Dye Analogues Research Articles

Synthesis, molecular dynamics, antimicrobial activity and wound healing application of new methylidene dyes based on pyrrolinone esters

A new methylidene dye based on the direct condensation of an aldehyde derivative with a pyrrolinone ester derivative was successfully prepared as well as its quaternary ammonium salt analogue. The structures of all synthesized dyes were confirmed using NMR, Mass and IR spectra. The absorption and emission spectra of the synthesized dyes were investigated. The synthesized methylidene dye and its cationic form showed high molar absorption coefficients and a significant emission of the cationic dye analogue solution was observed. The antibacterial affinity using the disk diffusion method was investigated for six potential skin infection causing microbial pathogens, including two Gram-negative species (Pseudomonas aeruginosa and Proteus mirabilis), two Gram-positive species (Staphylococcus aureus and Staphylococcus epidermidis), and two fungal species (Candida albicans and Rhizomucor miehei) by recording the inhibition zone as well as studying the killing time effect for the prepared dyes. The in vitro wound healing application and the effect of cationized Dye 2 on the healing progress showed very effective and faster healing at a concentration of 100 µg/mL (IC50). Molecular dynamics simulation studies of Dye 1 and Dye 2 were carried out to compute binding free energies using Generalized Born Surface Area (MM/GBSA) in molecular mechanics. Furthermore, computational studies revealed that Dye 2 showed high affinity toward the active site of DNA gyrase B, which provides a solid framework for new structure-based design initiatives.

Exploring how molluscan purple has survived throughout the Ages: The excited state dynamics of 6,6′-dibromoindigotin

The color purple has long been used as a symbol of royalty and power in art, fashion, and architecture. This correlation with aristocracy can be traced back to the use of molluscan purple, a rich purple dye that is still presently more expensive than gold, by royalty as early as the 18th century BCE. While the molluscan purple dye is composed of a mixture of various proteins, its color is derived from indigotin, indirubin and their brominated derivatives, including the molecule, 6,6′-dibromoindigotin, an analogue of the indigotin dye which is also widely used in various modern industries. Both dyes can exhibit high stability, in particular against photodamage from UV and Visible radiation. In this study, we present the gas phase absorption spectrum and excited-state lifetimes of 6,6′-dibromoindigotin combined with static calculations of the excited and ground-state potential energy surfaces. The lifetime measurements reveal that molluscan purple has nearly the same relaxation rate as indigotin providing new insights in the possible relaxation mechanisms of the indigotin family of dye molecules.

Cyclopentene ring effects in cyanine dyes: a handle to fine-tune photophysical properties.

The aim of this study is to investigate the photophysical properties of a cyanine dye analogue by performing first-principles calculations based on density functional theory (DFT) and time dependent-DFT. Cationic cyanine dyes are the subject of great importance due to their versatile applications and the tunability of their photophysical properties, such as by modifying their end groups and chain length. An example of this is the vinylene shift, which is experimentally known for these molecules, and it consists of a bathochromic (red) shift of approximately 100 nm of the 0-0 vibronic transition when a vinyl group is added to the polymethine chain. Our study shows that when the saturated moiety C2H4 of the cyclopentene ring is added to the chain, it interacts with the conjugated π-system, resulting in a smaller HOMO-LUMO gap. Here, we demonstrate the origin of this interaction and how it can be used to fine tune the absorption energies of this class of dyes.

Photostability of Mannich‐type dyed silk fibroin with pyrazolone‐containing aromatic primary amine dyes

AbstractMannich‐type dyeing of silk fibroin with aromatic primary amine dyes (APADs) is a novel reactive dyeing method that requires mild conditions and exhibits high selectivity and good wet fastness. However, the primary amine group in the APADs significantly decreases the photostability of Mannich‐type dyed silk fabrics. To reveal the structure–activity relationship and photofading mechanism of the APADs by Mannich‐type dyeing, six pyrazolone‐containing APADs with similar structures were designed and synthesised. Variation in amino electron density among the dye analogues was related to differences in colour fixation of the Mannich‐dyed fabrics, as determined from the calculated Mulliken charge densities. Using mass spectrometry to monitor the photodecomposition of the dyed silk, it is demonstrated that the Mannich‐type dyed silk fabrics undergo photooxidative fading, in contrast to the conventional acidic‐type dyed fabrics that undergo photoreductive fading. Furthermore, it is shown that the Mannich‐type dyed silk fabric has a higher light fastness than conventional acidic‐type dyed fabrics using the same pyrazolone‐containing APADs. Evaluation of dye dipole moment and Mannich‐type dyeing shows that the APADs with increased dipole moments generally demonstrated increased light fastness.

Non-Covalent Interactions between dUTP C5-Substituents and DNA Polymerase Decrease PCR Efficiency.

The approach based on molecular modeling was developed to study dNTP derivatives characterized by new polymerase-specific properties. For this purpose, the relative efficiency of PCR amplification with modified dUTPs was studied using Taq, Tth, Pfu, Vent, Deep Vent, Vent (exo-), and Deep Vent (exo-) DNA polymerases. The efficiency of PCR amplification with modified dUTPs was compared with the results of molecular modeling using the known 3D structures of KlenTaq polymerase-DNA-dNTP complexes. The dUTPs were C5-modified with bulky functional groups (the Cy5 dye analogs) or lighter aromatic groups. Comparing the experimental data and the results of molecular modeling revealed the decrease in PCR efficiency in the presence of modified dUTPs with an increase in the number of non-covalent bonds between the substituents and the DNA polymerase (about 15% decrease per one extra non-covalent bond). Generalization of the revealed patterns to all the studied polymerases of the A and B families is discussed herein. The number of non-covalent bonds between the substituents and polymerase amino acid residues is proposed to be a potentially variable parameter for regulating enzyme activity.

Synthesis of Pyridine Clubbed Tetrahydrobenzo[b]thiophene Azo Dye Analogues Using the Gewald Reaction: Catalytic Optimization, Antibacterial, and Dye Investigation

Synthesis of Pyridine Clubbed Tetrahydrobenzo[b]thiophene Azo Dye Analogues Using the Gewald Reaction: Catalytic Optimization, Antibacterial, and Dye Investigation

Elucidating the cellular uptake mechanisms of heptamethine cyanine dye analogues for their use as an anticancer drug-carrier molecule for the treatment of glioblastoma.

The development of chemotherapies for glioblastoma is hindered by their limited bioavailability and toxicity on normal brain function. To overcome these limitations, we investigated the structure-dependent activity of heptamethine cyanine dyes (HMCD), a group of tumour-specific and BBB permeable near-infrared fluorescent dyes, in both commercial (U87MG) and patient-derived GBM cell lines. HMCD analogues with strongly ionisable sulphonic acid groups were not taken up by patient-derived GBM cells, but were taken up by the U87MG cell line. HMCD uptake relies on a combination of transporter uptake through organic anion-transporting polypeptides (OATPs) and endocytosis into GBM cells. The uptake of HMCDs was not affected by p-glycoprotein efflux in GBM cells. Finally, we demonstrate structure-dependent cytotoxic activity at high concentrations (EC50 : 1-100 μM), likely due to mitochondrial damage-induced apoptosis. An in vivo orthotopic glioblastoma model highlights tumour-specific accumulation of our lead HMCD, MHI-148, for up to 7 days following a single intraperitoneal injection. These studies suggest that strongly ionisable groups like sulphonic acids hamper the cellular uptake of HMCDs in patient-derived GBM cell lines, highlighting cell line-specific differences in HMCD uptake. We envisage these findings will help in the design and structural modifications of HMCDs for drug-delivery applications for glioblastoma.

An antigen-strengthened dye-modified fully-human-nanobody-based immunoprobe for second near infrared bioimaging of metastatic tumors

Conventional immunoprobes have absorption capabilities across the visible to near infrared (NIR-I, 650–900 nm) region. Recently, second near infrared (NIR-II, 1000–1700 nm) window have gained much attention due to their deeper penetration depth and improved visualization. Here, we describe the design and synthesis of a fully human nanobody-based fluorescent immunoprobe (ICGM-n501) for NIR-II bioimaging with strengthened fluorescent emission by antigen for the first time. By site-directed conjugation of an FDA-approved dye analogue, indocyanine green decorated with maleimide (ICGM), into a tumor-specific n501, ICGM-n501 provides real-time monitoring of abdominal transportation pathway of antibody-based bioagents with high resolution (0.21 mm), presents better accuracy and lower dosage (0.21 μmol kg−1) in bioimaging of peritoneal metastatic tumors than bioluminescence agent D-luciferin. In this work, ICGM-n501 demonstrates its potential in clinical surgery guidance, provide an expanded category of available NIR-II fluorophores and a template for next-generation immunoassay bioagents.

Live-cell RNA imaging using the CRISPR-dCas13 system with modified sgRNAs appended with fluorescent RNA aptamers.

The development of RNA imaging strategies in live cells is essential to improve our understanding of their role in various cellular functions. We report an efficient RNA imaging method based on the CRISPR-dPspCas13b system with fluorescent RNA aptamers in sgRNA (CasFAS) in live cells. Using modified sgRNA attached to fluorescent RNA aptamers that showed reduced background fluorescence, this approach provides a simple, sensitive way to image and track endogenous RNA with high accuracy and efficiency. In addition, color switching can be easily achieved by changing the fluorogenic dye analogues in living cells through user-friendly washing and restaining operations. CasFAS is compatible with orthogonal fluorescent aptamers, such as Broccoli and Pepper, enabling multiple colors RNA labeling or intracellular RNA-RNA interaction imaging. Finally, the visualization of severe fever with thrombocytopenia syndrome virus (SFTSV) was achieved by CasFAS, which may facilitate further studies on this virus.

Colour and constitution of conjugate bases of benzodifurantrione, its ring-opened derivatives and benzodifuranone dye analogues.

The observation of ready deprotonation of the phenylogous enol of benzodifurantrione (BDT) to give a bright violet conjugate base has led to two follow up explorations. Extension of BDT enol by insertion of a p-phenylene unit into the enol C-O bond gives the known bright red 4-hydroxylated benzodifuranone dyes. Their deprotonation results in previously unreported near infrared-absorbing conjugate bases. These appear to aggregate in solution, the more so in less polar solvents. Ring-opened derivatives of BDT containing α-dicarbonyl substituents also give coloured conjugate bases, but α-keto-ester and -anilide derivatives differ substantially (ester yellow; anilide intense red). Investigation of this nonintuitive difference leads to the conclusion that while the anilide is essentially planar the ester is nonplanar. The contrast in conformation impacts on the auxochromic effects of the otherwise closely related α-dicarbonyl substituents and thus the variation in colour. The latter observation has potential across colour chemistry in general. In contrast to the readily observed BDT enol, no evidence has been adduced for enol tautomers amongst the ring-opened analogues.

Promising small molecule Pechmann dye analogue donors with low interfacial charge recombination for photovoltaic application: A DFT study

A series of donor–acceptor–donor (D-A-D) type small molecule (SM) donors containing Pechmann dye analogues (N, S, O) are designed and their geometrical, optoelectronic, charge transport, and photovoltaic properties are investigated using density functional theory (DFT). The structural modification of the donor backbone has been performed via additional sp2-nitrogen heteroatom incorporation in the Pechmann analogue acceptor cores. The N-heteroatom containing SM donors are found to be more air-stable due to having relatively deeper HOMO/LUMO levels than their unsubstituted counterparts. The maximum computed open-circuit voltage (Voc) is 1.53 V for the N-heteroatom substituted O-Pechmann core based donor. The designed donors are expected to harvest photon energy efficiently as their simulated absorption spectra lie in the visible region (575–724 nm). The N-heteroatom incorporation plays a significant role in lowering the charge recombination rate (KCR) and increasing the charge separation rate (KCS) at the SM donor/PC61BM interface. The ratio of interfacial KCS and KCR is found to be improved by 104−1010 times after sp2-nitrogen substitution in the Pechmann analogue cores. The maximum predicted power conversion efficiencies (PCEs) using the Scharber diagram reach up to ∼9% for the S-analogue of the Pechmann dye core based donor. This study sheds light on promising SM donors based on Pechmann dye analogues with low interfacial charge recombination rates and high charge separation rates and also demonstrates the impact of structural modification of Pechmann dye analogue cores on air-stability and overall photovoltaic performance.

ВИЗНАЧЕННЯ ВПЛИВУ ПОВЕРХНЕВО-АКТИВНИХ РЕЧОВИН НА ЯКІСТЬ ЗАБАРВЛЕННЯ ЗА МЕХАНІЗМОМ ГЕТЕРОКОАГУЛЯЦІЇ

To determine the eff ect of the type and concentration of surfactants on the coloring quality of a water-insoluble analogue of a straight dye of cotton textile materials by the mechanism of heterocoagulation. Method. Heterocoagulation mechanism was used to obtain dyeing of cotton textile materials with water insoluble direct dye form. Sample software was used to determine the color characteristics of colored samples of textile materials. Appropriate standard methods were used to determine the strengths of the obtained colors. Results. The concentrations of surfactant required for the combination of suffi cient intensity of the dyeing with the required strength of the dyeing to dry friction are determined. The analysis of the results shows that not only the particle size but also the nature of the interaction of the dye surfaces and the fi brous material, which is responsible for the depth of the fi rst low of the DLFO theory (Deriagin, Landau, Fairway, Overbeck theory), is important for heterocoagulation dyeing. Direct dye may be in the form of nanodispersion. In this situation, the diff usion of the dye into amorphous sections of the polymer is excluded. Dyeing is carried out on ly due to heterocoagulation - deposition of dye particles on the surface of the fi brous material. It has been investigated that the dispersion particle deposited on the surface by the mechanism of heterocoagulation is secured by the forces of intermolecular interaction and its stability on the surface is ensured by the balance of the forces of intermolecular interaction and the infl uence of mo lecules of the dispersion medium (Brownian motion eff ect). With the successive reduction of the size of the dye particles to the nanoscale, the infl uence of the forces of intermolecular interaction increases signifi cantly. Practical importance. Reducing the cost of the dyeing process and preventing the detection of structural heterogeneities of textile materials is possible when using a heterocoagulation dyeing mechanism.

Pentamethine sulfobenzoindocyanine dyes with low net charge states and high photostability.

A series of Cy5.5 dye analogs and targeted probes with net charges varied from -3 to 0 were synthesized by an optimized method, followed by comparing their spectral and photostability properties in saturated solutions of air, oxygen, and argon. The Cy5.5 analogs with reduced charge were relatively stable when irridated at their excitation maxima, with a trend of higher stability with lower net charge states. The photostability of dyes was markedly lower in pure oxygen and higher in inert argon relative to ambient atmospheric conditions. The stability of c(RGDyK) conjugates as models of targeted molecular imaging agents mirrored these results and demonstrated the practical utility of the new family of Cy5.5 fluorophores.

Development of Polyene-Bridged Hybrid Rhodamine Fluorophores for High-Resolution NIR-II Imaging

This work presents a polyene bridging strategy on Rhodamine-type dye analogues (Rh824, Rh926, and Rh1029) for tuning absorption and emission wavelengths from the first near-infrared window (NIR-I; ...

MiRNA-Specific Unlocking of Drug-Loaded Metal-Organic Framework Nanoparticles: Targeted Cytotoxicity toward Cancer Cells.

UiO-68 metal-organic framework nanoparticles (NMOFs) are loaded with a doxorubicin drug (fluorescent dye analogs) and locked by means of structurally engineered duplex nucleic acid structures, where one strand is covalently linked to the NMOFs and the second strand is hybridized with the anchor strand. Besides the complementarity of the second strand to the anchor sequence, it includes the complementary sequence to the microRNAs (miRNA)-21 or miRNA-221 that is specific miRNA biomarker for MCF-7 breast cancer cells or OVCAR-3 ovarian cancer cells. In the presence of the respective miRNA biomarkers, the miRNA-induced displacement of the strand associated with the anchor strand proceeds, resulting in the release of DNA/miRNA duplexes. The released duplexes are, however, engineered to be digested in the presence of exonuclease III, Exo III, a process that recycles the miRNAs and provides the autonomous amplified unlocking of the NMOFs and the release of the doxorubicin load (or the fluorescent dye analogs) even at low concentrations of miRNA. Preliminary cell experiments reveal that the respective NMOFs are unlocked by the miRNA-21 or miRNA-221, resulting in selective cytotoxicity toward MCF-7 breast cancer cells or OVCAR-3 ovarian cancer cells.

Transition-Metal-Free Benzannulation of Tricarbonyl Derivatives with Arynes: Access to 1,3-Dinaphthol Precursors for the Synthesis of Rhodamine Dye Analogues.

Herein, we report a transition-metal-free annulation reaction of benzynes and 1,3-oxopentanedioate for the synthesis of highly functionalized naphthalene derivatives for the first time. Additionally, the representative naphthalene derivatives have been successfully transformed into the new series of rhodamine dye analogues.

Toward the Rational Design of Sustainable Hair Dyes Using Cheminformatics Approaches: Step 2. Identification of Hair Dye Substance Database Analogs in the Max Weaver Dye Library

We report on part 2 of the cheminformatics-assisted development of sustainable hair dyes with enhanced technical and toxicological properties. In this study, an initial similarity search analysis was performed using two reference probes (C.I. Basic Orange 1 and Orange 2) as structural templates for the identification of potential analogs among the Max Weaver Dye Library (MWDL). The analysis revealed an interesting subset of 158 MWDL compounds that were close analogs of the classical aminoazobenzene dyes. A more detailed similarity search analysis of this subset ultimately led to the selection of four dyes for further in silico quantum calculations and experimental dye uptake (color depth on hair) studies. Results from quantum calculations indicated that the ESP surface properties of these dyes were consistent with nonionic interactions between dye and keratin. Among the four dye analogs, 2-amino-6-methyl-5-(phenyldiazenyl)pyrimidin-4-ol and 2-amino-4-chloro-1,6-dimethyl-5-(phenyldiazenyl)-pyrimidin-1-ium ...

Versatile Click Cyanine Amino Acid Conjugates Showing One‐Atom‐Influenced Recognition of DNA/RNA Secondary Structure and Mitochondrial Localisation in Living Cells

By a simple click CuAAC (copper(I)‐catalysed azide alkyne cycloaddition) procedure several cyanine dye analogues have been attached to the side‐chain of an amino acid to yield chromophore amino acid conjugates with the potential to fluoresce upon binding to a target. Due to the availabiltiy of the amino acid C and N termini for peptide coupling, these conjugates are suitable for easy incorporation into the backbone of peptides. The novel amino acid dyes prepared in this work, although intrinsically non‐fluorescent, gave rise to strong fluorimetric responses upon binding to double‐stranded (ds) DNA or RNA, the emission response to various polynucleotide secondary structures being controlled either by linker length or a halogen atom located on the cyanine part of the molecule. Molecular modelling confirmed the mode of binding to different polynucleotides, which was responsible for the recognition. Interestingly, cell localisation experiments showed that the dyes were specifically localised in mitochondria at variance with the localisation of the parent dyes, which accumulate in cell nuclei, which suggests that the amino acid tail (containing a triazole ring) might function as a novel mitochondria‐directing appendage.

DUTPs conjugated with zwitterionic Cy3 or Cy5 fluorophore analogues are effective substrates for DNA amplification and labelling by Taq polymerase.

To develop structural modifications of dNTPs that are compatible with Taq DNA polymerase activity, we synthesized eight dUTP derivatives conjugated with Cy3 or Cy5 dye analogues that differed in charge and charge distribution throughout the fluorophore. These dUTP derivatives and commercial Cy3− and Cy5-dUTP were studied in Taq polymerase-dependent polymerase chain reactions (PCRs) and in primer extension reactions using model templates containing one, two and three adjacent adenine nucleotides. The relative amounts of amplified DNA and the kinetic parameters Km and Vmax characterizing the incorporation of labelled dUMPs have been estimated using fluorescence measurements and analysed. The dUTPs labelled with electroneutral zwitterionic analogues of Cy3 or Cy5 fluorophores were used by Taq polymerase approximately one order of magnitude more effectively than the dUTPs labelled with negatively charged analogues of Cy3 or Cy5. The nucleotidyl transferase activity of Taq polymerase was also observed and resulted in the addition of dUMPs labelled with electroneutral or positively charged fluorophores to the 3′ ends of DNA. The introduction of mutually compensating charges into fluorophores or other functional groups conjugated to dNTPs can be considered a basis for the creation of PCR-compatible modified nucleoside triphosphates.

Substrate Properties of New Fluorescently Labeled Deoxycytidine Triphosphates in Enzymatic Synthesis of DNA with Polymerases of Families A and B

The efficiency of the incorporation of fluorescently labeled derivatives of 2'-deoxycytidine in DNA synthesized de novo has been studied using PCR with Taq and Tth polymerases of family A and Vent (exo-) and Deep Vent (exo-) polymerases of family B. Four derivatives of 5'-triphosphate-2'-deoxycytidine (dCTP) have different chemical structures of the indodicarbocyanine dye and Cy5 analogue attached to position 5 of cytosine. The kinetics of the accumulation of the PCR products and the intensity of the fluorescent signals in the hybridization analysis with immobilized DNA probes depend on the modification of the fluorescently labeled dCTP counterpart, its concentration, and the type of DNA polymerase. All labeled triphosphates showed some inhibitory effects on PCR. The best balance between the efficiency of incorporating labeled cytidine derivatives and the negative effect on the PCR kinetics has been shown in the case of Hot Taq polymerase in combination with the Cy5-dCTP analogue, which contains containing electrically neutral chro-mophore, the axis of which is a continuation of the linker between the chromophore and the pyrimidine base.