established through modeling of a newly released crystal structure. Moreover, for the far more common scenario where the structure of the ternary complex intermediate is unknown, the methods detailed in this work nonetheless consistently yield results that reliably follow experimental protein degradation trends, as established through seven retrospective case studies. These various case studies cover challenging yet common modeling situations, such as when the precise orientation of the PROTAC binding moiety in one (or both) of the protein pockets has not been experimentally established. Successful results are presented for one PROTAC targeting many proteins, for different PROTACs targeting the same protein, and even for degradation effected by an E3 ligase that has not been structurally characterized in a ternary complex. Overall, the computational modeling approaches detailed in this work should greatly facilitate PROTAC screening and design efforts, so that the many advantages of a PROTAC-based degradation approach can be effectively utilized both rapidly and at reduced cost.
Collapse
Affiliation(s)
| | - Andrew Henry
- Chemical Computing Group, Cambridge, CB4 0WS, United Kingdom
| | - Huifang Li
- Chemical Computing Group, Montreal, Quebec H3A 2R7, Canada
| | | |
Collapse
|
37
|
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: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [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.
Collapse
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
| |
Collapse
|
38
|
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] [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
| |
Collapse
|
39
|
Mechanisms of Action for Small Molecules Revealed by Structural Biology in Drug Discovery. Int J Mol Sci 2020; 21:ijms21155262. [PMID: 32722222 PMCID: PMC7432558 DOI: 10.3390/ijms21155262] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/08/2020] [Accepted: 07/20/2020] [Indexed: 12/26/2022] Open
Abstract
Small-molecule drugs are organic compounds affecting molecular pathways by targeting important proteins. These compounds have a low molecular weight, making them penetrate cells easily. Small-molecule drugs can be developed from leads derived from rational drug design or isolated from natural resources. A target-based drug discovery project usually includes target identification, target validation, hit identification, hit to lead and lead optimization. Understanding molecular interactions between small molecules and their targets is critical in drug discovery. Although many biophysical and biochemical methods are able to elucidate molecular interactions of small molecules with their targets, structural biology is the most powerful tool to determine the mechanisms of action for both targets and the developed compounds. Herein, we reviewed the application of structural biology to investigate binding modes of orthosteric and allosteric inhibitors. It is exemplified that structural biology provides a clear view of the binding modes of protease inhibitors and phosphatase inhibitors. We also demonstrate that structural biology provides insights into the function of a target and identifies a druggable site for rational drug design.
Collapse
|
40
|
Liu X, Zhang X, Lv D, Yuan Y, Zheng G, Zhou D. Assays and technologies for developing proteolysis targeting chimera degraders. Future Med Chem 2020; 12:1155-1179. [PMID: 32431173 PMCID: PMC7333641 DOI: 10.4155/fmc-2020-0073] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 03/18/2020] [Indexed: 02/06/2023] Open
Abstract
Targeted protein degradation by small-molecule degraders represents an emerging mode of action in drug discovery. Proteolysis targeting chimeras (PROTACs) are small molecules that can recruit an E3 ligase and a protein of interest (POI) into proximity, leading to induced ubiquitination and degradation of the POI by the proteasome system. To date, the design and optimization of PROTACs remain empirical due to the complicated mechanism of induced protein degradation. Nevertheless, it is increasingly appreciated that profiling step-by-step along the ubiquitin-proteasome degradation pathway using biochemical and biophysical assays are essential in understanding the structure-activity relationship and facilitating the rational design of PROTACs. This review aims to summarize these assays and to discuss the potential of expanding the toolbox with other new techniques.
Collapse
Affiliation(s)
- Xingui Liu
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA
| | - Xuan Zhang
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA
| | - Dongwen Lv
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA
| | - Yaxia Yuan
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA
| | - Guangrong Zheng
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA
| | - Daohong Zhou
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA
| |
Collapse
|
41
|
Khan S, He Y, Zhang X, Yuan Y, Pu S, Kong Q, Zheng G, Zhou D. PROteolysis TArgeting Chimeras (PROTACs) as emerging anticancer therapeutics. Oncogene 2020; 39:4909-4924. [PMID: 32475992 PMCID: PMC7319888 DOI: 10.1038/s41388-020-1336-y] [Citation(s) in RCA: 137] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/14/2020] [Accepted: 05/18/2020] [Indexed: 12/21/2022]
Abstract
Using PROteolysis TArgeting Chimeras (PROTACs) to degrade proteins that are important for tumorigenesis has emerged as a potential therapeutic strategy for cancer. PROTACs are heterobifunctional molecules consisting of one ligand for binding to a protein of interest (POI) and another to an E3 ubiquitin (E3) ligase, connected via a linker. PROTACs recruit the E3 ligase to the POI and cause proximity-induced ubiquitination and degradation of the POI by the ubiquitin proteasome system (UPS). PROTACs have been developed to degrade a variety of cancer targets with unprecedented efficacy against a multitude of tumor types. To date, most of the PROTACs developed have utilized ligands to recruit E3 ligases that are ubiquitously expressed in both tumor and normal tissues. These PROTACs can cause on-target toxicities if the POIs are not tumor-specific. Therefore, identifying and recruiting the E3 ligases that are enriched in tumors with minimal expression in normal tissues holds the potential to develop tumor-specific/selective PROTACs. In this review, we will discuss the potential of PROTACs to become anticancer therapeutics, chemical and bioinformatics approaches for PROTAC design, and safety concerns with a special focus on the development of tumor-specific/selective PROTACs. In addition, the identification of tumor types in terms of solid versus hematological malignancies that can be best targeted with PROTAC approach will be briefly discussed.
Collapse
Affiliation(s)
- Sajid Khan
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Yonghan He
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Xuan Zhang
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Yaxia Yuan
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Shaoyan Pu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Qingpeng Kong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Guangrong Zheng
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Daohong Zhou
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL, USA.
| |
Collapse
|
42
|
Foley CA, Potjewyd F, Lamb KN, James LI, Frye SV. Assessing the Cell Permeability of Bivalent Chemical Degraders Using the Chloroalkane Penetration Assay. ACS Chem Biol 2020; 15:290-295. [PMID: 31846298 DOI: 10.1021/acschembio.9b00972] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Bivalent chemical degraders provide a catalytic route to selectively degrade disease-associated proteins. By linking target-specific ligands with E3 ubiquitin ligase recruiting ligands, these compounds facilitate targeted protein ubiquitination and degradation by the proteasome. Due to the complexity of this multistep mechanism, the development of effective degrader molecules remains a difficult, lengthy, and unpredictable process. Since degraders are large heterobifunctional molecules, the efficacy of these compounds may be limited by poor cell permeability, and an efficient and reliable method to quantify the cell permeability of these compounds is lacking. Herein, we demonstrate that by the addition of a chloroalkane tag on the BRD4 specific degrader, MZ1, cell permeability can be quantified via the chloroalkane penetration assay. By extending this analysis to individual components of the degrader molecule, we have obtained structure-permeability relationships that will be informative for future degrader development, particularly as degraders move into the clinic as potential therapeutics.
Collapse
Affiliation(s)
- Caroline A. Foley
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Frances Potjewyd
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Kelsey N. Lamb
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Lindsey I. James
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Stephen V. Frye
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| |
Collapse
|
43
|
Sun X, Gao H, Yang Y, He M, Wu Y, Song Y, Tong Y, Rao Y. PROTACs: great opportunities for academia and industry. Signal Transduct Target Ther 2019; 4:64. [PMID: 31885879 PMCID: PMC6927964 DOI: 10.1038/s41392-019-0101-6] [Citation(s) in RCA: 354] [Impact Index Per Article: 70.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 11/17/2019] [Accepted: 11/21/2019] [Indexed: 02/07/2023] Open
Abstract
Although many kinds of therapies are applied in the clinic, drug-resistance is a major and unavoidable problem. Another disturbing statistic is the limited number of drug targets, which are presently only 20-25% of all protein targets that are currently being studied. Moreover, the focus of current explorations of targets are their enzymatic functions, which ignores the functions from their scaffold moiety. As a promising and appealing technology, PROteolysis TArgeting Chimeras (PROTACs) have attracted great attention both from academia and industry for finding available approaches to solve the above problems. PROTACs regulate protein function by degrading target proteins instead of inhibiting them, providing more sensitivity to drug-resistant targets and a greater chance to affect the nonenzymatic functions. PROTACs have been proven to show better selectivity compared to classic inhibitors. PROTACs can be described as a chemical knockdown approach with rapidity and reversibility, which presents new and different biology compared to other gene editing tools by avoiding misinterpretations that arise from potential genetic compensation and/or spontaneous mutations. PRTOACs have been widely explored throughout the world and have outperformed not only in cancer diseases, but also in immune disorders, viral infections and neurodegenerative diseases. Although PROTACs present a very promising and powerful approach for crossing the hurdles of present drug discovery and tool development in biology, more efforts are needed to gain to get deeper insight into the efficacy and safety of PROTACs in the clinic. More target binders and more E3 ligases applicable for developing PROTACs are waiting for exploration.
Collapse
Affiliation(s)
- Xiuyun Sun
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084 P. R. China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084 P. R. China
| | - Hongying Gao
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084 P. R. China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084 P. R. China
| | - Yiqing Yang
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084 P. R. China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084 P. R. China
| | - Ming He
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084 P. R. China
| | - Yue Wu
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084 P. R. China
| | - Yugang Song
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084 P. R. China
| | - Yan Tong
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084 P. R. China
| | - Yu Rao
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084 P. R. China
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001 China
| |
Collapse
|
44
|
Ciulli A, Farnaby W. Protein degradation for drug discovery. DRUG DISCOVERY TODAY. TECHNOLOGIES 2019; 31:1-3. [PMID: 31200853 DOI: 10.1016/j.ddtec.2019.04.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Alessio Ciulli
- Professor of Chemical & Structural Biology, School of Life Sciences, University of Dundee, Division of Biological Chemistry and Drug Discovery, James Black Centre, Dow Street, Dundee DD1 5EH, United Kingdom
| | - William Farnaby
- Professor of Chemical & Structural Biology, School of Life Sciences, University of Dundee, Division of Biological Chemistry and Drug Discovery, James Black Centre, Dow Street, Dundee DD1 5EH, United Kingdom
| |
Collapse
|