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Hartmann D, Smith JM, Mazzotti G, Chowdhry R, Booth MJ. Controlling gene expression with light: a multidisciplinary endeavour. Biochem Soc Trans 2020; 48:1645-1659. [PMID: 32657338 PMCID: PMC7458398 DOI: 10.1042/bst20200014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/19/2020] [Accepted: 06/22/2020] [Indexed: 12/21/2022]
Abstract
The expression of a gene to a protein is one of the most vital biological processes. The use of light to control biology offers unparalleled spatiotemporal resolution from an external, orthogonal signal. A variety of methods have been developed that use light to control the steps of transcription and translation of specific genes into proteins, for cell-free to in vivo biotechnology applications. These methods employ techniques ranging from the modification of small molecules, nucleic acids and proteins with photocages, to the engineering of proteins involved in gene expression using naturally light-sensitive proteins. Although the majority of currently available technologies employ ultraviolet light, there has been a recent increase in the use of functionalities that work at longer wavelengths of light, to minimise cellular damage and increase tissue penetration. Here, we discuss the different chemical and biological methods employed to control gene expression, while also highlighting the central themes and the most exciting applications within this diverse field.
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Affiliation(s)
- Denis Hartmann
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K
| | - Jefferson M. Smith
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K
| | - Giacomo Mazzotti
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K
| | - Razia Chowdhry
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K
| | - Michael J. Booth
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K
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2
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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: 100] [Impact Index Per Article: 20.0] [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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Santos FC, Soares AMS, Gonçalves MST, Costa SPG. Phototriggered release of tetrapeptide AAPV from coumarinyl and pyrenyl cages. Amino Acids 2017; 49:1077-1088. [PMID: 28283908 DOI: 10.1007/s00726-017-2405-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 02/28/2017] [Indexed: 11/30/2022]
Abstract
Ala-Ala-Pro-Val (AAPV) is a bioactive tetrapeptide that inhibits human neutrophil elastase, an enzyme involved in skin chronic inflammatory diseases like psoriasis. Caged derivatives of this peptide were prepared by proper N- and C-terminal derivatisation through a carbamate or ester linkage, respectively, with two photoactive moieties, namely 7-methoxycoumarin-2-ylmethyl and pyren-2-ylmethyl groups. These groups were chosen to assess the influence of the photosensitive group and the type of linkage in the controlled photo release of the active molecule. The caged peptides were irradiated at selected wavelengths of irradiation (254, 300, and 350 nm), and the photolytic process was monitored by HPLC-UV. The results established the applicability of the tested photoactive groups for the release of AAPV, especially for the derivative bearing the carbamate-linked pyrenylmethyl group, which displayed the shortest irradiation times for the release at the various wavelengths of irradiation (ca. 4 min at 254 nm, 8 min at 300 nm and 46 min at 350 nm).
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Affiliation(s)
- Filipa C Santos
- Centre of Chemistry, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Ana M S Soares
- Centre of Chemistry, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - M Sameiro T Gonçalves
- Centre of Chemistry, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Susana P G Costa
- Centre of Chemistry, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
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Hoecker J, Liffert R, Burch P, Wehlauch R, Gademann K. Caged retinoids as photoinducible activators: implications for cell differentiation and neurite outgrowth. Org Biomol Chem 2014; 11:3314-21. [PMID: 23538708 DOI: 10.1039/c3ob40106e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Aiming to control neurite formation and navigate the axonal growth by an extrinsic guidance, we report on the design, synthesis and biological evaluation of caged retinoids. Agonists of RARβ have been temporarily blocked either by the [(α-methyl-2-nitropiperonyl)oxy]carbonyl (MeNPOC) group or by immobilization using nitrocatechol linkers on TiO2 particles. Release on demand has been achieved by release under UV irradiation, leading to the biologically active compounds, which have been shown to induce neuronal differentiation and neurite outgrowth.
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Affiliation(s)
- Johannes Hoecker
- Department of Chemistry, NCCR Chemical Biology, University of Basel, Basel, Switzerland
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Karginov AV, Zou Y, Shirvanyants D, Kota P, Dokholyan NV, Young DD, Hahn KM, Deiters A. Light regulation of protein dimerization and kinase activity in living cells using photocaged rapamycin and engineered FKBP. J Am Chem Soc 2010; 133:420-3. [PMID: 21162531 DOI: 10.1021/ja109630v] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We developed a new system for light-induced protein dimerization in living cells using a photocaged analogue of rapamycin together with an engineered rapamycin binding domain. Using focal adhesion kinase as a target, we demonstrated successful light-mediated regulation of protein interaction and localization in living cells. Modification of this approach enabled light-triggered activation of a protein kinase and initiation of kinase-induced phenotypic changes in vivo.
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Affiliation(s)
- Andrei V Karginov
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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6
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Ouyang X, Chen JK. Synthetic strategies for studying embryonic development. ACTA ACUST UNITED AC 2010; 17:590-606. [PMID: 20609409 DOI: 10.1016/j.chembiol.2010.04.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2010] [Revised: 04/12/2010] [Accepted: 04/15/2010] [Indexed: 02/08/2023]
Abstract
Developmental biology has evolved from a descriptive science to one based on genetic principles and molecular mechanisms. Although molecular biology and genetic technologies have been the primary drivers of this transformation, synthetic strategies have been increasingly utilized to interrogate the mechanisms of embryonic patterning with spatial and temporal precision. In this review, we survey how chemical tools and engineered proteins have been used to perturb developmental processes at the DNA, RNA, protein, and cellular levels. We discuss the design principles, experimental capabilities, and limitations of each method, as well as future challenges for the chemical and developmental biology communities.
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Affiliation(s)
- Xiaohu Ouyang
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
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Sauers DJ, Temburni MK, Biggins JB, Ceo LM, Galileo DS, Koh JT. Light-activated gene expression directs segregation of co-cultured cells in vitro. ACS Chem Biol 2010; 5:313-20. [PMID: 20050613 DOI: 10.1021/cb9002305] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Light-directed gene patterning methods have been described as a means to regulate gene expression in a spatially and temporally controlled manner. Several methods have been reported that use photocaged forms of small molecule effectors to control ligand-dependent transcription factors. Whereas these methods offer many advantages including high specificity and transient light-sensitivity, the free diffusion of the uncaged effector can limit both the magnitude and resolution of localized gene induction. Methods to date have been limited by the small fraction of irradiated cells that have expression levels significantly above uninduced background and have not been shown to affect a defined biological response. The tetracycline-dependent transactivator/transrepressor system, RetroTET-ART, combined with a photocaged form of doxycycline (NvOC-Dox) can be used to form photolithographic patterns of induced expression wherein up to 85% of the patterned cells show expression levels above uninduced regions. The efficiency and inducibility of the RetroTET-ART system allows one to quantitatively measure the limits of resolution and the relative induction levels mediated by a small molecule photocaged effector for the first time. Well-defined patterns of reporter genes were reproducibly formed within 6-36 h with feature sizes as small as 300 microm. After photo-patterning, NvOC-Dox can be rapidly removed, rendering cells photoinsensitive and allowing one to monitor GFP product formation in real time. Patterned co-expression of the cell surface ligand ephrin A5 on cell monolayers creates well-defined patterns that are sufficient to direct and segregate co-cultured cells via either attractive or repulsive signaling cues. The ability to direct the arrangement of cells on living cell monolayers through the action of light may serve as a model system for engineering artificial tissues.
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Affiliation(s)
- Daniel J. Sauers
- Departments of Chemistry and Biochemistry and Biological Sciences, University of Delaware, Newark, Delaware 19716
| | - Murali K. Temburni
- Departments of Chemistry and Biochemistry and Biological Sciences, University of Delaware, Newark, Delaware 19716
| | - John B. Biggins
- Departments of Chemistry and Biochemistry and Biological Sciences, University of Delaware, Newark, Delaware 19716
| | - Luke M. Ceo
- Departments of Chemistry and Biochemistry and Biological Sciences, University of Delaware, Newark, Delaware 19716
| | - Deni S. Galileo
- Departments of Chemistry and Biochemistry and Biological Sciences, University of Delaware, Newark, Delaware 19716
| | - John T. Koh
- Departments of Chemistry and Biochemistry and Biological Sciences, University of Delaware, Newark, Delaware 19716
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Doxycycline-dependent photoactivated gene expression in eukaryotic systems. Nat Methods 2009; 6:527-31. [PMID: 19503080 DOI: 10.1038/nmeth.1340] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2009] [Accepted: 05/15/2009] [Indexed: 11/08/2022]
Abstract
High spatial and temporal resolution of conditional gene expression is typically difficult to achieve in whole tissues or organisms. We synthesized two reversibly inhibited, photoactivatable ('caged') doxycycline derivatives with different membrane permeabilities for precise spatial and temporal light-controlled activation of transgenes based on the 'Tet-on' system. After incubation with caged doxycycline or caged cyanodoxycycline, we induced gene expression by local irradiation with UV light or by two-photon uncaging in diverse biological systems, including mouse organotypic brain cultures, developing mouse embryos and Xenopus laevis tadpoles. The amount of UV light needed for induction was harmless as we detected no signs of toxicity. This method allows high-resolution conditional transgene expression at different spatial scales, ranging from single cells to entire complex organisms.
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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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Abstract
Biologically active compounds which are light-responsive offer experimental possibilities which are otherwise very difficult to achieve. Since light can be manipulated very precisely, for example, with lasers and microscopes rapid jumps in concentration of the active form of molecules are possible with exact control of the area, time, and dosage. The development of such strategies started in the 1970s. This review summarizes new developments of the last five years and deals with "small molecules", proteins, and nucleic acids which can either be irreversibly activated with light (these compounds are referred to as "caged compounds") or reversibly switched between an active and an inactive state.
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Affiliation(s)
- Günter Mayer
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany.
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Biggins JB, Hashimoto A, Koh JT. Photocaged Agonist for an Analogue-Specific form of the Vitamin D Receptor. Chembiochem 2007; 8:799-803. [PMID: 17393546 DOI: 10.1002/cbic.200600497] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Nuclear hormone receptors (NHRs) represent a diverse class of ligand-dependent transcriptional regulators. NHRs that have been rendered functionally inactive due to mutations that abrogate proper ligand binding can often be rescued by appropriately designed hormone analogues. The analogue-specific receptor-ligand pairs provide an ideal platform from which to develop new chemogenomic tools for the spatial and temporal control of gene expression. Here, we describe the synthesis and in vitro assessment of a photocaged VDR agonist specific to a mutant NHR that is associated with vitamin D-resistant rickets. The results provide insight into the utility of the agonist as a potential tool for photoinduced gene patterning.
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Affiliation(s)
- John B Biggins
- Department of Chemistry and Biochemistry, University of Delaware, Brown Laboratories, Newark, DE 19716, USA
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Ghosn B, Haselton FR, Gee KR, Monroe WT. Control of DNA Hybridization with Photocleavable Adducts¶. Photochem Photobiol 2007. [DOI: 10.1111/j.1751-1097.2005.tb01469.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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13
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Biggins JB, Koh JT. Chemical biology of steroid and nuclear hormone receptors. Curr Opin Chem Biol 2007; 11:99-110. [PMID: 17188557 DOI: 10.1016/j.cbpa.2006.10.042] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2006] [Accepted: 10/27/2006] [Indexed: 01/25/2023]
Abstract
The nuclear hormone receptors are ligand-gated transcription factors that modulate gene expression by directly acting upon genomic DNA, and have been of profound interest across all biological disciplines. Recent advancements in this area have included the expansion of transgene activation through ligand-receptor engineering, drug development from structural design and the exploitation of innate ligand-specific associations towards developing novel conditional protein-based recombinant and diagnostic tools. These advancements come on the heels of exciting new modes of hormone action that challenge and expand upon the classic paradigms of hormone receptor function.
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Affiliation(s)
- John B Biggins
- Department of Chemistry and Biochemistry, University of Delaware, Newark DE 19716, USA
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Hayashi KI, Hashimoto K, Kusaka N, Yamazoe A, Fukaki H, Tasaka M, Nozaki H. Caged gene-inducer spatially and temporally controls gene expression and plant development in transgenic Arabidopsis plant. Bioorg Med Chem Lett 2006; 16:2470-4. [PMID: 16480868 DOI: 10.1016/j.bmcl.2006.01.103] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2005] [Revised: 01/20/2006] [Accepted: 01/23/2006] [Indexed: 11/24/2022]
Abstract
Two new types of caged gene-inducers, caged 17beta-estradiol and caged dexamethazone, were synthesized. Caged gene-inducers were applied to transgenic Arabidopsis plants carrying a steroid hormone-inducible transactivation system. Light uncaged caged gene-inducers and controlled spatial and temporal expression of transgene in the transgenic plant. Furthermore, caged gene-inducers enabled the control of root development by light.
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Affiliation(s)
- Ken-ichiro Hayashi
- Department of Biochemistry, Okayama University of Science, 1-1 Ridai-cho, Okayama City 700-0005, Japan.
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Abstract
Many genes elicit their actions through their expression in precise spatial patterns in tissues. Photoregulated expression systems offer a means to remotely pattern gene expression in tissues. Using currently available photopatterning methods, gene expression is only transient. Herein is described a general method to permanently alter a cell's genome under the control of light. The photocaged estrogen receptor (ER) antagonists, nitroveratryl-hydroxytamoxifen (Nv-HTam) and nitroveratryl-hydroxytamoxifen aziridine (Nv-HTaz), mediate exposure-dependent recombination in cells expressing the Cre-ER, a fusion of the site-specific recombinase Cre and ER. Both Nv-HTam and Nv-HTaz only activate recombination by Cre-ER after exposure to light. When released only intracellularly, the covalent-modifying Taz can mediate significant amounts of recombination in an exposure-dependent manner. Nv-HTaz and Cre-ER represent perhaps the first compound that can be used to photopattern gene expression through recombination.
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Affiliation(s)
- Kristian H Link
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
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Ghosn B, Haselton FR, Gee KR, Monroe WT. Control of DNA Hybridization with Photocleavable Adducts¶. Photochem Photobiol 2005. [DOI: 10.1562/2004-11-15-ra-373r1.1] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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