2,5-Dimethylphenacyl carbonates: a photoremovable protecting group for alcohols and phenols.

Synthesis and photochemistry of a photochemically removable protecting group for alcohols and phenols, based on the 2,5-dimethylphenacyl (DMP) chromophore, is described. DMP carbonates release the corresponding hydroxy group containing molecules in high isolated yields (>70%), with quantum yields Phi= 0.1-0.2 in methanol and Phi= 0.36-0.51 in cyclohexane. The reactions proceed predominantly by the triplet pathway via E-photoenols, the lifetimes of which of approximately 2 s or 3 ms in cyclohexane or methanol, respectively, were determined by laser flash photolysis.     

Synthesis and reaction mechanism of a photoremovable protecting group based on 1,4-naphthoquinone.

5-(ethylen-2-yl)-1,4-naphthoquinone () is a photoremovable protecting group that absorbs up to 405 nm and provides fast and efficient release of bromide or diethyl phosphate. A convenient synthetic protocol to three derivatives of is described and their photochemistry in aqueous and acetonitrile solutions is investigated. The photoenol intermediates that expel the protected substrates were detected by laser flash photolysis and step-scan FTIR spectroscopy. The nucleofugacity of the leaving group and pH are the major factors that determine the reaction pathway.     

2,5-Dimethylphenacyl carbamate: a photoremovable protecting group for amines and amino acids.

2,5-Dimethylphenacyl (DMP) carbamates (1a-c) released the corresponding free amines or amino acids in high chemical yields, albeit with quantum yields Phi of only 0.04-0.09, upon irradiation in either aprotic or protic solvents. The photoreaction proceeded principally from the triplet excited state via the E-photoenol. The lifetimes of the triplet enol and the E- and Z-enols in the ground state were determined by laser flash photolysis. The primary photoinitiated transformation liberated a carbamic acid derivative, which subsequently decarboxylated to the amino group-containing compound. Exhaustive irradiation of a DMP-protected aniline (1a) in acetonitrile did not provide aniline in quantitative chemical yields, because it was involved in reductive cleavage of the starting material as an electron donor, thereby decreasing the overall deprotection yield (86%). Phenylalanine methyl ester, liberated from 1c, was, however, obtained in excellent chemical yield (97%). It was also found that the carbamates, while thermally stable, released amines with higher quantum yields in acidic methanol solutions. The DMP chromophore is proposed as an excellent photoremovable protecting group for amino acids and, under specific conditions, for amines in organic synthesis and biochemistry.     

Bichromophoric fluorescent photolabile protecting group for alcohols and carboxylic acids

Novel bichromophoric fluorescent photolabile protecting group, (5-dansyloxy-3-hydroxynaphthalen-2-yl)methyl (DNS-NQMP), allows for the independent photochemical release and fluorescent imaging of caged substrates. Irradiation of DNS-NQMP-caged alcohols and carboxylic acids with 300 or 350 nm light results in fast (k(release) ~ 10(5) s(-1)), efficient (Φ = 0.2), and quantitative release of the substrates. This uncaging chemistry is compatible with aqueous media and DNS-NQMP-protected hydroxy compounds are hydrolytically stable at neutral pH. Upon excitation with 400 nm light, caged compounds show intense green emission (λ(max) = 559 nm) with 21% fluorescence quantum yield. Fluorescent readout conducted using 400 nm or longer wavelengths does not cause substrate release. The DNS-NQMP chromophore retains its fluorescent properties after photo-uncaging reaction.     

The donor-acceptor biphenyl platform: a versatile chromophore for the engineering of highly efficient two-photon sensitive photoremovable protecting groups

Different photoremovable protecting groups in the o-nitrobenzyl, phenacyl, and 2-(o-nitrophenyl)propyl series with a donor-acceptor biphenyl backbone, known to display excellent two-photon absorption cross-sections, were investigated in order to develop efficient two-photon sensitive photoremovable protecting groups. The 2-(o-nitrophenyl)propyl series was a more versatile platform to increase the two-photon sensitivity of photoremovable protecting groups, leading to the p-alkoxy and p-bisalkylamino-4-nitro-[1,1'-biphenyl]-3-yl)propyl derivatives: PENB and EANBP respectively. Those two photoremovable protecting groups are to date the best caging groups for two-photon excitation at 800 and 740 nm respectively, offering attracting perspectives in chemical biology.     

Applications of p-hydroxyphenacyl (pHP) and coumarin-4-ylmethyl photoremovable protecting groups

Most applications of photoremovable protecting groups have used o-nitrobenzyl compounds and their (often commercially available) derivatives that, however, have several disadvantages. The focus of this review is on applications of the more recently developed title compounds, which are especially well suited for time-resolved biochemical and physiological investigations, because they release the caged substrates in high yield within a few nanoseconds or less. Together, these two chromophores cover the action spectrum for photorelease from >700 nm to 250 nm.     

Application of allyloxycarbonyl group as a protecting group to oligodeoxyribonucleotide synthesis

The allyloxycarbonyl (AOC) group, known as an efficient amino protective group in solution-phase synthesis of nucleotides, has been used for the first time in solid-phase oligonucleotide synthesis. The efficiency of the new procedure is compared with that of the conventional N-acyl protection.     

Fluorinated photoremovable protecting groups: the influence of fluoro substituents on the photo-Favorskii rearrangement.

To further explore the nature of the photo-Favorskii rearrangement and its commitment to substrate photorelease from p-hydroxyphenacyl (pHP), an array of ten new fluorinated pHP gamma-aminobutyric acid (GABA) derivatives was synthesized and photolyzed. The effects of fluorine substitution on the chromophore and the photophysical and photochemical properties of these new chromophores were shown to be derived primarily from the changes in the ground state pK(a) of the phenolic groups. The quantum yields and rate constants for release are clustered around Phi(dis) = 0.20 +/- 0.05 and k(r) = 8 +/- 7 x 10(7) s(-1) (H2O), respectively. The triplet lifetimes of the pHP GABA derivatives were concentrated in the range of 0.4-6.0 ns (H2O). The corresponding deprotonated conjugate bases displayed reduced efficiencies by 50% or more (one exception) and exhibited a weak fluorescence in pH 8.2 buffer. Pump-probe spectroscopy studies have further defined the rates of intersystem crossing and the lifetimes of the reactive triplet state of the fluoro pHP chromophore.     

Peptide substrate for caspase-3 with 2-aminoacridone as reporting group

Synthesis and properties of a new fluorescent/fluorogenic substrate Ac-DEVD-AMAC for caspase-3 are reported. The substrate is obtained by conventional Fmoc-based solid phase peptide synthesis and its properties are investigated with regard to fluorescence, sensitivity, applicability and kinetic constants. A non-traditional approach to assay the proteases activity using 2-aminoacridone labeled peptides is proposed. This approach utilizes the decrease of fluorescence intensity of a sample as a measure for the enzyme activity.     

Simple and efficient synthesis of chiral amino alcohols with an amino acid-based skeleton

Sodium bis(2-methoxyethoxy)aluminum hydride, NaAlH₂(OCH₂CH₂OCH₃)₂, commercially known as Vitride® or Red-Al®, enables rapid synthesis of pure optically active N-protected amino alcohols and peptide alcohols in very high yields. The method is very simple and attractive, as it does not require an additional step of N-protected amino acid derivatization and proceeds without the loss of enantiomeric homogeneity.     

Simple and efficient synthesis of chiral amino alcohols with an amino acid-based skeleton

Sodium bis(2-methoxyethoxy)aluminum hydride, NaAlH₂(OCH₂CH₂OCH₃)₂, commercially known as Vitride® or Red-Al®, enables rapid synthesis of pure optically active N-protected amino alcohols and peptide alcohols in very high yields. The method is very simple and attractive, as it does not require an additional step of N-protected amino acid derivatization and proceeds without the loss of enantiomeric homogeneity.     

Ninhydrin as a reversible protecting group of amino-terminal cysteine.

The proximity of the alpha-amine and beta-thiol of alpha-amino terminal-cysteine (NT-Cys) residues in peptides imparts unique chemical properties that have been exploited for inter- and intra-molecular ligation of unprotected peptides obtained through both synthetic and biological means. A reversible protecting group orthogonal to other protection strategies and reversible under mild conditions would be useful in simplifying the synthesis, cleavage, purification and handling of such NT-Cys peptides. It could also be useful for the sequential ligation of peptides. To this end, we explored tri-one chemistry and found that ninhydrin (indane-1,2,3 trione) reacted readily with cysteine or an NT-Cys-containing peptide on- or off-resin at pH 2-5 to form Ninhydrin-protected Cys (Nin-Cys) as a thiazolidine (Thz). The Thz ring, protecting both the amino and thiol groups in Nin-Cys, completely avoids the formylation and Thz side reactions found during hydrofluoric acid (HF) cleavage when N-pi-benzyloxymethyl histidine groups are present. Nin-Cys is stable during coupling reactions and various cleavage conditions with trifluoroacetic acid or HF, but is deprotected under thiolytic or reducing conditions. These properties enable a facile one-step deprotection and end-to-end-cyclization reaction of Nin-Cys peptides containing C-terminal thioesters.     

A new terbium(III) chelate as an efficient singlet oxygen fluorescence probe

A terbium(III) chelate fluorescence probe for detection of singlet oxygen (1O2) in aqueous media, N,N,N1,N1-[2,6-bis(3'-aminomethyl-1'-pyrazolyl)-4-(9'-anthryl)pyridine] tetrakis (acetate)-Tb3+ (PATA-Tb3+), was designed and synthesized. The new chelate is highly water soluble, is almost nonfluorescent, and can specifically react with 1O2 to yield a strongly fluorescent chelate, the endoperoxide of PATA-Tb3+, accompanied by a remarkable increase in the fluorescence quantum yield from 0.46 to 10.5%. The long fluorescence lifetime of the endoperoxide (2.76 ms) allows the probe to be used favorably for time-resolved fluorescence detection of 1O2. The studies of fluorescence property and reaction specificity indicate that the new probe is highly sensitive and selective for 1O2. The probe was used for quantitative detection of 1O2 generated from a MoO4(2-) -H2O2 system to give a detection limit of 10.8 nM. In addition, the good applicability of the probe was demonstrated by the real-time monitoring of the kinetic process of 1O2 generation in a horseradish peroxidase-catalyzed oxidation system of indole-3-acetic acid in a weakly acidic buffer.     

Synthesis of fructofuranosides: efficient glycosylation with N-phenyltrifluoroacetimidate as the leaving group

Fructofuranosyl trifluoroacetimidate 3 was demonstrated to be an effective glycosyl donor that exhibited good alpha-selectivity and good yield in fructosylation reactions. The reaction proceeds via neighboring group participation, which was proved by the isolation of a stable allylic orthoester intermediate.     

Synthesis of D-altritol nucleosides with a 3'-O-tert-butyldimethylsilyl protecting group

Four D-altritol nucleosides with a 3'-O-tert-butyldimethylsilyl protecting group are synthesized (base moieties are adenine, guanine, thymine and 5-methylcytosine). The nucleosides are obtained by ring opening reaction of 1,5:2,3-dianhydro-4,6-O-benzylidene-D-allitol. Optimal reaction circumstances (NaH, LiH, DBU, phase transfer, microwave irridation) for the introduction of the heterocycles are base-specific. For the introduction of the 3'-O-silyl protecting group, long reaction times and several equivalents of tert-butyldimethylsilyl chloride are needed.     

The use of the o-nitrophenyl group as a protecting/activating group for 2-acetamido-2-deoxyglucose

The o-nitrophenyl group, a protecting group with latent activation potential, was used as a protecting group for the glycosidic position. It is stable to common conditions used in synthesis and can be activated for displacement and glycoside formation by an alcohol, using zinc chloride as a catalyst. Good to excellent yields of beta-glycosides of the important amino sugar N-acetylglucosamine were obtained. A mechanism for the reaction is proposed.     

The box A domain of high mobility group box-1 protein as an efficient siRNA carrier with anti-inflammatory effects

High mobility group box‐1 (HMGB‐1) is a DNA binding nuclear protein and pro‐inflammatory cytokine. The box A domain of HMGB‐1 (rHMGB‐1A) exerts an anti‐inflammatory effect, inhibiting wild‐type HMGB‐1 (wtHMGB‐1). In this study, HMGB‐1A was evaluated as an siRNA carrier with anti‐inflammatory effects. HMGB‐1A was expressed and purified by consecutive nickel chelate chromatography, cationic exchange chromatography, and polymixin B chromatography. Purified rHMGB‐1A demonstrated an anti‐inflammatory effect, reducing tumor necrosis factor‐α (TNF‐α) in wtHMGB‐1 or lipopolysaccharide (LPS) activated macrophages. In gel retardation assay, rHMGB‐1A formed a stable complex with siRNA at or above a 1:2 weight ratio (siRNA:rHMGB‐1A). A heparin competition assay showed that an siRNA/rHMGB‐1A complex released siRNA more easily than an siRNA/polyethylenimine (PEI, 25 kDa) complex. Luciferase siRNA/rHMGB‐1A reduced firefly luciferase expression at a similar level as luciferase siRNA/PEI complex. Furthermore, TNF‐α siRNA/rHMGB‐1A synergistically reduced TNF‐α expression in LPS activated macrophages. Therefore, rHMGB‐1A may be useful as an siRNA carrier with anti‐inflammatory effects in siRNA therapy for various inflammatory diseases. J. Cell. Biochem. 113: 122–131, 2012. © 2011 Wiley Periodicals, Inc.     

Tailoring a low-molecular weight protein tyrosine phosphatase into an efficient reporting protein

Fusion reporter methods are important tools for biology and biotechnology. An ideal reporter protein in a fusion system should have little effects on its fusion partner and provide an easy and accurate readout. Therefore, a small monomeric protein with high activity for detection assays often has advantages as a reporter protein. For this purpose, we have tailored the human B-form low-molecular-weight phosphotyrosyl phosphatase (HPTP-B) to increase its general applicability as a potent reporter protein. With the aim to eliminate interference from cysteine residues in the native HPTP-B, combined with a systematic survey of N- and C-terminal truncated variants, a series of cysteine to serine mutations were introduced, which allowed isolation of an engineered soluble protein with suitable biophysical properties. When we deleted both the first six residues and the last two residues, we still obtained a soluble mutant protein with correct folding and similar activity with wild-type protein. This mutant with two cysteine to serine mutations, HPTP-B^{N_Δ6-C_Δ2-C90S-C109S}, has good potential as an optimal reporter.     

Green and scalable synthesis of chiral aromatic alcohols through an efficient biocatalytic system

Chiral aromatic alcohols have received much attention due to their widespread use in pharmaceutical industries. In the asymmetric synthesis processes, the excellent performance of alcohol dehydrogenase makes it a good choice for biocatalysts. In this study, a novel and robust medium-chain alcohol dehydrogenase RhADH from Rhodococcus R6 was discovered and used to catalyse the asymmetric reduction of aromatic ketones to chiral aromatic alcohols. The reduction of 2-hydroxyacetophenone (2-HAP) to (R)-(-)-1-phenyl-1,2-ethanediol ((R)-PED) was chosen as a template to evaluate its catalytic activity. A specific activity of 110 U mg⁻¹ and a 99% purity of e.e. was achieved in the presence of NADH. An efficient bienzyme-coupled catalytic system (RhADH and formate dehydrogenase, CpFDH) was established using a two-phase strategy (dibutyl phthalate and buffer), which highly raised the tolerated substrate concentration (60 g l⁻¹). Besides, a broad range of aromatic ketones were enantioselectively reduced to the corresponding chiral alcohols by this enzyme system with highly enantioselectivity. This system is of the potential to be applied at a commercial scale.