Synthesis of Fluorescent Dibenzofuran α-Amino Acids: Conformationally Rigid Analogues of Tyrosine

We report two synthetic strategies for the preparation of dibenzofuran α-amino acids, expanding the structural toolbox of fluorescent probes. The strategies involved dibenzofuran synthesis via a Pd(II)-catalyzed C-O cyclization, alongside an efficient Negishi coupling approach for faster access to analogues. These rigid tyrosine mimics possess enhanced fluorescent properties compared to proteinogenic amino acids as demonstrated by application of the lead compound as a FRET donor for monitoring peptide hydrolysis by a serine protease.

Expedient discovery of fluorogenic amino acid-based probes via one-pot palladium-catalysed arylation of tyrosine

To overcome the limitations of using large extrinsic chromophores for biological imaging, fluorescent unnatural α-amino acids have been widely adopted as intrinsic peptidic probes. Although various classes have been successfully utilised for imaging applications, novel amino acid probes readily prepared through operationally simple synthetic methodology are still required. Here, we report a new approach for the synthesis of unnatural α-amino acids via a one-pot process involving activation and palladium-catalysed arylation of tyrosine. Rapid access to a small library of novel α-amino acids has allowed the discovery of a dimethylaminobiphenyl analogue that displays strong charge transfer-based fluorescent properties and is both solvatochromic and pH sensitive with a significant hypsochromic shift in emission under acidic conditions. The imaging potential of the dimethylaminobiphenyl α-amino acid was demonstrated via its application as a FRET donor in a novel decapeptide substrate for monitoring and evaluating the kinetics of a serine protease.

Advances in Natural-Product-Based Fluorescent Agents and Synthetic Analogues for Analytical and Biomedical Applications

Fluorescence is a remarkable property exhibited by many chemical compounds and biomolecules. Fluorescence has revolutionized analytical and biomedical sciences due to its wide-ranging applications in analytical and diagnostic tools of biological and environmental importance. Fluorescent molecules are frequently employed in drug delivery, optical sensing, cellular imaging, and biomarker discovery. Cancer is a global challenge and fluorescence agents can function as diagnostic as well as monitoring tools, both during early tumor progression and treatment monitoring. Many fluorescent compounds can be found in their natural form, but recent developments in synthetic chemistry and molecular biology have allowed us to synthesize and tune fluorescent molecules that would not otherwise exist in nature. Naturally derived fluorescent compounds are generally more biocompatible and environmentally friendly. They can also be modified in cost-effective and target-specific ways with the help of synthetic tools. Understanding their unique chemical structures and photophysical properties is key to harnessing their full potential in biomedical and analytical research. As drug discovery efforts require the rigorous characterization of pharmacokinetics and pharmacodynamics, fluorescence-based detection accelerates the understanding of drug interactions via in vitro and in vivo assays. Herein, we provide a review of natural products and synthetic analogs that exhibit fluorescence properties and can be used as probes, detailing their photophysical properties. We have also provided some insights into the relationships between chemical structures and fluorescent properties. Finally, we have discussed the applications of fluorescent compounds in biomedical science, mainly in the study of tumor and cancer cells and analytical research, highlighting their pivotal role in advancing drug delivery, biomarkers, cell imaging, biosensing technologies, and as targeting ligands in the diagnosis of tumors.

Odd-Even Law Mediated Supramolecular Chirality of Luminescent Dipeptides for Chiroptical Energy Transfer

Inherent luminescent short peptides essentially provide opportunities to rationally manipulate supramolecular chirality and chiral luminescence. Herein, a facile protocol to construct a series of naphthalimide-appended dipeptides is reported that show ultrasound wave-activated supramolecular chirality regulated by odd-even law. Naphthalimide luminophores are conjugated to the dipeptide skeleton with variable alkyl spacers. The presence of tyrosine interferes the kinetic aggregation into achiral nanoparticles without chirality transfer to supramolecular scale. However, ultrasound treatment initiates the nanoparticle-to-helix transition accompanied with the appeared chiral optics, including Cotton effect and circularly polarized luminescence (CPL). The supramolecular chiral parameters, including handedness of helices and chiroptical behaviors, follow the odd-even law of alkyl spacers in dipeptides bearing non-substituted naphthalimides. The amine-substitution boosted the quantum yields of dipeptide whereas no odd-even effect. The two types of dipeptides constituted ideal energy transfer pairs that enable the efficient energy transfer as well as the transportation of odd-even law to dipeptides containing substituted naphthalimides. This work sheds light on the construction of luminescent dipeptides with applications in precise control over chirality transportation and chiral luminescence.

Fluorescent carbazole-derived α-amino acids: structural mimics of tryptophan

Fluorescent tags are commonly used for imaging of proteins and peptides during biological events; however, the large size of dyes can disrupt protein structure and function, and typically require the use of a chemical spacer. Herein, we report the synthesis of a new class of fluorescent unnatural α-amino acid, containing carbazole side-chains designed to mimic l-tryptophan and thus, readily incorporated into peptides. The amino acids were constructed using a Negishi cross-coupling reaction as the key step and exhibited strong fluorescent emission, with high quantum yields in both organic solvents and water. Compatible with solid phase peptide synthesis, the carbazole amino acids were used to replace tryptophan in a β-hairpin model peptide and shown to be a close structural mimic with retention of conformation. They were also found to be effective fluorescent molecular reporters for biological events. Incorporation into a proline-rich ligand of the WW domain protein demonstrated that the fluorescent properties of a carbazole amino acid could be used to measure the protein-protein binding interaction of this important biological signalling process.

Fluorescent Probes and Quenchers in Studies of Protein Folding and Protein-Lipid Interactions

Fluorescence spectroscopy provides numerous methodological tools for structural and functional studies of biological macromolecules and their complexes. All fluorescence-based approaches require either existence of an intrinsic probe or an introduction of an extrinsic one. Moreover, studies of complex systems often require an additional introduction of a specific quencher molecule acting in combination with a fluorophore to provide structural or thermodynamic information. Here, we review the fundamentals and summarize the latest progress in applications of different classes of fluorescent probes and their specific quenchers, aimed at studies of protein folding and protein-membrane interactions. Specifically, we discuss various environment-sensitive dyes, FRET probes, probes for short-distance measurements, and several probe-quencher pairs for studies of membrane penetration of proteins and peptides. The goals of this review are: (a) to familiarize the readership with the general concept that complex biological systems often require both a probe and a quencher to decipher mechanistic details of functioning and (b) to provide example of the immediate applications of the described methods.

Synthesis of Thiazoloindole α-Amino Acids: Chromophores Amenable to One- and Two-Photon Induced Fluorescence

Thiazoloindole α-amino acids have been synthesized in four steps from tryptophan using a dual-catalytic thiolation reaction and a copper-mediated intramolecular N-arylation process. Late-stage diversification of the thiazoloindole core with electron-deficient aryl substituents produced chromophores that on one-photon excitation displayed blue-green emission, mega-Stokes shifts, and high quantum yields. The thiazoloindole amino acids could also be excited via two-photon absorption in the near-infrared, demonstrating their potential for biomedical imaging applications.

Synthesis and Photophysical Properties of Charge-Transfer-Based Pyrimidine-Derived α-Amino Acids

The four-step synthesis of fluorescent pyrimidine-derived α-amino acids from an l-aspartic acid derivative is described. The key synthetic steps involved preparation of ynone intermediates via the reaction of alkynyl lithium salts with a Weinreb amide, followed by an ytterbium-catalyzed heterocyclization reaction with amidines. Variation of substituents at the C2- and C4-position of the pyrimidine ring allowed tuning of the photoluminescent properties of the α-amino acids. This revealed that a combination of highly conjugated or electron-rich aryl substituents with the π-deficient pyrimidine motif resulted in fluorophores with the highest quantum yields and overall brightness. Further analysis of the most fluorogenic α-amino acid demonstrated solvatochromism and sensitivity to pH.

Fluorescent α-amino acids via Heck-Matsuda reactions of phenylalanine-derived arenediazonium salts

The Heck-Matsuda coupling reaction of arenediazonium salts derived from L-phenylalanine with various alkenes has been developed. A two-step process involving the preparation of a tetrafluoroborate diazonium salt from a 4-aminophenylalanine derivative, followed by a palladium(0)-catalysed Heck-Matsuda coupling reaction allowed access to a range of unnatural α-amino acids with cinnamate, vinylsulfone and stilbene side-chains. Analysis of the photophysical properties of these unnatural α-amino acids demonstrated that the (E)-stilbene analogues exhibited fluorescent properties with red-shifted absorption and emission spectra and larger quantum yields than L-phenylalanine.

Rotamer-Controlled Dual Emissive α-Amino Acids

The synthesis and photoluminescent properties of novel α-amino acids are described in which the biaryl benzotriazinone-containing chromophores were found to display dual emission fluorescence via locally excited (LE) and twisted intramolecular charge transfer (TICT) states. The intensity of each emission band could be controlled by the electronics and position of the substituents, and this led to the design of a 2-methoxyphenyl analogue that, due to twisting, displayed bright TICT fluorescence, solvatochromism, and pH sensitivity.

Site-specific dual encoding and labeling of proteins via genetic code expansion

The ability to selectively modify proteins at two or more defined locations opens new avenues for manipulating, engineering, and studying living systems. As a chemical biology tool for the site-specific encoding of non-canonical amino acids into proteins in vivo, genetic code expansion (GCE) represents a powerful tool to achieve such modifications with minimal disruption to structure and function through a two-step "dual encoding and labeling" (DEAL) process. In this review, we summarize the state of the field of DEAL using GCE. In doing so, we describe the basic principles of GCE-based DEAL, catalog compatible encoding systems and reactions, explore demonstrated and potential applications, highlight emerging paradigms in DEAL methodologies, and propose novel solutions to current limitations.

Synthesis and Fluorescent Properties of Alkynyl- and Alkenyl-Fused Benzotriazole-Derived α-Amino Acids

Fluorescent unnatural α-amino acids are widely used as probes in chemical biology and medicinal chemistry. While a variety of structural classes have been developed, there is still a requirement for new environmentally sensitive analogues that can closely mimic proteinogenic α-amino acids. Here, we report the synthesis and fluorescent properties of highly conjugated, benzotriazole-derived α-amino acids designed to mimic l-tryptophan. Alkynyl-substituted analogues were prepared using three key steps, nucleophilic aromatic substitution with a 3-aminoalanine derivative, benzotriazole formation via a one-pot diazotization and cyclization process, and a Sonogashira cross-coupling reaction. E-Alkenyl-substituted benzotriazoles were accessed by stereoselective partial hydrogenation of the alkynes using zinc iodide and palladium catalysis. The alkynyl analogues were found to possess higher quantum yields and stronger brightness and, a solvatochromic study with the most fluorogenic α-amino acids demonstrated sensitivity to polarity.

Preparation of Deuterium Labeled Compounds by Pd/C-Al-D2O Facilitated Selective H-D Exchange Reactions

The chemo/regioselective H-D exchange of amino acids and synthetic building blocks by an environmentally benign Pd/C-Al-D₂O catalytic system is described. Due to the importance of isotope labeled compounds in medicinal chemistry and structural biology, notably their use as improved drug candidates and biological probes, the efficient and selective deuteration methods are of great interest. The approach is based on selective H-D exchange reactions where the deuterium source is simple D₂O. D₂ gas is generated in situ from the reaction of aluminum and D₂O, while the commercially available palladium catalyst assists the H-D exchange reaction. The high selectivity and efficiency, as well as the simplicity and safe nature of the procedure make this method an environmentally benign alternative to current alternatives.

Rational Design and Synthesis of Large Stokes Shift 2,6-Sulphur-Disubstituted BODIPYs for Cell Imaging

Five new disubstituted 2,6-thioaryl-BODIPY dyes were synthesized via selective aromatic electrophilic substitution from commercially available thiophenols. The analysis of the photophysical properties via absorption and emission spectroscopy showed unusually large Stokes shifts for BODIPY fluorophores (70–100 nm), which makes them suitable probes for bioimaging. Selected compounds were evaluated for labelling primary immune cells as well as different cancer cell lines using confocal fluorescence microscopy.

Automated Radiosynthesis of cis- and trans-4-[18F]Fluoro-l-proline Using [18F]Fluoride

The positron emission tomography imaging agents cis- and trans-4-[18F]fluoro-l-proline are used for the detection of numerous diseases such as pulmonary fibrosis and various carcinomas. These imaging agents are typically prepared by nucleophilic fluorination of 4-hydroxy-l-proline derivatives, with [18F]fluoride, followed by deprotection. Although effective radiofluorination reactions have been developed, the overall radiosynthesis process is suboptimal due to deprotection methods that are performed manually, require multiple steps, or involve harsh conditions. Here we describe the development of two synthetic routes that allow access to precursors, which undergo highly selective radiofluorination reactions and rapid deprotection, under mild acidic conditions. These methods were found to be compatible with automation, avoiding manual handling of radioactive intermediates.

Recent Advances in Fluorescence Imaging by Genetically Encoded Non-canonical Amino Acids

Technical innovations in protein labeling with a fluorophore at the specific residue have played a significant role in studying protein dynamics. The genetic code expansion (GCE) strategy enabled the precise installation of fluorophores at the tailored site of proteins in live cells with minimal perturbation of native functions. Considerable advances have been achieved over the past decades in fluorescent imaging using GCE strategies along with bioorthogonal chemistries. In this review, we discuss advances in the GCE-based strategies to site-specifically introduce fluorophore at a defined position of the protein and their bio-imaging applications.

Enantioselective Synthesis and Application of Small and Environmentally Sensitive Fluorescent Amino Acids for Probing Biological Interactions

Environmentally sensitive fluorescent amino acids (FlAAs) have been used extensively to probe biological interactions. However, most of these amino acids are large and do not resemble amino acid side chains. Here, we report the enantioselective synthesis of two small and environmentally sensitive fluorescent amino acids bearing 7-dialkylaminocoumarin side chains by alkylation of a Ni(II) glycine Schiff base complex. These amino acids exhibit a large increase in fluorescence as environment polarity decreases. One of these FLAAs was incorporated into a highly active analog of the cyclic lipopeptide antibiotic paenibacterin by Fmoc solid-phase peptide synthesis via a new and very efficient route. This peptide was used to probe the interaction of the antibiotic with model liposomes, lipopolysaccharides, and live bacteria.

Rhodaelectro-catalyzed access to chromones via formyl C-H activation towards peptide electro-labeling

Chromones represent a privileged scaffold in medicinal chemistry and are an omnipresent structural motif in natural products. Chemically encoded non-natural peptidomimetics feature improved stability towards enzymatic degradation, cell permeability and binding affinity, translating into a considerable impact on pharmaceutical industry. Herein, a strategy for the sustainable assembly of chromones via electro-formyl C–H activation is presented. The rational design of the rhodaelectro-catalysis is guided by detailed mechanistic insights and provides versatile access to tyrosine-based fluorogenic peptidomimetics.

The chromone scaffold is present in drugs and bioactive natural products, but conventional approaches to access chromones require stoichiometric amounts of oxidants. Here, the authors report rhodaelectro-catalyzed assembly of chromones by electrochemical formyl C–H activations, providing the basis for late-stage peptide diversification.

Facile synthesis of a novel genetically encodable fluorescent α-amino acid emitting greenish blue light

We report the facile synthesis and characterization of a novel fluorescent α-amino acid 4-phenanthracen-9-yl-l-phenylalanine (Phen-AA) (5) that emits greenish blue light in the visible region. This genetically encodable l-α-amino acid has excellent photostability with a 75% quantum yield. It readily gets into human cells, being clearly imaged upon 405 nm laser excitation. The synthetic procedure is resistant to racemization and only involves three simple steps which use mild conditions and generate the Phen-AA in reasonably good yield. It may find broad applications in research, biotechnology, and the pharmaceutical industry.

Phenothiazine-Biaryl-Containing Fluorescent RGD Peptides

Cyclic RGD peptides are well-known ligands of integrins. The integrins αV β3 and α5 β1 are involved in angiogenesis, and integrin αV β3 is abundantly present on cancer cells, thus representing a therapeutic target. Hence, synthetic and biophysical studies continuously are being directed towards the understanding of ligand-integrin interaction. In this context, the development of versatile synthetic strategies to obtain fluorescent building blocks that can add molecular diversity and modular spectral characteristics while not compromising binding affinity or selectivity is a relevant task. An on-resin intramolecular Suzuki-Miyaura cross-coupling (SMC) between l- or d-7-bromotryptophan (7BrTrp) and a phenothiazine (Ptz) boronic acid affords fluorescent cyclic RGD pseudopeptides, c(RGD(W/w)Ptz). Ring closure by SMC establishes a phenothiazine-indole moiety with axial chirality. An array of eight novel compounds has been synthesized, among them one fluorescent compound with good affinity to integrin αV β3 . The fluorescence properties of the analogues can be efficiently tuned depending on the substituents in Ptz moiety even for fluorescence emission in the visible (red) spectral range.

Core remodeling leads to long wavelength fluoro-coumarins

Low molecular weight, uncharged far-red and NIR dyes would be enabling for a range of imaging applications. Rational redesign of the coumarin scaffold leads to Fluoro-Coumarins (FCs), the lowest molecular weight dyes with emission maxima beyond 700, 800, and 900 nm. FCs display large Stokes shifts and high environmental sensitivity, with a 40-fold increase in emission intensity in hydrophobic solvents. Untargeted variants exhibit selective lipid droplet and nuclear staining in live cells. Furthermore, sulfo-lipid derivatization enables active targeting to the plasma membrane. Overall, these studies report a promising platform for the development of biocompatible, context-responsive imaging agents.

Fluoro-Coumarins are a novel class of far-red and near-infrared solvent sensitive dyes of exceptionally low molecular weight.

Coumarins into Polyurethanes for Smart and Functional Materials

Polyurethanes are of undoubted interest for the scientific community and the industry. Their outstanding versatility from tailor-made structures turns them into major polymers for use in a wide range of different applications. As with other polymers, new, emerging molecules and monomers with specific attributes can provide new functions and capabilities to polyurethanes. Natural and synthetic coumarin and its derivatives are characterised by interesting biological, photophysical and photochemical properties. Then, the polyurethanes can exploit those features of many coumarins which are present in their composition to achieve new functions and performances. This article reviews the developments in the proper use of the special properties of coumarins in polyurethanes to produce functional and smart materials that can be suitable for new specific applications.

4-Aminophthalimide Amino Acids as Small and Environment-Sensitive Fluorescent Probes for Transmembrane Peptides

Fluorescence probing of transmembrane (TM) peptides is needed to complement state-of-the art methods-mainly oriented circular dichroism and solid-state NMR spectroscopy-and to allow imaging in living cells. Three new amino acids incorporating the solvatofluorescent 4-aminophthalimide in their side chains were synthesized in order to examine the local polarity in the α-helical TM fragment of the human epidermal growth factor receptor. It was possible to distinguish their locations, either in the hydrophobic core of the lipid bilayer or at the membrane surface, by fluorescence readout, including blue shift and increased quantum yield. An important feature is the small size of the 4-aminophthalimide chromophore. It makes one of the new amino acids approximately isosteric to tryptophan, typically used as a very small fluorescent amino acid in peptides and proteins. In contrast to the only weakly fluorescent indole system in tryptophan, the 4-aminophthalimide moiety produces a significantly more informative fluorescence readout and is selectively excited outside the biopolymer absorption range.

Conformationally rigid pyrazoloquinazoline α-amino acids: one- and two-photon induced fluorescence

Conformationally rigid unnatural α-amino acids bearing a pyrazoloquinazoline ring system that are amenable to both one- and two-photon excitation have been developed as new fluorescent probes.

One-pot, two-step synthesis of unnatural α-amino acids involving the exhaustive aerobic oxidation of 1,2-diols

Herein, we report the nor-AZADO-catalyzed exhaustive aerobic oxidations of 1,2-diols to α-keto acids. Combining oxidation with transamination using dl-2-phenylglycine led to the synthesis of free α-amino acids (AAs) in one pot. This method enables the rapid and flexible preparation of a variety of valuable unnatural AAs, such as fluorescent AAs, photoactivatable AAs, and other functional AAs for bioorthogonal reactions.

Fluorogenic Trp(redBODIPY) cyclopeptide targeting keratin 1 for imaging of aggressive carcinomas

Keratin 1 (KRT1) is overexpressed in squamous carcinomas and associated with aggressive pathologies in breast cancer. Herein we report the design and preparation of the first Trp-based red fluorogenic amino acid, which is synthetically accessible in a few steps and displays excellent photophysical properties, and its application in a minimally-disruptive labelling strategy to prepare a new fluorogenic cyclopeptide for imaging of KRT1+ cells in whole intact tumour tissues.

Modifications of amino acids using arenediazonium salts

Aryl transfer reactions from arenediazonium salts have started to make their impact in chemical biology with initial forays in the arena of arylative modifications and bio-conjugations of amino acids, peptides and proteins.

Improving target amino acid selectivity in a permissive aminoacyl tRNA synthetase through counter-selection

The amino acid acridon-2-ylalanine (Acd) can be a valuable probe of protein dynamics, either alone or as part of a Förster resonance energy transfer (FRET) or photo-induced electron transfer (eT) probe pair. We have previously reported the genetic incorporation of Acd by an aminoacyl tRNA synthetase (RS). However, this RS, developed from a library of permissive RSs, also incorporates N-phenyl-aminophenylalanine (Npf), a trace byproduct of one Acd synthetic route. We have performed negative selections in the presence of Npf and analyzed the selectivity of the resulting AcdRSs by in vivo protein expression and detailed kinetic analyses of the purified RSs. We find that selection conferred a ∼50-fold increase in selectivity for Acd over Npf, eliminating incorporation of Npf contaminants, and allowing one to use a high yielding Acd synthetic route for improved overall expression of Acd-containing proteins. More generally, our report also provides a cautionary tale on the use of permissive RSs, as well as a strategy for improving selectivity for the target amino acid.

Full color palette of fluorescent d-amino acids for in situ labeling of bacterial cell walls

Fluorescent d-amino acids (FDAAs) enable efficient in situ labeling of peptidoglycan in diverse bacterial species. Conducted by enzymes involved in peptidoglycan biosynthesis, FDAA labeling allows specific probing of cell wall formation/remodeling activity, bacterial growth and cell morphology. Their broad application and high biocompatibility have made FDAAs an important and effective tool for studies of peptidoglycan synthesis and dynamics, which, in turn, has created a demand for the development of new FDAA probes. Here, we report the synthesis of new FDAAs, with emission wavelengths that span the entire visible spectrum. We also provide data to characterize their photochemical and physical properties, and we demonstrate their utility for visualizing peptidoglycan synthesis in Gram-negative and Gram-positive bacterial species. Finally, we show the permeability of FDAAs toward the outer-membrane of Gram-negative organisms, pinpointing the probes available for effective labeling in these species. This improved FDAA toolkit will enable numerous applications for the study of peptidoglycan biosynthesis and dynamics.

Hot off the press

A personal selection of 32 recent papers is presented covering various aspects of current developments in bioorganic chemistry and novel natural products such as kanamienamide from the marine cyanobacterium Moorea bouillonii.