Name: design, synthesis, and photochemical properties of clickable caged compounds
Uploaded: 2019-10-15T13:00:00.000+00:00
Duration: 9 min 44 s
Description: Watch this Scientific Journal Video about Design, Synthesis, and Photochemical Properties of Clickable Caged Compounds at JoVE.com

This work was supported by JSPS KAKENHI grant number JP16H01282 (TF), a Grant-in-Aid for Scientific Research on Innovative Areas &#34;Memory Dynamism,&#34; and JP19H05778 (TF), &#34;MolMovies.&#34;

1. Synthesis of the modular caging paBhc group for clickable caged compounds28,41
<ol>
	<li>Preparation of (6-bromo-7-hydroxycoumarin-4-yl)methyl chloride (Bhc-CH2Cl)
	<ol>
		<li>Place 4-bromoresorcinol (9.742 g, 51.5 mmol) in a 100 mL round-bottomed flask equipped with a stirrer bar.</li>
		<li>Add conc. H2SO4 (98%, 30 mL) to the flask and stir the mixture to dissolve.</li>
		<li>Add ethyl 4-chloroacetoacetate (10 mL, 74 mmol) dropwise.</li>
		<li>Continue stirring the mixture at ambient temperature for 5 days.</li>
		<li>Separately, place crushed ice cubes (~200 mL) in a 500 mL Erlenmeyer flask.</li>
		<li>Pour the reaction mixture into the ice and stir vigorously for 30 min until a finely powdered precipitate is obtained.</li>
		<li>Collect the precipitate via vacuum filtration. Wash the light brown precipitate with water five times.</li>
		<li>Dry the precipitate under vacuum overnight to yield BhcCH2Cl as a light brown powder (13.57 g, 46.9 mmol).</li>
	</ol>
	</li>
	<li>Preparation of (6-bromo-7-hydroxycoumarin-4-yl)methanol (BhcCH2OH)
	<ol>
		<li>Place the prepared BhcCH2Cl (1.1440 g, 3.95 mmol) and 1 M HCl (300 mL) in a 1 L round-bottomed flask equipped with a Dimroth condenser. Stir the mixture at 140 &#176;C for 5 days. After this time, cool the mixture to ambient temperature.</li>
		<li>Remove the water from the reaction by rotary evaporation under vacuum to yield BhcCH2OH (1) as a light brown powder (1.0359 g, 3.82 mmol, 97% yield). 
		NOTE: The use of 250 mL of 1 M HCl per 1 g of BhcCH2Cl gives a satisfactory result.</li>
	</ol>
	</li>
	<li>Preparation of paBhcCH2OH (2) via the Mannich reaction
	<ol>
		<li>Place paraformaldehyde (446.4 mg, 14.9 mmol) in a 50 mL round-bottomed flask. Add anhydrous ethanol (5 mL) and N-methylpropargylamine (1.25 mL, 14.8 mmol) to the flask.</li>
		<li>Stir the mixture at ambient temperature for 1 h under an Ar atmosphere.</li>
		<li>Add BhcCH2OH (1) (1.367 g, 5.04 mmol) to the flask. Heat the mixture to 80 &#176;C with a block heater apparatus, and continue stirring the mixture at 80 &#176;C for 2 h under an Ar atmosphere.</li>
		<li>Stop the block heater and cool the reaction mixture to room temperature.</li>
		<li>Collect the resulting light brown-yellow precipitate by vacuum filtration. Wash the precipitate twice with a small amount of anhydrous ethanol (1 mL each time).</li>
		<li>Remove the excess ethanol under vacuum to yield paBhcCH2OH (2) (1.393 g, 3.96 mmol).</li>
	</ol>
	</li>
</ol>
2. Preparation of clickable caged compounds
NOTE: The following procedures can be applied to the preparation of other clickable caged compounds containing hydroxyl, amino, and carboxylate functional groups.
<ol>
	<li>General Procedure 1: Preparation of a clickable caged amine
	<ol>
		<li>Place paBhcCH2OH (2) (709.6 mg, 2.02 mmol) and N,N&#8217;-carbonyl diimidazole (CDI, 397.6 mg, 2.45 mmol) in a 30 mL round-bottomed flask. Add dry CH2Cl2 (6 mL) and stir the solution at ambient temperature for 1 h.</li>
		<li>Add 4-dimethylaminopyridine (4-DMAP, 324.8 mg, 2.66 mmol) and tert-butyl (6-aminohexyl)carbamate (533.1 mg, 2.46 mmol). Stir the solution at ambient temperature for 3 h.</li>
		<li>Remove the solvent and other volatile materials using a rotary evaporator under vacuum. Purify the residue directly using silica gel flash column chromatography.</li>
	</ol>
	</li>
	<li>General Procedure 2: Preparation of a clickable caged alcohol
	<ol>
		<li>Place paclitaxel (PTX, 48.7 mg, 0.057 mmol) in a 30 mL round-bottomed flask equipped with a three-way stopcock and an Ar balloon. Add dry CH2Cl2 (1 mL), 4-DMAP (17.1 mg, 0.14 mmol), and 4-nitrophenyl chloroformate (26.0 mg, 0.13 mmol).</li>
		<li>Stir the solution at ambient temperature for 2.5 h under an Ar atmosphere.</li>
		<li>Add 4-DMAP (15.7 mg, 0.13 mmol) and paBhcCH2OH (2) (39.1 mg, 0.111 mmol) to the solution. Continue stirring the mixture at ambient temperature for 17 h.</li>
		<li>Add CHCl3 (10 mL) and 15% aqueous NaHCO3 (5 mL) to the mixture. Stir the mixture vigorously for approximately 3 min. Remove the aqueous layer with a pipette.</li>
		<li>Add 0.5 M citric acid (5 mL) to the flask containing the organic layer. Stir the mixture and remove the aqueous layer as above.</li>
		<li>Separate the organic layer using a phase separation column. Remove the solvents with a rotary evaporator under vacuum. Purify the product using standard silica gel flash column chromatography.</li>
	</ol>
	</li>
	<li>General Procedure 3: Preparation of a clickable caged carboxylic acid
	<ol>
		<li>Dissolve arachidonic acid (33.0 &#956;L, 0.100 mmol), paBhcCH2OH (2) (39.6 mg, 0.112 mmol), and 4-DMAP (14.1 mg, 0.115 mmol) in dry CH2Cl2 (2 mL). Add N,N&#697;-diisopropylcarbodiimide (DIPC, 17.0 &#956;L, 0.110 mmol) and stir the solution at ambient temperature for 140 min.</li>
		<li>Remove the solvent under vacuum. Purify the residue directly using silica gel flash column chromatography.</li>
	</ol>
	</li>
</ol>
3. Installation of a functional unit into the clickable caged compounds
<ol>
	<li>Dissolve copper(II) sulfate pentahydrate (249 mg) in ion-exchanged water (IEW, 10 mL) to give a 0.1 M CuSO4 solution.</li>
	<li>Dissolve 2&#697;-paBhcmoc-PTX (8.0 mg, 6.5 &#956;mol), tris(3-hydroxypropyltriazolylmethyl)amine (THPTA, 17.5 mg, 40.3 &#956;mol), sodium l-ascorbate (162.4 mg, 0.825 mmol), and 15-chloro-3,6,9-trioxapentadecyl azide (3.1 mg, 11 &#956;mol) in a mixed solvent of 0.1 M phosphate buffer (2.5 mL, pH 7.2) and dimethyl sulfoxide (DMSO, 0.5 mL).</li>
	<li>Add the 0.1 M CuSO4 solution (81.2 &#956;L, 8.1 &#956;mol) to the reaction mixture. Stir the mixture at ambient temperature for 80 min. Monitor the progress of the reaction using high-performance liquid chromatography (HPLC).</li>
	<li>Dissolve the precipitates by adding a 75% acetonitrile/water solution (3.5 mL). Apply the resulting solution directly to the semi-preparative HPLC system to purify the desired product. 
	NOTE: Solubilization of the reaction mixture by the addition of tert-butanol can accelerate the progression of the reaction.</li>
</ol>
4. Photolytic uncaging reaction of the caged compounds
<ol>
	<li>Preparation of the stock solutions
	<ol>
		<li>Dissolve the desired caged compound (5 &#956;mol) in DMSO (500 &#956;L) to prepare a 10 mM stock solution. Dispense an aliquot of each solution (10 &#956;L) into a 1.5 mL microcentrifuge tube and store in a freezer (&#8722;20 &#176;C) until just before use.</li>
		<li>6 mM K3[Fe(C2O4)3] (100 mL): Dissolve recrystallized potassium ferrioxalate (0.295 g, 0.675 mmol) in 80 mL of water. Add 0.5 M H2SO4 (10 mL) and an appropriate amount of IEW to make up the volume to 100 mL. 
		NOTE: Potassium ferrioxalate should be purified via recrystallization from hot water and stored in the dark. Recrystallized potassium ferrioxalate is obtained as the trihydrate; therefore, its formula is K3[Fe(C2O4)3]&#183;3H2O and a formula weight of 491.24 should be considered during preparation of the stock solution. Check the purity of the 6 mM solution by measuring its absorption at 510 nm. If the absorbance is &#60;0.02, it is suitable for use in the experiment.</li>
		<li>0.1% Buffer-phen (30 mL): Dissolve NaOAc&#183;3H2O (7.35 g), 1,10-phenanthroline (phen)&#183;H2O (30 mg), and conc. H2SO4 (0.9 mL) in IEW (20 mL). Add IEW to make up the volume to 30 mL. 
		NOTE: The solution contains 1.8 M NaOAc, 0.54 M H2SO4, and 0.1% 1,10-phenanthroline.</li>
	</ol>
	</li>
	<li>Measurement of the number of photons using ferrioxalate actinometry
	<ol>
		<li>Place 6 mM K3[Fe(C2O4)3] (V1 L) in a quartz cuvette. Irradiate the solution with 350 nm light for 5 s.</li>
		<li>Transfer the irradiated solution to a Pyrex cuvette with an l [cm] path length.</li>
		<li>Add 0.1% Buffer-phen (V2 L) to the irradiated sample solution and mix well by pipetting. Measure the absorbance of the sample at 510 nm. Calculate the average absorption change per unit time (&#916;A510 [s&#8722;1]).</li>
		<li>Calculate the number of moles of generated Fe2+ ions per unit time according to the following equation: 
		nFe2+ [mol s&#8722;1] = ((V1 + V2) [L] &#215; &#916;A510 [s&#8722;1])/(l [cm] &#215; &#949;510 [L mol&#8722;1 cm&#8722;1]), 
		where (V1 + V2) is the volume of the sample for the absorption measurement, l is the optical path length of the cuvette, and &#949;510 is the molar absorptivity of the Fe2+-phen complex at 510 nm. 
		NOTE: In the typical experimental conditions, values of V1 = 2.0 &#215; 10&#8722;3 L, V2 = 0.33 &#215; 10&#8722;3 L, l = 1.0 cm, and &#949;510 = 1.1 &#215; 104 L mol&#8722;1 cm&#8722;1 were used.</li>
		<li>Calculate the number of moles of photons that reach the sample (I0) using the following formula: 
		I0 [einstein cm&#8722;2 s&#8722;1] = nFe2+/&#934;350 
		where &#934; 350 is the quantum efficiency of photoreduction of the ferrioxalate at 350 nm. 
		NOTE: Although the quantum efficiency of the potassium ferrioxalate actinometer at 350 nm is not reported, the reported value of 1.2542 at 358 nm was employed.</li>
	</ol>
	</li>
	<li>Quantum efficiency measurements at 350 nm
	<ol>
		<li>Dilute the sample stock solution (in DMSO, 10 &#956;L) with K-MOPS buffer (pH 7.2, 10 mL) to give a 10 &#956;M solution in K-MOPS containing 0.1% DMSO. 
		NOTE: K-MOPS buffer consisted of 100 mM KCl and 10 mM 3-(N-morpholino)propanesulfonic acid (Mops) titrated to pH 7.2 with KOH.</li>
		<li>Transfer an aliquot of the solution (V1 L) into the same cuvette used in the photoreaction of the chemical actinometer. Irradiate the sample solution using the same setup as described in step 4.2.1.</li>
		<li>Remove an aliquot (50 &#956;L) from the irradiated solution periodically and analyze using HPLC.</li>
		<li>Determine the irradiation time, in seconds, in which 90% of the starting material reacted (t90%) by fitting plots of the time-dependent disappearance of the starting material. 
		NOTE: The absorbance of the irradiated sample must be maintained at &#60;0.1 so that the inner filtering of the radiation can be neglected. It is desirable that the photolytic consumption of the starting material can be approximated by single-exponential decay so that there is no undesired secondary effect that interferes with the photolysis process.</li>
		<li>Calculate the quantum yield of disappearance (&#934;dis) using the following equation28: 
		&#934;dis = 1/(t90% &#215; I0 &#215; &#963;350) 
		where t90% [s] is the irradiation time in which 90% of the starting material was consumed, I0 [einstein cm&#8722;2 s&#8722;1] is the number of moles of photons, and &#963;350 [cm2 mol&#8722;1] is the decadic extinction coefficient of the sample at 350 nm. 
		NOTE: &#963;350 [cm2 mol&#8722;1] = 103&#949;350 [M&#8722;1 cm&#8722;1].</li>
	</ol>
	</li>
</ol>
5. Targeting of a clickable caged compound with a HaloTag ligand
NOTE: Prior to use, maintain the HeLa cells in Dulbecco&#8217;s modified Eagle medium (DMEM, low glucose, sodium pyruvate, l-glutamine) supplemented with 10% fetal bovine serum (FBS) containing 1% antibiotics (streptomycin sulfate, penicillin G, and amphotericin) at 37 &#176;C and 5% CO2.
<ol>
	<li>Remove the medium and trypsinize the cells by treating with trypsin-ethylenediaminetetraacetic acid (EDTA, 1 mL) at 37 &#176;C for 1 min. Add DMEM (4 mL) to the cells and re-suspend the cells by pipetting gently. Seed approximately 5 &#215; 105 cells per dish into 35 mm glass bottom dishes in DMEM (2 mL) 24 h before transfection.</li>
	<li>For four dishes, in a 1.5 mL microcentrifuge tube, dilute the plasmid DNA (pcDNA3-Halo-EGFR, 14 &#956;g) in the reduced serum medium (700 &#956;L). Separately, dilute the lipofection reagent (5 &#956;L) in the reduced serum medium (150 &#956;L) into each of four tubes and allow them stand at ambient temperature for 5 min.</li>
	<li>Add a portion of the diluted plasmid DNA (150 &#956;L) to each of the diluted lipofection reagent samples. Incubate at ambient temperature for 5 min.</li>
	<li>After maintaining the cells at 37 &#176;C and 5% CO2 for 24 h, aspirate the DMEM and rinse the cells with phosphate-buffered saline (PBS, 2 mL). Add the reduced serum medium (1.5 mL).</li>
	<li>Add the plasmid-lipofection reagent (150 &#956;L) complex to each dish. Maintain the cells at 37 &#176;C and 5% CO2 for 48 h.</li>
	<li>Aspirate the medium, add a portion of freshly prepared DMEM (1 mL) containing 2 &#956;M paBhc-hex-FITC/Halo, and incubate the cells at 37 &#176;C and 5% CO2 for 30 min.</li>
	<li>Aspirate the medium containing the caged compound and rinse the cells twice with PBS+ (1 mL per rinse) to remove any unbound compounds. Add the reduced serum medium (500 &#956;L) and incubate the cells at 37 &#176;C and 5% CO2 for 30 min to remove the compounds that entered the cells. 
	NOTE: PBS+ is phosphate-buffered saline supplemented with 2 mM CaCl2 and 1 mM MgCl2.</li>
	<li>Remove the medium and rinse the cells twice with PBS+ (1 mL). Add a portion of a medium (1 mL) that does not contain phenol red. Record fluorescence images by laser scanning confocal fluorescence microscopy.</li>
</ol>
6. Photomediated modulation of a kinase localization using a clickable caged compound
NOTE: Prior to use, maintain the CHO-K1 cells in Ham&#8217;s F-12 medium supplemented with 10% FBS at 37 &#176;C and 5% CO2.
<ol>
	<li>Prepare a 100&#215; working solution (1 mM)of paBhc-AA (5) in DMSO. 
	NOTE: A 10 mM stock solution of the compound is prepared and stored in a freezer (-20 &#176;C).</li>
	<li>Seed approximately 5 &#215; 105 cells per dish into 35 mm glass bottom dishes in DMEM (2 mL) 24 h before transfection.</li>
	<li>Transfect CHO-K1 cells with a plasmid coding for GFP-DGK&#947; 48 h before the uncaging experiments. 
	NOTE: Transfection is performed according to steps 5.2&#8211;5.5.</li>
	<li>Replace the medium with a reduced serum medium (2 mL). Add the 100&#215; paBhc-AA working solution (20 &#956;L) and incubate the cells at 37 &#176;C and 5% CO2 for between 5 min and 1 h. 
	NOTE: The loading time depends on the compound employed.</li>
	<li>Place the cells on the objective stage of an inverted fluorescent microscope equipped with a dual light source fluorescence illuminator.</li>
	<li>Take a fluorescent image every 10 s. Irradiate the cells with 330&#8211;385 nm light through a microscope objective for an appropriate time. Alternatively, irradiate the cells with 405 nm light using a Xe lamp through flexible quartz fibers.</li>
	<li>Continue to record fluorescent images for 10 min.</li>
</ol>

We have nothing to disclose.

We previously developed Bhc caged compounds of various biologically active molecules that exhibit high photolytic efficiencies28,45,46,47. With the aim of expanding the repertoire of Bhc caging groups, we also reported platforms of modular caged compounds that can be modified easily by the introduction of various functional units32,40,41. The present protocol therefore represents a method for the synthesis of a clickable precursor of Bhc caging groups that can be modified via the copper(I)-catalyzed Huisgen cyclization. The synthesis of the clickable precursor, paBhcCH2OH (2), was achieved via a four-step reaction sequence starting from the commercially available 4-bromoresorcinol (Figure 1A). The advantage of the present protocol is that no laborious purification steps (e.g., column chromatographic separations) are required.
As clickable precursor paBhcCH2OH (2) can be used to mask various functional groups, clickable caged compounds of amines, alcohols, and carboxylic acids were synthesized using 2 as the precursor (Figure 1B). Amines were modified as their carbamates while alcohols were modified as their carbonates. In general procedures 1 and 2, CDI was used for the preparation of clickable carbamates, while 4-nitrophenyl chloroformate was used for the preparation of carbonates. As indicated by the reaction mechanism, both reagents can be used for the preparation of carbamates and carbonates. It should also be noted that the yield of the desired caged compound depends on the chemical structure of the molecule to be caged. Other examples can be seen in our previous reports28,30,33,48.
Click modification was then performed using a slight modification of the reported procedure49. The addition of tris(triazolylmethyl)amine-based ligands is necessary to obtain the desired products in good to high yields. Since a variety of azides are readily available both from commercial sources and from literature procedures, we can prepare various modular caged compounds with additional properties such as water solubility and cellular targeting ability (Figure 2).
The quantum yield of photolysis was then measured according to a reported procedure28,50. Figure 3 shows that the photolytic consumption of 2&#697;-glc-paBhcmoc-PTX and the release of PTX were approximated by single-exponential decay and rise, respectively, suggesting no inner filtering of the radiation or undesired secondary effects. Improved photolysis quantum yields (&#934;) and photolysis efficiencies (&#949;&#934;) were observed for the clickable paBhc caged compounds compared to those of the previously reported Bhc caged compounds (Table 1)41,43. Since the photolysis efficiencies (&#949;&#934;) of Bhc caged compounds are more than one hundred times higher than those of 2-nitrobenzyl-type caged compounds48, the marked improvement due to the presence of paBhc caging groups is clearly an advantage for this system.
As a proof-of-concept experiment, a hydrophilic moiety was introduced into 2&#697;-paBhcmoc-PTX (4) and a cellular targeting ligand was introduced into compound 3 (Figure 2). The water solubility of 2&#697;-glc-paBhcmoc-PTX was 650 times higher than that of the parent PTX (Table 1). Selective cellular targeting was achieved using a tag-probe system, and paBhcmoc-hex-FITC/Halo (8) bearing the HaloTag ligand was successfully targeted to the cell membrane of cultured mammalian cells expressing the HaloTag/EGFR fusion protein (Figure 4). Photo-mediated modulation of the subcellular localization of a kinase was also achieved using a clickable caged compound 5 (Figure 5).
In conclusion, we successfully demonstrated a method for the preparation of clickable platforms for photo-caged compounds of biologically interesting molecules that can be modified easily with additional properties, such as water solubility and a cellular targeting ability. Since the paBhc caging group can be used to prepare any molecules with modifiable functional groups, the application of the present protocol is not limited to the molecules described herein. Using a modular platform, namely the paBhc caging group, the desired caged compounds can be easily prepared, and their physical and chemical properties can be modulated via click modification.

Caged compounds are designed synthetic molecules whose original functions are temporally masked by covalently attached photo-removable protecting groups. Interestingly, caged compounds of biologically relevant molecules provide an indispensable method for the spatiotemporal control of the cellular physiology1,2,3,4,5,6. In 1977, Engels and Schlaeger reported the 2-nitrobenzyl ester of cAMP as a membrane permeable and photolabile derivative of cAMP7. The following year, Kaplan reported the 1-(2-nitrophenyl)ethyl ester of ATP (NPE-ATP) and named this compound &#8220;caged&#8221; ATP8. Since then, a range of photochemically removable protecting groups such as 2-nitrobenzyls, p-hydroxyphenacyls9, 2-(2-nitrophenyl)ethyls10,11, 7-nitroindolin-1-yls12,13, and (coumarin-4-yl)methyls14,15,16 have been used for the preparation of caged compounds.
The synthesis of caged compounds with desirable additional properties such as membrane permeability, water solubility, and cellular targeting ability would be expected to facilitate cell biological applications. Since the physical and photochemical properties of these molecules depend primarily on the chemical structure of the photochemically removable protecting groups used to prepare them, a diverse repertoire of photo-caging groups is required. However, the structural diversity of currently available caging groups that exhibit high photolysis efficiencies is limited. This could be an obstacle to increasing the use of caged compounds.
To address this issue, the repertoire of photo-caging groups has been expanded by the chemical modification of existing photoremovable protecting groups or the design of new photolabile chromophores with superior photophysical and photochemical properties. Examples include nitrodibenzofuran (NDBF)17, [3-(4,5-dimethoxy-2-nitrophenyl)-2-butyl] (DMNPB)18,19, a calcium-sensitive 2-nitrobenzyl photocage20, substituted coumarinylmethyls (DEAC45021, DEAdcCM22, 7-azetidinyl-4-methylcoumarin23, and styryl coumarins24), cyanine derivatives (CyEt-pan)25, and BODIPY derivatives26,27.
In addition, we previously developed the (6-bromo-7-hydroxycoumarin-4-yl)methyl (Bhc) group and successfully synthesized various caged compounds of neurotransmitters28, second messengers29,30, and oligonucleotides31,32,33 exhibiting large one- and two-photon excitation cross-sections. If additional properties can be installed easily into the caging groups without compromising their photosensitivity, then the repertoire of caged compounds can be expanded34,35,36,37,38,39. We therefore designed modular caged compounds that comprise three parts, namely the Bhc group as a photo-responsive core, chemical handles for the installation of additional functionalities, and the molecules that are to be masked40,41.
Thus, this article provides a practical method for the preparation of caged compounds of biologically relevant molecules. The present protocol describes methods for the preparation of a clickable platform for photo-caging groups, the introduction of additional functionalities to expand the repertoire of caged compounds, the measurement of their physical and photochemical properties, and the cell-type selective targeting of a clickable caged compound for further cellular application.

<table><tbody><tr><td>acetonitrile, EP</td><td>Nacalai</td><td>00404-75</td><td></td></tr><tr><td>acetonitrile, super dehydrated</td><td>FUJIFILM Wako</td><td>010-22905</td><td></td></tr><tr><td>Antibiotic-Antimycotic, 100X</td><td>Thermo Fisher</td><td>15240062</td><td></td></tr><tr><td>4-bromoresorcinol</td><td>TCI Chemicals</td><td>B0654</td><td></td></tr><tr><td>N,N&amp;rsquo;-carbonyldiimidazole</td><td>FUJIFILM Wako</td><td>034-10491</td><td></td></tr><tr><td>chloroform</td><td>Kanto</td><td>07278-71</td><td></td></tr><tr><td>Copper (II) Sulfate Pentahydrate, 99.9%</td><td>FUJIFILM Wako</td><td>032-12511</td><td></td></tr><tr><td>dichloromethane, dehydrated</td><td>Kanto</td><td>11338-05</td><td></td></tr><tr><td>N,N&#039;-Diisopropylcarbodiimide (DIPC)</td><td>TCI Chemicals</td><td>D0254</td><td></td></tr><tr><td>4-dimethylaminopyridine</td><td>TCI Chemicals</td><td>D1450</td><td></td></tr><tr><td>dimethylsulfoxide, dehydrated -super-</td><td>Kanto</td><td>10380-05</td><td></td></tr><tr><td>DMEM - Dulbecco&#039;s Modified Eagle Medium</td><td>Sigma</td><td>D6046-500ML</td><td></td></tr><tr><td>dual light source fluorescence illuminator, IX2-RFAW</td><td>Olympus</td><td></td><td></td></tr><tr><td>Ethanol (99.5)</td><td>FUJIFILM Wako</td><td>054-07225</td><td></td></tr><tr><td>Ethyl 4-Chloroacetoacetate</td><td>TCI Chemicals</td><td>C0911</td><td></td></tr><tr><td>Ham&#039;s F-12 with L-Glutamine and Phenol Red</td><td>FUJIFILM Wako</td><td>087-08335</td><td></td></tr><tr><td>hydrochloric acid</td><td>FUJIFILM Wako</td><td>087-01076</td><td></td></tr><tr><td>inverted fluorescent microscope IX-71</td><td>Olympus</td><td></td><td></td></tr><tr><td>ISOLUTE Phase Separator, 15 mL</td><td>Biotage</td><td>120-1906-D</td><td></td></tr><tr><td>L-(+)-Ascorbic Acid Sodium Salt</td><td>FUJIFILM Wako</td><td>196-01252</td><td></td></tr><tr><td>laser scanning fluorescence confocal microscopy, FLUOVIEW FV1200/IX-81</td><td>Olympus</td><td></td><td></td></tr><tr><td>Lipofectamine 2000 Transfection Reagent</td><td>Thermo Fisher</td><td>11668027</td><td>lipofection reagent</td></tr><tr><td>3-(N-morpholino)propanesulfonic acid</td><td>Dojindo</td><td>345-01804</td><td>MOPS</td></tr><tr><td>4-nitrophenylchloroformate (4-NPC)</td><td>TCI Chemicals</td><td>C1400</td><td></td></tr><tr><td>Opti-MEM I Reduced Serum Medium, no phenol red</td><td>Thermo Fisher</td><td>11058021</td><td>reduced serum medium contains no phenol red</td></tr><tr><td>1,10-Phenanthroline Monohydrate</td><td>Nacalai</td><td>26707-02</td><td></td></tr><tr><td>Photochemical reactor with RPR 350 nm lamps</td><td>Rayonet</td><td></td><td></td></tr><tr><td>Potassium Trioxalatoferrate (III) trihydrate</td><td>FUJIFILM Wako</td><td>W01SRM19-5000</td><td></td></tr><tr><td>Sodium Acetate Trihydrate</td><td>Nacalai</td><td>31115-05</td><td></td></tr><tr><td>Sodium Bicarbonate</td><td>FUJIFILM Wako</td><td>199-05985</td><td></td></tr><tr><td>Sulfuric Acid, 96-98%</td><td>FUJIFILM Wako</td><td>190-04675</td><td></td></tr><tr><td>Tris(3-hydroxypropyltriazolylmethyl)amine (THPTA)</td><td>ALDRICH</td><td>762342-100MG</td><td></td></tr><tr><td>tri-Sodium Citrate Dihydrate</td><td>Nacalai</td><td>31404-15</td><td></td></tr><tr><td>Xenon light source, MAX-303</td><td>Asahi Spectra</td><td></td><td></td></tr></tbody></table>

design, synthesis, and photochemical properties of clickable caged compounds

Caged compounds enable the photo-mediated manipulation of the cell physiology with high spatiotemporal resolution. However, the limited structural diversity of currently available caging groups and the difficulties in synthetic modification without sacrificing their photolysis efficiencies are obstacles to expanding the repertoire of caged compounds for live cell applications. As the chemical modification of coumarin-type photo-caging groups is a promising approach for the preparation of caged compounds with diverse physical and chemical properties, we report a method for the synthesis of clickable caged compounds that can be modified easily with various functional units via the copper(I)-catalyzed Huisgen cyclization. The modular platform molecule contains a (6-bromo-7-hydroxycoumarin-4-yl)methyl (Bhc) group as a photo-caging group, which exhibits a high photolysis efficiency compared to those of the conventional 2-nitrobenzyls. General procedures for the preparation of clickable caged compounds containing amines, alcohols, and carboxylates are presented. Additional properties such as the water solubility and cell targeting ability can be readily incorporated into clickable caged compounds. Furthermore, the physical and photochemical properties, including the photolysis quantum yield, were measured and were found to be superior to those of the corresponding Bhc caged compounds. The described protocol could therefore be considered a potential solution for the lack of structural diversity in the available caged compounds.

Clickable caged compounds of some biologically interesting molecules, including arachidonic acid and paclitaxel, were successfully synthesized (Figure 1)28,41. Additional properties such as the water solubility and cellular targeting ability were introduced into paBhcmoc-PTX via the copper(I)-catalyzed Huisgen cyclization (&#8220;Click&#8221; reaction) (Figure 2). These clickable caged PTXs were then photolyzed to produce their parent PTXs upon irradiation at 350 nm (Figure 3), and the physical and photochemical properties of the clickable caged compounds are summarized in Table 1. The quantum yields of clickable caged compounds 2&#697;-glc-paBhcmoc-PTX (&#934;dis 0.14) and paBhc-AA (&#934;dis 0.083) were more than twice those of conventional Bhc caged compounds 2&#697;-Bhcmoc-PTX (&#934;dis 0.040) and Bhc-AA (&#934;dis 0.038)43. In addition, an improved water solubility was observed for 2&#697;-glc-paBhcmoc-PTX, which contains a glucose moiety.
In live cell experiments, the targeting of paBhc-hex-FITC/Halo to the cultured mammalian cells transiently expressing a fusion protein of a HaloTag protein and epidermal growth factor receptor (EGFR) was achieved successfully. Green fluorescence of the fluorescein moiety of paBhc-hex-FITC/Halo was observed on the cell membrane (Figure 4). Photo-mediated modulation of the subcellular localization of a kinase was achieved using a paBhc caged compound. The translocation of diacylglycerol kinase &#947; (DGK&#947;) has been reported to be activated in the presence of arachidonic acid (AA)44. CHO-K1 cells transiently expressing GFP-DGK&#947; were treated with either AA or paBhc-AA (5). Addition of AA caused the modulation of the subcellular localization of DGK&#947; (Figure 5A,B). Similar changes in the localization of DGK&#947; were observed for the paBhc-AA-treated cells after exposure to UV light (Figure 5C,D).
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/60021/60021fig01.jpg" /> 
Figure 1: Preparation of the clickable caged compounds. 
(A) Reagents and conditions: a. ethyl 4-chloroacetoacetate/conc. H2SO4/rt/7 days/91% yield, b. 1 M HCl/reflux/3 days/97% yield. c. N-methylpropargylamine /HCHO/EtOH, then add (1) and heat at reflux for 17 h/79% yield. (B) Syntheses of the clickable caged amine, PTX, and arachidonic acid. <a href="https://www.jove.com/files/ftp_upload/60021/60021fig01large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 2" class="xfigimg" src="/files/ftp_upload/60021/60021fig02.jpg" /> 
Figure 2: Installation of functional units into clickable caged compounds. 
(A) Synthesis of a water-soluble caged PTX via the copper(I)-catalyzed Huisgen cyclization. (B) Structures of clickable caged compounds containing the HaloTag ligand for cellular targeting. <a href="https://www.jove.com/files/ftp_upload/60021/60021fig02large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 3" class="xfigimg" src="/files/ftp_upload/60021/60021fig03.jpg" /> 
Figure 3: Photolysis of 2&#697;-glc-paBhcmoc-PTX (6). 
Samples (10 &#956;M) in K-MOPS solution (pH 7.2) were irradiated at 350 nm. (A) Typical HPLC traces for the photolysis of 6 (measured at 254 nm). Samples were analyzed at the specified irradiation time. (B) Time course for the photolysis of 6. Blue circles show the consumption of 6. The solid line shows the least-squares curve fit for a simple decaying exponential for 6. Red squares show the yield of PTX. The error bars represent the standard deviation (&#177;SD). <a href="https://www.jove.com/files/ftp_upload/60021/60021fig03large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 4" class="xfigimg" src="/files/ftp_upload/60021/60021fig04.jpg" /> 
Figure 4: Fluorescence images of cultured mammalian cells incubated with paBhc-hex-FITC/Halo (8). 
Cells transfected with pcDNA3-Halo-EGFR were incubated with a 2 &#956;M solution of compound 8 at 37 &#176;C for 30 min. The images were obtained after repeated washing with PBS+. Mock-treated HEK293T cells (A: differential interference contrast (DIC) image and D: fluorescence image). HEK293T cells (B and E) and HeLa cells (C and F) transiently expressing Halo-EGFR (B and C: DIC images and E and F: fluorescence images). <a href="https://www.jove.com/files/ftp_upload/60021/60021fig04large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 5" class="xfigimg" src="/files/ftp_upload/60021/60021fig05.jpg" /> 
Figure 5: Fluorescence images after UV irradiation of the CHO-K1 cells incubated with Bhc caged arachidonic acid. CHO-K1 cells were transfected with a fusion protein DGK&#947;-EGFP. 
(A) A fluorescence image of the transfected cells. (B) 100 s after the addition of a 10 &#956;M solution of arachidonic acid. (C) Cells were incubated with a 10 &#956;M solution of paBhc-AA (5) at 37 &#176;C for 5 min. (D) 100 s after 20-s UV irradiation (330&#8211;385 nm). <a href="https://www.jove.com/files/ftp_upload/60021/60021fig05large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>compounds</td>
			<td>&#955;max (nm)a</td>
			<td>&#949;max (M-1 cm-1)b</td>
			<td>&#981;disc</td>
			<td>&#949;&#981;disd</td>
			<td>Solubility (&#956;M)e</td>
		</tr>
		<tr>
			<td>PTX</td>
			<td></td>
			<td></td>
			<td></td>
			<td></td>
			<td>1.0</td>
		</tr>
		<tr>
			<td>2&#39;-Bhcmoc-PTX</td>
			<td>340</td>
			<td>10500</td>
			<td>0.040</td>
			<td>400</td>
			<td>55</td>
		</tr>
		<tr>
			<td>2&#39;-paBhcmoc-PTX</td>
			<td>359</td>
			<td>9300</td>
			<td>0.059</td>
			<td>670</td>
			<td>8.3</td>
		</tr>
		<tr>
			<td>2&#39;-glc-Bhcmoc-PTX</td>
			<td>373</td>
			<td>12300</td>
			<td>0.14</td>
			<td>1280</td>
			<td>650</td>
		</tr>
		<tr>
			<td>Bhc-AA</td>
			<td>341</td>
			<td>10800</td>
			<td>0.038</td>
			<td>390</td>
			<td></td>
		</tr>
		<tr>
			<td>paBhc-AA</td>
			<td>366</td>
			<td>10300</td>
			<td>0.083</td>
			<td>750</td>
			<td></td>
		</tr>
	</tbody>
</table>
Table 1: Physical and photochemical properties of the clickable caged compounds. 
a. Absorption maximum (nm), b. Molar absorptivity at &#955;max (M&#8722;1 cm&#8722;1), c. Quantum yield of the disappearance of the starting materials at 350 nm, d. The product of molar absorptivity and the quantum yield of disappearance at 350 nm, e. The concentration of the saturated solution in K-MOPS (pH 7.2) (&#956;g mL&#8722;1).

Watch this Scientific Journal Video about Design, Synthesis, and Photochemical Properties of Clickable Caged Compounds at JoVE.com

Design, Synthesis, and Photochemical Properties of Clickable Caged Compounds

A protocol for the synthesis and measurement of the photochemical properties of modular caged compounds with clickable moieties is presented.

Caged compounds enable the photo-mediated manipulation of the cell physiology with high spatiotemporal resolution. However, the limited structural ...

design-synthesis-photochemical-properties-clickable-caged

Research

JoVE Journal

Chemistry

12.1K Views.  Toho University. A protocol for the synthesis and measurement of the photochemical properties of modular caged compounds with clickable moieties is presented.

Video: Design, Synthesis, and Photochemical Properties of Clickable Caged Compounds

Identification of Small Molecule-binding Proteins in a Native Cellular Environment by Live-cell Photoaffinity Labeling

Identifying the molecular target(s) of small molecules is a challenging but necessary step towards understanding their mechanism of action. While several target identification methods have been developed and used to successfully elucidate the binding proteins of a variety of small molecules, these techniques have drawbacks that make them unsuitable for detecting certain types of small molecule-target interactions. In particular, non-covalent interactions that depend on native cellular conditions, such as those of membrane proteins whose structures may be perturbed upon cell lysis, are often not amenable to affinity-based target identification methods. Here, we demonstrate a method wherein a probe containing a photolabile group is used to covalently crosslink to the small molecule binding protein within the environment of the live cell, allowing the detection and isolation of the target protein without the need for maintenance of the interaction after cell lysis. This technique is a valuable tool for studying biologically interesting small molecules with unknown mechanisms, both in the context of basic biology as well as drug discovery.

We describe here a method for identification of small molecule-binding proteins using photoaffinity labeling. The advantage of this technique is that binding and covalent labeling of the target proteins occurs within the live cellular environment, removing the risk of disrupting native protein structure and binding conditions upon cell lysis.

Identifying the molecular target(s) of small molecules is a challenging but necessary step towards understanding their mechanism of action. While several ...

Biochemistry

Efficient and Site-specific Antibody Labeling by Strain-promoted Azide-alkyne Cycloaddition

There are currently many chemical tools available to introduce chemical probes into proteins to study their structure and function. A useful method is protein conjugation by genetically introducing an unnatural amino acid containing a bioorthogonal functional group. This report describes a detailed protocol for site-specific antibody conjugation. The protocol includes experimental details for the genetic incorporation of an azide-containing amino acid, and the conjugation reaction by strain-promoted azide-alkyne cycloaddition (SPAAC). This strain-promoted reaction proceeds by simple mixing of the reacting molecules at physiological pH and temperature, and does not require additional reagents such as copper(I) ions and copper-chelating ligands. Therefore, this method would be useful for general protein conjugation and development of antibody drug conjugates (ADCs).

Here, we present a protocol to site-specifically introduce chemical probes into an antibody fragment by genetically incorporating an azide-containing amino acid, and subsequently coupling the azide with a chemical probe by strain-promoted azide-alkyne cycloaddition (SPAAC).

There are currently many chemical tools available to introduce chemical probes into proteins to study their structure and function. A useful method is ...

An Optimized Protocol for the Efficient Radiolabeling of Gold Nanoparticles by Using a 125I-labeled Azide Prosthetic Group

Here, we demonstrate a detailed protocol for the radiosynthesis of a 125I-labeled azide prosthetic group and its application to the efficient radiolabeling of DBCO-group-functionalized gold nanoparticles using a copper-free click reaction. Radioiodination of the stannylated precursor (2) was carried out by using [125I]NaI and chloramine T as an oxidant at room temperature for 15 min. After HPLC purification of the crude product, the purified 125I-labeled azide (1) was obtained with high radiochemical yield (75 &plusmn; 10%, n = 8) and excellent radiochemical purity (&gt;99%). For the synthesis of radiolabeled 13-nm-sized gold nanoparticles, the DBCO-functionalized gold nanoparticles (3) were prepared by using a thiolated polyethylene glycol polymer. A copper-free click reaction between 1 and 3 gave the 125I-labeled gold nanoparticles (4) with more than 95% of radiochemical yield as determined by radio-thin-layer chromatography (radio-TLC). These results clearly indicate that the present radiolabeling method using a strain-promoted copper-free click reaction will be useful for the efficient and convenient radiolabeling of DBCO-group-containing nanomaterials.

An Optimized Protocol for the Efficient Radiolabeling of Gold Nanoparticles by Using a 125I-labeled Azide Prosthetic Group

A detailed procedure for the synthesis of a 125I-labeled azide and the radiolabeling of dibenzocyclooctyne (DBCO)-group-conjugated, 13-nm-sized gold nanoparticles using a copper-free click reaction is described.

Here, we demonstrate a detailed protocol for the radiosynthesis of a 125I-labeled azide prosthetic group and its application to the efficient ...

Chemoselective Modification of Viral Surfaces via Bioorthogonal Click Chemistry

The modification of virus particles has received a significant amount of attention for its tremendous potential for impacting gene therapy, oncolytic applications and vaccine development.1,2,3 Current approaches to modifying viral surfaces, which are mostly genetics-based, often suffer from attenuation of virus production, infectivity and cellular transduction.4,5 Using chemoselective click chemistry, we have developed a straightforward alternative approach which sidesteps these issues while remaining both highly flexible and accessible.1,2
The goal of this protocol is to demonstrate the effectiveness of using bioorthogonal click chemistry to modify the surface of adenovirus type 5 particles. This two-step process can be used both therapeutically1 or analytically,2,6 as it allows for chemoselective ligation of targeting molecules, dyes or other molecules of interest onto proteins pre-labeled with azide tags. The three major advantages of this method are that (1) metabolic labeling demonstrates little to no impact on viral fitness,1,7 (2) a wide array of effector ligands can be utilized, and (3) it is remarkably fast, reliable and easy to access.1,2,7
In the first step of this procedure, adenovirus particles are produced bearing either azidohomoalanine (Aha, a methionine surrogate) or the unnatural sugar O-linked N-azidoacetylglucosamine (O-GlcNAz), both of which contain the azide (-N3) functional group. After purification of the azide-modified virus particles, an alkyne probe containing the fluorescent TAMRA moiety is ligated in a chemoselective manner to the pre-labeled proteins or glycoproteins. Finally, an SDS-PAGE analysis is performed to demonstrate the successful ligation of the probe onto the viral capsid proteins. Aha incorporation is shown to label all viral capsid proteins (Hexon, Penton and Fiber), while O-GlcNAz incorporation results in labeling of Fiber only.
In this evolving field, multiple methods for azide-alkyne ligation have been successfully developed; however only the two we have found to be most convenient are demonstrated herein &#x2013; strain-promoted azide-alkyne cycloaddition (SPAAC) and copper-catalyzed azide-alkyne cycloaddition (CuAAC) under deoxygenated atmosphere.

Adenovirus particles are engineered to contain either the unnatural amino acid analogue azidohomoalanine or the azido sugar O-GlcNAz. The azide group of each is chemoselectively ligated via "click" chemistry reactions as a means of viral surface modification.

The modification of virus particles has received a significant amount of attention for its tremendous potential for impacting gene therapy, oncolytic ...

Immunology and Infection

Optimizing the Genetic Incorporation of Chemical Probes into GPCRs for Photo-crosslinking Mapping and Bioorthogonal Chemistry in Live Mammalian Cells

The genetic incorporation of non-canonical amino acids (ncAAs) via amber stop codon suppression is a powerful technique to install artificial probes and reactive moieties onto proteins directly in the live cell. Each ncAA is incorporated by a dedicated orthogonal suppressor-tRNA/amino-acyl-tRNA-synthetase (AARS) pair that is imported into the host organism. The incorporation efficiency of different ncAAs can greatly differ, and be unsatisfactory in some cases. Orthogonal pairs can be improved by manipulating either the AARS or the tRNA. However, directed evolution of tRNA or AARS using large libraries and dead/alive selection methods are not feasible in mammalian cells. Here, a facile and robust fluorescence-based assay to evaluate the efficiency of orthogonal pairs in mammalian cells is presented. The assay allows screening tens to hundreds of AARS/tRNA variants with a moderate effort and within a reasonable time. Use of this assay to generate new tRNAs that significantly improve the efficiency of the pyrrolysine orthogonal system is described, along with the application of ncAAs to the study of G-protein coupled receptors (GPCRs), which are challenging objects for ncAA mutagenesis. First, by systematically incorporating a photo-crosslinking ncAA throughout the extracellular surface of a receptor, binding sites of different ligands on the intact receptor are mapped directly in the live cell. Second, by incorporating last-generation ncAAs into a GPCR, ultrafast catalyst-free receptor labeling with a fluorescent dye is demonstrated, which exploits bioorthogonal strain-promoted inverse Diels Alder cycloaddition (SPIEDAC) on the live cell. As ncAAs can be generally applied to any protein independently on its size, the method is of general interest for a number of applications. In addition, ncAA incorporation does not require any special equipment and is easily performed in standard biochemistry labs.

A facile fluorescence assay is presented to evaluate the efficiency of amino-acyl-tRNA-synthetase/tRNA pairs incorporating non-canonical amino-acids (ncAAs) into proteins expressed in mammalian cells. The application of ncAAs to study G-protein coupled receptors (GPCRs) is described, including photo-crosslinking mapping of binding sites and bioorthogonal GPCR labeling on live cells.

The genetic incorporation of non-canonical amino acids (ncAAs) via amber stop codon suppression is a powerful technique to install artificial probes and ...

Harnessing the Bioorthogonal Inverse Electron Demand Diels-Alder Cycloaddition for Pretargeted PET Imaging

Due to their exquisite affinity and specificity, antibodies have become extremely promising vectors for the delivery of radioisotopes to cancer cells for PET imaging. However, the necessity of labeling antibodies with radionuclides with long physical half-lives often results in high background radiation dose rates to non-target tissues. In order to circumvent this issue, we have employed a pretargeted PET imaging strategy based on the inverse electron demand Diels-Alder cycloaddition reaction. The methodology decouples the antibody from the radioactivity and thus exploits the positive characteristics of antibodies, while eschewing their pharmacokinetic drawbacks. The system is composed of four steps: (1) the injection of a mAb-trans-cyclooctene (TCO) conjugate; (2) a localization time period during which the antibody accumulates in the tumor and clears from the blood; (3) the injection of the radiolabeled tetrazine; and (4) the in vivo click ligation of the components followed by the clearance of excess radioligand. In the example presented in the work at hand, a 64Cu-NOTA-labeled tetrazine radioligand and a trans-cyclooctene-conjugated humanized antibody (huA33) were successfully used to delineate SW1222 colorectal cancer tumors with high tumor-to-background contrast. Further, the pretargeting methodology produces high quality images at only a fraction of the radiation dose to non-target tissue created by radioimmunoconjugates directly labeled with 64Cu or 89Zr. Ultimately, the modularity of this protocol is one of its greatest assets, as the trans-cyclooctene moiety can be appended to any non-internalizing antibody, and the tetrazine can be attached to a wide variety of radioisotopes.

The bioorthogonal inverse electron demand Diels-Alder cycloaddition has been harnessed to create an effective and modular pretargeted PET imaging strategy for cancer. In this protocol, the steps of this methodology are described in the context of a model system employing the colorectal cancer targeted antibody huA33 and a 64Cu-labeled radioligand.

Due to their exquisite affinity and specificity, antibodies have become extremely promising vectors for the delivery of radioisotopes to cancer cells for ...

Bioengineering

Spatiotemporally Controlled Nuclear Translocation of Guests in Living Cells Using Caged Molecular Glues as Photoactivatable Tags

The cell nucleus is one of the most important organelles as a subcellular drug-delivery target, since modulation of gene replication and expression is effective for treating various diseases. Here, we demonstrate light-triggered nuclear translocation of guests using caged molecular glue (CagedGlue-R) tags, whose multiple guanidinium ion (Gu+) pendants are protected by an anionic photocleavable group (butyrate-substituted nitroveratryloxycarbonyl; BANVOC). Guests tagged with CagedGlue-R are taken up into living cells via endocytosis and remain in endosomes. However, upon photoirradiation, CagedGlue-R is converted into uncaged molecular glue (UncagedGlue-R) carrying multiple Gu+ pendants, which facilitates the endosomal escape and subsequent nuclear translocation of the guests. This method is promising for site-selective nuclear-targeting drug delivery, since the tagged guests can migrate into the cytoplasm followed by the cell nucleus only when photoirradiated. CagedGlue-R tags can deliver macromolecular guests such as quantum dots (QDs) as well as small-molecule guests. CagedGlue-R tags can be uncaged with not only UV light but also two-photon near-infrared (NIR) light, which can deeply penetrate into tissue.

This protocol describes light-triggered nuclear translocation of guests in living cells using caged molecular glue tags. This method is promising for site-selective nuclear-targeting drug delivery.

The cell nucleus is one of the most important organelles as a subcellular drug-delivery target, since modulation of gene replication and expression is ...

Constructing Cyclic Peptides Using an On-Tether Sulfonium Center

In recent years, cyclic peptides have attracted increasing attention in the field of drug discovery due to their excellent biological activities, and, as a consequence, they are now used clinically. It is, therefore, critical to seek effective strategies for synthesizing cyclic peptides to promote their application in the field of drug discovery. This paper reports a detailed protocol for the efficient synthesis of cyclic peptides using on-resin or intramolecular (intermolecular) bisalkylation. Using this protocol, linear peptides were synthesized by taking advantage of solid-phase peptide synthesis with cysteine (Cys) and methionine (Met) coupled simultaneously on the resin. Further, cyclic peptides were synthesized via bisalkylation between Met and Cys using a tunable tether and an on-tether sulfonium center. The whole synthetic route can be divided into three major processes: the deprotection of Cys on the resin, the coupling of the linker, and the cyclization between Cys and Met in a trifluoroacetic acid (TFA) cleavage solution. Furthermore, inspired by the reactivity of the sulfonium center, a propargyl group was attached to the Met to trigger thiol-yne addition and form a cyclic peptide. After that, the crude peptides were dried and dissolved in acetonitrile, separated, and then purified by high-performance liquid chromatography (HPLC). The molecular weight of the cyclic peptide was confirmed by liquid chromatography-mass spectrometry (LC-MS), and the stability of the cyclic peptide combination with the reductant was further confirmed using HPLC. In addition, the chemical shift in the cyclic peptide was analyzed by 1H nuclear magnetic resonance (1H NMR) spectra. Overall, this protocol aimed to establish an effective strategy for synthesizing cyclic peptides.

This protocol presents the synthesis of cyclic peptides via bisalkylation between cysteine and methionine and the facile thiol-yne reaction triggered by the propargyl sulfonium center.

In recent years, cyclic peptides have attracted increasing attention in the field of drug discovery due to their excellent biological activities, and, as ...

Genetically-encoded Molecular Probes to Study G Protein-coupled Receptors

To facilitate structural and dynamic studies of G protein-coupled receptor (GPCR) signaling complexes, new approaches are required to introduce informative probes or labels into expressed receptors that do not perturb receptor function. We used amber codon suppression technology to genetically-encode the unnatural amino acid, p-azido-L-phenylalanine (azF) at various targeted positions in GPCRs heterologously expressed in mammalian cells. The versatility of the azido group is illustrated here in different applications to study GPCRs in their native cellular environment or under detergent solubilized conditions. First, we demonstrate a cell-based targeted photocrosslinking technology to identify the residues in the ligand-binding pocket of GPCR where a tritium-labeled small-molecule ligand is crosslinked to a genetically-encoded azido amino acid. We then demonstrate site-specific modification of GPCRs by the bioorthogonal Staudinger-Bertozzi ligation reaction that targets the azido group using phosphine derivatives. We discuss a general strategy for targeted peptide-epitope tagging of expressed membrane proteins in-culture and its detection using a whole-cell-based ELISA approach. Finally, we show that azF-GPCRs can be selectively tagged with fluorescent probes. The methodologies discussed are general, in that they can in principle be applied to any amino acid position in any expressed GPCR to interrogate active signaling complexes.

We genetically-encode the unnatural amino acid, p-azido-L-phenylalanine at various targeted positions in GPCRs and show the versatility of the azido group in different applications. These include a targeted photocrosslinking technology to identify residues in the ligand-binding pocket of a GPCR, and site-specific bioorthogonal modification of GPCRs with a peptide-epitope tag or fluorescent probe.

To facilitate structural and dynamic studies of G protein-coupled receptor (GPCR) signaling complexes, new approaches are required to introduce ...

Biology

Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors

REPLACE is a unique strategy developed to more effectively target protein-protein interactions (PPIs). It aims to expand available drug target space by providing improved methodology for the identification of inhibitors for such binding sites and which represent the majority of potential drug targets. The main goal of this paper is to provide a methodological overview of the use and application of the REPLACE strategy which involves computational and synthetic chemistry approaches. REPLACE is exemplified through its application to the development of non-ATP competitive cyclin dependent kinases (CDK) inhibitors as anti-tumor therapeutics. CDKs are frequently deregulated in cancer and hence are considered as important targets for drug development. Inhibition of CDK2/cyclin A in S phase has been reported to promote selective apoptosis of cancer cells in a p53 independent manner through the E2F1 pathway. Targeting the protein-protein interaction at the cyclin binding groove (CBG) is an approach which will allow the specific inhibition of cell cycle over transcriptional CDKs. The CBG is recognized by a consensus sequence derived from CDK substrates and tumor suppressor proteins termed the cyclin binding motif (CBM). The CBM has previously been optimized to an octapeptide from p21Waf (HAKRRIF) and then further truncated to a pentapeptide retaining sufficient activity (RRLIF). Peptides in general are not cell permeable, are metabolically unstable and therefore the REPLACE (REplacement with Partial Ligand Alternatives through Computational Enrichment) strategy has been applied in order to generate more drug-like inhibitors. The strategy begins with the design of Fragment ligated inhibitory peptides (FLIPs) that selectively inhibit cell cycle CDK/cyclin complexes. FLIPs were generated by iteratively replacing residues of HAKRRLIF/RRLIF with fragment like small molecules (capping groups), starting from the N-terminus (Ncaps), followed by replacement on the C-terminus. These compounds are starting points for the generation of non-ATP competitive CDK inhibitors as anti-tumor therapeutics.

We describe implementation of the REPLACE strategy for targeting protein-protein interactions. REPLACE is an iterative strategy involving synthetic and computational approaches for the conversion of optimized peptidic inhibitors into drug like molecules.

REPLACE is a unique strategy developed to more effectively target protein-protein interactions (PPIs). It aims to expand available drug target space by ...