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Light-triggered release of photocaged therapeutics - Where are we now? J Control Release 2019; 298:154-176. [PMID: 30742854 DOI: 10.1016/j.jconrel.2019.02.006] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 02/04/2019] [Accepted: 02/06/2019] [Indexed: 01/02/2023]
Abstract
The current available therapeutics face several challenges such as the development of ideal drug delivery systems towards the goal of personalized treatments for patients benefit. The application of light as an exogenous activation mechanism has shown promising outcomes, owning to the spatiotemporal confinement of the treatment in the vicinity of the diseased tissue, which offers many intriguing possibilities. Engineering therapeutics with light responsive moieties have been explored to enhance the bioavailability, and drug efficacy either in vitro or in vivo. The tailor-made character turns the so-called photocaged compounds highly desirable to reduce the side effects of drugs and, therefore, have received wide research attention. Herein, we seek to highlight the potential of photocaged compounds to obtain a clear understanding of the mechanisms behind its use in therapeutic delivery. A deep overview on the progress achieved in the design, fabrication as well as current and possible future applications in therapeutics of photocaged compounds is provided, so that novel formulations for biomedical field can be designed.
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2
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Salahi F, Purohit V, Ferraudi G, Stauffacher C, Wiest O, Helquist P. pHP-Tethered N-Acyl Carbamate: A Photocage for Nicotinamide. Org Lett 2018; 20:2547-2550. [PMID: 29652162 DOI: 10.1021/acs.orglett.8b00697] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The synthesis of a new photocaged nicotinamide having an N-acyl carbamate linker and a p-hydroxyphenacyl (pHP) chromophore is described. The photophysical and photochemical studies showed an absorption maximum at λ = 330 nm and a quantum yield for release of 11% that are dependent upon both pH and solvent. While the acyl carbamate releases nicotinamide efficiently, a simpler amide linker was inert to photocleavage. This photocaged nicotinamide has significant advantages with respect to quantum yield, absorbance wavelength, rate of release, and solubility that make it the first practical example of a photocaged amide.
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Affiliation(s)
- Farbod Salahi
- Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , Indiana 46556 , United States
| | - Vatsal Purohit
- Department of Biological Sciences , Purdue University , 915 West State Street , West Lafayette , Indiana 47907 , United States
| | - Guillermo Ferraudi
- Notre Dame Radiation Research Laboratory , Notre Dame , Indiana 46556 , United States
| | - Cynthia Stauffacher
- Department of Biological Sciences , Purdue University , 915 West State Street , West Lafayette , Indiana 47907 , United States
| | - Olaf Wiest
- Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , Indiana 46556 , United States.,Laboratory of Computational Chemistry and Drug Design, School of Chemical Biology and Biotechnology , Peking University, Shenzhen Graduate School , Shenzhen 518055 , China
| | - Paul Helquist
- Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , Indiana 46556 , United States
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3
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Tang X, Zhang J, Sun J, Wang Y, Wu J, Zhang L. Caged nucleotides/nucleosides and their photochemical biology. Org Biomol Chem 2013; 11:7814-24. [PMID: 24132515 DOI: 10.1039/c3ob41735b] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Nucleotides and nucleosides are not only key units of DNA/RNA that store genetic information, but are also the regulators of many biological events of our lives. By caging the key functional groups or key residues of nucleotides with photosensitive moieties, it will be possible to trigger biological events of target nucleotides with spatiotemporal resolution and amplitude upon light activation or photomodulate polymerase reactions with the caged nucleotide analogues for next-generation sequencing (NGS) and bioorthogonal labeling. This review highlights three different caging strategies for nucleotides and demonstrates the photochemical biology of these caged nucleotides.
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Affiliation(s)
- Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs, the School of Pharmaceutical Sciences, Peking University, No. 38, Xueyuan Rd., Beijing 100191, China.
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4
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Bourbon P, Peng Q, Ferraudi G, Stauffacher C, Wiest O, Helquist P. Development of carbamate-tethered coumarins as phototriggers for caged nicotinamide. Bioorg Med Chem Lett 2013; 23:6321-4. [PMID: 24125882 DOI: 10.1016/j.bmcl.2013.09.067] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 09/18/2013] [Accepted: 09/23/2013] [Indexed: 11/29/2022]
Abstract
The syntheses of 7-diethylaminocoumarin- or modified DEACM-nicotinamide and 6-bromo-7-methoxycoumarin- or BMCM-nicotinamide have been accomplished by reaction of nicotinoyl isocyanate with the corresponding coumarin allylic alcohol derivatives. The resulting compounds contain an N-acyl O-alkyl carbamate as a new type of linkage for the caging of nicotinamide with a coumarin phototrigger, which undergoes cleavage upon photolysis. Our design of specific caged-nicotinamides was based upon NBO and TD-FT calculations to predict absorption wavelengths and photocleavage potential. This work provides a potentially general method for the caging of amides with coumarin photolabile protecting groups.
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Affiliation(s)
- Pauline Bourbon
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA
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5
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Morigaki K, Mizutani K, Kanemura E, Tatsu Y, Yumoto N, Imaishi H. Photoregulation of cytochrome P450 activity by using caged compound. Anal Chem 2011; 84:155-60. [PMID: 22085411 DOI: 10.1021/ac202189h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cytochrome P450 (P450) species play an important role in the metabolism of xenobiotics, and assaying the activities of P450 is important for evaluating the toxicity of chemicals in drugs and food. However, the lag time caused by the introduction and mixing of sample solutions can become sources of error as the throughput is heightened by increasing the sample number and decreasing the sample volume. To amend this technological obstacle, we developed a methodology to photoregulate the activity of P450 by using photoprotected (caged) compounds. We synthesized caged molecules of nicotinamide adenine dinucleotide phosphate (NADP(+)) and glucose 6-phosphate (G6P), which are involved in the generation of NADPH (cofactor of P450). The use of caged-G6P completely blocked the P450 catalysis before the UV illumination, whereas caged-NADP(+) resulted in a little background reaction. Upon UV illumination, more than 90% of the enzymatic activity could be restored. The use of caged-G6P enabled assays in isolated microchambers (width, 50 μm; height, 50 μm) by encapsulating necessary ingredients in advance and initiating the reaction by UV illumination. The initiation of enzymatic reaction could be observed in a single microchamber. Minimizing uncertainties caused by the introduction and mixing of solutions led to significantly reduced errors of obtained kinetic constants.
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Affiliation(s)
- Kenichi Morigaki
- National Institute of Advanced Industrial Science and Technology (AIST), Midorigaoka, Ikeda 563-8577, Japan.
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6
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Silanskas A, Foss M, Wende W, Urbanke C, Lagunavicius A, Pingoud A, Siksnys V. Photocaged variants of the MunI and PvuII restriction enzymes. Biochemistry 2011; 50:2800-7. [PMID: 21410225 DOI: 10.1021/bi2000609] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Regulation of proteins by light is a new and promising strategy for the external control of biological processes. In this study, we demonstrate the ability to regulate the catalytic activity of the MunI and PvuII restriction endonucleases with light. We used two different approaches to attach a photoremovable caging compound, 2-nitrobenzyl bromide (NBB), to functionally important regions of the two enzymes. First, we covalently attached a caging molecule at the dimer interface of MunI to generate an inactive monomer. Second, we attached NBB at the DNA binding site of the single-chain variant of PvuII (scPvuII) to prevent binding and cleavage of the DNA substrate. Upon removal of the caging group by UV irradiation, nearly 50% of the catalytic activity of MunI and 80% of the catalytic activity of PvuII could be restored.
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Affiliation(s)
- Arunas Silanskas
- Institute of Biotechnology, Vilnius University, Graiciuno 8, LT-02241 Vilnius, Lithuania
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7
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Bandara HMD, Walsh TP, Burdette SC. A Second-Generation Photocage for Zn2+ Inspired by TPEN: Characterization and Insight into the Uncaging Quantum Yields of ZinCleav Chelators. Chemistry 2011; 17:3932-41. [DOI: 10.1002/chem.201001982] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Revised: 10/26/2010] [Indexed: 11/08/2022]
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8
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Schaper K, Madani Mobarekeh SA, Doro P, Maydt D. The α,5-dicarboxy-2-nitrobenzyl caging group, a tool for biophysical applications with improved hydrophilicity: synthesis, photochemical properties and biological characterization. Photochem Photobiol 2010; 86:1247-54. [PMID: 20880228 DOI: 10.1111/j.1751-1097.2010.00803.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Earlier we reported on the synthesis of α,4-dicarboxy-2-nitrobenyzl caged compounds (Schaper, K. et al. [2002] Eur. J. Org. Chem., 1037-1046). These compounds have the advantage of an increased hydrophilicity compared with the well-established α-carboxy-2-nitrobenzyl caged compounds; however, the release of the active compound becomes slower due to the introduction of the additional carboxy group. Based upon theoretical calculations we predicted that the release would become faster when the additional carboxy group is moved to the 5-position. Here we describe the synthesis and the photochemical and biological characterization of an α,5-dicarboxy-2-nitrobenyzl caged compound. The high hydrophilicity of the new caging group is maintained due to the fact that the additional carboxy moiety is preserved, while the release of the active species from the new derivative is even faster than for the reference, an α-CNB caged compound.
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Affiliation(s)
- Klaus Schaper
- Group for Organic Photochemistry, Institute for Organic Chemistry and Macromolecular Chemistry, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany.
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9
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DeGraw AJ, Hast MA, Xu J, Mullen D, Beese LS, Barany G, Distefano MD. Caged protein prenyltransferase substrates: tools for understanding protein prenylation. Chem Biol Drug Des 2008; 72:171-81. [PMID: 18844669 DOI: 10.1111/j.1747-0285.2008.00698.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Originally designed to block the prenylation of oncogenic Ras, inhibitors of protein farnesyltransferase currently in preclinical and clinical trials are showing efficacy in cancers with normal Ras. Blocking protein prenylation has also shown promise in the treatment of malaria, Chagas disease and progeria syndrome. A better understanding of the mechanism, targets and in vivo consequences of protein prenylation are needed to elucidate the mode of action of current PFTase (Protein Farnesyltransferase) inhibitors and to create more potent and selective compounds. Caged enzyme substrates are useful tools for understanding enzyme mechanism and biological function. Reported here is the synthesis and characterization of caged substrates of PFTase. The caged isoprenoid diphosphates are poor substrates prior to photolysis. The caged CAAX peptide is a true catalytically caged substrate of PFTase in that it is to not a substrate, yet is able to bind to the enzyme as established by inhibition studies and X-ray crystallography. Irradiation of the caged molecules with 350 nm light readily releases their cognate substrate and their photolysis products are benign. These properties highlight the utility of those analogs towards a variety of in vitro and in vivo applications.
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Affiliation(s)
- Amanda J DeGraw
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
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10
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Lo KKW, Sze KS, Tsang KHK, Zhu N. Luminescent Tricarbonylrhenium(I) Dipyridoquinoxaline Indole Complexes as Sensitive Probes for Indole-Binding Proteins. Organometallics 2007. [DOI: 10.1021/om0700617] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kenneth Kam-Wing Lo
- Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, People's Republic of China, and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, People's Republic of China
| | - Ka-Shing Sze
- Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, People's Republic of China, and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, People's Republic of China
| | - Keith Hing-Kit Tsang
- Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, People's Republic of China, and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, People's Republic of China
| | - Nianyong Zhu
- Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, People's Republic of China, and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, People's Republic of China
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11
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Rathert P, Raskó T, Roth M, Slaska-Kiss K, Pingoud A, Kiss A, Jeltsch A. Reversible inactivation of the CG specific SssI DNA (cytosine-C5)-methyltransferase with a photocleavable protecting group. Chembiochem 2007; 8:202-7. [PMID: 17195251 DOI: 10.1002/cbic.200600358] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Caging of proteins by conjugation with a photocleavable group is a powerful approach for reversibly blocking enzymatic activity. Here we describe the covalent modification of the bacterial SssI DNA methyltransferase (M.SssI) with the cysteine-specific reagent 4,5-dimethoxy-2-nitrobenzylbromide (DMNBB). M.SssI contains two cysteine residues; replacement of the active-site Cys141 with Ser resulted in an approximately 100-fold loss of enzymatic activity; this indicates an important role for this residue in catalysis. However, replacement of Cys368 with Ala did not affect methyltransferase activity. Treatment of the Cys368Ala mutant enzyme with DMNBB led to an almost complete loss of activity. Irradiation of the inactivated enzyme with near-ultraviolet light (320-400 nm) restored 60 % of the catalytic activity. This indicates that caging by DMNBB can be used for the reversible inactivation of M.SssI.
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Affiliation(s)
- Philipp Rathert
- Biochemistry Laboratory International University Bremen, School of Engineering and Science, Campus Ring 1, 28759 Bremen, Germany
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12
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Parkesh R, Vasudevan S, Berry A, Galione A, ChurchillI G. Chemo-enzymatic synthesis and biological evaluation of photolabile nicotinic acid adenine dinuclotide phosphate (NAADP+). Org Biomol Chem 2006; 5:441-3. [PMID: 17252124 PMCID: PMC2518626 DOI: 10.1039/b617344f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A chemo-enzymatic synthesis of novel caged NAADP+ without the formation of multiple cage compounds has been achieved. The biological activity of the caged NAADP+ was demonstrated by its fast uncaging in intact sea-urchin eggs.
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13
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Höbartner C, Silverman SK. Modulation of RNA tertiary folding by incorporation of caged nucleotides. Angew Chem Int Ed Engl 2006; 44:7305-9. [PMID: 16229043 DOI: 10.1002/anie.200502928] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Claudia Höbartner
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
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14
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Höbartner C, Silverman SK. Modulation of RNA Tertiary Folding by Incorporation of Caged Nucleotides. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200502928] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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15
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Kantevari S, Narasimhaji CV, Mereyala HB. Bis(4,5-dimethoxy-2-nitrophenyl)ethylene glycol: a new and efficient photolabile protecting group for aldehydes and ketones. Tetrahedron 2005. [DOI: 10.1016/j.tet.2005.04.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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16
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Joubert F, Fales HM, Wen H, Combs CA, Balaban RS. NADH enzyme-dependent fluorescence recovery after photobleaching (ED-FRAP): applications to enzyme and mitochondrial reaction kinetics, in vitro. Biophys J 2004; 86:629-45. [PMID: 14695307 PMCID: PMC1303832 DOI: 10.1016/s0006-3495(04)74141-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
NADH enzyme-dependent fluorescence recovery after photobleaching (ED-FRAP) was evaluated for studying enzyme kinetics in vitro and in isolated mitochondria. Mass, optical, and nuclear magnetic resonance spectroscopy data were consistent with the UV NADH photolysis reaction being NADH --> NAD* + H+ + e-. The overall net reaction was O2 + 2NADH + 2H+ --> 2NAD+ + 2H2O, or in the presence of other competing electron acceptors such as cytochrome c, NADH + 2Cyt(ox) --> NAD+ + H+ + 2Cyt(red). Solution pH could differentiate between these free-radical scavenging pathways. These net reactions represent the photooxidation of NADH to NAD+. Kinetic models and acquisition schemes were developed, varying [NADH] and [NAD] by altering NADH photolysis levels, for extracting kinetic parameters. UV irradiation levels used did not damage mitochondrial function or enzymatic activity. In mitochondria, [NADH] is a high affinity product inhibitor that significantly reduced the NADH regeneration rate. Matrix NADH regeneration only slightly exceeded the net rate of NADH consumption, suggesting that the NADH regeneration process is far from equilibrium. Evaluation of NADH regeneration in active mitochondria, in comparison to rotenone-treated preparations, revealed other regulatory elements in addition to matrix [NADH] and [NAD] that have yet to be fully characterized. These studies demonstrate that the rapid UV photolysis of NADH to NAD is an effective tool in evaluating the steady-state kinetic properties of enzyme systems. Initial data support the notion that the NADH regeneration process is far from equilibrium in mitochondria and is potentially controlled by NADH levels as well as several other matrix factors.
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Affiliation(s)
- Frederic Joubert
- Laboratory of Cardiac Energetics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892-1061, USA
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17
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Katritzky AR, Xu YJ, Vakulenko AV, Wilcox AL, Bley KR. Model compounds of caged capsaicin: design, synthesis, and photoreactivity. J Org Chem 2004; 68:9100-4. [PMID: 14604387 DOI: 10.1021/jo034616t] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Molecules were prepared with substituted nitrobenzyl groups covalently bonded to N-(4-hydroxy-3-methoxybenzyl)acetamide (2) by ether or carbonate linkages. These compounds decomposed under irradiation at 363 nm. Those with carbonate linkages decomposed at slower rates than those with ether linkages. Molecules with dimethoxy-substituted benzyl groups decomposed more slowly than monomethoxy-substituted benzyl groups due to the electronic characteristics of the benzylic carbon.
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Affiliation(s)
- Alan R Katritzky
- Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA.
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18
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Pelliccioli AP, Wirz J. Photoremovable protecting groups: reaction mechanisms and applications. Photochem Photobiol Sci 2002; 1:441-58. [PMID: 12659154 DOI: 10.1039/b200777k] [Citation(s) in RCA: 538] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photolabile protecting groups enable biochemists to control the release of bioactive compounds in living tissue. 'Caged compounds' (photoactivatable bioagents) have become an important tool to study the events that follow chemical signalling in, e.g., cell biology and the neurosciences. The possibilities are by no means exhausted. Progress will depend on the development of photoremovable protecting groups that satisfy the diverse requirements of new applications--a challenging task for photochemists.
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Affiliation(s)
- Anna Paola Pelliccioli
- Institut für Physikalische Chemie, Universität Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
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19
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Schaper K, Mobarekeh S, Grewer C. Synthesis and Photophysical Characterization of a New, Highly Hydrophilic Caging Group. European J Org Chem 2002. [DOI: 10.1002/1099-0690(200203)2002:6<1037::aid-ejoc1037>3.0.co;2-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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20
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Kurita K, Hayakawa M, Nishiyama Y, Harata M. Polymeric asymmetric reducing agents: preparation and reducing performance of chitosan/dihydronicotinamide conjugates having l- and d-phenylalanine spacer arms. Carbohydr Polym 2002. [DOI: 10.1016/s0144-8617(00)00345-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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21
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Abstract
Caged compounds have covalently attached groups that are rapidly cleaved upon exposure to UV light. Attachment of photolabile groups makes the molecule inert until photolysis releases it in its bioactive form. When caged compounds are applied to the experimental system in advance, the concentration jump of biologically active substances can be brought about immediately in a limited area upon irradiation with pulsed and focused UV light. Therefore, caged compounds of low molecular weight, which are commercially available, have been used effectively to study the mechanisms of temporal biological phenomena, such as muscle contraction, intracellular signaling, and neurotransmission. Because many proteins and peptides play important roles in these phenomena, their caged derivatives should serve as powerful tools to clarify complex biological systems. To prepare caged proteins and peptides, several groups have improved upon a chemical modification method, as well as developed two new methods: (1) nonsense codon suppression and (2) solid-phase peptide synthesis. In this review, we summarize recent advances made in the design, preparation, and application of caged peptides and proteins.
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Affiliation(s)
- Y Shigeri
- National Institute of Advanced Industrial Science and Technology (AIST), 1-8-31 Midorigaoka, Ikeda, Osaka 563-8577, Japan.
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22
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Affiliation(s)
- K Moffat
- Department of Biochemistry & Molecular Biology, Institute for Biophysical Dynamics, Center for Advanced Radiation Sources, University of Chicago, 920 East 58th Street, Chicago, Illinois 60637, USA.
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23
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Stoddard BL. Trapping reaction intermediates in macromolecular crystals for structural analyses. Methods 2001; 24:125-38. [PMID: 11384188 DOI: 10.1006/meth.2001.1174] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The development of "time-resolved" crystallographic methods, including trapping of reaction intermediates and rapid data collection, allows the comparative study of discrete structural species formed during a macromolecular reaction, such as enzymatic catalysis, ribozyme cleavage, or a protein photocycle. The primary technical details that must be addressed in such studies are the reaction initiation, the accumulation of a specific reaction species throughout the crystal, the lifetime of that species and of the crystal under the experimental conditions, and the method used to collect X-ray data. Methods of reaction initiation range from substrate diffusion, which is appropriate for the visualization of very long-lived intermediates, to photolysis, which is appropriate for the accumulation of rate-limited species with half-lives ranging from milliseconds to nanoseconds. This review discusses various methods for initiating turnover in crystals and trapping rate-limiting species for structural studies.
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Affiliation(s)
- B L Stoddard
- Division of Basic Sciences, Program in Structural Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, A3-023, Seattle, Washington 98109, USA.
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24
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Coenzymes of Oxidation—Reduction Reactions. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50018-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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25
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Salerno CP, Magde D, Patron AP. Enzymatic synthesis of caged NADP cofactors: aqueous NADP photorelease and optical properties. J Org Chem 2000; 65:3971-81. [PMID: 10866616 DOI: 10.1021/jo9917846] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The synthesis of caged NADP analogues 18, 19, and 20 has been accomplished by utilizing the transglycosidase activity of solubilized NAD glycohydrolase (porcine brain) to incorporate caged nicotinamides 2, 3, and 4 into NADP. The synthesis of several nicotinamides modified at the carboxamide with o-nitrobenzyl photolabile groups is demonstrated as well as their potential for enzymatic transglycosidation. These results further demonstrate the feasibility of direct enzymatic transglycosidation of sterically hindered substrates into NAD(P), although high nicotinamide analogue water solubility was found to be a necessary trait for yield enhancement with certain analogues. Caged analogues were surveyed under aqueous conditions for net NADP photorelease, while the UV and fluorescent properties of both analogues and their photobyproducts were assessed for compatibility with systems that rely on optical monitoring of enzyme activity. A highly water-soluble alpha-methyl-o-nitrobenzyl group 8 was developed for the synthesis of 20 in order to enhance net NADP photorelease. Compound 20 demonstrated a high 75% net NADP photoreleased without substantial UV optical blackening or fluorescent byproducts. Analogues 18 and 19 were shown by ESI/MALDI-MS to photogenerate primarily adducts of NADP with deleterious UV and fluorescent properties. Our work stresses the superior release properties conferred by alpha-methyl substitution on aqueous carboxamide photorelease from o-nitrobenzyl compounds.
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Affiliation(s)
- C P Salerno
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093-0506, USA
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Namiki S, Kaneda F, Ikegami M, Arai T, Fujimori K, Asada S, Hama H, Kasuya Y, Goto K. Bis-N-nitroso-caged nitric oxides: photochemistry and biological performance test by rat aorta vasorelaxation. Bioorg Med Chem 1999; 7:1695-702. [PMID: 10482461 DOI: 10.1016/s0968-0896(99)00084-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Three new caged nitric oxides (NOs)-BNN3, BNN5Na, and BNN5M were tested for biological use. BNNs have a strong ultraviolet (UV) absorption band (lambda(max): 300 nm, epsilon: 13.5 mM(-1) cm (-1)) extended to 420 nm and produce NO upon irradiation with 300-360 nm light in quantum yields about 2. A photoexcited BNN molecule yields two NOs with time constants of less than 10 ns for phase 1 and less than 20 micros for phase 2 at 37 degrees C, suggesting usefulness of BNNs for measuring in vivo and in vitro fast NO reactions. Upon irradiating with UV light, caged nitric oxides-loaded rat aortic strips maintained in a state of active tonic contraction effectively relaxed ( < 3 microM BNN5M loading solution concentration). BNN3 is incorporated in the lipid membrane. BNN5Na, insoluble in organic solvents but water soluble, localizes in the water phase. BNN5M, is muscle-cell-permeable and hydrolysed to BNN5Na to remain in cytosol. BNNs were thermally stable and demonstrated no observable toxicity.
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Affiliation(s)
- S Namiki
- Department of Chemistry, University of Tsukuba, Ibaraki, Japan
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Stoddard BL, Cohen BE, Brubaker M, Mesecar AD, Koshland DE. Millisecond Laue structures of an enzyme-product complex using photocaged substrate analogs. NATURE STRUCTURAL BIOLOGY 1998; 5:891-7. [PMID: 9783749 DOI: 10.1038/2331] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The structure of a rate-limited product complex formed during a single initial round of turnover by isocitrate dehydrogenase has been determined. Photolytic liberation of either caged substrate or caged cofactor and Laue X-ray data collection were used to visualize the complex, which has a minimum half-life of approximately 10 milliseconds. The experiment was conducted with three different photoreactive compounds, each possessing a unique mechanism leading to the formation of the enzyme-substrate (ES) complex. Photoreaction efficiency and subsequent substrate affinities and binding rates in the crystal are critical parameters for these experiments. The structure suggests that CO2 dissociation is a rapid event that may help drive product formation, and that small conformational changes may contribute to slow product release.
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Affiliation(s)
- B L Stoddard
- Division of Basic Sciences, Program in Structural Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.
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