TRANS-CYCLOOCTENES WITH HIGH REACTIVITY AND FAVORABLE PHYSIOCHEMICAL PROPERTIES
20230331652 · 2023-10-19
Assignee
Inventors
- Joseph M. Fox (Landenberg, PA, US)
- Jessica Pigga (Pawcatuck, CT, US)
- Samantha Jo Boyd (Wilmington, DE, US)
Cpc classification
C07D207/408
CHEMISTRY; METALLURGY
C07C35/21
CHEMISTRY; METALLURGY
International classification
C07C35/21
CHEMISTRY; METALLURGY
C07D207/408
CHEMISTRY; METALLURGY
Abstract
The present invention discloses a new class of trans-cyclooctenes (TCOs), “a-TCOs,” that are prepared in high yield via stereocontrolled 1,2-additions of nucleophiles to trans-cyclooct-4-enone, which itself was prepared on large scale in two steps from 1,5-cyclooctadiene. Computational transition state models rationalize the diastereoselectivity of 1,2-additions to deliver a-TCO products, which were also shown to be more reactive than standard TCOs and less hydrophobic than even a trans-oxocene analog. Illustrating the favorable physicochemical properties of a-TCOs, a fluorescent TAMRA derivative in live HeLa cells was shown to be cell-permeable through intracellular Diels-Alder chemistry and to washout more rapidly than other TCOs.
Claims
1. A trans-cyclooct-4-eneone having the following formula (2): ##STR00048## wherein the trans-cyclooct-4-eneone 2 characterized by .sup.1H NMR (400 MHz, CDCl.sub.3) includes peaks at 5.27 ppm and 2.91 ppm.
2. The trans-cyclooct-4-enone of claim 1, wherein the trans-cyclooct-4-enone is in an isolated form.
3. The trans-cyclooct-4-enone of claim 1, wherein the trans-cyclooct-4-enone is at least 90% pure.
4. The trans-cyclooct-4-enone of claim 1, produced by a photochemical flow method comprising irradiating cis-cyclooct-4-enone with light from a low-pressure mercury lamp for a time sufficient to form the trans-cyclooct-4-enone.
5. A substituted axial hydroxy-trans-cyclooctene, having the following formula (2a): ##STR00049## where R is selected from hydrogen, alkyl, aryl, and heteroaryl.
6. The substituted axial hydroxy-trans-cyclooctene of claim 5, wherein R is selected from hydrogen, allyl, acetate, cyano, acetohydrazide, hydroxyethyl, (prop-2-yn-1-yloxy)ethyl, amino ethyl, hydroxysuccinyl acetate, phenyl, and phenylethynyl.
7. The substituted axial hydroxy-trans-cyclooctene of claim 5, wherein the trans-cyclooctene exists as a single diastereoisomer.
8. The substituted axial hydroxy-trans-cyclooctene of claim 5 having one of the following structures: ##STR00050## ##STR00051##
9. An alpha-substituted trans-cyclooct-4-enone, having the formula: ##STR00052## where R′ is selected from the group consisting of alkyl, aryl, carboxylic acid, alkene, and alkyne.
10. An oxime conjugate having the following formula: ##STR00053## where R″ is selected from the group consisting of hydrogen, aryl, and alkyl.
11. The oxime conjugate of claim 10 having one of the following structures: ##STR00054##
12. A method of producing the substituted axial hydroxy-trans-cyclooctene of claim 5, the method comprising contacting trans-cyclooct-4-enone with a nucleophile for a stereocontrolled 1,2-addition of the nucleophile to the trans-cyclooct-4-enone, wherein nucleophilic addition to the trans-cyclooct-4-eneone take place exclusively from the equatorial-face of the trans-cyclooctennone to produce an axial hydroxy-trans-cyclooctene as a single diastereomer, wherein the nucleophile is a Grignard reagent, an organolithium, or an organozinc.
13. The method of claim 12, wherein nucleophile is selected from lithium phenyl acetylene, methyl α-lithioacetate, lithioacetonitrile, and lithium bis(trimethylsilyl)amide.
14. The method of claim 12, wherein the substituted axial hydroxy-trans-cyclooctene is produced as a single diastereoisomer.
15. The method of claim 12, wherein the substituted axial hydroxy-trans-cyclooctene is produced with a yield of at least 80%.
16. The method of claim 12, wherein the substituted axial hydroxy-trans-cyclooctene is at least 95% pure.
17. A method of producing the alpha-substituted trans-cyclooct-4-enone of claim 9 comprising treating a trans-cyclooct-4-enone, having the following formula (2), with a base followed by the addition of an electrophile, ##STR00055## wherein the trans-cyclooct-4-eneone 2 characterized by .sup.1H NMR (400 MHz, CDCl.sub.3) includes peaks at 5.27 ppm and 2.91 ppm.
18. The method of claim 17, where the electrophile is selected from alkyl halides, alkyl sulfonates, epoxides, aldehydes, or ketones.
19. The method of claim 17, wherein the substituted axial hydroxy-trans-cyclooctene is produced as a single diastereoisomer.
20. The method of claim 19, wherein the substituted axial hydroxy-trans-cyclooctene is produced with a yield of at least 80%.
Description
BRIEF DESCRIPTION OF THE DRAWINGS
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DETAILED DESCRIPTION OF THE INVENTION
[0045] As used herein, the term “alkyl group” refers to a saturated aliphatic hydrocarbon group such as a methyl group, an ethyl group, an n-propyl group, an isopropyl group, an n-butyl group, a sec-butyl group, or a tert-butyl group, and the alkyl group may have a substituent or no substituent. In an embodiment, the alkyl group is an unsubstituted alkyl. In another embodiment, the alkyl group is a substituted alkyl group. The term “substituted alkyl group” refers to an alkyl group bonded to a substituent, the additional substituent is not particularly limited. Examples of the additional substituent include an alkyl group, a halogen, an aryl group, and a heteroaryl group, and the same holds true in the description below. An alkyl group substituted with a halogen is also referred to as a haloalkyl group. The number of carbon atoms in the alkyl group is not particularly limited, and is preferably in the range of 1 to 12.
[0046] As used herein, the term “aryl group” refers to an aromatic hydrocarbon group such as a phenyl group, a biphenyl group, a naphthalene group, a terphenyl group. The aryl group may have a substituent or no substituent. In an embodiment, the aryl group is an unsubstituted aryl. In another embodiment, the aryl group is a substituted aryl group. The term “substituted aryl group” refers to an aryl group bonded to a substituent, the additional substituent is not particularly limited. An aryl group substituted with a halogen is also referred to as a haloaryl group. The number of carbon atoms in the aryl group is not particularly limited, and is preferably in the range of 6 to 14.
[0047] In a substituted phenyl group having two adjacent carbon atoms each having a substituent, the substituents may form a ring structure. The resulting group may correspond to any one or more of a “substituted phenyl group”, an “aryl group having a structure in which two or more rings are condensed”, and a “heteroaryl group having a structure in which two or more rings are condensed” depending on the structure.
[0048] As used herein, the term “heteroaryl group” refers to a cyclic aromatic group having one or a plurality of atoms other than carbon in the ring, such as a pyridyl group, a furanyl group, a thiophenyl group, a quinolinyl group, an isoquinolinyl group, a pyrazinyl group, a pyrimidyl group, a pyridazinyl group, a pyrrolyl group, an imidazolyl group, an oxazolyl group, an isoxazolyl group, a thiazolyl group, an isothiazolyl group, an indazolyl group, a benzofuranyl group, a benzothiophenyl or a triazinyl group. The heteroaryl group may have a substituent or no substituent. The number of carbon atoms in the heteroaryl group is not particularly limited, and is preferably in the range of 2 to 12.
[0049] As used herein, the term “halide” refers to an ion selected from fluoride, chloride, bromide, and iodide.
[0050] As used herein, the term “acyl group” refers to a functional group having an alkyl group, a cycloalkyl group, an alkenyl group, an alkynyl group, an aryl group, or a heteroaryl group bonded via a carbonyl group, such as an acetyl group, a propionyl group, a benzoyl group, or an acrylyl group, and these substituents may be further substituted. The number of carbon atoms in the acyl group is not particularly limited, and is 2 to 10.
[0051] As shown in
Experiment 1
[0052] Ketone 1 was prepared simply in a single step by the Wacker oxidation (5 mol % Pd(OAc).sub.2, AcOH, benzoquinone) of 1,5-cyclooctadiene 3 on multigram scale (
[0053] Computation was used to predict if nucleophilic addition to TCO 2 would be diastereoselective (
[0054] Nucleophilic additions with a diverse array of nucleophiles were preformed to create a library of a-TCOs (Scheme 1, shown in
[0055] The diastereoselective additions of 2 with methyl α-lithioacetate or lithioacetonitrile provided a straightforward path to introduce handles for conjugation via amide bond or ether formation. The reaction of ketone 2 with lithium bis(trimethylsilyl)amide (LiHMDS)/methyl acetate produced ester 9 in 86% yield. Similarly, the combination of 2 with LiHMDS and acetonitrile produced nitrile 10 in 98% yield. Hydrolysis of 9 with trimethyltin hydroxide followed by DIC-mediated coupling with N-hydroxysuccinimide gave NHS ester 11 in 89% yield (
[0056] a-TCO derivatives also display rapid kinetics in Diels-Alder reactions compared to most other TCOs. The kinetics for the reaction of a-TCO derivative 14 toward a 3,6-dipyridyl-s-tetrazinyl succinamic acid derivative 20 were measured by stopped flow kinetics at 25° C. in 95:5 PBS:MeOH (
[0057] The stability of a-TCO 14 is very similar to that of axial-5-hydroxy-trans-cyclooctene 4a, which is used broadly for applications in bioorthogonal chemistry. In MeOD, 35 mM solutions of both 14 and 4a are >99% stable after 1 week at room temperature (
[0058] The fluorescent conjugate TAMRA-a-TCO 12 was shown to be cell permeable through selective bioorthogonal reaction inside live cells using the HaloTag self-labeling platform (
[0059] The advantage of the increased hydrophilicity for a-TCO conjugates was demonstrated by comparing the washout times for fluorescent derivatives in mammalian cells. While TCO-derivatives offer rapid labeling kinetics, a consideration for labeling by fluorophore-tagged TCOs has been the background fluorescence due to non-covalent cellular binding that can be ameliorated only by extended washout times. More hydrophilic oxo- and dioxo-trans-cyclooctenes with backbone oxygens offer improvements, but are difficult to synthesize and, for dioxo-TCO, display reduced Diels-Alder kinetics. As shown in
[0060] In summary, a-TCOs are a class of trans-cyclooctenes with favorable physiochemical properties that can be prepared in high yield through the stereocontrolled additions of nucleophiles to trans-cyclooct-4-enone (2), a trans-cyclooctene that can be prepared on large scale in two steps from 1,5-cyclooctadiene. Computation was used to rationalize diastereoselectivity of 1,2-additions to deliver a-TCO products. The strategy can be applied to the synthesis of a range of usefully functionalized a-TCOs with high yield, selectivity. a-TCOs were also shown to be more reactive than standard TCOs and less hydrophobic than even hydrophilic oxo-TCO analogs. As a demonstration of the favorable physicochemical properties of a-TCOs, a fluorescent TAMRA derivative was shown to be cell-permeable by demonstrating intracellular Diels-Alder chemistry in live cells and to washout of HeLa cells more rapidly and completely than TCO and oxo-TCO analogs.
Experiment 2
[0061] Alkylation of 2 was carried out to produce an alpha-substituted trans-cyclooct-4-ene 20 with a variety of R groups, including but not limited to alkyl, benzylic, carboxylic acid, alkene, and alkyne. This included reaction of 2 with LiHMDS followed by addition of an alkylhalide electrophile.
##STR00010##
Experiment 3
[0062] .sup.1H NMR (400 MHz) spectrum of trans-cyclooct-4-eneone 2 in CDCl.sub.3 was taken and peaks were compared with those reported by Nagendrappa in Tetrahedron 1982, 38, 2429-2433. As shown in
[0063] Additionally, the structure of trans-cyclooct-4-eneone 2 of the present invention was unambiguously confirmed by converting 2 into axial-5-hydroxy-trans-cyclooctene, which is well known, commercially available, and has been converted into a crystallographically characterized derivative as described in FIG. 2 of Maksim Royzen, Glenn P. A. Yap, and Joseph M. Fox Journal of the American Chemical Society 2008 130 (12), 3760-3761, reproduced here as
[0064] Additionally, inventors also took the spectrum of both axial-5-hydroxy-trans-cyclooctene and equatorial-5-hydroxy-trans-cyclooctene, and compared to the spectral report by Nagendrappa. The spectra differ, but due to a large spectral window for the impure mixture of Nagendrappa, it is not clear if axial-5-hydroxy-trans-cyclooctene was a component of their mixture.
ASPECTS OF THE INVENTION
[0065] Certain illustrative, non-limiting aspects of the invention may be summarized as follows: [0066] Aspect 1. A trans-cyclooct-4-eneone having the following formula (2):
##STR00011## [0067] wherein the trans-cyclooct-4-eneone characterized by .sup.1H NMR (400 MHz, CDCl.sub.3) includes peaks at 5.27 ppm and 2.91 ppm. [0068] Aspect 2. The trans-cyclooct-4-enone of Aspect 1, wherein the trans-cyclooct-4-enone is in an isolated form. [0069] Aspect 3. The trans-cyclooct-4-enone of Aspect 1, wherein the trans-cyclooct-4-enone is at least 90% pure. [0070] Aspect 4. The trans-cyclooct-4-enone of Aspect 1, produced by a photochemical flow method comprising irradiating cis-cyclooct-4-enone with light from a low-pressure mercury lamp for a time sufficient to form the trans-cyclooct-4-enone. [0071] Aspect 5. A substituted axial hydroxy-trans-cyclooctene, having the following formula (2a):
##STR00012## [0072] where R is selected from hydrogen, alkyl, aryl, and heteroaryl. [0073] Aspect 6. The substituted axial hydroxy-trans-cyclooctene of Aspect 5, wherein R is selected from hydrogen, allyl, acetate, cyano, acetohydrazide, hydroxyethyl, (prop-2-yn-1-yloxy)ethyl, amino ethyl, hydroxysuccinyl acetate, phenyl, and phenylethynyl. [0074] Aspect 7. The substituted axial hydroxy-trans-cyclooctene of Aspect 5, wherein the trans-cyclooctene exists as a single diastereoisomer. [0075] Aspect 8. The substituted axial hydroxy-trans-cyclooctene of Aspect 5 having one of the following structures:
##STR00013## ##STR00014## [0076] Aspect 9. An alpha-substituted trans-cyclooct-4-enone, having the formula:
##STR00015## [0077] where R′ is selected from the group consisting of alkyl, aryl, carboxylic acid, alkene, and alkyne. [0078] Aspect 10. An oxime conjugate having the following formula:
##STR00016## [0079] where R″ is selected from the group consisting of hydrogen, alkyl, and aryl. [0080] Aspect 11. The oxime conjugate of Aspect 10 having one of the following structures:
##STR00017## [0081] Aspect 12. A method of producing the substituted axial hydroxy-trans-cyclooctene of Aspect 5, the method comprising contacting trans-cyclooct-4-enone with a nucleophile for a stereocontrolled 1,2-addition of the nucleophile to the trans-cyclooct-4-enone, wherein nucleophilic addition to the trans-cyclooct-4-eneone take place exclusively from the equatorial-face of the trans-cyclooctennone to produce an axial hydroxy-trans-cyclooctene as a single diastereomer, and wherein the nucleophile is a Grignard reagent, an organolithium, or an organozinc. [0082] Aspect 13. The method of Aspect 12, wherein the nucleophile is selected from lithium phenyl acetylene, methyl α-lithioacetate, lithioacetonitrile, and lithium bis(trimethylsilyl)amide. [0083] Aspect 14. The method of Aspect 12, wherein the substituted axial hydroxy-trans-cyclooctene is produced as a single diastereoisomer. [0084] Aspect 15. The method of Aspect 12, wherein the substituted axial hydroxy-trans-cyclooctene is produced in a yield of at least 80%. [0085] Aspect 16. The method of Aspect 12, wherein the substituted axial hydroxy-trans-cyclooctene is at least 95% pure. [0086] Aspect 17. A method of producing the alpha-substituted trans-cyclooct-4-enone of Aspect 9 comprising treating the trans-cyclooct-4-enone of Aspect 1 with a base followed by the addition of an electrophile. [0087] Aspect 18. The method of Aspect 17, where the electrophile is selected from alkyl halides, alkyl sulfonates, epoxides, aldehydes, or ketones. [0088] Aspect 19. The method of Aspect 17, wherein the substituted axial hydroxy-trans-cyclooctene is produced as a single diastereoisomer. [0089] Aspect 20. The method of Aspect 19, wherein the substituted axial hydroxy-trans-cyclooctene is produced with a yield of at least 80%.
[0090] As used herein, when an amount, concentration, or other value or parameter is given as either a range, preferred range, or a list of upper preferable values and lower preferable values, this is to be understood as specifically disclosing all ranges formed from any pair of any upper range limit or preferred value and any lower range limit or preferred value, regardless of whether ranges are separately disclosed. Where a range of numerical values is recited herein, unless otherwise stated, the range is intended to include the endpoints thereof, and all integers and fractions within the range. It is not intended that the scope of the invention be limited to the specific values recited when defining a range.
[0091] Within this specification, embodiments have been described in a way which enables a clear and concise specification to be written, but it is intended and will be appreciated that embodiments may be variously combined or separated without departing from the invention. For example, it will be appreciated that all preferred features described herein are applicable to all aspects of the invention described herein.
EXAMPLES
[0092] Examples of the present invention will now be described. The technical scope of the present invention is not limited to the examples described below.
[0093] Materials
[0094] Materials and their source are listed below:
[0095] Anhydrous methylene chloride, diethyl ether, and THF were obtained from an alumina column solvent purification system. Other reagents were purchased from commercial sources and used without further purification. 3-Methyl-6-(4-aminomethylphenyl)-s-tetrazine was purchased from Click Chemistry Tools.
[0096] Methods
[0097] Chromatography
[0098] Normal phase silica gel chromatography was performed on Silicycle Siliaflash P60 silica gel (40-63 μm, 60 Å) and reverse phase chromatography on prepacked Yamazen Universal Column C18-silica gel (40-60 μm, 120 Å) using automated chromatography (Teledyne Isco Combiflash Rf).
[0099] NMR Spectrometry
[0100] NMR spectra were obtained on a Bruker AV400 (.sup.1H: 400 MHz, .sup.13C: 101 MHz) and AV600 (.sup.1H: 600 MHz, .sup.13C: 150 MHz) instruments. Chemical shifts (δ) were reported in ppm and referenced according to the residual nondeuterated solvent peak: CDCl.sub.3 (7.26 ppm), benzene-d.sub.6 (7.16 ppm), MeOD (3.31 ppm), and DMSO-d.sub.6 (2.50 ppm) for .sup.1H NMR, and CDCl.sub.3 (77.0 ppm), benzene-d.sub.6 (128.0 ppm), MeOD (49.0 ppm), and DMSO-d.sub.6 (39.5 ppm) for .sup.13C NMR. Coupling constants (3) were reported to the nearest 0.1 Hz for the .sup.1H NMR spectra and the .sup.13C NMR resonances were proton decoupled. Peak multiplicities were reported as singlet (s), doublet (d), triplet (t), quartet (q), pentet (pent), multiplet (m), ‘broad’ (br), and ‘apparent’ (app). An APT pulse sequence was used for .sup.13C NMR, where the secondary (CH.sub.2) and quaternary (C) carbons appeared ‘up’, and tertiary (CH.sub.3) and primary (CH) carbons appeared ‘down’. Exceptions were for methine carbons of alkynes, which usually have the same phase as ‘normal’ methylene and quaternary carbons.
[0101] pD and pH Measurements
[0102] Phosphate buffered D.sub.2O (pD=7.4) was prepared by combining anhydrous sodium dihydrogen phosphate (NaH.sub.2PO.sub.4, 77.1 mg) and anhydrous disodium hydrogen phosphate (Na.sub.2HPO.sub.4, 204.4 mg) with 20 mL of D.sub.2O to make a 0.1 M solution. The pD was measured on a Fisher Scientific AB15 Plus pH meter and pH values were converted to pD by adding 0.4 units. The pD was adjusted to 7.4 with DCI (35 wt. % in D.sub.2O) and NaOD (40 wt. % in D.sub.2O) as necessary.
[0103] Stopped-Flow Kinetics Measurements
[0104] Stopped-flow kinetics measurements were performed on a SX18MV-R stopped-flow spectrophotometer (Applied Photophysics Ltd.) with temperature control (25° C.).
[0105] Mass Spectrometry
[0106] Mass spectrometry was conducted on a Waters GCT Premier and Thermo Q-Exactive Orbitrap.
GENERAL CONSIDERATIONS EXPERIMENTAL PROCEDURES
[0107] All reactions were conducted under a nitrogen atmosphere with glassware that was flame-dried under vacuum.
[0108] For purposes of long-term storage, trans-cyclooctene derivatives that are oils were stored as solutions in Et.sub.2O in a −20° C. freezer. cLogP calculations were carried out using ALOGPS 2.1 program (available online from Virtual Computational Chemistry Laboratory).
[0109] Photoisomerization Apparatus
[0110] A previously described photoisomerization protocol was utilized with some modification. A Southern New England Ultraviolet Company Rayonet® reactor (model RPR-100 or RPR-200) was stocked with 8 low-pressure mercury lamps (2537 Å), and a 500 mL quartz flask (Southern New England Ultraviolet Company) containing the reaction solution was suspended in the reactor. A Biotage® SNAP cartridge (‘50 g’) was used to house silica gel and AgNO.sub.3-silica gel. The bottom of the column was interfaced to PTFE tubing (⅛″ OD×0.063″ ID, flanged with a thermoelectric flanging tool), equipped with flangeless nylon fittings (¼-28 thread, IDEX part no. P-582), using a female luer (¼-28 thread, IDEX part no. P-628). The top of the column was interfaced using a male luer (¼-28 thread, IDEX part no. P-675). A fluid metering pump (Fluid Metering, Inc, model RP-D equipped with pumphead FMI R405) was interfaced to the PTFE tubing (IDEX, part no. U-510) and was used for recirculating the reaction solution through the photolysis apparatus.
[0111] Silver Nitrate Silica Gel
[0112] Flash silica gel (90 g, Silicycle, cat #R12030B, 60 Å) was suspended in 100 mL of water in a 2 L round bottomed flask. The flask was covered with aluminum foil and a silver nitrate (10 g) solution in water (10 mL) was added. The resulting mixture was thoroughly mixed. Water was evaporated under reduced pressure via rotary evaporation (bath temperature ˜65° C.) using a bump trap equipped with a coarse fritted disk. To remove the remaining traces of water, toluene (2×200 mL) was added and subsequently concentrated via rotary evaporation. The 10% silver nitrate adsorbed on silica gel was dried under vacuum overnight at room temperature then was stored in a dry, dark place.
Keto-TCO Synthesis
Example 1: (Z)-Cyclooct-4-enone (1)
[0113] ##STR00018##
[0114] (Z)-Cyclooct-4-enone (1) can be prepared by the oxidation of commercially available 5-hydroxy-cis-cyclooctene (Combi-Blocks, QB-7357) with Dess-Martin reagent. Alternatively, 1 can be prepared from 1,5-cyclooctadiene as described below.
[0115] A round bottom flask with a magnetic stir bar was charged with Pd(OAc).sub.2 (1.04 g, 4.62 mmol), benzoquinone (1.01 g, 9.27 mmol), acetic acid (462 mL), 1,5-cyclooctadiene (11.3 mL, 92.4 mmol), and hydrogen peroxide (30% in H.sub.2O, 15.7 mL, 138 mmol). After stirring for 20 hours at room temperature, the reaction mixture was diluted with 2 L of 1:1 ether/pentane which was then washed with H.sub.2O (4×500 mL) and 8 M NaOH (4×350 mL). All aqueous washes were chilled to 0° C., combined, then stirred for 15 minutes at 0° C. The combined aqueous washes were brought to room temperature and then were extracted with 1:1 ether/pentane until all product was removed from the aqueous phase (TLC monitored). The combined organic extracts were dried with MgSO.sub.4, filtered, and then concentrated by rotary evaporation. The residue was purified by silica gel chromatography (0-3% diethyl ether in hexanes) to afford 5.03 g (40.5 mmol, 44% yield) of a pale-yellow oil. NMR spectra were in agreement with previously reported data.
Example 2: (E)-Cyclooct-4-enone (2)
[0116] ##STR00019##
[0117] (Z)-Cyclooct-4-enone (4.00 g, 32.2 mmol), methyl benzoate (8.80 g, 64.6 mmol), and 400 mL of 15% Et.sub.2O in hexanes were added to a 500 mL quartz flask. The flask was placed in a Rayonet® reactor containing 8 low-pressure mercury lamps (2537 Å). and connected via PTFE tubing to a column (Biotage® SNAP, 50 g) and an FMI pump. Five Biotage® SNAP cartridge (‘50 g’) columns were each packed with 7 cm of dry silica gel and topped with 16.3 g of 10% silver nitrate silica gel. The FMI pump was set at a flow rate of 100 mL/minute and the first column was flushed with 400 mL of 15% Et.sub.2O in hexanes. The contents of the quartz flask were irradiated for 4 hours under continuous flow, after which the column was flushed with 20% Et.sub.2O in hexanes and dried by a stream of compressed air. The flushed contents were concentrated by rotary evaporation and the recovered starting material and methyl benzoate were added back into the quartz flask. The next column was connected to the tubing and the process was repeated for each column.
[0118] After flushing the fifth column, the 10% silver nitrate silica gel from all of the columns was combined. The contents were stirred in 400 mL of ammonium hydroxide and 400 mL of CH.sub.2Cl.sub.2 for 10 minutes. The silica gel was filtered off and the filtrate was transferred to a separatory funnel. The aqueous layer was extracted with CH.sub.2Cl.sub.2 then the combined organic phases were washed with water and brine. The organics were next dried with Na.sub.2SO.sub.4, filtered, and concentrated by rotary evaporation in a 10° C. water bath. The crude oil was purified by silica gel chromatography (0-5% Et.sub.2O in pentane) to afford 2.5 g (20.1 mmol, 62.5% yield) of the title compound as a pale-yellow oil. The product was stored as a 0.2 M solution in Et.sub.2O at −20° C. .sup.1H NMR (400 MHz, C.sub.6D.sub.6) δ 5.43 (ddd, J=15.3, 11.1, 3.6 Hz, 1H), 5.21 (ddd, J=15.7, 11.2, 3.6 Hz, 1H), 2.52-2.37 (m, 1H), 2.35-2.23 (m, 1H), 2.23-2.15 (m, 1H), 2.09-1.98 (m, 2H), 1.91-1.75 (m, 1H), 1.73-1.50 (m, 3H), 1.47-1.38 (m, 1H). .sup.13C NMR (101 MHz, C.sub.6D.sub.6) δ 214.2 (C), 133.8 (CH), 131.9 (CH), 49.1 (CH.sub.2), 43.2 (CH.sub.2), 34.6 (CH.sub.2), 33.5 (CH.sub.2), 28.3 (CH.sub.2). FTMS (ESI+) calculated [M+H].sup.+ for C.sub.8H.sub.13O 125.0966; found 125.0961.
[0119] Additionally, .sup.1H NMR spectrum of trans-cyclooct-4-enone 2 in CDCl.sub.3 was taken and peaks were compared with those reported by Nagendrappa in Tetrahedron 1982, 38, 2429-2433. As shown in
A-TCO Syntheses
Example 3: 5-ax-Hydroxy-trans-cyclooctene (4a)
[0120] ##STR00020##
[0121] Procedure 1: (E)-Cyclooct-4-enone (104 mg, 0.837 mmol) and 1.6 mL of anhydrous MeOH were added to a round bottom flask equipped with a magnetic stir bar. The reaction mixture was cooled in an ice bath, and then NaBH.sub.4 (66 mg, 1.7 mmol) was added in portions over the course of 10 minutes while stirring vigorously. The reaction mixture was removed from the ice bath and then stirred for 20 minutes before quenching with 1.2 mL of water at 0° C. The reaction mixture was brought to room temperature, extracted with ether, dried with Na.sub.2SO.sub.4, filtered, and concentrated by rotary evaporation. The crude oil was purified by silica gel chromatography (0-8% Et.sub.2O in hexanes) to afford 95.1 mg (0.754 mmol, 90% yield) of the title compound as a colorless oil.
[0122] Procedure 2: To a flame-dried, nitrogen-purged flask was added (E)-cyclooct-4-enone (31.4 mg, 0.253 mmol) in THF (2.5 mL). The flask was placed in an ice bath and LiAlH.sub.4 (12.5 mg, 0.329 mmol) was added in one portion. The mixture was allowed to stir at room temperature for 30 minutes, after which the flask was placed in an ice bath and the reaction mixture was quenched with water. The reaction solution was extracted with CH.sub.2Cl.sub.2, dried over MgSO.sub.4, filtered, and concentrated via rotary evaporation. The crude oil was purified by silica gel column chromatography (20% Et2O in hexanes) to afford 21.3 mg (0.169 mmol, 67% yield) of the title compound as a colorless oil.
[0123] NMR spectra were in agreement with previously reported data.
Example 4: 5-ax-Hydroxy-5-eq-propargyl-trans-cyclooctene (5)
[0124] ##STR00021##
[0125] Propargyl magnesium bromide was synthesized according to a previously published procedure. Zinc bromide (140 mg, 0.621 mmol) and ground magnesium turnings (650 mg, 26.7 mmol) were added to a round bottom flask that was then thoroughly flame dried under vacuum. The flask was then charged with Et.sub.2O (10 mL) and stirred vigorously. A solution of propargyl bromide (1.0 mL, 13 mmol) in 8 mL of Et.sub.2O was added dropwise at room temperature until the reaction initiated, after which it was chilled to 0° C. while the remaining solution was added at a flow rate of 13.5 mL/min. The reaction mixture was stirred at 0° C. for an additional hour and formed a light green supernatant.
[0126] A round bottom flask with a magnetic stir bar was flame dried and nitrogen purged. (E)-Cyclooct-4-enone (100 mg, 0.805 mmol) and 8 mL of dry THF were added and the flask was cooled by an ice bath. The propargyl magnesium bromide solution (3 mL) was added dropwise to the flask by syringe. The reaction was monitored by TLC and then quenched with 2.5 mL of saturated NH.sub.4Cl aqueous solution after 25 minutes. The aqueous phase was extracted with Et.sub.2O and then the combined organic phases were dried with MgSO.sub.4, filtered, and concentrated by rotary evaporation. The compound was purified by silica gel chromatography (0-4% ether in hexanes) to afford 113 mg (0.690 mmol, 86% yield) of the title compound as a colorless oil. .sup.1H NMR (400 MHz, C.sub.6D.sub.6) δ 5.68 (ddd, J=15.1, 10.6, 3.8 Hz, 1H), 5.40 (ddd, J=15.5, 11.3, 3.3 Hz, 1H), 2.39 (app dtd, J=12.3, 11.3, 4.5 Hz, 1H), 2.24-2.10 (m, 1H), 2.06-1.92 (m, 3H), 1.92-1.82 (m, 1H), 1.78-1.54 (m, 5H), 1.49 (ddd, J=14.0, 12.8, 4.9 Hz, 1H), 1.35 (s, 1H), 1.21 (app dd, J=15.6, 11.5 Hz, 1H). .sup.13C NMR (101 MHz, C.sub.6D.sub.6) δ 134.7 (CH), 132.3 (CH), 81.5 (C), 71.7 (C), 71.3 (CH), 47.3 (CH.sub.2), 39.1 (CH.sub.2), 38.9 (CH.sub.2), 34.4 (CH.sub.2), 30.8 (CH.sub.2), 27.8 (CH.sub.2). FTMS (ESI+) calculated [M+H].sup.+ for C.sub.11H.sub.17O, 165.1279; found 165.1271.
Example 5: 5-eq-Allyl-5-ax-hydroxy-trans-cyclooctene (6)
[0127] ##STR00022##
[0128] An oven-dried 4 mL vial equipped with a magnetic stir bar was charged with (E)-Cyclooct-4-enone (100 mg, 0.805 mmol), allyl bromide (99 μL, 1.17 mmol), DMF (800 μL), and 20 mesh zinc (79.0 mg, 1.21 mmol). The contents were stirred vigorously at room temperature to initiate the reaction which was indicated by a color change to brown (˜10 minutes). The reaction was monitored by TLC and quenched with saturated NH.sub.4Cl aqueous solution 20 minutes after initiation. The aqueous phase was extracted with Et.sub.2O then the combined extracts were dried with Na.sub.2SO.sub.4, filtered, and concentrated via rotary evaporation. The crude product was purified by silica gel chromatography (0-4% Et.sub.2O in hexanes) to afford 113 mg (0.681 mmol, 85% yield) of the title compound as a colorless oil. .sup.1H NMR (400 MHz, C.sub.6D.sub.6) δ 5.75 (ddt, J=17.3, 10.2, 7.3 Hz, 1H), 5.61 (ddd, J=15.9, 10.5, 3.7 Hz, 1H), 5.45 (ddd, J=15.9, 11.2, 3.3 Hz, 1H), 5.03 (dm, J=10.1 Hz, 1H), 4.96 (dm, J=17.2 Hz, 1H), 2.37 (app qd, J=11.8, 4.7 Hz, 1H), 2.25-2.10 (m, 1H), 2.05-1.90 (m, 3H), 1.85-1.52 (m, 5H), 1.40 (ddd, J=14.0, 12.8, 4.8 Hz, 1H), 1.18-1.03 (m, 1H), 0.88 (s, 1H). .sup.13C NMR (101 MHz, C.sub.6D.sub.6) δ 134.9 (CH), 134.2 (CH), 133.1 (CH), 118.3 (CH.sub.2), 71.8 (C), 53.6 (CH.sub.2), 48.0 (CH.sub.2), 39.0 (CH.sub.2), 34.6 (CH.sub.2), 30.9 (CH.sub.2), 27.8 (CH.sub.2). FTMS (ESI+) calculated [M+H].sup.+ for C.sub.11H.sub.19O 167.1436; found 167.1427.
Example 6: 5-ax-Hydroxy-5-eq-phenylethynyl-trans-cyclooctene (7)
[0129] ##STR00023##
[0130] Phenyl acetylene (88 μL, 0.80 mmol) and 2 mL of THF were added to a round bottom flask with a magnetic stir bar and was then cooled by a bath of dry ice/acetone. n-Butyllithium (350 μL, 2.5 M in hexane) was added dropwise followed by TMEDA (121 μL, 0.806 mmol) and the mixture was stirred for 1 hour at −78° C. (E)-Cyclooct-4-enone (50 mg, 0.403 mmol) in 50 μL of THF was added dropwise and the reaction mixture was stirred for 2.5 hours after which it was quenched with 1 mL of H.sub.2O and brought to room temperature. The product was extracted with EtOAc then the combined organic extracts were washed with brine, dried with Na.sub.2SO.sub.4, filtered, and concentrated via rotary evaporation. The crude product was purified by silica gel chromatography (0-5% EtOAc in hexanes) to afford 84 mg (0.37 mmol, 92% yield) of title compound as a thick, colorless oil. .sup.1H NMR (400 MHz, C.sub.6D.sub.6) δ7.45-7.38 (m, 2H), 7.05-6.93 (m, 3H), 5.76 (ddd, J=15.4, 11.1, 3.8 Hz, 1H), 5.42 (ddd, J=15.6, 11.2, 3.3 Hz, 1H), 2.55-2.32 (m, 3H), 2.19-2.09 (m, 1H), 2.02-1.79 (m, 3H), 1.73 (app td, J=11.3, 4.6 Hz, 1H), 1.68-1.55 (m, 2H), 1.31 (s, 1H). .sup.13C NMR (101 MHz, C.sub.6D.sub.6) δ 135.7 (CH), 131.8 (CH), 131.3 (CH), 128.6 (CH), 128.3 (CH), 123.9 (C), 98.8 (C), 81.9 (C), 68.2 (C), 49.6 (CH.sub.2), 42.1 (CH.sub.2), 34.1 (CH.sub.2), 30.4 (CH.sub.2), 28.1 (CH.sub.2). FTMS (ESI+) calculated [M+H].sup.+ for C.sub.16H.sub.19O 227.1436; found 227.1426.
Example 7: 5-ax-Hydroxy-5-eq-phenyl-trans-cyclooctene (8)
[0131] ##STR00024##
[0132] A round bottom flask equipped with a magnetic stir bar was charged with phenyl bromide (84 μL, 0.806 mmol) and 1.6 mL of THF. The flask was then cooled by a bath of dry ice/acetone. n-Butyllithium (350 μL, 2.5 M in hexanes) was added dropwise and the reaction mixture was stirred for 30 minutes. (E)-Cyclooct-4-enone (50 mg, 0.403 mmol) in 100 μL of THF was added dropwise. The reaction was monitored by TLC and quenched after 45 minutes with 1 mL of saturated NH.sub.4Cl aqueous solution. The product was extracted with Et.sub.2O, dried with Na.sub.2SO.sub.4, filtered, and concentrated via rotary evaporation. The crude oil was purified via silica gel chromatography (0-5% EtOAc in hexanes) to afford 80 mg (0.40 mmol, 98% yield) of the title compound as a white solid. .sup.1H NMR (400 MHz, C.sub.6D.sub.6) δ 7.33 (dd, J=8.6, 1.3 Hz, 2H), 7.25-7.18 (m, 2H), 7.12-7.04 (m, 1H), 5.65-5.45 (m, 2H), 2.38-2.21 (m, 1H), 2.17-2.07 (m, 1H), 2.00-1.88 (m, 2H), 1.88-1.78 (m, 2H), 1.78-1.56 (m, 3H), 1.55-1.43 (m, 1H), 1.29 (s, 1H). .sup.13C NMR (101 MHz, C.sub.6D.sub.6) δ 156.0 (C), 134.5 (CH), 132.9 (CH), 128.3 (CH), 125.9 (CH), 123.6 (CH), 74.1 (C), 50.8 (CH.sub.2), 42.2 (CH.sub.2), 34.2 (CH.sub.2), 31.3 (CH.sub.2), 28.3 (CH.sub.2). FTMS (ESI+) calculated [M+H].sup.+ for C.sub.14H.sub.19O 203.1436; found 203.1427.
Example 8: (E)-Methyl-2-(1-ax-hydroxycyclooct-4-en-1-yl)acetate (9)
[0133] ##STR00025##
[0134] A round bottom flask equipped with a magnetic stir bar was charged with LiHMDS (4.1 mL, 1M in THF) and cooled by a bath of dry ice/acetone. Methyl acetate (0.3 mL, 3.72 mmol) was added dropwise and the reaction mixture was stirred for 30 minutes. (E)-Cyclooct-4-enone (308 mg, 2.48 mmol) in 250 μL of THF was added dropwise over 10 minutes. The reaction mixture was stirred for 3 hours then quenched with 3 mL of saturated aq. NH.sub.4Cl and brought to room temperature. The product was extracted from the aqueous phase with Et.sub.2O, dried with MgSO.sub.4, filtered, and concentrated via rotary evaporation. The crude product was purified by silica gel chromatography using 30% CH.sub.2Cl.sub.2 in hexanes to elute traces of starting material then was changed to 5% Et.sub.2O in hexanes. The purification afforded 423 mg (2.14 mmol, 86% yield) of the title compound as a white solid. .sup.1H NMR (400 MHz, C.sub.6D.sub.6) δ 5.97 (ddd, J=15.4, 11.3, 3.7 Hz, 1H), 5.44 (ddd, J=15.4, 11.3, 3.3 Hz, 1H), 3.76 (s, 1H), 3.19 (s, 3H), 2.67 (app qd, J=11.8, 4.8 Hz, 1H), 2.29-2.22 (m, 1H), 2.13 (app d, J=15.8 Hz, 2H), 2.04-1.89 (m, 2H), 1.83-1.70 (m, 2H), 1.68-1.59 (m, 1H), 1.49 (dd, J=15.1, 6.6 Hz, 1H), 1.35 (td, J=13.3, 4.8 Hz, 1H), 1.26 (dd, J=15.2, 11.8 Hz, 1H). .sup.13C NMR (101 MHz, C.sub.6D.sub.6) δ 173.9 (C), 135.5 (CH), 131.5 (CH), 70.9 (C), 51.1 (CH.sub.3), 50.3 (CH.sub.2), 47.9 (CH.sub.2), 39.7 (CH.sub.2), 34.7 (CH.sub.2), 30.7 (CH.sub.2), 27.6 (CH.sub.2). FTMS (ESI+) calculated [M+H].sup.+ for C.sub.11H.sub.19O.sub.3 199.1334; found 199.1325.
Example 9: (E)-2-(1-ax-Hydroxycyclooct-4-en-1-yl)acetonitrile (10)
[0135] ##STR00026##
[0136] A round bottom flask equipped with a magnetic stir bar was charged with LiHMDS (17.7 mL, 1 M in THF) and THF (7.6 mL) and was then cooled by a bath of dry ice/acetone. Anhydrous acetonitrile (841 μL, 16.1 mmol) was added dropwise and the reaction mixture was stirred for 30 minutes. (E)-Cyclooct-4-enone (200 mg, 1.61 mmol) in THF (2.1 mL) was added dropwise to the flask over 15 minutes. The reaction was monitored by TLC and a change in color from yellow to orange was observed. The reaction mixture was quenched after 2 hours with 5 mL of saturated NH.sub.4Cl aqueous solution then brought to room temperature. The aqueous layer was extracted with Et.sub.2O, dried with MgSO.sub.4, filtered, and concentrated via rotary evaporation. The crude oil was purified by silica gel chromatography (10% EtOAc in hexanes) to afford 261 mg (1.58 mmol, 98% yield) of the title compound as a white solid. .sup.1H NMR (400 MHz, C.sub.6D.sub.6) δ 5.31 (ddd, J=16.0, 10.6, 3.7 Hz, 1H), 5.20 (ddd, J=15.9, 10.9, 3.2 Hz, 1H), 2.13-1.96 (m, 2H), 1.85-1.75 (m, 1H), 1.63-1.51 (m, 4H), 1.48-1.40 (m, 2H), 1.37-1.21 (m, 2H), 1.10-0.96 (m, 2H). .sup.13C NMR (101 MHz, C.sub.6D.sub.6) δ 134.3 (CH), 132.4 (CH), 117.7 (C), 71.2 (C), 46.8 (CH.sub.2), 38.7 (CH.sub.2), 36.8 (CH.sub.2), 33.9 (CH.sub.2), 30.3 (CH.sub.2), 27.4 (CH.sub.2). FTMS (ESI+) calculated [M+H].sup.+ for C.sub.10H.sub.16NO 166.1232; found 166.1224.
Example 10A: (E)-N-Hydroxysuccinyl 2-(1-ax-hydroxycyclooct-4-en-1-yl)acetate (11)
[0137] ##STR00027##
[0138] Procedure 1: A round bottom flask equipped with a magnetic stir bar and a condenser was charged with (E)-methyl-2-(1-ax-hydroxycyclooct-4-en-1-yl)acetate (412 mg, 2.08 mmol), Me.sub.3SnOH (3.8 g, 21 mmol), and dichloroethane (21 mL). The reaction flask was immersed in an 80° C. oil bath for 5 hours then was cooled to room temperature. The reaction mixture was directly loaded onto a silica gel column and chromatographed (20-50% EtOAc in hexanes) to afford a carboxylic acid intermediate as a white solid that was used directly in the next step. To the white solid in CH.sub.2Cl.sub.2 (21 mL) was added N-hydroxysuccinimide (359 mg, 3.12 mmol) and N,N′-diisopropylcarbodiimide (0.49 mL, 3.12 mmol). The mixture was stirred at room temperature and monitored by TLC. It was quenched with 8 mL of H.sub.2O after 20 minutes of stirring. The product was extracted from the aqueous phase with CH.sub.2Cl.sub.2, washed with brine, dried with Na.sub.2SO.sub.4, filtered, and concentrated via rotary evaporation. The crude product was purified by silica gel chromatography (0-2% acetone in CH.sub.2Cl.sub.2) to afford 521 mg (1.85 mmol, 89% yield) of the title compound as a white solid.
Example 10B: (E)-N-Hydroxysuccinyl 2-(1-ax-hydroxycyclooct-4-en-1-yl)acetate (11)
[0139] ##STR00028##
[0140] Procedure 2: A 7 mL vial equipped with a magnetic stir bar was charged with (E)-methyl-2-(1-ax-hydroxycyclooct-4-en-1-yl)acetate (100 mg, 0.505 mmol), 2.5 mL of 3:1 MeOH/H.sub.2O, and lithium hydroxide monohydrate (64 mg, 1.52 mmol). The reaction mixture was stirred for 48 hours. The methanol was removed by rotary evaporation and aqueous solution was diluted with 4 mL of ethyl acetate. The mixture was acidified to ˜pH 4 via the dropwise addition of 2M HCl while stirring vigorously. The ethyl acetate was removed, and the aqueous layer was extracted with ethyl acetate several more times. The acidification and extraction processes were repeated until all product was extracted (TLC monitored). The combined organic layers were washed with brine, dried with Na.sub.2SO.sub.4, filtered, and concentrated by rotary evaporation to afford a carboxylic acid intermediate as a white solid that was used directly in the next step. The solid was diluted in 2.9 mL of CH.sub.2Cl.sub.2 and transferred to a 50 mL round bottom flask. N-hydroxysuccinimide (50 mg, 0.432 mmol) was added followed by N,N′-diisopropylcarbodiimide (68 μL, 0.432 mmol). The reaction mixture was stirred at room temperature and monitored by TLC. It was quenched with 2 mL of H.sub.2O after 20 minutes. The aqueous layer was extracted with CH.sub.2Cl.sub.2, the organics were washed with brine then dried with Na.sub.2SO.sub.4, filtered, and concentrated by rotary evaporation. The crude product was purified by silica gel chromatography (0-2% acetone in CH.sub.2Cl.sub.2) to afford 66 mg (0.23 mmol, 46% yield) of the title compound as a white solid.
[0141] .sup.1H NMR (400 MHz, C.sub.6D.sub.6) δ 5.75 (ddd, J=15.1, 10.9, 3.7 Hz, 1H), 5.36 (ddd, J=15.4, 11.4, 3.3 Hz, 1H), 2.55 (s, 1H), 2.50 (app qd, J=12.1, 5.0 Hz, 1H), 2.29 (d, J=14.7 Hz, 1H), 2.25 (d, J=14.7 Hz, 1H), 2.20-2.07 (m, 1H), 2.03-1.91 (m, 1H), 1.91-1.78 (m, 2H), 1.81-1.34 (m, 8H), 1.28 (dd, J=15.2, 11.6 Hz, 1H). .sup.13C NMR (101 MHz, C.sub.6D.sub.6) δ 168.9 (C), 167.9 (C), 135.2 (CH), 131.6 (CH), 71.8 (C), 48.6 (CH.sub.2), 47.5 (CH.sub.2), 39.0 (CH.sub.2), 34.4 (CH.sub.2), 30.6 (CH.sub.2), 27.6 (CH.sub.2), 25.2 (CH.sub.2). FTMS (ESI+) calculated [M+H].sup.+ for C.sub.14H.sub.20NO.sub.5 282.1341; found 282.1340.
Example 11: (R,E)-2-(6-(dimethylamino)-3-(dimethyliminio)-3H-xanthen-9-yl)-5-((5-(2-(1-hydroxycyclooct-4-en-1-yl)acetamido)pentyl)carbamoyl)benzoate (TAMRA-a-TCO) (12)
[0142] ##STR00029##
[0143] To a solution of 5-TAMRA Cadaverine TFA salt (5.1 mg, 8.1 μmol), CH.sub.2Cl.sub.2 (4 mL), and triethylamine (5.6 μL, 40 μmol) in a 25 mL vial was added (E)-N-hydroxysuccinyl-2-(1-ax-hydroxycyclooct-4-en-1-yl)acetate (5.3 mg, 19 μmol) in 1.5 mL of CH.sub.2Cl.sub.2. The reaction mixture was stirred for 30 minutes at room temperature before concentrating by rotary evaporation and redissolving in a minimal amount of 1:1 MeOH/H.sub.2O. The solution was directly injected onto a revered phase prepackaged C-18 column (14 g) and the separation was conducted on the Teledyne Isco (Combiflash® RF) using a 0-100% MeOH in H.sub.2O gradient. The fractions containing product were concentrated using the Biotage® V-10 Touch evaporation system to afford 4.3 mg (6.3 μmol, 79% yield) the title product as a purple solid. .sup.1H NMR (600 MHz, MeOD) δ 8.51 (d, J=1.8 Hz, 1H), 8.04 (dd, J=7.9, 1.9 Hz, 1H), 7.36 (d, J=7.9 Hz, 1H), 7.26 (d, J=9.5 Hz, 2H), 7.02 (dd, J=9.4, 2.5 Hz, 2H), 6.93 (d, J=2.5 Hz, 2H), 5.64 (ddd, J=14.6, 10.5, 3.6 Hz, 1H), 5.51 (ddd, J=14.7, 11.1, 2.9 Hz, 1H), 3.46 (t, J=7.0 Hz, 2H), 3.28 (s, 12H), 3.22 (t, J=6.9 Hz, 2H), 2.43 (qd, J=12.0, 4.6 Hz, 1H), 2.26-2.16 (m, 3H), 2.04-1.99 (m, 1H), 1.94-1.88 (m, 1H), 1.85-1.75 (m, 2H), 1.74-1.65 (m, 5H), 1.63-1.55 (m, 2H), 1.51-1.43 (m, 3H). FTMS (ESI+) calculated [M+H].sup.+ for C.sub.40H.sub.49N.sub.4O.sub.6 681.3652; found 681.3644.
Example 12: (E)-2-(1-ax-Hydroxycyclooct-4-en-1-yl)acetohydrazide (13)
[0144] ##STR00030##
[0145] A round bottom flask equipped with a magnetic stir bar was charged with (E)-N-hydroxysuccinyl-2-(1-ax-hydroxycyclooct-4-en-1-yl)acetate (50 mg, 0.18 mmol), THF (1.8 mL), and hydrazine monohydrate (17.4 μL, 0.355 mmol). The reaction was monitored by TLC and concentrated after 20 minutes of stirring. The crude mixture was purified by silica gel chromatography (0-2.5% MeOH in CH.sub.2Cl.sub.2) to afford 35 mg (0.18 mmol, quant.) of the title compound as a white solid. The compound was stored at −20° C. as a solution in Et.sub.2O. .sup.1H NMR (400 MHz, DMSO) δ 5.56 (ddd, J=15.6, 10.2, 3.2 Hz, 1H), 5.44 (ddd, J=15.9, 10.9, 3.2 Hz, 1H), 3.52 (br s, 4H), 2.32 (app qd, J=11.5, 4.6 Hz, 1H), 2.20-2.09 (m, 1H), 2.06 (app d, J=2.3 Hz, 2H), 1.98-1.88 (m, 1H), 1.86-1.76 (m, 1H), 1.76-1.65 (m, 2H), 1.65-1.51 (m, 3H), 1.39-1.26 (m, 1H). .sup.13C NMR (101 MHz, DMSO) δ 171.6 (C), 134.9 (CH), 131.7 (CH), 71.0 (C), 49.4 (CH.sub.2), 47.6 (CH.sub.2), 39.0 (CH.sub.2), 34.2 (CH.sub.2), 30.2 (CH.sub.2), 27.2 (CH.sub.2). FTMS (ESI+) calculated [M+H].sup.+ for C.sub.10H.sub.19N.sub.2O.sub.2 199.1446; found 199.1436.
Example 13: 5-ax-Hydroxy-5-eq-(2-hydroxyethyl)-trans-cyclooctene (14)
[0146] ##STR00031##
[0147] A Schlenk flask equipped with a magnetic stir bar was charged with LiAlH.sub.4 (57.3 mg, 1.51 mmol) and THF (2.2 mL) then chilled to 0° C. A solution of (E)-methyl-2-(1-ax-hydroxycyclooct-4-en-1-yl)acetate (100 mg, 0.505 mmol) in THF (0.55 mL) was added to the flask dropwise and some bubbling was observed. After addition, the mixture was immediately diluted with 6 mL of THF then quenched by the dropwise addition of 1.2 mL of water and 1.2 mL of 10% NaOH in water. The mixture was stirred for 5 minutes then allowed to warm to room temperature, after which Na.sub.2SO.sub.4 was added. The reaction mixture was stirred another 5 minutes before filtering, rinsing the solids with Et.sub.2O, and concentrating via rotary evaporation. The product was purified by silica gel chromatography (20-40% Et.sub.2O in hexanes) to afford 76 mg (0.45 mmol, 89% yield) of the title compound as a white solid. .sup.1H NMR (600 MHz, C.sub.6D.sub.6) δ 5.57 (ddd, J=15.7, 10.7, 3.8 Hz, 1H), 5.47 (ddd, J=15.8, 11.2, 3.3 Hz, 1H), 3.63-3.47 (m, 2H), 2.41 (qd, J=12.0, 4.9 Hz, 1H), 2.23 (s, 1H), 2.21-2.14 (m, 1H), 2.06-2.01 (m, 1H), 2.01-1.95 (m, 1H), 1.88-1.81 (m, 1H), 1.79-1.69 (m, 2H), 1.66-1.54 (m, 2H), 1.43 (ddd, J=14.3, 7.3, 4.4 Hz, 1H), 1.33-1.24 (m, 2H), 1.13-1.07 (m, 1H). .sup.13C NMR (101 MHz, C.sub.6D.sub.6) δ 133.9 (CH), 133.4 (CH), 73.5 (C), 60.0 (CH.sub.2), 48.13 (CH.sub.2), 48.08 (CH.sub.2), 39.3 (CH.sub.2), 34.5 (CH.sub.2), 30.7 (CH.sub.2), 27.5 (CH.sub.2). FTMS (ESI+) calculated [M+H].sup.+ for C.sub.10H.sub.19O.sub.2 171.1385; found 171.1376.
Example 14: 5-ax-Hydroxy-5-eq-(2-(prop-2-yn-1-yloxy)ethyl)-trans-cyclooctene (15)
[0148] ##STR00032##
[0149] A round bottom flask equipped with a magnetic stir bar was charged with 5-ax-hydroxy-5-eq-(2-hydroxyethyl)-trans-cyclooctene (30 mg, 0.18 mmol) and THF (0.9 mL). NaH (14 mg, 0.35 mmol, 60% in mineral oil) was added in one portion and the reaction mixture was stirred for 30 minutes. Propargyl bromide (38 μL, 0.35 mmol, 9.2 mol/L in toluene) was added dropwise followed by the addition of tetrabutylammonium iodide (2.8 mg, 8.8 μmol). The reaction was monitored by TLC and quenched with 1 mL of water after stirring 1 hour. The product was extracted from the aqueous phase with Et.sub.2O, washed with brine, dried with Na.sub.2SO.sub.4, filtered, and concentrated by rotary evaporation. The product was purified by silica gel chromatography (0-10% Et.sub.2O in hexanes) to afford 35.1 mg (0.167 mmol, 96% yield) of the title compound as a pale-yellow oil. .sup.1H NMR (600 MHz, C.sub.6D.sub.6) δ 5.82 (ddd, J=15.3, 11.1, 3.8 Hz, 1H), 5.51 (ddd, J=15.4, 11.4, 3.4 Hz, 1H), 3.68 (dd, J=15.9, 2.3 Hz, 1H), 3.67 (dd, J=15.9, 2.3 Hz, 1H), 3.47-3.37 (m, 2H), 2.57 (app qd, J=11.9, 4.8 Hz, 1H), 2.29-2.24 (m, 1H), 2.12 (s, 1H), 2.07-2.01 (m, 1H), 1.98 (t, J=2.4 Hz, 1H), 1.94-1.75 (m, 3H), 1.68-1.58 (m, 2H), 1.55 (ddd, J=14.3, 6.8, 5.7 Hz, 1H), 1.46 (app dt, J=14.2, 6.0 Hz, 1H), 1.36 (app td, J=13.1, 4.7 Hz, 1H), 1.18 (dd, J=14.4, 11.6 Hz, 1H). .sup.13C NMR (151 MHz, C.sub.6D.sub.6) δ 134.7 (CH), 132.6 (CH), 79.9 (C), 74.7 (CH), 72.1 (C), 67.2 (CH.sub.2), 58.2 (CH.sub.2), 48.2 (CH.sub.2), 46.8 (CH.sub.2), 39.4 (CH.sub.2), 34.8 (CH.sub.2), 30.8 (CH.sub.2), 27.6 (CH.sub.2). FTMS (ESI+) calculated [M+H].sup.+ for C.sub.13H.sub.21O.sub.2 209.1541; found 209.1536.
Example 15: 5-ax-Hydroxy-5-eq-(2-aminoethyl)-trans-cyclooctene (16)
[0150] ##STR00033##
[0151] A round bottom flask equipped with a magnetic stir bar was charged with (E)-2-(1-ax-hydroxycyclooct-4-en-1-yl)acetonitrile (50 mg, 0.30 mmol) and Et.sub.2O (3.4 mL) then was chilled to −15° C. LiAlH.sub.4 (354 mg, 0.91 mmol) was added in portions and the reaction was monitored by TLC. The mixture was quenched after 15 minutes of stirring with a 1 drop of water followed by 2 drops of 10% aq. NaOH and 0.1 mL of water. The reaction mixture was warmed to room temperature and stirred for 10 minutes. MgSO.sub.4 was added and the mixture was stirred another 15 minutes. The solids were filtered off and rinsed with ethyl acetate. The product was concentrated via rotary evaporation to afford 48 mg (0.28 mmol, 93% yield) of a colorless oil. .sup.1H NMR (400 MHz, C.sub.6D.sub.6) δ 6.08 (ddd, J=15.5, 11.0, 3.8 Hz, 1H), 5.61 (ddd, J=15.5, 11.6, 3.6 Hz, 1H), 2.84 (app qd, J=11.6, 4.2 Hz, 1H), 2.49-2.32 (m, 3H), 2.25-2.01 (m, 2H), 2.00-1.83 (m, 2H), 1.79-1.69 (m, 1H), 1.63 (dd, J=15.0, 6.9 Hz, 1H), 1.41 (app td, J=13.1, 4.7 Hz, 1H), 1.33-1.16 (m, 2H), 1.15-1.04 (m, 1H). .sup.13C NMR (101 MHz, C.sub.6D.sub.6) δ 135.1 (CH), 132.4 (CH), 72.9 (C), 49.3 (CH.sub.2), 47.1 (CH.sub.2), 39.9 (CH.sub.2), 38.4 (CH.sub.2), 35.2 (CH.sub.2), 31.0 (CH.sub.2), 27.5 (CH.sub.2). FTMS (ESI+) calculated [M+H].sup.+ for C.sub.10H.sub.20NO 170.1544; found 170.1539.
Example 16: (R,E)-N-(2-(2,5-dioxo-2,5-dihydro-1H-pyrrol-1-yl)ethyl)-2-(1-hydroxycyclooct-4-en-1-yl)acetamide (17)
[0152] ##STR00034##
[0153] A round bottomed flask equipped with a magnetic stir bar was charged with 1-(2-aminoethyl)maleimide hydrochloride (103 mg, 0.586 mmol), triethylamine (0.27 mL, 1.955 mmol), and CH.sub.2Cl.sub.2 (3.9 mL) and was stirred briefly before (E)-N-hydroxysuccinyl 2-(1-ax-hydroxycyclooct-4-en-1-yl)acetate (110 mg, 0.391 mmol) in CH.sub.2Cl.sub.2 (3.9 mL) was added. The reaction was monitored by TLC. After 20 minutes, the reaction was loaded directly onto a silica gel column and chromatographed (30-60% ethyl acetate in hexanes) to afford 103 mg (0.336 mmol, 86% yield) of the title compound as a white solid. The compound was stored at −20° C. as a solution in methanol. .sup.1H NMR (400 MHz, C.sub.6D.sub.6) δ 6.06 (ddd, J=15.3, 11.2, 3.7 Hz, 1H), 5.72 (s, 2H), 5.54 (ddd, J=15.4, 11.4, 3.3 Hz, 1H), 4.94 (s, 1H), 4.76 (brs, 1H), 3.20-3.05 (m, 2H), 3.03-2.88 (m, 2H), 2.77 (app qd, J=11.8, 4.6 Hz, 1H), 2.37-2.26 (m, 1H), 2.15-1.96 (m, 2H), 1.93-1.75 (m, 3H), 1.73-1.63 (m, 2H), 1.48 (dd, J=14.9, 6.6 Hz, 1H), 1.36 (dd, J=13.0, 4.7 Hz, 1H), 1.32-1.23 (m, 1H). .sup.13C NMR (101 MHz, C.sub.6D.sub.6) δ 173.3 (C), 170.5 (C), 135.7 (CH), 133.6 (CH), 131.7 (CH), 71.4 (C), 51.0 (CH.sub.2), 48.3 (CH.sub.2), 39.9 (CH.sub.2), 38.1 (CH.sub.2), 37.4 (CH.sub.2), 34.9 (CH.sub.2), 30.7 (CH.sub.2), 27.8 (CH.sub.2). FTMS (ESI+) calculated [M+H].sup.+ for C.sub.16H.sub.23N.sub.2O.sub.4 307.1658; found 307.1642.
Example 17: (E)-Cyclooct-4-enone Oxime (18)
[0154] ##STR00035##
[0155] An oven-dried, 7 mL vial equipped with a magnetic stir bar was charged with hydroxylamine hydrochloride (196 mg, 2.82 mmol), 0.26 mL of pyridine, and 1 mL of MeOH and was then stirred for 10 minutes. (E)-Cyclooct-4-enone (100 mg, 0.805 mmol) in 1 mL of MeOH was added, and the reaction was monitored by TLC. After 3.5 hours of stirring, the mixture was partitioned between Et.sub.2O and water. The product was extracted from the aqueous phase with Et.sub.2O, dried with Na.sub.2SO.sub.4, filtered, then concentrated by rotary evaporation. The crude product was purified by silica column chromatography (10-20% EtOAc in hexanes) to afford 91 mg (0.65 mmol, 81% yield) of the title compound as a white solid and as a 4:1 mixture of geometric isomers as judged by .sup.1H NMR.
[0156] Peaks attributed to major product: .sup.1H NMR (400 MHz, CDCl.sub.3) δ 8.05 (br s, 1H), 5.77-5.62 (m, 1H), 5.48-5.34 (m, 1H), 2.82 (ddd, J=13.1, 5.6, 1.7 Hz, 1H), 2.72-2.59 (m, 1H), 2.56-2.15 (m, 5H), 2.08-1.85 (m, 2H), 1.41 (td, J=12.8, 1.7 Hz, 1H). .sup.13C NMR (101 MHz, CDCl.sub.3) δ 164.0 (C), 135.0 (CH), 132.4 (CH), 42.3 (CH.sub.2), 35.5 (CH.sub.2), 34.0 (CH.sub.2), 32.5 (CH.sub.2), 28.2 (CH.sub.2).
[0157] Peaks attributed to minor product: .sup.1H NMR (400 MHz, CDCl.sub.3) δ 8.05 (br s, 1H), 5.77-5.62 (m, 1H), 5.48-5.34 (m, 1H), 3.41 (app dd, J=11.6, 4.6 Hz, 1H), 2.56-2.15 (m, 5H), 2.08-1.85 (m, 2H), 1.83-1.68 (m, 1H), 1.59 (ddd, J=14.4, 12.8, 1.7 Hz, 1H). .sup.13C NMR (101 MHz, CDCl.sub.3) δ 164.7 (C), 134.3 (CH), 133.1 (CH), 37.1 (CH.sub.2), 35.1 (CH.sub.2), 34.1 (CH.sub.2), 33.4 (CH.sub.2), 32.1 (CH.sub.2).
[0158] FTMS (ESI+) calculated [M+H].sup.+ for C.sub.8H.sub.14NO 140.1075; found 140.1070.
Example 18: (E)-Cyclooct-4-enone O-benzyl Oxime (19)
[0159] ##STR00036##
[0160] (E)-Cyclooct-4-enone (50 mg, 0.40 mmol), 2.2 mL of ethanol, and 0.2 mL of pyridine were added to a round bottom flask equipped with a magnetic stir bar. O-Benzylhydroxylamine hydrochloride (129 mg, 0.806 mmol) was added in portions while vigorously stirring. The reaction was monitored by TLC and stirred for 18 hours, after which the mixture was concentrated by rotary evaporation and dissolved in a 1:1: CH.sub.2Cl.sub.2 and EtOAc solution. The precipitate formed was filtered off and rinsed with CH.sub.2Cl.sub.2 and EtOAc. The crude product was purified by silica gel chromatography (0-3% Et.sub.2O in hexanes) to afford 76 mg (0.33 mmol, 83% yield) of a white solid that was a 3:1 mixture of geometric isomers as judged by .sup.1H NMR.
[0161] Peaks attributed to major product: .sup.1H NMR (400 MHz, C.sub.6D.sub.6) δ 7.39-7.30 (m, 2H), 7.21-7.13 (m, 2H), 7.11-7.05 (m, 1H), 5.45-5.28 (m, 2H), 5.22-5.05 (m, 2H), 2.73 (ddd, J=28.1, 12.8, 5.3 Hz, 2H), 2.41-2.24 (m, 2H), 2.23-2.03 (m, 2H), 1.97-1.81 (m, 1H), 1.78-1.60 (m, 2H), 1.03 (app td, J=12.8, 1.7 Hz, 1H). .sup.13C NMR (101 MHz, C.sub.6D.sub.6) δ 162.8 (C), 139.3 (C), 134.8 (CH), 132.6 (CH), 128.6 (CH), 75.8 (CH.sub.2), 42.3 (CH.sub.2), 35.9 (CH.sub.2), 34.1 (CH.sub.2), 32.9 (CH.sub.2), 28.9 (CH.sub.2).
[0162] Peaks attributed to minor product: .sup.1H NMR (400 MHz, C.sub.6D.sub.6) δ 7.39-7.30 (m, 2H), 7.21-7.13 (m, 2H), 7.11-7.05 (m, 1H), 5.45-5.28 (m, 2H), 5.22-5.05 (m, 2H), 3.40 (app dd, J=11.8, 4.7 Hz, 1H), 2.61-2.46 (m, 1H), 2.41-2.24 (m, 1H), 2.23-2.03 (m, 2H), 1.97-1.81 (m, 1H), 1.78-1.60 (m, 2H), 1.51 (app td, J=12.2, 5.1 Hz, 1H), 1.13 (ddd, J=14.3, 12.6, 1.8 Hz, 1H). .sup.13C NMR (101 MHz, C.sub.6D.sub.6) δ 163.5 (C), 139.5 (C), 134.4 (CH), 133.0 (CH), 128.5 (CH), 75.7 (CH.sub.2), 37.7 (CH.sub.2), 35.1 (CH.sub.2), 34.3 (CH.sub.2), 33.8 (CH.sub.2), 32.37 (CH.sub.2).
[0163] FTMS (ESI+) calculated [M+H].sup.+ for C.sub.15H.sub.20NO 230.1545; found 230.1535.
OXO-TCO-Tamra Synthesis
[0164] (R,E)-(3,4,7,8-tetrahydro-2H-oxocin-2-yl)methanol (oxo-TCO) was synthesized according to a previously published procedure (Brown et al., Chem. Soc. Rev. 2017, 46, 6532-6552).
##STR00037##
Example 19: (R,E)-4-nitrophenyl ((3,4,7,8-tetrahydro-2H-oxocin-2-yl)methyl) carbonate
[0165] ##STR00038##
[0166] A dry round bottom flask was charged with (R,E)-(3,4,7,8-tetrahydro-2H-oxocin-2-yl)methanol (202 mg, 1.42 mmol) and a magnetic stir bar. 4-Nitrophenyl chloroformate (344 mg, 1.70 mmol) dissolved in anhydrous CH.sub.2Cl.sub.2 (7 mL) and pyridine (0.458 mL, 5.68 mmol) was added by syringe. After stirring under nitrogen at room temperature overnight, the resulting solution was concentrated by rotary evaporation. A yellow oil (400 mg, 1.30 mmol, 92%) was obtained after column chromatography (0-5% EtOAc in CH.sub.2Cl.sub.2). .sup.1H NMR (400 MHz, C.sub.6D.sub.6) δ 7.73-7.59 (m, 2H), 6.83-6.66 (m, 2H), 5.73 (ddd, J=15.4, 11.4, 3.4 Hz, 1H), 5.13 (ddd, J=15.4, 10.9, 3.8 Hz, 1H), 4.03 (dd, J=10.8, 7.6 Hz, 1H), 3.98-3.88 (m, 1H), 3.82 (dd, J=10.8, 4.4 Hz, 1H), 2.91 (td, J=11.7, 3.3 Hz, 1H), 2.86-2.72 (m, 1H), 2.37-2.13 (m, 2H), 1.99-1.76 (m, 2H), 1.70-1.49 (m, 1H), 1.39-1.33 (m, 1H). .sup.13C NMR (101 MHz, C.sub.6D.sub.6) δ 155.4 (C), 152.9 (C), 145.6 (C), 140.8 (CH), 127.1 (CH), 125.2 (CH), 121.5 (CH), 82.2 (CH), 74.19 (CH.sub.2), 72.15 (CH.sub.2), 38.2 (CH.sub.2), 37.2 (CH.sub.2), 34.1 (CH.sub.2). HRMS (ESI+) calculated [M+H].sup.+ for C.sub.15H.sub.18O.sub.6N 308.1134; found 308.1128.
Example 20: (S,E)-2-(6-(dimethylamino)-3-(dimethyliminio)-3H-xanthen-9-yl)-5-((5-((((3,4,7,8-tetrahydro-2H-oxocin-2-yl)methoxy)carbonyl)amino)pentyl)carbamoyl)benzoate (TAMRA-oxo-TCO)
[0167] ##STR00039##
[0168] A dry round bottom flask was charged with 5-TAMRA Cadaverine TFA salt (3.8 mg, 6.1 μmol) and a magnetic stir bar. Anhydrous CH.sub.2Cl.sub.2 (1 mL), triethylamine (8.5 mL, 61 μmol) and (R,E)-4-nitrophenyl ((3,4,7,8-tetrahydro-2H-oxocin-2-yl)methyl) carbonate (3.7 mg, 12 μmol) were added by syringe. After stirring under nitrogen at room temperature overnight, the resulting mixture was concentrated by rotary evaporation. A purple solid (1.6 mg, 2.3 μmol, 39%) was obtained after reverse phase column chromatography with a 14 g Yamazan column (0-50% acetonitrile in H.sub.2O with 0.05% NH.sub.4OH). .sup.1H NMR (600 MHz, MeOD) δ 8.50 (d, J=1.8 Hz, 1H), 8.04 (dd, J=7.9, 1.9 Hz, 1H), 7.35 (d, J=7.9 Hz, 1H), 7.25 (d, J=9.5 Hz, 2H), 7.02 (dd, J=9.5, 2.5 Hz, 2H), 6.93 (d, J=2.4 Hz, 2H), 5.67 (ddd, J=15.4, 11.4, 3.4 Hz, 1H), 5.40 (ddd, J=15.5, 10.8, 3.9 Hz, 1H), 4.02 (dd, J=12.0, 6.1 Hz, 1H), 3.92 (dd, J=10.9, 7.5 Hz, 1H), 3.85 (dd, J=11.1, 4.8 Hz, 1H), 3.46 (t, J=7.1 Hz, 2H), 3.28 (s, 12H), 3.13 (t, J=6.9 Hz, 2H), 2.46-2.41 (m, 1H), 2.35-2.26 (m, 1H), 2.25-2.13 (m, 2H), 1.87 (dd, J=14.2, 5.0 Hz, 1H), 1.74-1.65 (m, 3H), 1.62-1.54 (m, 3H), 1.54-1.42 (m, 3H). HRMS (ESI+) calculated for [M+H].sup.+ C.sub.39H.sub.47O.sub.7N.sub.4 683.3445; found 683.3428.
Stability Assays
Example 21: Stability of TCO 14 in methanol-d.SUB.4 .(35 mM)
[0169] A solution of 14 (4.5 mg, 26 μmol) in methanol-d.sub.4 (750 μL) was monitored by quantitative .sup.1H NMR on a 600 MHz instrument to observe the decomposition of the trans-isomer over time. Methyl tert-butyl ether (3.1 μL, 26 μmol) was used as an internal standard. There was no observable decomposition of TCO 14 after 7 days (
Example 22: Stability of TCO 4a in methanol-d.SUB.4 .(35 mM)
[0170] A solution of 4a (3.3 mg, 26 μmol) in methanol-d.sub.4 (750 μL) was monitored by quantitative .sup.1H NMR on a 600 MHz instrument to observe the decomposition of the trans-isomer over time. Methyl tert-butyl ether (3.1 μL, 26 μmol) was used as an internal standard. There was no observable decomposition of TCO 4a after 7 days (
Example 23: Stability of a-TCO 14 in Phosphate Buffered D.SUB.20., pD=7.4 (33 mM)
[0171] A solution of 14 (4.3 mg, 25 μmol) in phosphate buffered D.sub.2O (750 μL, pD=7.4) was monitored by quantitative .sup.1H NMR on a 600 MHz instrument to observe the decomposition of the trans-isomer over time. Methyl tert-butyl ether (3.0 μL, 26 μmol) was used as an internal standard. After 1 day, 90% of 14 remained and after 5 days, 39% remained (
Example 24: Stability of TCO 4a in Phosphate Buffered D.SUB.20., pD=7.4 (33 mM)
[0172] A solution of 4a (3.2 mg, 25 μmol) in phosphate buffered D.sub.2O (750 μL, pD=7.4) was monitored by quantitative .sup.1H NMR on a 600 MHz instrument to observe the decomposition of the trans-isomer over time. Methyl tert-butyl ether (3.0 μL, 26 μmol) was used as an internal standard. After 1 day, 85% of 4a remained and after 5 days, 35% remained (
Example 25: Stability of a-TCO 14 in Phosphate Buffered D.SUB.20 .and Mercaptoethanol, pD=7.4 (25 mM)
[0173] TCO 14 (3.1 mg, 18 μmol) in a solution of mercaptoethanol in phosphate buffered D.sub.2O (720 μL, 18 μmol, 25 mM, pD=7.4) was monitored by quantitative 1H NMR on a 600 MHz instrument to observe the decomposition of the trans-isomer over time. Methyl tert-butyl ether (2.1 μL, 18 μmol) was used as an internal standard. After 4 hours, 93% of 14 remained and 49% of 14 remained after 20 hours. (
Example 26: Stability of TCO 4a in Phosphate Buffered D.SUB.20 .and Mercaptoethanol, pD=7.4 (25 mM)
[0174] TCO 4a (2.3 mg, 18 μmol) in a solution of mercaptoethanol in phosphate buffered D.sub.2O (720 μL, 18 μmol, 25 mM, pD=7.4) was monitored by quantitative 1H NMR on a 600 MHz instrument to observe the decomposition of the trans-isomer over time. Methyl tert-butyl ether (2.1 μL, 18 μmol) was used as an internal standard. After 4 hours, 89% of 4a and 49% of 4a remained after 20 hours. (
Stopped-Flow Kinetic Measurements
Example 27: Kinetic Measurements for the Reaction of 5-ax-hydroxy-5-eq-(2-hydroxyethyl)-trans-cyclooctene (14) and 3,6-dipyridyl-s-tetrazine-mono-succinamic Acid (20)
[0175] ##STR00040##
[0176] The reaction between 5-ax-hydroxy-5-eq-(2-hydroxyethyl)-trans-cyclooctene 14 and 3,6-dipyridyl-s-tetrazine-mono-succinamic acid 20 was monitored by a SX18MV-R stopped-flow spectrophotometer (Applied Photophysics Ltd.) at 325 nm by measuring the exponential decay of tetrazine under pseudo-first order conditions. Solutions of 14 (0.98, 1.46, 1.95, and 2.63 mM in 9:1 PBS/MeOH) and tetrazine (0.1 mM in PBS) were mixed in the stopped-flow spectrophotometer in equal volumes resulting in final concentrations of 0.49 mM, 0.73 mM, 0.97 mM, and 1.31 mM of 14 and 0.05 mM of tetrazine in 95:5 PBS/MeOH. Three independent samples were prepared for each TCO concentration and measurements were taken in duplicate every 0.1 ms for 0.1 sat 25° C. The observed rates k.sub.obs for each run were determined by nonlinear regression analysis of the data points using Prism software (Version 8.00, GraphPad Software Inc). The average k.sub.obs values were plotted against the concentrations of 14 to obtain the bimolecular rate constant k.sub.2 from the slope of the plot. The average k.sub.2 was measured as 150,000±8000 M.sup.−1s.sup.−1.
[0177] The observed rates (k.sub.obs) of 5-ax-hydroxy-5-eq-(2-hydroxyethyl)-trans-cyclooctene 14 (10-30 equivalents) and 3,6-dipyridyl-s-tetrazine-mono-succinamic acid 20 were measured using stopped-flow kinetics. The final concentrations of 14 after injection were (A) 0.49 mM, (B) 0.73 mM, (C) 0.97 mM, and (D) 1.31 mM and the concentration of tetrazine was 0.05 mM in 95:5 PBS/MeOH at 25° C. Duplicate measurements were obtained for three independent samples for each concentration of 14. The averages and the nonlinear best fit curve) were calculated using Prism software and are summarized below in Table 1.
TABLE-US-00001 TABLE 1 A (0.49 mM) B (0.73 mM) C (0.97 mM) D (1.31 mM) K.sub.obs 76.13 121.4 162.4 200.2 R.sup.2 0.9995 0.9996 0.9986 0.9934
Example 28: Kinetic Measurements for the Reaction of 5-ax-hydroxy-trans-cyclooctene (4a) and 3,6-dipyridyl-s-tetrazine-mono-succinamic Acid (20)
[0178] ##STR00041##
[0179] The reaction between 5-ax-hydroxy-trans-cyclooctene 4a and 3,6-dipyridyl-s-tetrazine-mono-succinamic acid 20 was monitored by a SX18MV-R stopped-flow spectrophotometer (Applied Photophysics Ltd.) at 325 nm by measuring the exponential decay of tetrazine under pseudo-first order conditions. Solutions of 4a (100, 200, 300, and 400 μM in 9:1 PBS/MeOH) and tetrazine (20 μM in PBS) were mixed in the stopped-flow spectrophotometer in equal volumes resulting in final concentrations of 50 μM, 100 μM, 150 μM, and 200 μM of 4a and 10 μM of tetrazine in 95:5 PBS/MeOH. Three independent samples were prepared for each TCO concentration and measurements were taken in duplicate every 0.1 ms for 0.2 s at 25° C. The observed rates k.sub.obs for each run were determined by nonlinear regression analysis of the data points using Prism software (Version 8.00, GraphPad Software Inc). The average k.sub.obs values were plotted against the concentrations of 4a to obtain the bimolecular rate constant k.sub.2 from the slope of the plot. The average k.sub.2 was measured as 70,000±1800 M.sup.−1s.sup.−1.
[0180] The observed rates (k.sub.obs) of 5-ax-hydroxy-trans-cyclooctene 4a (5-20 equivalents) and 3,6-dipyridyl-s-tetrazine-mono-succinamic acid 20 were measured using stopped-flow kinetics. The final concentrations of 4a after injection were (A) 50 μM, (B) 100 μM, (C) 150 μM, and (D) 200 μM and the concentration of tetrazine was 10 μM in 95:5 PBS/MeOH at 25° C. Duplicate measurements were obtained for three independent samples for each concentration of 4a. The averages and the nonlinear best fit curve were calculated using Prism software, and summarized below in Table 2.
TABLE-US-00002 TABLE 2 A (0.49 mM) B (0.73 mM) C (0.97 mM) D (1.31 mM) K.sub.obs 3.407 6.966 10.09 13.86 R.sup.2 0.9983 0.9931 0.9926 0.9943
TAMRA-A-TCO Permeability Assay
Example 29: 4-((4-(6-methyl-1,2,4,5-tetrazin-3-yl)benzyl)-N-(2-(2-((6-chlorohexyl)oxy)ethoxy)ethyl)amide (21) was Prepared According to a Previously Published Procedure as Described in Scinto et al., J. Am. Chem. Soc. 2019, 141, 10932-10937
[0181] ##STR00042##
[0182] Plasmids: Halo-H2B-GFP and Halo-GAP43-GFP plasmids were gifts from Pfizer.
[0183] HeLa Cell Culture and Transfection: HeLa cells were grown in Dulbecco's modified eagle medium (DMEM, Life Technologies) supplemented with 10% (v:v) heat inactivated fetal bovine serum (Life Technologies), 2 mM I-glutamine, and 100 units/mL penicillin/streptomycin (Life Technologies) in a humidified incubator at 37° C./5% CO.sub.2. Transfection was performed with cells at 70% confluency using Lipofectamine 3000 according to the manufacturer's instructions. HeLa cells were incubated for 5 hours at 37° C./5% CO.sub.2 before being exchanged with antibiotic free growth media for 16-20 hours prior to experimental procedures.
[0184] HeLa Cell Labeling: HeLa cells expressing localized HaloTag were grown on poly-1-lysine coated coverslips and labeled with 10 μM 4-((4-(6-methyl-1,2,4,5-tetrazin-3-yl)benzyl)-N-(2-(2-((6-chlorohexyl)oxy)ethoxy)ethyl)amide 21 for 30 minutes at 37° C./5% CO.sub.2. After incubation, cells were washed 3× with DPBS and incubated for an hour in 2 mL of new media to remove excess ligand. After an additional media swap, cells were treated with 1 μM TAMRA-a-TCO 12 for 30 minutes. After fluorophore incubation, unreacted TAMRA-a-TCO 12 was quenched by washing the cells with quenching buffer (100 μM 3-methyl-6-(4-aminomethylphenyl)-s-tetrazine in PBS). The cells were then allowed to sit for 1 hour in media to wash out any remaining dye. To fix cells, media was aspirated, and the wells were washed 3× with PBS before fixation with 4% paraformaldehyde at room temperature for 10 minutes. Cells were washed 3× for 5 minutes in PBS before being mounted onto coverslips with Vectashield HardSet Mounting Medium with DAPI and stored at 4° C. Images were acquired using the Airyscan mode of the Zeiss LSM 880 confocal microscope with the 63 ×1.4NA Plan-Apochromat objective.
[0185] TAMRA-TCO Comparative Washout Assay
[0186] HeLa cells were seeded at 5×10.sup.3 cells per well in a poly-L-lysine (0.1 mg/mL) coated 48-well plate and allowed to grow for 48 hours in Dulbecco's modified eagle medium (DMEM, Life Technologies) supplemented with 5% FBS (Life Technologies), 1 mM L-glutamine, and 1% penicillin/streptomycin (Life Technologies). Cells were then incubated with media containing 5 μM of TAMRA-TCO, TAMRA-oxo-TCO, or TAMRA-a-TCO 12 (1 mM stock solutions in DMSO, diluted twice into media) for 30 mins at 37° C. All wells were washed three times with DPBS before adding fresh media. Cells were imaged after 2 DPBS washes and again after the 3.sup.rd DPBS wash, then incubated for additional time intervals: 10 minutes, 40 minutes, and 2 hour. At each time point, the media was removed from the designated wells and replaced with fresh media before imaging. Images were taken with an EVOS M7000 and all images were taken with the same laser power and gain. Fluorescence intensity was calculated for each sample in 3 replicates using ImageJ and the fluorescence data was normalized with the cell count of each image.
Computational Analysis
[0187] Method: M062X/6-311+G(d,p) scrf=(smd,solvent=THF)
[0188] Keto-TCO Ground State (Crown Conformation)
##STR00043##
TABLE-US-00003 Electronic Energy (a.u.) −639.57964 Sum of electronic and zero-point Energies −639.36404 Sum of electronic and thermal Energies −639.3505 Sum of electronic and thermal Enthalpies −639.34956 Sum of electronic and thermal Free Energies −639.40429
[0189] Atomic Coordinates in Angstroms
TABLE-US-00004 Atom x y z C −0.658834 −1.104451 −0.918879 C −3.022731 −0.929489 0.112482 C −0.893470 2.166554 0.098905 C −2.498211 0.366386 0.644257 C −2.125185 1.352717 −0.171711 C −1.770144 −1.817816 −0.118156 C 0.263959 1.348753 −0.548393 H 0.069083 −1.852243 −1.254861 H −3.535667 −0.771588 −0.840710 H −0.714622 2.252795 1.173742 H −2.100391 0.347195 1.659865 H −2.480108 1.345310 −1.202478 H −1.073795 −0.623028 −1.806098 H −3.706258 −1.439993 0.794539 H −0.912767 3.167193 −0.335463 H −2.060739 −2.723112 −0.655746 H 1.235178 1.737318 −0.236561 H −1.361026 −2.133679 0.845607 H 0.187505 1.402632 −1.637072 C 0.148201 −0.103063 −0.113417 O 0.712648 −0.481451 0.905956 Li 2.336408 −0.295635 1.778618 H 3.112378 −0.191160 −1.564127 H 3.397909 0.967291 0.803940 Al 3.965454 −0.214976 −0.201289 H 5.553859 −0.157253 −0.361618 H 3.466639 −1.472017 0.739767
[0190] Transition State of Nucleophilic Addition of Lithium Aluminum Hydride to Axial Face of Keto-TCO
##STR00044##
TABLE-US-00005 Electronic Energy (a.u.) −639.55363 au Sum of electronic and zero-point −639.3388 au Energies Sum of electronic and thermal −639.326 au Energies Sum of electronic and thermal −639.32506 au 15.375 Kcal/mol Enthalpies Sum of electronic and thermal Free −639.37744 au 16.846 Kcal/mol Energies Imaginary frequency 370.25722i cm.sup.−1
[0191] Atomic Coordinates in Angstroms
TABLE-US-00006 Atom x y z C 0.580167 −0.432529 1.514642 C 2.474039 −1.164238 −0.130275 C 0.576219 1.935789 −0.972479 C 1.905536 −0.135931 −1.049359 C 1.801232 1.136004 −0.669996 C 1.279683 −1.588819 0.763706 C −0.335886 1.794399 0.265681 H 0.119339 −0.864101 2.404999 H 3.259306 −0.735372 0.499865 H 0.066599 1.534229 −1.852071 H 1.258490 −0.501400 −1.844337 H 2.418174 1.490808 0.156015 H 1.342408 0.274906 1.860202 H 2.877084 −2.041831 −0.640700 H 0.764567 2.999631 −1.138294 H 1.643363 −2.290614 1.519927 H −1.324381 2.209879 0.051574 H 0.544464 −2.128521 0.160905 H 0.088009 2.395575 1.082733 C −0.570286 0.420978 0.921033 H −3.255355 0.039070 −0.842775 O −1.674525 0.291295 1.503251 Li −3.354913 0.517573 0.892911 Al −2.110809 −1.076576 −1.240230 H −2.049111 −1.260735 −2.831135 H −0.740070 −0.392963 −0.642473 H −2.375664 −2.410068 −0.383914
[0192] Transition State of Nucleophilic Addition of Lithium Aluminum Hydride to Equatorial Face of Keto-TCO
##STR00045##
TABLE-US-00007 Electronic Energy (a.u.) −639.55967 au Sum of electronic and zero-point −639.34398 au Energies Sum of electronic and thermal −639.33139 au Energies Sum of electronic and thermal −639.33045 au 11.994 Kcal/mol Enthalpies Sum of electronic and thermal Free −639.38184 au 14.086 Kcal/mol Energies Imaginary frequency 477.2191i cm.sup.−1
Example 30: Synthesis of (E)-8-methylcyclooct-4-en-1-one
[0193] ##STR00046##
[0194] A round bottom flask equipped with a magnetic stir bar was charged with LiHMDS (0.36 mL, 1M in THF) then was chilled to 0° C. (E)-Cyclooct-4-enone (30 mg, 0.24 mmol) in 0.16 mL of THF was added dropwise and stirred for 30 minutes before chilling to −78° C. Methyl iodide (21 μL, 0.34 mmol) was added dropwise and stirred at −78° C. for 40 mins before warming to 0° C. and stirring for another 2.5 hour. The reaction was quenched with 0.5 mL of NH.sub.4Cl sat. solution and the aqueous layer was extracted with Et.sub.2O. The organic layer was washed with brine, dried with MgSO.sub.4, filtered and concentrated. The crude was purified by column chromatography (0-2% diethyl ether in hexanes) to afford 14.5 mg of a 3:1 mixture of monoalkylation (33% yield) to dialkylation product as determined by .sup.1H NMR analysis as clear, colorless oil. Further purification afforded a 10:1 mixture of monoalkylation to dialkylation that was utilized to further characterize the monoalkylation product.
[0195] Peaks attributed to monoalkylation product: .sup.1H NMR (600 MHz, C.sub.6D.sub.6) δ 5.42 (ddd, J=15.4, 11.2, 3.7 Hz, 1H), 5.24 (ddd, J=15.7, 11.3, 3.7 Hz, 1H), 2.52-2.42 (m, 1H), 2.27 (ddd, J=12.6, 10.4, 5.9 Hz, 1H), 2.18 (app dd, J=10.4, 5.9 Hz, 1H), 2.13-2.07 (m, 1H), 2.05-2.00 (m, 1H), 1.94-1.78 (m, 2H), 1.67 (app qd, J=11.5, 5.2 Hz, 1H), 1.24 (app dd, J=12.6, 5.3 Hz, 1H), 0.77 (d, J=6.5 Hz, 3H). .sup.13C NMR (151 MHz, C.sub.6D.sub.6) δ 217.2 (C), 134.5 (CH), 131.2 (CH), 48.4 (CH), 48.0 (CH.sub.2), 37.1 (CH.sub.2), 34.7 (CH.sub.2), 33.3 (CH.sub.2), 17.5 (CH.sub.3). FTMS (ESI+) calculated [M+H].sup.+ for C.sub.9H.sub.15O 139.1123; found 139.1116.
[0196] Peaks attributed to dialkylation product: .sup.1H NMR (600 MHz, C.sub.6D.sub.6) δ 5.57 (ddd, J=16.3, 11.0, 3.9 Hz, 1H), 5.30-5.20 (m, 1H), 2.65 (ddd, J=12.9, 10.3, 4.8 Hz, 1H), 2.61-2.53 (m, 1H), 2.07-1.93 (m, 2H), 1.93-1.79 (m, 2H), 1.14-1.07 (m, 2H), 0.93 (s, 3H), 0.86 (s, 3H). .sup.13C NMR (151 MHz, C.sub.6D.sub.6) δ 217.2 (C), 134.3 (CH), 130.1 (CH), 46.2 (C), 44.6 (CH.sub.2), 42.9 (CH.sub.2), 35.5 (CH.sub.2), 30.2 (CH.sub.2), 29.6 (CH.sub.3), 22.2 (CH.sub.3).
Example 31: Other Derivatives Synthesized by the Method Described in Example 30 Include the Following
[0197] ##STR00047##
[0198] Although the invention is illustrated and described herein with reference to specific embodiments, the invention is not intended to be limited to the details shown. Rather, various modifications may be made in the details within the scope and range of equivalents of the claims and without departing from the invention.
[0199] While preferred embodiments of the invention have been shown and described herein, it will be understood that such embodiments are provided by way of example only. Numerous variations, changes and substitutions will occur to those skilled in the art without departing from the spirit of the invention. Accordingly, it is intended that the appended claims cover all such variations as fall within the spirit and scope of the invention.