1
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Schwalm MP, Saxena K, Müller S, Knapp S. Luciferase- and HaloTag-based reporter assays to measure small-molecule-induced degradation pathway in living cells. Nat Protoc 2024:10.1038/s41596-024-00979-z. [PMID: 38637703 DOI: 10.1038/s41596-024-00979-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 01/31/2024] [Indexed: 04/20/2024]
Abstract
The rational development of small-molecule degraders (e.g., proteolysis targeting chimeras) remains a challenge as the rate-limiting steps that determine degrader efficiency are largely unknown. Standard methods in the field of targeted protein degradation mostly rely on classical, low-throughput endpoint assays such as western blots or quantitative proteomics. Here we applied NanoLuciferase- and HaloTag-based screening technologies to determine the kinetics and stability of small-molecule-induced ternary complex formation between a protein of interest and a selected E3 ligase. A collection of live-cell assays were designed to probe the most critical steps of the degradation process while minimizing the number of required expression constructs, making the proposed assay pipeline flexible and adaptable to the requirements of the users. This approach evaluates the underlying mechanism of selective target degraders and reveals the exact characteristics of the developed degrader molecules in living cells. The protocol allows scientists trained in basic cell culture and molecular biology to carry out small-molecule proximity-inducer screening via tracking of the ternary complex formation within 2 weeks of establishment, while degrader screening using the HiBiT system requires a CRISPR-Cas9 engineered cell line whose generation can take up to 3 months. After cell-line generation, degrader screening and validation can be carried out in high-throughput manner within days.
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Affiliation(s)
- Martin P Schwalm
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany.
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Frankfurt am Main, Germany.
- German Cancer Consortium (DKTK)/German Cancer Research Center (DKFZ), DTKT Site Frankfurt-Mainz, Heidelberg, Germany.
| | - Krishna Saxena
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Frankfurt am Main, Germany
| | - Susanne Müller
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Frankfurt am Main, Germany
| | - Stefan Knapp
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany.
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Frankfurt am Main, Germany.
- German Cancer Consortium (DKTK)/German Cancer Research Center (DKFZ), DTKT Site Frankfurt-Mainz, Heidelberg, Germany.
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2
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Nguyen KQT, Nguyen HH, Phung HTT, Chung KL, Vu TY. A close-up shot of protein-protein docking, from experiment to theory and reverse with the PROTAC performers. J Biomol Struct Dyn 2024:1-8. [PMID: 38284361 DOI: 10.1080/07391102.2024.2308778] [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: 08/11/2023] [Accepted: 01/14/2024] [Indexed: 01/30/2024]
Abstract
PROTACs (Proteolysis Targeting Chimeras), heterobifunctional molecules, exhibit selectivity in degrading target proteins through E3 ubiquitin ligases. Designing effective PROTACs requires a deep understanding of the intricate binding interactions in the ternary complex (POI/PROTAC/E3 ligase), crucial for efficient target protein degradation. To address this challenge, we introduce a novel computational virtual screening method that considers essential amino acid interactions between the protein of interest and the chosen E3 ligase. This approach enhances accuracy and reliability, facilitating the strategic development of potent PROTACs. Utilizing a crystallized model of the VHL:PROTAC:SMARCA2BD ternary complex (PDB: 7Z6L), we assessed the effectiveness of our method. Our study reveals that increasing the number of essential restraints between the two proteins reduces the generated docking poses, leading to closer alignment with the experimental ternary complex. Specifically, utilizing three restraints showed the closest resemblance to the published complex, highlighting crucial interactions such as an H-bond between A:Gln 89 and B:Asn 67, along with two hydrophobic interactions: A:Gly 22 with B:Arg 69 and A:Glu 37 with B:Pro 99. This resulted in a significant decrease in the mean RMSD value from 31.8 and 31.0 Å to 24.4 Å, respectively. This underscores the importance of incorporating multiple essential restraints to enhance docking accuracy. Building on this progress, we introduce a systematic approach to design potential PROTACs between the Estrogen receptor and the E3 ligase, utilizing bridging intermediates with 4, 6, or 7 carbon atoms. By providing a more accurate and efficient means of identifying optimal PROTAC candidates, this approach has the potential to accelerate the development of targeted therapies and reduce the time and costs associated with drug discovery.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Hieu Hien Nguyen
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Huong Thi Thu Phung
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Khanh Linh Chung
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Thien Y Vu
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam
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3
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Thomas K, Bouguenina H, Miller DSJ, Sialana FJ, Hayhow TG, Choudhary JS, Rossanese OW, Bellenie BR. Degradation by Design: New Cyclin K Degraders from Old CDK Inhibitors. ACS Chem Biol 2024; 19:173-184. [PMID: 38193430 PMCID: PMC10804372 DOI: 10.1021/acschembio.3c00616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/22/2023] [Accepted: 12/27/2023] [Indexed: 01/10/2024]
Abstract
Small molecules that induce protein degradation hold the potential to overcome several limitations of the currently available inhibitors. Monovalent or molecular glue degraders, in particular, enable the benefits of protein degradation without the disadvantages of high molecular weight and the resulting challenge in drug development that are associated with bivalent molecules like Proteolysis Targeting Chimeras. One key challenge in designing monovalent degraders is how to build in the degrader activity─how can we convert an inhibitor into a degrader? If degradation activity requires very specific molecular features, it will be difficult to find new degraders and challenging to optimize those degraders toward drugs. Herein, we demonstrate that an unexpectedly wide range of modifications to the degradation-inducing group of the cyclin K degrader CR8 are tolerated, including both aromatic and nonaromatic groups. We used these findings to convert the pan-CDK inhibitors dinaciclib and AT-7519 to Cyclin K degraders, leading to a novel dinaciclib-based compound with improved degradation activity compared to CR8 and confirm the mechanism of degradation. These results suggest that general design principles can be generated for the development and optimization of monovalent degraders.
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Affiliation(s)
- Katie
L. Thomas
- Centre
for Cancer Drug Discovery, The Institute
of Cancer Research, London SM2 5NG, U.K.
| | - Habib Bouguenina
- Centre
for Cancer Drug Discovery, The Institute
of Cancer Research, London SM2 5NG, U.K.
| | - Daniel S. J. Miller
- Centre
for Cancer Drug Discovery, The Institute
of Cancer Research, London SM2 5NG, U.K.
| | - Fernando J. Sialana
- Functional
Proteomics Group, The Institute of Cancer
Research, London SW3 6JB, U.K.
| | - Thomas G. Hayhow
- Oncology
R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0AA, U.K.
| | - Jyoti S. Choudhary
- Functional
Proteomics Group, The Institute of Cancer
Research, London SW3 6JB, U.K.
| | - Olivia W. Rossanese
- Centre
for Cancer Drug Discovery, The Institute
of Cancer Research, London SM2 5NG, U.K.
| | - Benjamin R. Bellenie
- Centre
for Cancer Drug Discovery, The Institute
of Cancer Research, London SM2 5NG, U.K.
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4
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Ma Z, Bolinger AA, Zhou J. RIPTACs: A groundbreaking approach to drug discovery. Drug Discov Today 2023; 28:103774. [PMID: 37734702 PMCID: PMC11144445 DOI: 10.1016/j.drudis.2023.103774] [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: 07/25/2023] [Revised: 09/04/2023] [Accepted: 09/14/2023] [Indexed: 09/23/2023]
Abstract
Regulated induced proximity targeting chimeras (RIPTACs), a new class of heterobifunctional molecules, show promise in specifically targeting and eliminating cancer cells while leaving healthy cells unharmed. As a groundbreaking drug discovery approach, RIPTACs work by forming a stable complex with two proteins, one specifically found in cancer cells (target protein, TP) and the other pan-essential for cell survival (effector protein, EP), selectively disrupting the function of the EP in cancer cells and causing cell death. Interestingly, the TPs need not be linked to disease progression, broadening the spectrum of potential drug targets. This review summarizes the discovery and recent advances of the RIPTAC strategy. Additionally, it discusses the associated opportunities and challenges as well as future perspectives in this field.
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Affiliation(s)
- Zonghui Ma
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, TX 77555, USA
| | - Andrew A Bolinger
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, TX 77555, USA
| | - Jia Zhou
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, TX 77555, USA.
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5
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Konstantinidou M, Visser EJ, Vandenboorn E, Chen S, Jaishankar P, Overmans M, Dutta S, Neitz RJ, Renslo AR, Ottmann C, Brunsveld L, Arkin MR. Structure-Based Optimization of Covalent, Small-Molecule Stabilizers of the 14-3-3σ/ERα Protein-Protein Interaction from Nonselective Fragments. J Am Chem Soc 2023; 145:20328-20343. [PMID: 37676236 PMCID: PMC10515640 DOI: 10.1021/jacs.3c05161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Indexed: 09/08/2023]
Abstract
The stabilization of protein-protein interactions (PPIs) has emerged as a promising strategy in chemical biology and drug discovery. The identification of suitable starting points for stabilizing native PPIs and their subsequent elaboration into selective and potent molecular glues lacks structure-guided optimization strategies. We have previously identified a disulfide fragment that stabilized the hub protein 14-3-3σ bound to several of its clients, including ERα and C-RAF. Here, we show the structure-based optimization of the nonselective fragment toward selective and highly potent small-molecule stabilizers of the 14-3-3σ/ERα complex. The more elaborated molecular glues, for example, show no stabilization of 14-3-3σ/C-RAF up to 150 μM compound. Orthogonal biophysical assays, including mass spectrometry and fluorescence anisotropy, were used to establish structure-activity relationships. The binding modes of 37 compounds were elucidated with X-ray crystallography, which further assisted the concomitant structure-guided optimization. By targeting specific amino acids in the 14-3-3σ/ERα interface and locking the conformation with a spirocycle, the optimized covalent stabilizer 181 achieved potency, cooperativity, and selectivity similar to the natural product Fusicoccin-A. This case study showcases the value of addressing the structure, kinetics, and cooperativity for molecular glue development.
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Affiliation(s)
- Markella Konstantinidou
- Department
of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco, California 94143, United States
| | - Emira J. Visser
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
for Complex Molecular Systems (ICMS), Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Edmee Vandenboorn
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
for Complex Molecular Systems (ICMS), Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Sheng Chen
- Department
of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco, California 94143, United States
| | - Priyadarshini Jaishankar
- Department
of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco, California 94143, United States
| | - Maurits Overmans
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
for Complex Molecular Systems (ICMS), Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Shubhankar Dutta
- Department
of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco, California 94143, United States
| | - R. Jeffrey Neitz
- Department
of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco, California 94143, United States
| | - Adam R. Renslo
- Department
of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco, California 94143, United States
| | - Christian Ottmann
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
for Complex Molecular Systems (ICMS), Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Luc Brunsveld
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
for Complex Molecular Systems (ICMS), Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Michelle R. Arkin
- Department
of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco, California 94143, United States
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6
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Teng M, Gray NS. The rise of degrader drugs. Cell Chem Biol 2023; 30:864-878. [PMID: 37494935 DOI: 10.1016/j.chembiol.2023.06.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/30/2023] [Accepted: 06/21/2023] [Indexed: 07/28/2023]
Abstract
The cancer genomics revolution has served up a plethora of promising and challenging targets for the drug discovery community. The field of targeted protein degradation (TPD) uses small molecules to reprogram the protein homeostasis system to destroy desired target proteins. In the last decade, remarkable progress has enabled the rational development of degraders for a large number of target proteins, with over 20 molecules targeting more than 12 proteins entering clinical development. While TPD has been fully credentialed by the prior development of immunomodulatory drug (IMiD) class for the treatment of multiple myeloma, the field is poised for a "Gleevec moment" in which robust clinical efficacy of a rationally developed novel degrader against a preselected target is firmly established. Here, we endeavor to provide a high-level evaluation of exciting developments in the field and comment on steps that may realize the full potential of this new therapeutic modality.
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Affiliation(s)
- Mingxing Teng
- Center for Drug Discovery, Department of Pathology & Immunology, and Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Nathanael S Gray
- Department of Chemical and Systems Biology, ChEM-H, Stanford Cancer Institute, School of Medicine, Stanford University, Stanford, CA 94305, USA.
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7
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Stein RR, Fouché M, Kearns JD, Roth HJ. A model-informed method to retrieve intrinsic from apparent cooperativity and project cellular target occupancy for ternary complex-forming compounds. RSC Chem Biol 2023; 4:512-523. [PMID: 37415863 PMCID: PMC10320841 DOI: 10.1039/d2cb00216g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 05/19/2023] [Indexed: 07/08/2023] Open
Abstract
There is an increasing interest to develop therapeutics that modulate challenging or undruggable target proteins via a mechanism that involves ternary complexes. In general, such compounds can be characterized by their direct affinities to a chaperone and a target protein and by their degree of cooperativity in the formation of the ternary complex. As a trend, smaller compounds have a greater dependency on intrinsic cooperativity to their thermodynamic stability relative to direct target (or chaperone) binding. This highlights the need to consider intrinsic cooperativity of ternary complex-forming compounds early in lead optimization, especially as they provide more control over target selectivity (especially for isoforms) and more insight into the relationship between target occupancy and target response via estimation of ternary complex concentrations. This motivates the need to quantify the natural constant of intrinsic cooperativity (α) which is generally defined as the gain (or loss) in affinity of a compound to its target in pre-bound vs. unbound state. Intrinsic cooperativities can be retrieved via a mathematical binding model from EC50 shifts of binary binding curves of the ternary complex-forming compound with either a target or chaperone relative to the same experiment but in the presence of the counter protein. In this manuscript, we present a mathematical modeling methodology that estimates the intrinsic cooperativity value from experimentally observed apparent cooperativities. This method requires only the two binary binding affinities and the protein concentrations of target and chaperone and is therefore suitable for use in early discovery therapeutic programs. This approach is then extended from biochemical assays to cellular assays (i.e., from a closed system to an open system) by accounting for differences in total ligand vs. free ligand concentrations in the calculations of ternary complex concentrations. Finally, this model is used to translate biochemical potency of ternary complex-forming compounds into expected cellular target occupancy, which could ultimately serve as a way for validation or de-validation of hypothesized biological mechanisms of action.
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Affiliation(s)
- Richard R Stein
- Novartis Institutes for BioMedical Research Basel Switzerland
| | - Marianne Fouché
- Novartis Institutes for BioMedical Research Basel Switzerland
| | | | - Hans-Joerg Roth
- Novartis Institutes for BioMedical Research Basel Switzerland
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8
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Li Q, Zhou L, Qin S, Huang Z, Li B, Liu R, Yang M, Nice EC, Zhu H, Huang C. Proteolysis-targeting chimeras in biotherapeutics: Current trends and future applications. Eur J Med Chem 2023; 257:115447. [PMID: 37229829 DOI: 10.1016/j.ejmech.2023.115447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 05/02/2023] [Accepted: 05/02/2023] [Indexed: 05/27/2023]
Abstract
The success of inhibitor-based therapeutics is largely constrained by the acquisition of therapeutic resistance, which is partially driven by the undruggable proteome. The emergence of proteolysis targeting chimera (PROTAC) technology, designed for degrading proteins involved in specific biological processes, might provide a novel framework for solving the above constraint. A heterobifunctional PROTAC molecule could structurally connect an E3 ubiquitin ligase ligand with a protein of interest (POI)-binding ligand by chemical linkers. Such technology would result in the degradation of the targeted protein via the ubiquitin-proteasome system (UPS), opening up a novel way of selectively inhibiting undruggable proteins. Herein, we will highlight the advantages of PROTAC technology and summarize the current understanding of the potential mechanisms involved in biotherapeutics, with a particular focus on its application and development where therapeutic benefits over classical small-molecule inhibitors have been achieved. Finally, we discuss how this technology can contribute to developing biotherapeutic drugs, such as antivirals against infectious diseases, for use in clinical practices.
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Affiliation(s)
- Qiong Li
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Li Zhou
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400016, PR China
| | - Siyuan Qin
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Zhao Huang
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Bowen Li
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Ruolan Liu
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, PR China
| | - Mei Yang
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Edouard C Nice
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Huili Zhu
- Department of Reproductive Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second University Hospital of Sichuan University, Chengdu, 610041, PR China.
| | - Canhua Huang
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China; School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, PR China.
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9
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Miñarro-Lleonar M, Bertran-Mostazo A, Duro J, Barril X, Juárez-Jiménez J. Lenalidomide Stabilizes Protein-Protein Complexes by Turning Labile Intermolecular H-Bonds into Robust Interactions. J Med Chem 2023; 66:6037-6046. [PMID: 37083375 PMCID: PMC10184122 DOI: 10.1021/acs.jmedchem.2c01692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
Targeted protein degradation is a promising therapeutic strategy, spearheaded by the anti-myeloma drugs lenalidomide and pomalidomide. These drugs stabilize very efficiently the complex between the E3 ligase Cereblon (CRBN) and several non-native client proteins (neo-substrates), including the transcription factors Ikaros and Aiolos and the enzyme Caseine Kinase 1α (CK1α,), resulting in their degradation. Although the structures for these complexes have been determined, there are no evident interactions that can account for the high efficiency of formation of the ternary complex. We show that lenalidomide's stabilization of the CRBN-CK1α complex is largely due to hydrophobic shielding of intermolecular hydrogen bonds. We also find a quantitative relationship between hydrogen bond robustness and binding affinities of the ternary complexes. These results pave the way to further understand cooperativity effects in drug-induced protein-protein complexes and could help in the design of improved molecular glues and more efficient protein degraders.
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Affiliation(s)
- Marina Miñarro-Lleonar
- Unitat de Fisicoquímica, Departament de Farmàcia i Tecnologia Farmacèutica, i Fisicoquímica, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona (UB), Av. Joan XXIII, 27-31, 08028 Barcelona, Spain
- Institut de Química Teòrica i Computacional (IQTC), Facultat de Química i Física, Universitat de Barcelona (UB), C. Martí i Franquès, 1, 08028 Barcelona, Spain
- Institut de Biomedicina, Facultat de Biologia, Universitat de Barcelona (UB), Av. Diagonal, 643, 08028 Barcelona, Spain
| | - Andrea Bertran-Mostazo
- Unitat de Fisicoquímica, Departament de Farmàcia i Tecnologia Farmacèutica, i Fisicoquímica, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona (UB), Av. Joan XXIII, 27-31, 08028 Barcelona, Spain
- Institut de Biomedicina, Facultat de Biologia, Universitat de Barcelona (UB), Av. Diagonal, 643, 08028 Barcelona, Spain
| | - Jorge Duro
- Unitat de Fisicoquímica, Departament de Farmàcia i Tecnologia Farmacèutica, i Fisicoquímica, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona (UB), Av. Joan XXIII, 27-31, 08028 Barcelona, Spain
- Institut de Química Teòrica i Computacional (IQTC), Facultat de Química i Física, Universitat de Barcelona (UB), C. Martí i Franquès, 1, 08028 Barcelona, Spain
| | - Xavier Barril
- Unitat de Fisicoquímica, Departament de Farmàcia i Tecnologia Farmacèutica, i Fisicoquímica, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona (UB), Av. Joan XXIII, 27-31, 08028 Barcelona, Spain
- Institut de Química Teòrica i Computacional (IQTC), Facultat de Química i Física, Universitat de Barcelona (UB), C. Martí i Franquès, 1, 08028 Barcelona, Spain
- Institut de Biomedicina, Facultat de Biologia, Universitat de Barcelona (UB), Av. Diagonal, 643, 08028 Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Pg. Lluís Companys, 23 08010 Barcelona, Spain
| | - Jordi Juárez-Jiménez
- Unitat de Fisicoquímica, Departament de Farmàcia i Tecnologia Farmacèutica, i Fisicoquímica, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona (UB), Av. Joan XXIII, 27-31, 08028 Barcelona, Spain
- Institut de Química Teòrica i Computacional (IQTC), Facultat de Química i Física, Universitat de Barcelona (UB), C. Martí i Franquès, 1, 08028 Barcelona, Spain
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10
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Zhou QQ, Xiao HT, Yang F, Wang YD, Li P, Zheng ZG. Advancing targeted protein degradation for metabolic diseases therapy. Pharmacol Res 2023; 188:106627. [PMID: 36566001 DOI: 10.1016/j.phrs.2022.106627] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/12/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022]
Abstract
The development and application of traditional drugs represented by small molecule chemical drugs and biological agents, especially inhibitors, have become the mainstream drug development. In recent years, targeted protein degradation (TPD) technology has become one of the most promising methods to remove specific disease-related proteins using cell self-destruction mechanisms. Many different TPD strategies are emerging based on the ubiquitin-proteasome system (UPS) and the autophagy-lysosomal pathway (ALP), including but not limited to proteolysis-targeting chimeras (PROTAC), molecular glues (MG), lysosome targeting chimeras (LYTAC), chaperone-mediated autophagy (CMA)-targeting chimeras, autophagy-targeting chimera (AUTAC), autophagosome-tethering compound (ATTEC), and autophagy-targeting chimera (AUTOTAC). The advent of targeted degradation technology can change most protein targets in human cells from undruggable to druggable, greatly expanding the therapeutic prospect of refractory diseases such as metabolic syndrome. Here, we summarize the latest progress of major TPD technologies, especially in metabolic syndrome and look forward to providing new insights for drug discovery.
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Affiliation(s)
- Qian-Qian Zhou
- State Key Laboratory of Natural Medicines, Department of Pharmacognosy, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 210009, Nanjing, Jiangsu, China
| | - Hai-Tao Xiao
- State Key Laboratory of Natural Medicines, Department of Pharmacognosy, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 210009, Nanjing, Jiangsu, China
| | - Fan Yang
- State Key Laboratory of Natural Medicines, Department of Pharmacognosy, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 210009, Nanjing, Jiangsu, China
| | - Yong-Dan Wang
- State Key Laboratory of Natural Medicines, Department of Pharmacognosy, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 210009, Nanjing, Jiangsu, China
| | - Ping Li
- State Key Laboratory of Natural Medicines, Department of Pharmacognosy, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 210009, Nanjing, Jiangsu, China
| | - Zu-Guo Zheng
- State Key Laboratory of Natural Medicines, Department of Pharmacognosy, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 210009, Nanjing, Jiangsu, China.
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11
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Raina K, Forbes CD, Stronk R, Rappi JP, Eastman KJ, Gerritz SW, Yu X, Li H, Bhardwaj A, Forgione M, Hundt A, King MP, Posner ZM, Denny A, McGovern A, Puleo DE, Garvin E, Chenard R, Zaware N, Mousseau JJ, Macaluso J, Martin M, Bassoli K, Jones K, Garcia M, Howard K, Smith LM, Chen JM, De Leon CA, Hines J, Kayser-Bricker KJ, Crews CM. Regulated Induced Proximity Targeting Chimeras (RIPTACs): a Novel Heterobifunctional Small Molecule Therapeutic Strategy for Killing Cancer Cells Selectively. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.01.522436. [PMID: 36711980 PMCID: PMC9881854 DOI: 10.1101/2023.01.01.522436] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
While specific cell signaling pathway inhibitors have yielded great success in oncology, directly triggering cancer cell death is one of the great drug discovery challenges facing biomedical research in the era of precision oncology. Attempts to eradicate cancer cells expressing unique target proteins, such as antibody-drug conjugates (ADCs), T-cell engaging therapies, and radiopharmaceuticals have been successful in the clinic, but they are limited by the number of targets given the inability to target intracellular proteins. More recently, heterobifunctional small molecules such as Proteolysis Targeting Chimera (PROTACs) have paved the way for protein proximity inducing therapeutic modalities. Here, we describe a proof-of-concept study using novel heterobifunctional small molecules called Regulated Induced Proximity Targeting Chimeras or RIPTACs, which elicit a stable ternary complex between a target protein selectively expressed in cancer tissue and a pan-expressed protein essential for cell survival. The resulting cooperative protein:protein interaction (PPI) abrogates the function of the essential protein, thus leading to cell death selectively in cells expressing the target protein. This approach not only opens new target space by leveraging differentially expressed intracellular proteins but also has the advantage of not requiring the target to be a driver of disease. Thus, RIPTACs can address non-target mechanisms of resistance given that cell killing is driven by inactivation of the essential protein. Using the HaloTag7-FKBP model system as a target protein, we describe RIPTACs that incorporate a covalent or non-covalent target ligand connected via a linker to effector ligands such as JQ1 (BRD4), BI2536 (PLK1), or multi-CDK inhibitors such as TMX3013 or dinaciclib. We show that these RIPTACs exhibit positive co-operativity, accumulate selectively in cells expressing HaloTag7-FKBP, form stable target:RIPTAC:effector trimers in cells, and induce an anti-proliferative response in target-expressing cells. We propose that RIPTACs are a novel heterobifunctional therapeutic modality to treat cancers that are known to selectively express a specific intracellular protein.
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Affiliation(s)
- Kanak Raina
- co-corresponding authors
- Halda Therapeutics OpCo Inc, New Haven CT USA
| | | | | | | | | | | | - Xinheng Yu
- Halda Therapeutics OpCo Inc, New Haven CT USA
| | - Hao Li
- Halda Therapeutics OpCo Inc, New Haven CT USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Kelli Jones
- Halda Therapeutics OpCo Inc, New Haven CT USA
| | | | | | | | | | - Cesar A De Leon
- Department of Molecular, Cellular, & Developmental Biology, Yale University New Haven CT USA
| | - John Hines
- Department of Molecular, Cellular, & Developmental Biology, Yale University New Haven CT USA
| | | | - Craig M Crews
- co-corresponding authors
- Department of Molecular, Cellular, & Developmental Biology, Yale University New Haven CT USA
- Department of Pharmacology, Yale University New Haven CT USA
- Department of Chemistry, Yale University New Haven CT USA
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12
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Nussinov R, Zhang M, Maloney R, Liu Y, Tsai CJ, Jang H. Allostery: Allosteric Cancer Drivers and Innovative Allosteric Drugs. J Mol Biol 2022; 434:167569. [PMID: 35378118 PMCID: PMC9398924 DOI: 10.1016/j.jmb.2022.167569] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/11/2022] [Accepted: 03/25/2022] [Indexed: 01/12/2023]
Abstract
Here, we discuss the principles of allosteric activating mutations, propagation downstream of the signals that they prompt, and allosteric drugs, with examples from the Ras signaling network. We focus on Abl kinase where mutations shift the landscape toward the active, imatinib binding-incompetent conformation, likely resulting in the high affinity ATP outcompeting drug binding. Recent pharmacological innovation extends to allosteric inhibitor (GNF-5)-linked PROTAC, targeting Bcr-Abl1 myristoylation site, and broadly, allosteric heterobifunctional degraders that destroy targets, rather than inhibiting them. Designed chemical linkers in bifunctional degraders can connect the allosteric ligand that binds the target protein and the E3 ubiquitin ligase warhead anchor. The physical properties and favored conformational state of the engineered linker can precisely coordinate the distance and orientation between the target and the recruited E3. Allosteric PROTACs, noncompetitive molecular glues, and bitopic ligands, with covalent links of allosteric ligands and orthosteric warheads, increase the effective local concentration of productively oriented and placed ligands. Through covalent chemical or peptide linkers, allosteric drugs can collaborate with competitive drugs, degrader anchors, or other molecules of choice, driving innovative drug discovery.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Mingzhen Zhang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA
| | - Ryan Maloney
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA
| | - Yonglan Liu
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA
| | - Chung-Jung Tsai
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA
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13
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Domostegui A, Nieto-Barrado L, Perez-Lopez C, Mayor-Ruiz C. Chasing molecular glue degraders: screening approaches. Chem Soc Rev 2022; 51:5498-5517. [PMID: 35723413 DOI: 10.1039/d2cs00197g] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Protein-protein interactions (PPIs) govern all biological processes. Some small molecules modulate PPIs through induced protein proximity. In particular, molecular glue degraders are monovalent compounds that orchestrate interactions between a target protein and an E3 ubiquitin ligase, prompting the proteasomal degradation of the former. This and other pharmacological strategies of targeted protein degradation (e.g. proteolysis-targeting chimeras - PROTACs) overcome some limitations of traditional occupancy-based therapeutics. Here, we provide an overview of the "molecular glue" concept, with a special focus on natural and synthetic inducers of proximity to E3s. We then briefly highlight the serendipitous discoveries of some clinical and preclinical molecular glue degraders, and discuss the first examples of intentional discoveries. Specifically, we outline the different screening strategies reported in this rapidly evolving arena and our thoughts on future perspectives. By mastering the ability to influence PPIs, molecular glue degraders can induce the degradation of unligandable proteins, thus providing an exciting path forward to broaden the targetable proteome.
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Affiliation(s)
- Ana Domostegui
- IRB Barcelona - Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac, 10, 08028 Barcelona, Spain.
| | - Luis Nieto-Barrado
- IRB Barcelona - Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac, 10, 08028 Barcelona, Spain.
| | - Carles Perez-Lopez
- IRB Barcelona - Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac, 10, 08028 Barcelona, Spain.
| | - Cristina Mayor-Ruiz
- IRB Barcelona - Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac, 10, 08028 Barcelona, Spain.
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14
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Soini L, Leysen S, Davis J, Ottmann C. Molecular glues to stabilise protein-protein interactions. Curr Opin Chem Biol 2022; 69:102169. [PMID: 35749929 DOI: 10.1016/j.cbpa.2022.102169] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 04/21/2022] [Accepted: 05/11/2022] [Indexed: 11/27/2022]
Abstract
Targeting protein-protein interactions (PPIs) has become a common approach to tackle various diseases whose pathobiology is driven by their mis-regulation in important signalling pathways. Modulating PPIs has tremendous untapped therapeutic potential and different approaches can be used to modulate PPIs. Initially, therapeutic effects were mostly sought by inhibiting PPIs. However, by gaining insight in the mode of action of certain therapeutic compounds, it became clear that stabilising (i.e. enhancing) PPIs can also be useful. The latter strategy is recently gaining a lot of attention, as stabilising physiologic, or even inducing novel interactions of a target protein with E3 ubiquitin ligases forms the basis of the targeted protein degradation (TPD) approach. An emerging additional example for drug discovery based on PPI stabilisation are the 14-3-3 proteins, a family of regulatory proteins, which engages in many protein-protein interactions, some of which might become therapeutical targets.
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Affiliation(s)
- Lorenzo Soini
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands; Department of Structural Biology and Biophysics, UCB Biopharma UK, Slough, UK
| | - Seppe Leysen
- Department of Structural Biology and Biophysics, UCB Biopharma UK, Slough, UK
| | - Jeremy Davis
- Department of Chemistry, UCB Biopharma UK, Slough, UK.
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands.
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15
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Abstract
AbstractThe druggable genome is limited by structural features that can be targeted by small molecules in disease-relevant proteins. While orthosteric and allosteric protein modulators have been well studied, they are limited to antagonistic/agonistic functions. This approach to protein modulation leaves many disease-relevant proteins as undruggable targets. Recently, protein-protein interaction modulation has emerged as a promising therapeutic field for previously undruggable protein targets. Molecular glues and heterobifunctional degraders such as PROTACs can facilitate protein interactions and bring the proteasome into proximity to induce targeted protein degradation. In this review, we discuss the function and rational design of molecular glues, heterobifunctional degraders, and hydrophobic tag degraders. We also review historic and novel molecular glues and targets and discuss the challenges and opportunities in this new therapeutic field.
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16
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Richardson PG, Mateos MV, Vangsted AJ, Ramasamy K, Abildgaard N, Ho PJ, Quach H, Bahlis NJ. The role of E3 ubiquitin ligase in multiple myeloma: potential for cereblon E3 ligase modulators in the treatment of relapsed/refractory disease. Expert Rev Proteomics 2022; 19:235-246. [PMID: 36342226 DOI: 10.1080/14789450.2022.2142564] [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: 11/09/2022]
Abstract
INTRODUCTION Insights into the mechanisms of protein homeostasis and proteasomal degradation have led to new strategies of redirecting the ubiquitin-proteasome system (UPS) to reduce or eliminate proteins or survival factors key to malignant pathobiology, multiple myeloma (MM) in particular. These strategies have enabled researchers to target proteins that were previously considered difficult to modulate by pharmacological means. AREAS COVERED This review provides a brief overview of UPS biology, particularly the role of the CRL4CRBN E3 ubiquitin ligase complex, and summarizes current strategies for co-opting the UPS, including CELMoD compounds, SNIPERs, PROTACs, and degronimids. A detailed discussion is provided on lead CELMoD compounds iberdomide and mezigdomide, which are currently being evaluated in clinical trials in patients with MM. EXPERT OPINION Since a high proportion of patients develop drug resistance, it is vital to have novel therapeutic agents for treating relapsed patients with MM more effectively. It is encouraging that the expanding pathophysiological insight into cellular signaling pathways in MM increasingly translates into the development of novel therapeutic agents such as targeted protein degraders. This holds promise for improving outcomes in MM and beyond.
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Affiliation(s)
- Paul G Richardson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | - Karthik Ramasamy
- Department of Clinical Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Niels Abildgaard
- Hematology Research Unit, Department of Hematology, Odense University Hospital, Odense, Denmark; and Department of Clinical Research.,Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - P Joy Ho
- Institute of Haematology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia.,Sydney Medical School, University of Sydney, Camperdown, NSW, Australia
| | - Hang Quach
- Department of Haematology, St Vincent's Hospital, Melbourne, Australia
| | - Nizar J Bahlis
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB, Canada
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17
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Cowan AD, Ciulli A. Driving E3 Ligase Substrate Specificity for Targeted Protein Degradation: Lessons from Nature and the Laboratory. Annu Rev Biochem 2022; 91:295-319. [PMID: 35320687 DOI: 10.1146/annurev-biochem-032620-104421] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Methods to direct the degradation of protein targets with proximity-inducing molecules that coopt the cellular degradation machinery are advancing in leaps and bounds, and diverse modalities are emerging. The most used and well-studied approach is to hijack E3 ligases of the ubiquitin-proteasome system. E3 ligases use specific molecular recognition to determine which proteins in the cell are ubiquitinated and degraded. This review focuses on the structural determinants of E3 ligase recruitment of natural substrates and neo-substrates obtained through monovalent molecular glues and bivalent proteolysis-targeting chimeras. We use structures to illustrate the different types of substrate recognition and assess the basis for neo-protein-protein interactions in ternary complex structures. The emerging structural and mechanistic complexity is reflective of the diverse physiological roles of protein ubiquitination. This molecular insight is also guiding the application of structure-based design approaches to the development of new and existing degraders as chemical tools and therapeutics. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Angus D Cowan
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, United Kingdom;
| | - Alessio Ciulli
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, United Kingdom;
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18
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Yamanaka S, Horiuchi Y, Matsuoka S, Kido K, Nishino K, Maeno M, Shibata N, Kosako H, Sawasaki T. A proximity biotinylation-based approach to identify protein-E3 ligase interactions induced by PROTACs and molecular glues. Nat Commun 2022; 13:183. [PMID: 35013300 PMCID: PMC8748630 DOI: 10.1038/s41467-021-27818-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 12/02/2021] [Indexed: 12/24/2022] Open
Abstract
Proteolysis-targeting chimaeras (PROTACs) as well as molecular glues such as immunomodulatory drugs (IMiDs) and indisulam are drugs that induce interactions between substrate proteins and an E3 ubiquitin ligases for targeted protein degradation. Here, we develop a workflow based on proximity-dependent biotinylation by AirID to identify drug-induced neo-substrates of the E3 ligase cereblon (CRBN). Using AirID-CRBN, we detect IMiD-dependent biotinylation of CRBN neo-substrates in vitro and identify biotinylated peptides of well-known neo-substrates by mass spectrometry with high specificity and selectivity. Additional analyses reveal ZMYM2 and ZMYM2-FGFR1 fusion protein-responsible for the 8p11 syndrome involved in acute myeloid leukaemia-as CRBN neo-substrates. Furthermore, AirID-DCAF15 and AirID-CRBN biotinylate neo-substrates targeted by indisulam and PROTACs, respectively, suggesting that this approach has the potential to serve as a general strategy for characterizing drug-inducible protein-protein interactions in cells.
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Affiliation(s)
- Satoshi Yamanaka
- Division of Cell-Free Sciences, Proteo-Science Center, Ehime University, Matsuyama, 790-8577, Japan
| | - Yuto Horiuchi
- Division of Cell-Free Sciences, Proteo-Science Center, Ehime University, Matsuyama, 790-8577, Japan
| | - Saya Matsuoka
- Division of Cell-Free Sciences, Proteo-Science Center, Ehime University, Matsuyama, 790-8577, Japan
| | - Kohki Kido
- Division of Cell-Free Sciences, Proteo-Science Center, Ehime University, Matsuyama, 790-8577, Japan
| | - Kohei Nishino
- Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Tokushima University, Tokushima, 770-8503, Japan
| | - Mayaka Maeno
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Nagoya, 466-8555, Japan
| | - Norio Shibata
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Nagoya, 466-8555, Japan
| | - Hidetaka Kosako
- Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Tokushima University, Tokushima, 770-8503, Japan
| | - Tatsuya Sawasaki
- Division of Cell-Free Sciences, Proteo-Science Center, Ehime University, Matsuyama, 790-8577, Japan.
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19
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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: 88] [Impact Index Per Article: 29.3] [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.
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20
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St-Cyr D, Ceccarelli DF, Orlicky S, van der Sloot AM, Tang X, Kelso S, Moore S, James C, Posternak G, Coulombe-Huntington J, Bertomeu T, Marinier A, Sicheri F, Tyers M. Identification and optimization of molecular glue compounds that inhibit a noncovalent E2 enzyme-ubiquitin complex. SCIENCE ADVANCES 2021; 7:eabi5797. [PMID: 34705497 PMCID: PMC10763754 DOI: 10.1126/sciadv.abi5797] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 09/04/2021] [Indexed: 06/13/2023]
Abstract
Pharmacological control of the ubiquitin-proteasome system (UPS) is of intense interest in drug discovery. Here, we report the development of chemical inhibitors of the ubiquitin-conjugating (E2) enzyme CDC34A (also known as UBE2R1), which donates activated ubiquitin to the cullin-RING ligase (CRL) family of ubiquitin ligase (E3) enzymes. A FRET-based interaction assay was used to screen for novel compounds that stabilize the noncovalent complex between CDC34A and ubiquitin, and thereby inhibit the CDC34A catalytic cycle. An isonipecotamide hit compound was elaborated into analogs with ~1000-fold increased potency in stabilizing the CDC34A-ubiquitin complex. These analogs specifically inhibited CDC34A-dependent ubiquitination in vitro and stabilized an E2~ubiquitin thioester reaction intermediate in cells. The x-ray crystal structure of a CDC34A-ubiquitin-inhibitor complex uncovered the basis for analog structure-activity relationships. The development of chemical stabilizers of the CDC34A-ubiquitin complex illustrates a general strategy for de novo discovery of molecular glue compounds that stabilize weak protein interactions.
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Affiliation(s)
- Daniel St-Cyr
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Québec H3T 1J4, Canada
| | - Derek F. Ceccarelli
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Stephen Orlicky
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Almer M. van der Sloot
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Québec H3T 1J4, Canada
| | - Xiaojing Tang
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Susan Kelso
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Susan Moore
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Québec H3T 1J4, Canada
| | - Clint James
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Québec H3T 1J4, Canada
| | - Ganna Posternak
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Jasmin Coulombe-Huntington
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Québec H3T 1J4, Canada
| | - Thierry Bertomeu
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Québec H3T 1J4, Canada
| | - Anne Marinier
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Québec H3T 1J4, Canada
- Department of Chemistry, University of Montreal, Montreal, Québec H3C 3J7, Canada
| | - Frank Sicheri
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Mike Tyers
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Québec H3T 1J4, Canada
- Department of Medicine, University of Montreal, Montreal, Québec H3C 3J7, Canada
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21
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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: 247] [Impact Index Per Article: 82.3] [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.
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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.
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22
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Soini L, Redhead M, Westwood M, Leysen S, Davis J, Ottmann C. Identification of molecular glues of the SLP76/14-3-3 protein-protein interaction. RSC Med Chem 2021; 12:1555-1564. [PMID: 34667951 PMCID: PMC8459327 DOI: 10.1039/d1md00172h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/01/2021] [Indexed: 12/12/2022] Open
Abstract
The stabilisation of protein-protein interactions (PPIs) through molecular glues is a novel and promising approach in drug discovery. In stark contrast to research in protein-protein inhibition the field of stabilisation remains underdeveloped with comparatively few examples of small-molecule stabilisers of PPIs reported to date. At the same time identifying molecular glues has received recent sustained interest, especially in the fields of targeted protein degradation and 14-3-3 PPIs. The hub-protein 14-3-3 has a broad interactome with more than 500 known protein partners which presents a great opportunity for therapeutic intervention. In this study we have developed an HTRF assay suitable for HTS of the 14-3-3/SLP76 PPI and have completed a proof of concept screen against a chemically diverse library of 20 K molecules. The adaptor protein SLP76 has been reported to interact with 14-3-3 proteins downstream of the TCR playing an important role in mediating its own proteasomal degradation. We believe that stabilisation of this PPI could be exploited to potentiate degradation of SLP76 and therefore inhibit TCR signalling. This would represent an interesting alternative to other approaches in the field of targeted protein degradation. Here we disclose 16 novel stabilisers of the 14-3-3/SLP76 PPI across multiple different chemotypes. Based on the early results presented here we would recommend this approach to find molecular glues with broad applicability in the field of 14-3-3 PPIs.
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Affiliation(s)
- Lorenzo Soini
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology Eindhoven The Netherlands .,Department of Chemistry, UCB Celltech Slough UK
| | - Martin Redhead
- Exscientia Ltd, Schrodinger Building, Oxford Science Park Oxford OX44GE UK
| | - Marta Westwood
- Structural Biology, Discovery, Charles River, Chesterford Research Park UK
| | - Seppe Leysen
- Department of Structural Biology and Biophysics, UCB Celltech Slough UK
| | | | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology Eindhoven The Netherlands
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23
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Dong G, Ding Y, He S, Sheng C. Molecular Glues for Targeted Protein Degradation: From Serendipity to Rational Discovery. J Med Chem 2021; 64:10606-10620. [PMID: 34319094 DOI: 10.1021/acs.jmedchem.1c00895] [Citation(s) in RCA: 138] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Targeted protein degradation is a promising area in the discovery and development of innovative therapeutics. Molecular glues mediate proximity-induced protein degradation and have intrinsic advantages over heterobifunctional proteolysis-targeting chimeras, including unprecedented mechanisms, distinct biological activities, and favorable physicochemical properties. Classical molecular glue degraders have been identified serendipitously, but rational discovery and design strategies are emerging rapidly. In this review, we aim to highlight the recent advances in molecular glues for targeted protein degradation and discuss the challenges in developing molecular glues into therapeutic agents. In particular, discovery strategies, action mechanisms, and representative case studies will be addressed.
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Affiliation(s)
- Guoqiang Dong
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, China
| | - Yu Ding
- Neurology Department at Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, School of Life Sciences, Fudan University, 220 Handan Road, Shanghai 200433, China
| | - Shipeng He
- Institute of Translational Medicine, Shanghai University, 99 Shangda Road, Shanghai 200444, China
| | - Chunquan Sheng
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, China
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24
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Wang L, Diwu W, Tan N, Wang H, Hu J, Xu B, Wang X. Pathway-based protein-protein association network to explore mechanism of α-glucosidase inhibitors from Scutellaria baicalensis Georgi against type 2 diabetes. IET Syst Biol 2021; 15:126-135. [PMID: 33900023 PMCID: PMC8675860 DOI: 10.1049/syb2.12019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 03/28/2021] [Accepted: 04/08/2021] [Indexed: 11/20/2022] Open
Abstract
Natural products have been widely used in the treatment of type 2 diabetes (T2D). However, their mechanisms are often obscured due to multi-components and multi-targets. The authors constructed a pathway-based protein-protein association (PPA) network for target proteins of 13 α-glucosidase inhibitors (AGIs) identified from Scutellaria baicalensis Georgi (SBG), designed to explore the underlying mechanisms. This network contained 118 nodes and 1167 connections. An uneven degree distribution and small-world property were observed, characterised by high clustering coefficient and short average path length. The PPA network had an inherent hierarchy as C(k)∼k-0.71 . It also exhibited potential weak disassortative mixing pattern, coupled with a decreased function Knn (k) and negative value of assortativity coefficient. These properties indicated that a few nodes were crucial to the network. PGH2, GNAS, MAPK1, MAPK3, PRKCA, and MAOA were then identified as key targets with the highest degree values and centrality indices. Additionally, a core subnetwork showed that chrysin, 5,8,2'-trihydroxy-7-methoxyflavone, and wogonin were the main active constituents of these AGIs, and that the serotonergic synapse pathway was the critical pathway for SBG against T2D. The application of a pathway-based protein-protein association network provides a novel strategy to explore the mechanisms of natural products on complex diseases.
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Affiliation(s)
- Le Wang
- Key Laboratory of PhytochemistryCollege of Chemistry and Chemical EngineeringBaoji University of Arts and SciencesBaojiChina
| | - Wenbo Diwu
- Key Laboratory of PhytochemistryCollege of Chemistry and Chemical EngineeringBaoji University of Arts and SciencesBaojiChina
| | - Nana Tan
- Key Laboratory of PhytochemistryCollege of Chemistry and Chemical EngineeringBaoji University of Arts and SciencesBaojiChina
| | - Huan Wang
- College of Computer Science and TechnologyBaoji University of Arts and SciencesBaojiChina
| | - Jingbo Hu
- College of Electronic and Electrical Engineering, College of Chemistry and Chemical EngineeringBaoji University of Arts and SciencesBaojiChina
| | - Bailu Xu
- Key Laboratory of PhytochemistryCollege of Chemistry and Chemical EngineeringBaoji University of Arts and SciencesBaojiChina
| | - Xiaoling Wang
- Key Laboratory of PhytochemistryCollege of Chemistry and Chemical EngineeringBaoji University of Arts and SciencesBaojiChina
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25
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Izert MA, Klimecka MM, Górna MW. Applications of Bacterial Degrons and Degraders - Toward Targeted Protein Degradation in Bacteria. Front Mol Biosci 2021; 8:669762. [PMID: 34026843 PMCID: PMC8138137 DOI: 10.3389/fmolb.2021.669762] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 04/15/2021] [Indexed: 12/28/2022] Open
Abstract
A repertoire of proteolysis-targeting signals known as degrons is a necessary component of protein homeostasis in every living cell. In bacteria, degrons can be used in place of chemical genetics approaches to interrogate and control protein function. Here, we provide a comprehensive review of synthetic applications of degrons in targeted proteolysis in bacteria. We describe recent advances ranging from large screens employing tunable degradation systems and orthogonal degrons, to sophisticated tools and sensors for imaging. Based on the success of proteolysis-targeting chimeras as an emerging paradigm in cancer drug discovery, we discuss perspectives on using bacterial degraders for studying protein function and as novel antimicrobials.
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Affiliation(s)
| | | | - Maria Wiktoria Górna
- Structural Biology Group, Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland
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26
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Bond MJ, Crews CM. Proteolysis targeting chimeras (PROTACs) come of age: entering the third decade of targeted protein degradation. RSC Chem Biol 2021; 2:725-742. [PMID: 34212149 PMCID: PMC8190915 DOI: 10.1039/d1cb00011j] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 03/11/2021] [Indexed: 12/12/2022] Open
Abstract
With the discovery of PROteolysis TArgeting Chimeras (PROTACs) twenty years ago, targeted protein degradation (TPD) has changed the landscape of drug development. PROTACs have evolved from cell-impermeable peptide-small molecule chimeras to orally bioavailable clinical candidate drugs that degrade oncogenic proteins in humans. As we move into the third decade of TPD, the pace of discovery will only accelerate. Improved technologies are enabling the development of ligands for "undruggable" proteins and the recruitment of new E3 ligases. Moreover, enhanced computing power will expedite identification of active degraders. Here we discuss the strides made in these areas and what advances we can look forward to as the next decade in this exciting field begins.
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Affiliation(s)
- Michael J Bond
- Department of Pharmacology, Yale University New Haven CT 06511 USA
| | - Craig M Crews
- Department of Pharmacology, Yale University New Haven CT 06511 USA
- Department of Molecular, Cellular, and Developmental Biology, Yale University New Haven CT 06511 USA
- Department of Chemistry, Yale University New Haven CT 06511 USA
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27
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Kastl JM, Davies G, Godsman E, Holdgate GA. Small-Molecule Degraders beyond PROTACs-Challenges and Opportunities. SLAS DISCOVERY 2021; 26:524-533. [PMID: 33632029 DOI: 10.1177/2472555221991104] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Targeted protein degradation (TPD) is a recent strategy, utilizing the cell's proteostasis machinery to deplete specific proteins. This represents a paradigm shift in early drug discovery, away from occupancy-driven to event-driven mechanisms.Recent efforts have focused on the development of proteolysis-targeting chimeras (PROTACs). These heterobifunctional molecules combine a target-specific binding moiety linked to an E3 ligase ligand and trigger selective ubiquitination of the target protein, marking it for proteasomal degradation. While these molecules can be highly efficacious, they generally have unfavorable physicochemical properties due to their large size.In contrast, smaller molecules that induce degradation could represent an attractive, simple option to overcoming the limitations of both traditional modulators and PROTACs. These molecules may have a range of mechanisms: recruitment of an E3 ligase (molecular glues), introduction of hydrophobic areas, or inducing local unfolding, each of which triggers degradation.We recently completed a high-throughput screen of 111,000 compounds in a cellular HiBiT assay in an effort to identify such molecules. Preliminary analysis indicates that we have been able to identify alternative small-molecule degraders. We highlight methods for triage, characterization, selectivity, and mode of action. In summary, we believe that these types of small-molecule degraders, which may possibly have more acceptable physicochemical properties than the inherently larger heterobifunctional molecules, are an exciting approach for inducing TPD, and we illustrate that a general screening approach can be successful in identifying useful start points for developing such molecules.
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Affiliation(s)
- Johanna M Kastl
- Hit Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Alderley Park, UK
| | - Gareth Davies
- Hit Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Alderley Park, UK
| | - Eleanor Godsman
- Hit Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Alderley Park, UK
| | - Geoffrey A Holdgate
- Hit Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Alderley Park, UK
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28
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Zinn N, Werner T, Doce C, Mathieson T, Boecker C, Sweetman G, Fufezan C, Bantscheff M. Improved Proteomics-Based Drug Mechanism-of-Action Studies Using 16-Plex Isobaric Mass Tags. J Proteome Res 2021; 20:1792-1801. [PMID: 33621079 DOI: 10.1021/acs.jproteome.0c00900] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Multiplexed quantitative proteomics enabled complex workflows to study the mechanisms by which small molecule drugs interact with the proteome such as thermal proteome profiling (TPP) or multiplexed proteome dynamics profiling (mPDP). TPP measures changes in protein thermal stability in response to drug treatment and thus informs on direct targets and downstream regulation events, while the mPDP approach enables the discovery of regulated protein synthesis and degradation events caused by small molecules and other perturbations. The isobaric mass tags available for multiplexed proteomics have thus far limited the efficiency and sensitivity by which such experiments could be performed. Here we evaluate a recent generation of 16-plex isobaric mass tags and demonstrate the sensitive and time efficient identification of Staurosporine targets in HepG2 cell extracts by recording full thermal denaturation/aggregation profiles of vehicle and compound treated samples in a single mass spectrometry experiment. In 2D-TPP experiments, isothermal titration over seven concentrations per temperature enabled comprehensive selectivity profiling of Staurosporine with EC50 values for kinase targets tightly matching to the kinobeads gold standard assay. Finally, we demonstrate time and condition-based multiplexing of dynamic SILAC labeling experiments to delineate proteome-wide effects of the molecular glue Indisulam on synthesis and degradation rates.
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Affiliation(s)
- Nico Zinn
- Cellzome GmbH, a GSK Company, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Thilo Werner
- Cellzome GmbH, a GSK Company, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Carola Doce
- Cellzome GmbH, a GSK Company, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Toby Mathieson
- Cellzome GmbH, a GSK Company, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Christine Boecker
- Cellzome GmbH, a GSK Company, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Gavain Sweetman
- Cellzome GmbH, a GSK Company, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Christian Fufezan
- Cellzome GmbH, a GSK Company, Meyerhofstr. 1, 69117 Heidelberg, Germany.,Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, 69120 Heidelberg, Germany
| | - Marcus Bantscheff
- Cellzome GmbH, a GSK Company, Meyerhofstr. 1, 69117 Heidelberg, Germany
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29
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Fuchs O, Bokorova R. Preclinical Studies of PROTACs in Hematological Malignancies. Cardiovasc Hematol Disord Drug Targets 2021; 21:7-22. [PMID: 33687890 DOI: 10.2174/1871529x21666210308111546] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 01/01/2021] [Accepted: 01/23/2021] [Indexed: 06/12/2023]
Abstract
Incorrectly expressed or mutated proteins associated with hematologic malignancies have been generally targeted by chemotherapy using small-molecule inhibitors or monoclonal antibodies. But the majority of these intracellular proteins are without active sites and antigens. PROTACs, proteolysis targeting chimeras, are bifunctional molecules designed to polyubiquitinate and degrade specific pathological proteins of interest (POIs) by hijacking the activity of E3-ubiquitin ligases for POI polyubiquitination and subsequent degradation by the proteasome. This strategy utilizes the ubiquitin-proteasome system for the degradation of specific proteins in the cell. In many cases, including hematologic malignancies, inducing protein degradation as a therapeutic strategy offers therapeutic benefits over classical enzyme inhibition connected with resistance to inhibitors. Limitations of small-molecule inhibitors are shown. PROTACs can polyubiquitinate and mark for degradation of "undruggable"proteins, e.g. transcription factor STAT3 and scaffold proteins. Today, this technology is used in preclinical studies in various hematologic malignancies, mainly for targeting drug-resistant bromodomain and extraterminal proteins and Bruton tyrosine kinase. Several mechanisms limiting selectivity and safety of PROTAC molecules function are also discussed.
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Affiliation(s)
- Ota Fuchs
- Department of Genomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Radka Bokorova
- Department of Genomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
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30
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Casement R, Bond A, Craigon C, Ciulli A. Mechanistic and Structural Features of PROTAC Ternary Complexes. Methods Mol Biol 2021; 2365:79-113. [PMID: 34432240 DOI: 10.1007/978-1-0716-1665-9_5] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The rapid and ever-growing advancements from within the field of proteolysis-targeting chimeras (PROTAC)-induced protein degradation have driven considerable development to gain a deeper understanding of their mode of action. The ternary complex formed by PROTACs with their target protein and E3 ubiquitin ligase is the key species in their substoichiometric catalytic mechanism. Here, we describe the theoretical framework that underpins ternary complexes, including a current understanding of the three-component binding model, cooperativity, hook effect and structural considerations. We discuss in detail the biophysical methods used to interrogate ternary complex formation in vitro, including X-ray crystallography, AlphaLISA, FRET, FP, ITC and SPR. Finally, we provide detailed ITC methods and discuss approaches to assess binary and ternary target engagement, target ubiquitination and degradation that can be used to obtain a more holistic understanding of the mode of action within a cellular environment.
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Affiliation(s)
- Ryan Casement
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, Scotland, UK
| | - Adam Bond
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, Scotland, UK
| | - Conner Craigon
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, Scotland, UK
| | - Alessio Ciulli
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, Scotland, UK.
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31
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Miller MA, Sletten EM. Perfluorocarbons in Chemical Biology. Chembiochem 2020; 21:3451-3462. [PMID: 32628804 PMCID: PMC7736518 DOI: 10.1002/cbic.202000297] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/03/2020] [Indexed: 01/10/2023]
Abstract
Perfluorocarbons, saturated carbon chains in which all the hydrogen atoms are replaced with fluorine, form a separate phase from both organic and aqueous solutions. Though perfluorinated compounds are not found in living systems, they can be used to modify biomolecules to confer orthogonal behavior within natural systems, such as improved stability, engineered assembly, and cell-permeability. Perfluorinated groups also provide handles for purification, mass spectrometry, and 19 F NMR studies in complex environments. Herein, we describe how the unique properties of perfluorocarbons have been employed to understand and manipulate biological systems.
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Affiliation(s)
- Margeaux A Miller
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E Young Dr E, Los Angeles, CA, 90095, USA
| | - Ellen M Sletten
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E Young Dr E, Los Angeles, CA, 90095, USA
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32
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Leissing TM, Luh LM, Cromm PM. Structure driven compound optimization in targeted protein degradation. DRUG DISCOVERY TODAY. TECHNOLOGIES 2020; 37:73-82. [PMID: 34895657 DOI: 10.1016/j.ddtec.2020.11.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/22/2020] [Accepted: 11/23/2020] [Indexed: 06/14/2023]
Abstract
Small molecule induced protein degradation has created tremendous excitement in drug discovery within recent years. Not being confined to target inhibition and being able to remove disease-causing protein targets via engagement and subsequent ubiquitination has provided scientists with a powerful tool to expand the druggable space. At the center of this approach sits the ternary complex formed between an E3 ubiquitin ligase, the small molecule degrader, and the target protein. A productive ternary complex is pivotal for a ubiquitin to be transferred to a surface lysine of the target protein resulting in poly-ubiquitination which enables recognition and finally degradation by the proteasome. As understanding the ternary complex means understanding the degradation process, many efforts are put into obtaining structural information of the ternary complex and getting a snapshot of the underlying conformations and molecular contacts. Locking this transient trimeric intermediate in a crystalline state has proven to be very demanding but the obtained results have tremendously improved our understanding of small molecule degraders. This review discusses target protein degradation from a structural perspective and highlights the evolution of certain degraders based on the obtained structural insights.
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Affiliation(s)
| | - Laura M Luh
- Research and Development, Pharmaceuticals, Bayer AG, 13353 Berlin, Germany
| | - Philipp M Cromm
- Research and Development, Pharmaceuticals, Bayer AG, 13353 Berlin, Germany.
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33
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Kounde CS, Tate EW. Photoactive Bifunctional Degraders: Precision Tools To Regulate Protein Stability. J Med Chem 2020; 63:15483-15493. [PMID: 33226810 DOI: 10.1021/acs.jmedchem.0c01542] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Targeted protein degradation with bifunctional degraders is positioned as a remarkable game-changing strategy to control cellular protein levels and promises a new therapeutic modality in drug discovery. Light activation of a degrader to achieve exquisite spatiotemporal control over protein stability in cells has attracted the interest of multiple research groups, with recent reports demonstrating optical control of proteolysis with chimeric molecules bearing photolabile or photoswitchable motifs. In this context of targeted proteolysis research spurring the emergence of innovative tools, we examine the design, synthesis, and properties of light-activated degraders. The significant impact of this approach in regulating disease-relevant protein levels in a light-dependent manner is highlighted with key examples, and future developments to fully harness the potential of light-induced protein degradation with photoactive bifunctional molecules are discussed.
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Affiliation(s)
- Cyrille S Kounde
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London W12 0BZ, United Kingdom
| | - Edward W Tate
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London W12 0BZ, United Kingdom
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34
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Weninger S, Sperling B, Alexander R, Ivarsson M, Menzies FM, Powchik P, Weber CJ, Altar CA, Crystal RG, Haggarty SJ, Loring J, Bain LJ, Carrillo MC. Active immunotherapy and alternative therapeutic modalities for Alzheimer's disease. ALZHEIMERS & DEMENTIA-TRANSLATIONAL RESEARCH & CLINICAL INTERVENTIONS 2020; 6:e12090. [PMID: 33083513 PMCID: PMC7550557 DOI: 10.1002/trc2.12090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 09/11/2020] [Indexed: 12/17/2022]
Abstract
As knowledge of Alzheimer's disease (AD) progression improves, the field has recognized the need to diversify the pipeline, broaden strategies and approaches to therapies, as well as delivery mechanisms. A better understanding of the earliest biological processes of AD/dementia would help inform drug target selection. Currently there are a number of programs exploring these alternate avenues. This meeting will allow experts in the field (academia, industry, government) to provide perspectives and experiences that can help elucidate what the pipeline looks like today and what avenues hold promise in developing new therapies across the stages of AD. The focus here is on Active Immunotherapies and Alternative Therapeutic Modalities. This topic includes active vaccines, antisense oligomers, and cell-based therapy among others, and highlights new clinical developments that utilize these modalities.
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Affiliation(s)
| | | | - Robert Alexander
- Takeda Pharmaceuticals International Co. Cambridge Massachusetts USA
| | - Magnus Ivarsson
- Rodin Therapeutics 300 Technology Square Cambridge Massachusetts USA
| | | | - Peter Powchik
- United Neuroscience 9 Exchange Place, I. F. S. C Dublin Ireland
| | | | | | - Ronald G Crystal
- Department of Genetic Medicine Weill Cornell Medicine New York New York USA
| | - Stephen J Haggarty
- Chemical Neurobiology Laboratory Center for Genomic Medicine Department of Neurology Massachusetts General Hospital and Harvard Medical School Boston Massachusetts USA
| | | | - Lisa J Bain
- Independent Science Writer Elverson Pennsylvania USA
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35
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Luh LM, Scheib U, Juenemann K, Wortmann L, Brands M, Cromm PM. Prey for the Proteasome: Targeted Protein Degradation-A Medicinal Chemist's Perspective. Angew Chem Int Ed Engl 2020; 59:15448-15466. [PMID: 32428344 PMCID: PMC7496094 DOI: 10.1002/anie.202004310] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Indexed: 12/12/2022]
Abstract
Targeted protein degradation (TPD), the ability to control a proteins fate by triggering its degradation in a highly selective and effective manner, has created tremendous excitement in chemical biology and drug discovery within the past decades. The TPD field is spearheaded by small molecule induced protein degradation with molecular glues and proteolysis targeting chimeras (PROTACs) paving the way to expand the druggable space and to create a new paradigm in drug discovery. However, besides the therapeutic angle of TPD a plethora of novel techniques to modulate and control protein levels have been developed. This enables chemical biologists to better understand protein function and to discover and verify new therapeutic targets. This Review gives a comprehensive overview of chemical biology techniques inducing TPD. It explains the strengths and weaknesses of these methods in the context of drug discovery and discusses their future potential from a medicinal chemist's perspective.
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Affiliation(s)
- Laura M. Luh
- Research and DevelopmentPharmaceuticalsBayer AG13353BerlinGermany
| | - Ulrike Scheib
- Research and DevelopmentPharmaceuticalsBayer AG13353BerlinGermany
| | - Katrin Juenemann
- Research and DevelopmentPharmaceuticalsBayer AG13353BerlinGermany
| | - Lars Wortmann
- Research and DevelopmentPharmaceuticalsBayer AG13353BerlinGermany
| | - Michael Brands
- Research and DevelopmentPharmaceuticalsBayer AG13353BerlinGermany
| | - Philipp M. Cromm
- Research and DevelopmentPharmaceuticalsBayer AG13353BerlinGermany
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36
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Design and Applications of Bifunctional Small Molecules in Biology. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1869:140534. [PMID: 32871274 DOI: 10.1016/j.bbapap.2020.140534] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 08/17/2020] [Accepted: 08/27/2020] [Indexed: 12/12/2022]
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37
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Han B. A suite of mathematical solutions to describe ternary complex formation and their application to targeted protein degradation by heterobifunctional ligands. J Biol Chem 2020; 295:15280-15291. [PMID: 32859748 PMCID: PMC7650257 DOI: 10.1074/jbc.ra120.014715] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 08/25/2020] [Indexed: 01/30/2023] Open
Abstract
Small molecule–induced targeted protein degradation by heterobifunctional ligands or molecular glues represents a new modality in drug development, allowing development of therapeutic agents for targets previously considered undruggable. Successful target engagement requires the formation of a ternary complex (TC) when the ligand brings its target protein in contact with an E3 ubiquitin ligase. Unlike traditional drugs, where target engagement can be described by a simple bimolecular equilibrium equation, similar mathematical tools are currently not available to describe TC formation in a universal manner. This current limitation substantially increases the challenges of developing drugs with targeted protein degradation mechanism. In this article, I provide a full, exact, and universal mathematical description of the TC system at equilibrium for the first time. I have also constructed a comprehensive suite of mathematical tools for quantitative measurement of target engagement and equilibrium constants from experimental data. Mechanistic explanations are provided for many common challenges associated with developing this type of therapeutic agent. Insights from these analyses provide testable hypotheses and grant direction to drug development efforts in this promising area. The mathematical and analytical tools described in this article may also have broader applications in other areas of biology and chemistry in which ternary complexes are observed.
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Affiliation(s)
- Bomie Han
- Department of Molecular Pharmacology, Discovery Chemistry Research and Technologies, Lilly Research Laboratories, Eli Lilly and Co., Indianapolis, Indiana, USA.
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38
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Luh LM, Scheib U, Juenemann K, Wortmann L, Brands M, Cromm PM. Beute für das Proteasom: Gezielter Proteinabbau aus medizinalchemischer Perspektive. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004310] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Laura M. Luh
- Research and Development Pharmaceuticals Bayer AG 13353 Berlin Germany
| | - Ulrike Scheib
- Research and Development Pharmaceuticals Bayer AG 13353 Berlin Germany
| | - Katrin Juenemann
- Research and Development Pharmaceuticals Bayer AG 13353 Berlin Germany
| | - Lars Wortmann
- Research and Development Pharmaceuticals Bayer AG 13353 Berlin Germany
| | - Michael Brands
- Research and Development Pharmaceuticals Bayer AG 13353 Berlin Germany
| | - Philipp M. Cromm
- Research and Development Pharmaceuticals Bayer AG 13353 Berlin Germany
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39
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Bueno AB, Sun B, Willard FS, Feng D, Ho JD, Wainscott DB, Showalter AD, Vieth M, Chen Q, Stutsman C, Chau B, Ficorilli J, Agejas FJ, Cumming GR, Jiménez A, Rojo I, Kobilka TS, Kobilka BK, Sloop KW. Structural insights into probe-dependent positive allosterism of the GLP-1 receptor. Nat Chem Biol 2020; 16:1105-1110. [PMID: 32690941 DOI: 10.1038/s41589-020-0589-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 06/09/2020] [Indexed: 12/19/2022]
Abstract
Drugs that promote the association of protein complexes are an emerging therapeutic strategy. We report discovery of a G protein-coupled receptor (GPCR) ligand that stabilizes an active state conformation by cooperatively binding both the receptor and orthosteric ligand, thereby acting as a 'molecular glue'. LSN3160440 is a positive allosteric modulator of the GLP-1R optimized to increase the affinity and efficacy of GLP-1(9-36), a proteolytic product of GLP-1(7-36). The compound enhances insulin secretion in a glucose-, ligand- and GLP-1R-dependent manner. Cryo-electron microscopy determined the structure of the GLP-1R bound to LSN3160440 in complex with GLP-1 and heterotrimeric Gs. The modulator binds high in the helical bundle at an interface between TM1 and TM2, allowing access to the peptide ligand. Pharmacological characterization showed strong probe dependence of LSN3160440 for GLP-1(9-36) versus oxyntomodulin that is driven by a single residue. Our findings expand protein-protein modulation drug discovery to uncompetitive, active state stabilizers for peptide hormone receptors.
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Affiliation(s)
| | | | - Francis S Willard
- Quantitative Biology, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
| | - Dan Feng
- ConfometRx, Santa Clara, CA, USA
| | - Joseph D Ho
- Lilly Biotechnology Center San Diego, San Diego, CA, USA
| | - David B Wainscott
- Quantitative Biology, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
| | - Aaron D Showalter
- Diabetes and Complications, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
| | - Michal Vieth
- Lilly Biotechnology Center San Diego, San Diego, CA, USA
| | - Qi Chen
- Discovery Chemistry Research and Technologies, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
| | - Cynthia Stutsman
- Diabetes and Complications, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
| | - Betty Chau
- Lilly Biotechnology Center San Diego, San Diego, CA, USA
| | - James Ficorilli
- Diabetes and Complications, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
| | | | | | | | | | | | | | - Kyle W Sloop
- Diabetes and Complications, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA.
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40
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Gerry CJ, Schreiber SL. Recent achievements and current trajectories of diversity-oriented synthesis. Curr Opin Chem Biol 2020; 56:1-9. [DOI: 10.1016/j.cbpa.2019.08.008] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 08/21/2019] [Accepted: 08/26/2019] [Indexed: 12/14/2022]
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41
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Hassan MM, Olaoye OO. Recent Advances in Chemical Biology Using Benzophenones and Diazirines as Radical Precursors. Molecules 2020; 25:E2285. [PMID: 32414020 PMCID: PMC7288102 DOI: 10.3390/molecules25102285] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 05/06/2020] [Accepted: 05/09/2020] [Indexed: 12/19/2022] Open
Abstract
The use of light-activated chemical probes to study biological interactions was first discovered in the 1960s, and has since found many applications in studying diseases and gaining deeper insight into various cellular mechanisms involving protein-protein, protein-nucleic acid, protein-ligand (drug, probe), and protein-co-factor interactions, among others. This technique, often referred to as photoaffinity labelling, uses radical precursors that react almost instantaneously to yield spatial and temporal information about the nature of the interaction and the interacting partner(s). This review focuses on the recent advances in chemical biology in the use of benzophenones and diazirines, two of the most commonly known light-activatable radical precursors, with a focus on the last three years, and is intended to provide a solid understanding of their chemical and biological principles and their applications.
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Affiliation(s)
- Muhammad Murtaza Hassan
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road North, Mississauga, ON L5L 1C6, Canada;
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| | - Olasunkanmi O. Olaoye
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road North, Mississauga, ON L5L 1C6, Canada;
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
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42
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Gerry CJ, Schreiber SL. Unifying principles of bifunctional, proximity-inducing small molecules. Nat Chem Biol 2020; 16:369-378. [PMID: 32198490 PMCID: PMC7312755 DOI: 10.1038/s41589-020-0469-1] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 01/07/2020] [Indexed: 01/14/2023]
Abstract
Nature uses a variety of tools to mediate the flow of information in cells, many of which control distances between key biomacromolecules. Researchers have thus generated compounds whose activities stem from interactions with two (or more) proteins simultaneously. In this Perspective, we describe how these 'bifunctional' small molecules facilitate the study of an increasingly wide range of complex biological phenomena and enable the drugging of otherwise challenging therapeutic targets and processes. Despite their structural and functional differences, all bifunctional molecules employ Nature's strategy of altering interactomes and inducing proximity to modulate biology. They therefore exhibit a shared set of chemical and biophysical principles that have not yet been appreciated fully. By highlighting these commonalities-and their wide-ranging consequences-we hope to chip away at the artificial barriers that threaten to constrain this interdisciplinary field. Doing so promises to yield remarkable benefits for biological research and therapeutics discovery.
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Affiliation(s)
- Christopher J Gerry
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA, USA
- Vertex Pharmaceuticals, Boston, MA, USA
| | - Stuart L Schreiber
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA, USA.
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43
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Li J, Wang L, Tian J, Zhou Z, Li J, Yang H. Nongenetic engineering strategies for regulating receptor oligomerization in living cells. Chem Soc Rev 2020; 49:1545-1568. [DOI: 10.1039/c9cs00473d] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nongenetic strategies for regulating receptor oligomerization in living cells based on DNA, protein, small molecules and physical stimuli.
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Affiliation(s)
- Jingying Li
- MOE Key Laboratory for Analytical Science of Food Safety and Biology
- Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety
- State Key Laboratory of Photocatalysis on Energy and Environment
- College of Chemistry
- Fuzhou University
| | - Liping Wang
- MOE Key Laboratory for Analytical Science of Food Safety and Biology
- Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety
- State Key Laboratory of Photocatalysis on Energy and Environment
- College of Chemistry
- Fuzhou University
| | - Jinmiao Tian
- Institute of Molecular Medicine
- Renji Hospital
- School of Medicine
- Shanghai Jiao Tong University
- Shanghai
| | - Zhilan Zhou
- Institute of Molecular Medicine
- Renji Hospital
- School of Medicine
- Shanghai Jiao Tong University
- Shanghai
| | - Juan Li
- MOE Key Laboratory for Analytical Science of Food Safety and Biology
- Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety
- State Key Laboratory of Photocatalysis on Energy and Environment
- College of Chemistry
- Fuzhou University
| | - Huanghao Yang
- MOE Key Laboratory for Analytical Science of Food Safety and Biology
- Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety
- State Key Laboratory of Photocatalysis on Energy and Environment
- College of Chemistry
- Fuzhou University
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44
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Vavers E, Zvejniece L, Maurice T, Dambrova M. Allosteric Modulators of Sigma-1 Receptor: A Review. Front Pharmacol 2019; 10:223. [PMID: 30941035 PMCID: PMC6433746 DOI: 10.3389/fphar.2019.00223] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 02/22/2019] [Indexed: 11/13/2022] Open
Abstract
Allosteric modulators of sigma-1 receptor (Sig1R) are described as compounds that can increase the activity of some Sig1R ligands that compete with (+)-pentazocine, one of the classic prototypical ligands that binds to the orthosteric Sig1R binding site. Sig1R is an endoplasmic reticulum membrane protein that, in addition to its promiscuous high-affinity ligand binding, has been shown to have chaperone activity. Different experimental approaches have been used to describe and validate the activity of allosteric modulators of Sig1R. Sig1R-modulatory activity was first found for phenytoin, an anticonvulsant drug that primarily acts by blocking the voltage-gated sodium channels. Accumulating evidence suggests that allosteric Sig1R modulators affect processes involved in the pathophysiology of depression, memory and cognition disorders as well as convulsions. This review will focus on the description of selective and non-selective allosteric modulators of Sig1R, including molecular structure properties and pharmacological activity both in vitro and in vivo, with the aim of providing the latest overview from compound discovery approaches to eventual clinical applications. In this review, the possible mechanisms of action will be discussed, and future challenges in the development of novel compounds will be addressed.
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Affiliation(s)
- Edijs Vavers
- Laboratory of Pharmaceutical Pharmacology, Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Liga Zvejniece
- Laboratory of Pharmaceutical Pharmacology, Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Tangui Maurice
- MMDN, University of Montpellier, INSERM, EPHE, UMR-S1198, Montpellier, France
| | - Maija Dambrova
- Laboratory of Pharmaceutical Pharmacology, Latvian Institute of Organic Synthesis, Riga, Latvia
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Drummond ML, Williams CI. In Silico Modeling of PROTAC-Mediated Ternary Complexes: Validation and Application. J Chem Inf Model 2019; 59:1634-1644. [DOI: 10.1021/acs.jcim.8b00872] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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