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Light Controlled Modulation of Gene Expression by Chemical Optoepigenetic Probes

View Article: PubMed Central - PubMed

ABSTRACT

Epigenetic gene regulation is a dynamic process orchestrated by chromatin-modifying enzymes. Many of these master regulators exert their function through covalent modification of DNA and histone proteins. Aberrant epigenetic processes have been implicated in the pathophysiology of multiple human diseases. Small-molecule inhibitors have been essential to advancing our understanding of the underlying molecular mechanisms of epigenetic processes. However, the resolution offered by small molecules is often insufficient to manipulate epigenetic processes with high spatio-temporal control. Here, we present a novel and generalizable approach, referred to as ‘Chemo-Optical Modulation of Epigenetically-regulated Transcription’ (COMET), enabling high-resolution, optical control of epigenetic mechanisms based on photochromic inhibitors of human histone deacetylases using visible light. COMET probes may translate into novel therapeutic strategies for diseases where conditional and selective epigenome modulation is required.

No MeSH data available.


Overview of photochromic HDAC inhibitor design for use in COMET(a) Schematic of azobenzene trans/cis isomerization. (b) Theoretical model of the dose-dependent activity of a photochromatic inhibitor as a function of the trans/cis isomer ratio. (c) Azobenzene-based COMET HDAC inhibitor design combining elements of DABCYL and the class I HDAC-selective HDAC inhibitors CI-994 and compound C60 to produce the hybrid structure of BG14 and BG48, respectively. (d) Structures of control compound BG12 and HDAC1/2-biased COMET probe BG47. (e) Density functional theory (DFT) calculations (Gaussian 09) of the electrostatic potentials of CI-994, cis-BG14 and trans-BG14 showed that the electrostatic potential of the zinc-chelating moieties (carbonyl oxygen and aniline nitrogen) in cis-BG14 are very similar to CI-994 and less negative than trans-BG14.
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Figure 1: Overview of photochromic HDAC inhibitor design for use in COMET(a) Schematic of azobenzene trans/cis isomerization. (b) Theoretical model of the dose-dependent activity of a photochromatic inhibitor as a function of the trans/cis isomer ratio. (c) Azobenzene-based COMET HDAC inhibitor design combining elements of DABCYL and the class I HDAC-selective HDAC inhibitors CI-994 and compound C60 to produce the hybrid structure of BG14 and BG48, respectively. (d) Structures of control compound BG12 and HDAC1/2-biased COMET probe BG47. (e) Density functional theory (DFT) calculations (Gaussian 09) of the electrostatic potentials of CI-994, cis-BG14 and trans-BG14 showed that the electrostatic potential of the zinc-chelating moieties (carbonyl oxygen and aniline nitrogen) in cis-BG14 are very similar to CI-994 and less negative than trans-BG14.

Mentions: The limited success in developing light-controlled enzyme modulators is in part inherent to the molecular properties of currently employed photoswitches. Generally, a photochromic ligand can adopt two distinct geometries, which represent the thermodynamic ground state and a metastable higher-energy state 10. With azobenzenes, the most widely used photochromic ligand for biological studies to date, the respective states correspond to the trans and cis isomers (Fig. 1a). Trans/cis isomerization can be induced with ultraviolet (UV)/visible (Vis) light, and the ratio of both isomers obtained after irradiation under equilibrium conditions inversely correlates to the absorbance coefficient at the wavelength used for isomerization. In virtually all reported examples, both isomers have absorbance overlap at any given wavelength, and the ratio of the respective absorption coefficients is generally less than 10. Therefore, light-induced isomerization can never be quantitative in terms of complete transformation as it does not allow for >10:1 enrichment, and consequently light-induced “deactivation” will generally retain >5 % of the active isomer 15. While this can be sufficient for modulating a threshold-based biological function, such as an ion channel opening, it is generally not suitable to study differential enzymatic activity in a cellular context (Fig. 1b). In contrast, thermal relaxation from the metastable state (cis) to the thermodynamic ground state (trans) is quantitative. However, the rate constants depend highly on the electronic nature of the substituents, and half-lives can vary from microseconds to weeks15.


Light Controlled Modulation of Gene Expression by Chemical Optoepigenetic Probes
Overview of photochromic HDAC inhibitor design for use in COMET(a) Schematic of azobenzene trans/cis isomerization. (b) Theoretical model of the dose-dependent activity of a photochromatic inhibitor as a function of the trans/cis isomer ratio. (c) Azobenzene-based COMET HDAC inhibitor design combining elements of DABCYL and the class I HDAC-selective HDAC inhibitors CI-994 and compound C60 to produce the hybrid structure of BG14 and BG48, respectively. (d) Structures of control compound BG12 and HDAC1/2-biased COMET probe BG47. (e) Density functional theory (DFT) calculations (Gaussian 09) of the electrostatic potentials of CI-994, cis-BG14 and trans-BG14 showed that the electrostatic potential of the zinc-chelating moieties (carbonyl oxygen and aniline nitrogen) in cis-BG14 are very similar to CI-994 and less negative than trans-BG14.
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Related In: Results  -  Collection

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Figure 1: Overview of photochromic HDAC inhibitor design for use in COMET(a) Schematic of azobenzene trans/cis isomerization. (b) Theoretical model of the dose-dependent activity of a photochromatic inhibitor as a function of the trans/cis isomer ratio. (c) Azobenzene-based COMET HDAC inhibitor design combining elements of DABCYL and the class I HDAC-selective HDAC inhibitors CI-994 and compound C60 to produce the hybrid structure of BG14 and BG48, respectively. (d) Structures of control compound BG12 and HDAC1/2-biased COMET probe BG47. (e) Density functional theory (DFT) calculations (Gaussian 09) of the electrostatic potentials of CI-994, cis-BG14 and trans-BG14 showed that the electrostatic potential of the zinc-chelating moieties (carbonyl oxygen and aniline nitrogen) in cis-BG14 are very similar to CI-994 and less negative than trans-BG14.
Mentions: The limited success in developing light-controlled enzyme modulators is in part inherent to the molecular properties of currently employed photoswitches. Generally, a photochromic ligand can adopt two distinct geometries, which represent the thermodynamic ground state and a metastable higher-energy state 10. With azobenzenes, the most widely used photochromic ligand for biological studies to date, the respective states correspond to the trans and cis isomers (Fig. 1a). Trans/cis isomerization can be induced with ultraviolet (UV)/visible (Vis) light, and the ratio of both isomers obtained after irradiation under equilibrium conditions inversely correlates to the absorbance coefficient at the wavelength used for isomerization. In virtually all reported examples, both isomers have absorbance overlap at any given wavelength, and the ratio of the respective absorption coefficients is generally less than 10. Therefore, light-induced isomerization can never be quantitative in terms of complete transformation as it does not allow for >10:1 enrichment, and consequently light-induced “deactivation” will generally retain >5 % of the active isomer 15. While this can be sufficient for modulating a threshold-based biological function, such as an ion channel opening, it is generally not suitable to study differential enzymatic activity in a cellular context (Fig. 1b). In contrast, thermal relaxation from the metastable state (cis) to the thermodynamic ground state (trans) is quantitative. However, the rate constants depend highly on the electronic nature of the substituents, and half-lives can vary from microseconds to weeks15.

View Article: PubMed Central - PubMed

ABSTRACT

Epigenetic gene regulation is a dynamic process orchestrated by chromatin-modifying enzymes. Many of these master regulators exert their function through covalent modification of DNA and histone proteins. Aberrant epigenetic processes have been implicated in the pathophysiology of multiple human diseases. Small-molecule inhibitors have been essential to advancing our understanding of the underlying molecular mechanisms of epigenetic processes. However, the resolution offered by small molecules is often insufficient to manipulate epigenetic processes with high spatio-temporal control. Here, we present a novel and generalizable approach, referred to as ‘Chemo-Optical Modulation of Epigenetically-regulated Transcription’ (COMET), enabling high-resolution, optical control of epigenetic mechanisms based on photochromic inhibitors of human histone deacetylases using visible light. COMET probes may translate into novel therapeutic strategies for diseases where conditional and selective epigenome modulation is required.

No MeSH data available.