Developing visible fluorogenic 'click-on' dyes for cellular imaging

Synthesis and structure-activity relationship (SAR) studies of 1,2,3-triazole, amide, and ester-based benzothiazole derivatives as potential molecular probes for tau protein

The pyridinyl-butadienyl-benzothiazole (PBB3 15) scaffold was used to develop tau ligands with improved in vitro and in vivo properties for imaging applications to provide insights into the etiology and characteristics of Alzheimer's disease. The photoisomerisable trans-butadiene bridge of PBB3 was replaced with 1,2,3-triazole, amide, and ester moieties and in vitro fluorescence staining studies revealed that triazole derivatives showed good visualisation of Aβ plaques, but failed to detect the neurofibrillary tangles (NFTs) in human brain sections. However, NFTs could be observed using the amide 110 and ester 129. Furthermore, the ligands showed low to high affinities (Ki = >1.5 mM-0.46 nM) at the shared binding site(s) with PBB3.

One-Pot Reductive Methylation of Nitro- and Amino-Substituted (Hetero)Aromatics with DMSO/HCOOH: Concise Synthesis of Fluorescent Dimethylamino-Functionalized Bibenzothiazole Ligands with Tunable Emission Color upon Complexation

One-pot reductive N,N-dimethylation of suitable nitro- and amino-substituted (hetero)arenes can be achieved using a DMSO/HCOOH/Et₃N system acting as a low-cost but efficient reducing and methylating agent. The transformation of heteroaryl-amines can be accelerated by using dimethyl sulfoxide/oxalyl chloride or chloromethyl methyl sulfide as the source of active CH₃SCH₂⁺ species, while the exclusion of HCOOH in the initial stage of the reaction allows avoiding N-formamides as resting intermediates. The developed procedures are applicable in multigram-scale synthesis, and because of the lower electrophilicity of CH₃SCH₂⁺, they also work in pathological cases, where common methylating agents provide N,N-dimethylated products in no yield or inferior yields due to concomitant side reactions. The method is particularly useful in one-pot reductive transformation of 2-H-nitrobenzazoles to corresponding N,N-dimethylamino-substituted heteroarenes. These, upon Cu(II)-catalyzed oxidative homocoupling, afford 2,2'-bibenzazoles substituted with dimethylamino groups as charge-transfer N^N ligands with intensive absorption/emission in the visible region. The fluorescence of NMe₂-functionalized bibenzothiazoles remains intensive even upon complexation with ZnCl₂, while emission maxima are bathochromically shifted from the green/yellow to orange/red spectral region, making these small-molecule fluorophores, exhibiting large emission quantum yields and Stokes shifts, an attractive platform for the construction of various functional dyes and light-harvesting materials with tunable emission color upon complexation.

Hetero-Trifunctional Malonate-Based Nanotheranostic System for Targeted Breast Cancer Therapy

Designing multifunctional linkers is crucial for tricomponent theranostic targeted nanomedicine development as they are essential to enrich polymeric systems with different functional moieties. Herein, we have obtained a hetero-trifunctional linker from malonic acid and demonstrated its implication as an amphiphilic targeted nanotheranostic system (CB DX UN PG FL). We synthesized it with varying hydrophilic segment to fine-tune the hydrophobic/hydrophilic ratio to optimize its self-assembly. pH-responsive hydrazone-linked doxorubicin was conjugated to the backbone (UN PG FL) containing folate as a targeting ligand. Cobalt carbonyl complex was used for T₂-weighted magnetic resonance imaging (MRI). Electron micrographs of optimized molecule CB DX UN PG_(4 kDa) FL in an aqueous system have demonstrated about 50-60 nm-sized uniform micelles. The relaxivity study and the one-dimensional (1D) imaging experiments clearly revealed the effect of the nanotheranostics system on transverse relaxation (T₂) of water molecules, which validated the system as a T₂-weighted MRI contrast agent. The detailed in vitro biological studies validated the targeted delivery and anticancer potential of CB DX UN PG_(4 kDa) FL. Combining the data on transverse relaxation, folate mediated uptake, and anticancer activity, the designed molecule will have a significant impact on the development of targeted theranostic.

Synthesis and spectral properties of 6′-triazolyl-dihydroxanthene-hemicyanine fused near-infrared dyes

Copper(i)-catalyzed azide alkyne cycloaddition (CuAAC) to explore the fluorogenic potential of near-infrared (NIR) dihydroxanthene (DHX) triazole dyes.

Iodine mediated oxidative cross-coupling of unprotected anilines and heteroarylation of benzothiazoles with 2-methylquinoline

Iodine-promoted oxidative C-H/C-H cross-coupling of unprotected anilines and 2-methylquinoline to furnish C4-carbonylated aniline (4-aminophenyl)(quinoline-2-yl) methanones in moderate to good yields has been demonstrated. This work provides the first site-selective approach for the synthesis of free amino groups containing methanones including unprecedented C-H functionalization rather than the N-H functionalization of unprotected anilines via the Kornblum oxidation of 2-methylquinoline. Furthermore, we noticed that the incorporation of KOH under standard conditions provides 2-heteroarylbenzothiazoles from benzothiazoles and 2-methylquinoline in good to excellent yields. These transformations do not require any transition metals or peroxides and tolerate various functional groups such as methoxy, hydroxy, bromo, chloro and nitro groups. Moreover, a plausible mechanistic pathway is proposed.

The ULTIMATE Reagent: A Universal Photocleavable and Clickable Reagent for the Regiospecific and Reversible End Labeling of Any Nucleic Acid

There is a need for methods to chemically incorporate photocleavable labels into synthetic and biologically sourced nucleic acids in a chemically defined and reversible manner. We have previously demonstrated that the light-cleaved diazo di-methoxy nitro phenyl ethyl (diazo-DMNPE) group has a remarkable regiospecificity for modifying terminally phosphorylated siRNA. Building on this observation, we have identified conditions under which a diazo-DMNPE reagent that we designed (diazo-DMNPE-azide or DDA) is able to singly modify any nucleic acid (RNA, DNA, single-stranded, double-stranded, 3' or 5' phosphate). It can then be modified with any clickable reagent to incorporate arbitrary labels such as fluorophores into the nucleic acid. Finally, native nucleic acid can be regenerated directly through photolysis of the reagent. Use of the described approach should allow for the tagging of any nucleic acid, from any source-natural or unnatural-while allowing for the light-induced regeneration of native nucleic acid.

Design and Synthesis of Aza-Bicyclononene Dienophiles for Rapid Fluorogenic Ligations

Fluorogenic bioorthogonal reactions enable visualization of biomolecules under native conditions with excellent signal-to-noise ratio. Here, we present the design and synthesis of conformationally-strained aziridine-fused trans-cyclooctene (aza-TCO) dienophiles, which lead to the formation of fluorescent products in tetrazine ligations without the need for attachment of an extra fluorophore moiety. The presented aza-TCOs adopt the highly strained "half-chair" conformation, which was predicted computationally and confirmed by NMR measurements and X-ray crystallography. Kinetic studies revealed that the aza-TCOs belong to the most reactive dienophiles known to date. The potential of the newly developed aza-TCO probes for bioimaging applications is demonstrated by protein labeling experiments, imaging of cellular glycoconjugates and peptidoglycan imaging of live bacteria.

Sydnone-coumarins as clickable turn-on fluorescent sensors for molecular imaging

Sydnone-coumarin compounds are interesting turn-on fluorogenic probes for protein labeling.

A cell-permeable and triazole-forming fluorescent probe for glycoconjugate imaging in live cells

A new fluorescence-forming probe, coumOCT, designed by fusing cyclooctyne with a coumarin fluorophore was successfully used for the imaging of azido-glycoconjugates in living HeLa cells.

N-Iodosuccinimide involved one-pot metal-free synthesis of 2-heteroaromatic benzothiazole compounds

A metal-free and operationally simple protocol for the synthesis of structurally diverse 2-hetarylbenzothiazoles via oxidative condensation of the sp³ C–H bond with benzothiazoles has been described.

Synthesis and evaluation of benzothiazole-triazole and benzothiadiazole-triazole scaffolds as potential molecular probes for amyloid-β aggregation

Fluorescent scaffolds that can be easily modifiedviaclick chemistry were investigated as probes for Aβ-plaque deposits in mouse tissue.

Stereodivergent, Diels-Alder-initiated organocascades employing α,β-unsaturated acylammonium salts: scope, mechanism, and application

Chiral α,β-unsaturated acylammonium salts are novel dienophiles enabling enantioselective Diels–Alder-lactonization (DAL) organocascades leading to cis- and trans-fused, bicyclic γ- and δ-lactones.

Chiral α,β-unsaturated acylammonium salts are novel dienophiles enabling enantioselective Diels–Alder-lactonization (DAL) organocascades leading to cis- and trans-fused, bicyclic γ- and δ-lactones from readily prepared dienes, commodity acid chlorides, and a chiral isothiourea organocatalyst under mild conditions. We describe extensions of stereodivergent DAL organocascades to other racemic dienes bearing pendant secondary and tertiary alcohols, and application to a formal synthesis of (+)-dihydrocompactin is described. A combined experimental and computational investigation of unsaturated acylammonium salt formation and the entire DAL organocascade pathway provide a rationalization of the effect of Brønsted base additives and enabled a controllable, diastereodivergent DAL process leading to a full complement of possible stereoisomeric products. Evaluation of free energy and enthalpy barriers in conjunction with experimentally observed temperature effects revealed that the DAL is a rare case of an entropy-controlled diastereoselective process. NMR analysis of diene alcohol–Brønsted base interactions and computational studies provide a plausible explanation of observed stabilization of exo transition-state structures through hydrogen-bonding effects.

1,2,3-Triazole pharmacophore-based benzofused nitrogen/sulfur heterocycles with potential anti-Moraxella catarrhalis activity

Versatile 1,2,3-triazole pharmacophore-based benzofused heterocycles containing halogen-substituted aromatic (9-17 and 25-28), 7-substituted coumarin (18-23 and 29-30) or penciclovir-like subunit (31a,b-38a) were designed and synthesized to evaluate their antibacterial activities against selected Gram-positive and Gram-negative bacteria. Hybridization approach using environmentally friendly Cu(I)-catalyzed click reaction under microwave irradiation was adopted in the synthesis of regioselective 1,4-disubstituted 1,2,3-triazole tethered heterocycles (9-23 and 25-30), while post-N-alkylation of NH-1,2,3-triazoles afforded both 2,4- (31a-38a) and 1,4-disubstituted (31b-33b, 35b-37b) 1,2,3-triazole regioisomers. The compounds 18-23 and 25-30 revealed fluorescence in the violet region of the visible spectrum with a strong influence of phenyl spacer in 25-30 on both wavelength and emission intensity. Fusion of selected subunits led to new hybrid architecture, benzothiazole-1,2,3-triazole-coumarin 29 that demonstrated extremely narrow spectrum activity towards fastidious Gram-negative bacteria Moraxella catarrhalis. Selected hybrid showed the potency against Moraxella catarrhalis (MIC⩽0.25μg/mL) comparable to that of reference antibiotic azithromycin, which suggested that further investigations are necessary to optimize this potential hit compound as a new anti-Moraxella catarrhalis agent.

Highly selective fluorescent and colorimetric probe for live-cell monitoring of sulphide based on bioorthogonal reaction

H₂S is the third endogenously generated gaseous signaling compound and has also been known to involve a variety of physiological processes. To better understand its physiological and pathological functions, efficient methods for monitoring of H₂S are desired. Azide fluorogenic probes are popular because they can take place bioorthogonal reactions. In this work, by employing a fluorescein derivative as the fluorophore and an azide group as the recognition unit, we reported a new probe 5-azidofluorescein for H₂S with improved sensitivity and selectivety. The probe shows very low background fluorescence in the absence of H₂S. In the presence of H₂S, however, a significant enhancement for excited fluorescence were observed, resulting in a high sensitivity to H₂S in buffered (10 mmol/L HEPES, pH 7.0) aqueous acetonitrile solution (H₂O/CH₃CN = 1:3, v/v) with a detection limit of 0.035 μmol/L observed, much lower than the previously reported probes. All these features are favorable for direct monitoring of H₂S with satisfactory sensitivity, demonstrating its value of practical application.

Design strategies for bioorthogonal smart probes

Bioorthogonal chemistry has enabled the selective labeling and detection of biomolecules in living systems. Bioorthogonal smart probes, which become fluorescent or deliver imaging or therapeutic agents upon reaction, allow for the visualization of biomolecules or targeted delivery even in the presence of excess unreacted probe. This review discusses the strategies used in the development of bioorthogonal smart probes and highlights the potential of these probes to further our understanding of biology.

Imaging bacterial peptidoglycan with near-infrared fluorogenic azide probes

Fluorescent probes designed for activation by bioorthogonal chemistry have enabled the visualization of biomolecules in living systems. Such activatable probes with near-infrared (NIR) emission would be ideal for in vivo imaging but have proven difficult to engineer. We present the development of NIR fluorogenic azide probes based on the Si-rhodamine scaffold that undergo a fluorescence enhancement of up to 48-fold upon reaction with terminal or strained alkynes. We used the probes for mammalian cell surface imaging and, in conjunction with a new class of cyclooctyne D-amino acids, for visualization of bacterial peptidoglycan without the need to wash away unreacted probe.

Target validation using in-cell small molecule clickable imaging probes

The application of click chemistry to the visualization of chemical probes in in-cell chemical biology experiments is reviewed and the influence this research has had on target validation and molecular mode of action studies is also highlighted.

Oligonucleotide Labelling Using a Fluorogenic “Click” Reaction with a Hemicarboxonium Salt

Two fluorescent streptocyanine labelled oligonucleotides have been synthesized by a simple “click” reaction between a non-fluorescent hemicarboxonium salt and aminoalkyl functionalized thymidines within the oligonucleotide and their spectrophotometric properties have been studied.

Relative performance of alkynes in copper-catalyzed azide-alkyne cycloaddition

Copper-catalyzed azide-alkyne cycloaddition (CuAAC) has found numerous applications in a variety of fields. We report here only modest differences in the reactivity of various classes of terminal alkynes under typical bioconjugative and preparative organic conditions. Propargyl compounds represent an excellent combination of azide reactivity, ease of installation, and cost. Electronically activated propiolamides are slightly more reactive, at the expense of increased propensity for Michael addition. Certain alkynes, including tertiary propargyl carbamates, are not suitable for bioconjugation due to copper-induced fragmentation. A fluorogenic probe based on such reactivity is available in one step from rhodamine 110 and can be useful for optimization of CuAAC conditions.

Ultra Pseudo-Stokes Shift Near Infrared Dyes Based on Energy Transfer

Novel fluorescent dyes with ultra pseudo-Stokes Shift were prepared based on intramolecular energy transfer between a fluorescent donor and a Cyanine-7 acceptor. The prepared dyes could be excited at ~ 320 nm and emit fluorescence at ~ 780 nm. The energy transfer efficiencies of the system are found to be > 94 %.

Fluorogenic azidofluoresceins for biological imaging

Fluorogenic probes activated by bioorthogonal chemical reactions can enable biomolecule imaging in situations where it is not possible to wash away unbound probe. One challenge for the development of such probes is the a priori identification of structures that will undergo a dramatic fluorescence enhancement by virtue of the chemical transformation. With the aid of density functional theory calculations reported previously by Nagano and co-workers, we identified azidofluorescein derivatives that were predicted to undergo an increase in fluorescence quantum yield upon Cu-catalyzed or Cu-free cycloaddition with linear or cyclic alkynes, respectively. Four derivatives were experimentally verified in model reactions, and one, a 4-azidonaphthylfluorescein analogue, was further shown to label alkyne-functionalized proteins in vitro and glycoproteins on cells with excellent selectivity. The azidofluorescein derivative also enabled cell imaging under no-wash conditions with good signal above background. This work establishes a platform for the rational design of fluorogenic azide probes with spectral properties tailored for biological imaging.

In situ synthesis of fluorescent membrane lipids (ceramides) using click chemistry

Ceramide analogues containing azide groups either in the polar head or in the hydrocarbon chains are non-fluorescent. When incorporated into phospholipid bilayers, they can react in situ with a non-fluorescent 1,8-naphthalimide using click chemistry giving rise to fluorescent ceramide derivatives emitting at ≈440 nm. When incorporated into giant unilamellar vesicles, two-photon excitation at 760 nm allows visualization of the ceramide-containing bilayers. This kind of method may be of general applicability in the study of model and cell membranes.

A benzothiazole alkyne fluorescent sensor for Cu detection in living cell

A new type of alkyne dye, 6-dimethylaminobenzothiazole alkyne (1), was developed for Cu sensing in biological system. Dye (1) offered excellent selective over a panel of ions, only Cu(I) could change the fluorescence of dye (I) by forming copper acetylide between the terminal alkyne and Cu(I). Its potential of detecting Cu in biological system was demonstrated in cell culture.