1
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Miura K, Nakamura H. Development of carbonic anhydrase IX-targeting molecular-targeted photodynamic therapy. Bioorg Med Chem Lett 2024; 109:129821. [PMID: 38810709 DOI: 10.1016/j.bmcl.2024.129821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 05/23/2024] [Accepted: 05/27/2024] [Indexed: 05/31/2024]
Abstract
The efficacy of molecular-targeted photodynamic therapy (MT-PDT) targeting carbonic anhydrase (CA) IX, a cancer-specific molecule, was demonstrated. CA ligand-directed photosensitizers 1-3 were evaluated for their ability to deactivate CAIX protein in cells. Compounds 2 and 3 selectively deactivated CAIX protein under 540 nm light without affecting internal standard proteins. Mechanistic studies revealed that compound 3 not only induced CAIX-selective light inactivation via singlet oxygen but also induced cell membrane damage, resulting in an anti-tumor effect. In vivo studies of CAIX-targeting MT-PDT revealed that treatment with compound 3 followed by light irradiation exhibited remarkable anti-tumor activity, leading to tumor degeneration and necrosis.
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Affiliation(s)
- Kazuki Miura
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Hiroyuki Nakamura
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8501, Japan.
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2
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Ogorek AN, Zhou X, Martell JD. Switchable DNA Catalysts for Proximity Labeling at Sites of Protein-Protein Interactions. J Am Chem Soc 2023; 145:16913-16923. [PMID: 37463457 DOI: 10.1021/jacs.3c05578] [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] [Indexed: 07/20/2023]
Abstract
Proximity labeling (PL) has emerged as a powerful approach to elucidate proteomes within a defined radius around a protein of interest (POI). In PL, a catalyst is attached to the POI and tags nearby endogenous proteins, which are then isolated by affinity purification and identified by mass spectrometry. Although existing PL methods have yielded numerous biological insights, proteomes with greater spatial resolution could be obtained if PL catalysts could be activated at more specific subcellular locations, such as sites where both the POI and a chemical stimulus are present or sites of protein-protein interactions (PPIs). Here, we report DNA-based switchable PL catalysts that are attached to a POI and become activated only when a secondary molecular trigger is present. The DNA catalysts consist of a photocatalyst and a spectral quencher tethered to a DNA oligomer. They are catalytically inactive by default but undergo a conformational change in response to a specific molecular trigger, thus activating PL. We designed a system in which the DNA catalyst becomes activated on living mammalian cells specifically at sites of Her2-Her3 heterodimers and c-Met homodimers, PPIs known to increase the invasion and growth of certain cancers. While this study employs a Ru(bpy)3-type complex for tagging proteins with biotin phenol, the switchable DNA catalyst design is compatible with diverse synthetic PL photocatalysts. Furthermore, the switchable DNA PL catalysts can be constructed from conformation-switching DNA aptamers that respond to small molecules, ions, and proteins, opening future opportunities for PL in highly specific subcellular locations.
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Affiliation(s)
- Ashley N Ogorek
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Xu Zhou
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Jeffrey D Martell
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53726, United States
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3
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Miura K, Wen Y, Tsushima M, Nakamura H. Photodynamic Therapy by Glucose Transporter 1-Selective Light Inactivation. ACS OMEGA 2022; 7:34685-34692. [PMID: 36188330 PMCID: PMC9520747 DOI: 10.1021/acsomega.2c05042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 09/07/2022] [Indexed: 06/16/2023]
Abstract
Chromophore-assisted light inactivation (CALI) was applied to molecule-targeted photodynamic therapy (PDT). In order to identify organic photosensitizers suitable for CALI, the carbonic anhydrase II (CAII) ligand, 4-sulfamoylbenzoic acid 1, was conjugated with several photosensitizers to produce compounds 2-7, whose CALI ability was evaluated by measuring their effect on CAII enzymatic activity. Di-iodinated BODIPY (I2BODIPY) exhibited excellent CAII inactivation ability, similar to that of Ru(bpy)3. The glucose-I2BODIPY conjugate (8) was synthesized as an inactivation of glucose transporter 1 (GLUT1), a protein overexpressed in many cancer cells. Under light irradiation, 8 exhibited concentration-dependent cytotoxicity with half maximal inhibitory concentration (IC50) values of 5.49, 11.14, and 8.73 μM, against human cervical carcinoma (HeLa), human lung carcinoma (A549), and human hepatocellular carcinoma (HepG2) cell lines, respectively. The GLUT1 inhibitor phloretin suppressed the cytotoxicity induced by 8 under light irradiation in a concentration-dependent manner. Western blot analysis indicated that GLUT1 was not detected in cell lines treated with 10 μM 8 under light irradiation. Furthermore, 8 reduced the levels of epidermal growth factor receptor tyrosine kinase (EGFR), phospho-ERK (Y204), and GLUT1 without affecting ERK, α-tubulin, and PCNA protein levels, whereas talaporfin sodium, a clinically approved photosensitizer for PDT, nonspecifically reduced intracellular protein levels in HeLa cells, indicating that 8 has a GLUT1-specific inactivation ability and causes light-induced cytotoxicity by modulating the EGFR/MAPK signaling pathway.
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Affiliation(s)
- Kazuki Miura
- Laboratory
for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Yijin Wen
- School
of Life Science and Technology, Tokyo Institute
of Technology, 4259 Nagatsuta-cho,
Midori-ku, Yokohama 226-8501, Japan
| | - Michihiko Tsushima
- School
of Life Science and Technology, Tokyo Institute
of Technology, 4259 Nagatsuta-cho,
Midori-ku, Yokohama 226-8501, Japan
| | - Hiroyuki Nakamura
- Laboratory
for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
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4
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Trowbridge AD, Seath CP, Rodriguez-Rivera FP, Li BX, Dul BE, Schwaid AG, Buksh BF, Geri JB, Oakley JV, Fadeyi OO, Oslund RC, Ryu KA, White C, Reyes-Robles T, Tawa P, Parker DL, MacMillan DWC. Small molecule photocatalysis enables drug target identification via energy transfer. Proc Natl Acad Sci U S A 2022; 119:e2208077119. [PMID: 35969791 PMCID: PMC9407219 DOI: 10.1073/pnas.2208077119] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 07/14/2022] [Indexed: 12/24/2022] Open
Abstract
Over half of new therapeutic approaches fail in clinical trials due to a lack of target validation. As such, the development of new methods to improve and accelerate the identification of cellular targets, broadly known as target ID, remains a fundamental goal in drug discovery. While advances in sequencing and mass spectrometry technologies have revolutionized drug target ID in recent decades, the corresponding chemical-based approaches have not changed in over 50 y. Consigned to outdated stoichiometric activation modes, modern target ID campaigns are regularly confounded by poor signal-to-noise resulting from limited receptor occupancy and low crosslinking yields, especially when targeting low abundance membrane proteins or multiple protein target engagement. Here, we describe a broadly general platform for photocatalytic small molecule target ID, which is founded upon the catalytic amplification of target-tag crosslinking through the continuous generation of high-energy carbene intermediates via visible light-mediated Dexter energy transfer. By decoupling the reactive warhead tag from the small molecule ligand, catalytic signal amplification results in unprecedented levels of target enrichment, enabling the quantitative target and off target ID of several drugs including (+)-JQ1, paclitaxel (Taxol), dasatinib (Sprycel), as well as two G-protein-coupled receptors-ADORA2A and GPR40.
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Affiliation(s)
| | - Ciaran P. Seath
- Merck Center for Catalysis, Princeton University, Princeton, NJ 08544
| | | | - Beryl X. Li
- Merck Center for Catalysis, Princeton University, Princeton, NJ 08544
| | - Barbara E. Dul
- Department of Chemistry, Princeton University, Princeton, NJ 08544
| | | | - Benito F. Buksh
- Merck Center for Catalysis, Princeton University, Princeton, NJ 08544
| | - Jacob B. Geri
- Merck Center for Catalysis, Princeton University, Princeton, NJ 08544
| | - James V. Oakley
- Merck Center for Catalysis, Princeton University, Princeton, NJ 08544
| | | | - Rob C. Oslund
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA 02141
| | - Keun Ah Ryu
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA 02141
| | - Cory White
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA 02141
| | | | - Paul Tawa
- Pharmacology, Merck & Co., Inc., Kenilworth, NJ 07033
| | - Dann L. Parker
- Discovery Chemistry, Merck & Co., Inc., Kenilworth, NJ 07033
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5
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Nakane K, Niwa T, Tsushima M, Tomoshige S, Taguchi H, Nakamura H, Ishikawa M, Sato S. BODIPY Catalyzes Proximity‐Dependent Histidine Labelling. ChemCatChem 2022. [DOI: 10.1002/cctc.202200077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Keita Nakane
- Tohoku University: Tohoku Daigaku Graduate School of Life Science JAPAN
| | - Tatsuya Niwa
- Tokyo Institute of Technology: Tokyo Kogyo Daigaku Cell Biology Center, Institute of Innovative research JAPAN
| | - Michihiko Tsushima
- Tokyo Institute of Technology: Tokyo Kogyo Daigaku Laboratory for Chemistry and Life Science, Institute of Innovative Research JAPAN
| | - Shusuke Tomoshige
- Tohoku University: Tohoku Daigaku Graduate School of Life Sciences JAPAN
| | - Hideki Taguchi
- Tokyo Institute of Technology: Tokyo Kogyo Daigaku Cell Biology Center, Institute of Innovative Research JAPAN
| | - Hiroyuki Nakamura
- Tokyo Institute of Technology: Tokyo Kogyo Daigaku Laboratory for Chemistry and Life Science, Institute of Innovative Research JAPAN
| | - Minoru Ishikawa
- Tohoku University: Tohoku Daigaku Graduate School of Life Sciences JAPAN
| | - Shinichi Sato
- Tohoku University: Tohoku Daigaku Frontier Research Institute for Interdisciplinary Sciences 2-1-1 Katahira, Aoba-ku, Sendai-shi 980-8577 Miyagi JAPAN
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6
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Sato S. Protein Chemical Modification Using Highly Reactive Species and Spatial Control of Catalytic Reactions. Chem Pharm Bull (Tokyo) 2022; 70:95-105. [PMID: 35110442 DOI: 10.1248/cpb.c21-00915] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Protein bioconjugation has become an increasingly important research method for introducing artificial functions in to protein with various applications, including therapeutics and biomaterials. Due to its amphiphilic nature, only a few tyrosine residues are exposed on the protein surface. Therefore, tyrosine residue has attracted attention as suitable targets for site-specific modification, and it is the most studied amino acid residue for modification reactions other than lysine and cysteine residues. In this review, we present the progress of our tyrosine chemical modification studies over the past decade. We have developed several different catalytic approaches to selectively modify tyrosine residues using peroxidase, laccase, hemin, and ruthenium photocatalysts. In addition to modifying tyrosine residues by generating radical species through single-electron transfer, we have developed a histidine modification method that utilizes singlet oxygen generated by photosensitizers. These highly reactive chemical species selectively modify proteins in close proximity to the enzyme/catalyst. Taking advantage of the spatially controllable reaction fields, we have developed novel methods for site-specific antibody modification, detecting hotspots of oxidative stress, and target identification of bioactive molecules.
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Affiliation(s)
- Shinichi Sato
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University
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7
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Liu W, Watson EE, Winssinger N. Photocatalysis in Chemical Biology: Extending the Scope of Optochemical Control and Towards New Frontiers in Semisynthetic Bioconjugates and Biocatalysis. Helv Chim Acta 2021. [DOI: 10.1002/hlca.202100179] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Weilong Liu
- Department of Organic Chemistry NCCR Chemical Biology Faculty of Science University of Geneva 30 quai Ernest Ansermet CH-1211 Geneva Switzerland
| | - Emma E. Watson
- Department of Organic Chemistry NCCR Chemical Biology Faculty of Science University of Geneva 30 quai Ernest Ansermet CH-1211 Geneva Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry NCCR Chemical Biology Faculty of Science University of Geneva 30 quai Ernest Ansermet CH-1211 Geneva Switzerland
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8
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Lechner VM, Nappi M, Deneny PJ, Folliet S, Chu JCK, Gaunt MJ. Visible-Light-Mediated Modification and Manipulation of Biomacromolecules. Chem Rev 2021; 122:1752-1829. [PMID: 34546740 DOI: 10.1021/acs.chemrev.1c00357] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Chemically modified biomacromolecules-i.e., proteins, nucleic acids, glycans, and lipids-have become crucial tools in chemical biology. They are extensively used not only to elucidate cellular processes but also in industrial applications, particularly in the context of biopharmaceuticals. In order to enable maximum scope for optimization, it is pivotal to have a diverse array of biomacromolecule modification methods at one's disposal. Chemistry has driven many significant advances in this area, and especially recently, numerous novel visible-light-induced photochemical approaches have emerged. In these reactions, light serves as an external source of energy, enabling access to highly reactive intermediates under exceedingly mild conditions and with exquisite spatiotemporal control. While UV-induced transformations on biomacromolecules date back decades, visible light has the unmistakable advantage of being considerably more biocompatible, and a spectrum of visible-light-driven methods is now available, chiefly for proteins and nucleic acids. This review will discuss modifications of native functional groups (FGs), including functionalization, labeling, and cross-linking techniques as well as the utility of oxidative degradation mediated by photochemically generated reactive oxygen species. Furthermore, transformations at non-native, bioorthogonal FGs on biomacromolecules will be addressed, including photoclick chemistry and DNA-encoded library synthesis as well as methods that allow manipulation of the activity of a biomacromolecule.
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Affiliation(s)
- Vivian M Lechner
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Manuel Nappi
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Patrick J Deneny
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Sarah Folliet
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - John C K Chu
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Matthew J Gaunt
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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9
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Interrogating biological systems using visible-light-powered catalysis. Nat Rev Chem 2021; 5:322-337. [PMID: 37117838 DOI: 10.1038/s41570-021-00265-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/24/2021] [Indexed: 12/12/2022]
Abstract
Light-powered catalysis has found broad utility as a chemical transformation strategy, with widespread impact on energy, environment, drug discovery and human health. A noteworthy application impacting human health is light-induced sensitization of cofactors for photodynamic therapy in cancer treatment. The clinical adoption of this photosensitization approach has inspired the search for other photochemical methods, such as photoredox catalysis, to influence biological discovery. Over the past decade, light-mediated catalysis has enabled the discovery of valuable synthetic transformations, propelling it to become a highly utilized chemical synthesis strategy. The reaction components required to achieve a photoredox reaction are identical to photosensitization (catalyst, light source and substrate), making it ideally suited for probing biological environments. In this Review, we discuss the therapeutic application of photosensitization and advancements made in developing next-generation catalysts. We then highlight emerging uses of photoredox catalytic methods for protein bioconjugation and probing complex cellular environments in living cells.
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10
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Beard HA, Hauser JR, Walko M, George RM, Wilson AJ, Bon RS. Photocatalytic proximity labelling of MCL-1 by a BH3 ligand. Commun Chem 2019; 2:133. [PMID: 33763603 PMCID: PMC7610391 DOI: 10.1038/s42004-019-0235-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Ligand-directed protein labelling allows the introduction of diverse chemical functionalities onto proteins without the need for genetically encoded tags. Here we report a method for the rapid labelling of a protein using a ruthenium-bipyridyl (Ru(II)(bpy)3)-modified peptide designed to mimic an interacting BH3 ligand within a BCL-2 family protein-protein interactions. Using sub-stoichiometric quantities of (Ru(II)(bpy)3)-modified NOXA-B and irradiation with visible light for 1 min, the anti-apoptotic protein MCL-1 can be photolabelled with a variety of functional tags. In contrast with previous reports on Ru(II)(bpy)3-mediated photolabelling, tandem mass spectrometry experiments reveal that the labelling site is a cysteine residue of MCL-1. MCL-1 can be labelled selectively in mixtures with other proteins, including the structurally related BCL-2 member, BCL-xL. These results demonstrate that proximity-induced photolabelling is applicable to interfaces that mediate protein-protein interactions, and pave the way towards future use of ligand-directed proximity labelling for dynamic analysis of the interactome of BCL-2 family proteins.
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Affiliation(s)
- Hester A Beard
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK.,Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
| | - Jacob R Hauser
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK.,Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
| | - Martin Walko
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK.,Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
| | - Rachel M George
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
| | - Andrew J Wilson
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK.,Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
| | - Robin S Bon
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK.,Leeds Institute of Cardiovascular and Metabolic Medicine, LIGHT laboratories, University of Leeds, Leeds LS2 9JT, UK
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11
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Protein Chemical Labeling Using Biomimetic Radical Chemistry. Molecules 2019; 24:molecules24213980. [PMID: 31684188 PMCID: PMC6864698 DOI: 10.3390/molecules24213980] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 10/30/2019] [Accepted: 10/31/2019] [Indexed: 01/17/2023] Open
Abstract
Chemical labeling of proteins with synthetic low-molecular-weight probes is an important technique in chemical biology. To achieve this, it is necessary to use chemical reactions that proceed rapidly under physiological conditions (i.e., aqueous solvent, pH, low concentration, and low temperature) so that protein denaturation does not occur. The radical reaction satisfies such demands of protein labeling, and protein labeling using the biomimetic radical reaction has recently attracted attention. The biomimetic radical reaction enables selective labeling of the C-terminus, tyrosine, and tryptophan, which is difficult to achieve with conventional electrophilic protein labeling. In addition, as the radical reaction proceeds selectively in close proximity to the catalyst, it can be applied to the analysis of protein–protein interactions. In this review, recent trends in protein labeling using biomimetic radical reactions are discussed.
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12
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Angerani S, Winssinger N. Visible Light Photoredox Catalysis Using Ruthenium Complexes in Chemical Biology. Chemistry 2019; 25:6661-6672. [PMID: 30689234 DOI: 10.1002/chem.201806024] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Indexed: 12/24/2022]
Abstract
The development of bioorthogonal reactions have had a transformative impact in chemical biology and the quest to expand this toolbox continues. Herein we review recent applications of ruthenium-catalyzed photoredox reactions used in chemical biology.
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Affiliation(s)
- Simona Angerani
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 Quai Ernest-Ansermet, 1205, Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 Quai Ernest-Ansermet, 1205, Geneva, Switzerland
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