Potential charge transfer probe induced conformational changes of model plasma protein human serum albumin: Spectroscopic, molecular docking, and molecular dynamics simulation study

A multi-wavelength cross-reactive fluorescent sensor ensemble for fingerprinting flavonoids in serum and urine

Flavonoids are a kind of natural polyphenols which are closely related to human health, and the identification of flavonoids with similar structures is an important but difficult issue. We herein easily constructed a powerful fluorescent sensor ensemble by using surfactant cetyltrimethylammoniumbromide (CTAB) encapsulating two commercially available fluorescent probes (F1 and F2) with multi-wavelength emission. Fluorescence measurements illustrate the present sensor ensemble exhibits turn-off responses to flavones and flavonols but ratiometric responses to isoflavones, owing to different FRET processes. The heat map and linear discriminant analysis (LDA) results show that this single sensor can effectively distinguish 6 flavonoids belong to three subgroups by collecting the fluorescence variation at four typical wavelengths. Moreover, it can be applied to identify different flavonoids even in biofluids like serum and urine, providing potential practical application.

A flaw in applying the FRET technique to evaluate the distance between ligands and tryptophan residues in human serum albumin: Proposal of correction

Due to its primordial function as a drug carrier, human serum albumin (HSA) is extensively studied regarding its binding affinity with developing drugs. Förster resonance energy transfer (FRET) is frequently applied as a spectroscopic molecular ruler to measure the distance between the binding site and the ligand. In this work, we have shown that most of the published results that use the FRET technique to estimate the distance from ligands to the binding sites do not corroborate the crystallography data. By comparing the binding affinity of dansyl-proline with HSA and ovotransferrin, we demonstrated that FRET explains the quenching provoked by the interaction of ligands in albumin. So, why does the distance calculation via FRET not corroborate the crystallography data? We have shown that this inconsistency is related to the fact that a one-to-one relationship between donor and acceptor is not present in most experiments. Hence, the quenching efficiency used for calculating energy transfer depends on distance and binding constant, which is inconsistent with the correct application of FRET as a molecular ruler. We have also shown that the indiscriminate attribution of 2/3 to the relative orientation of transition dipoles of the acceptor and donor (κ²) generates inconsistencies. We proposed corrections based on the experimental equilibrium constant and theoretical orientation of transition dipoles to correct the FRET results.

A novel highly selective FRET sensor for Fe(III) and DFT mechanistic evaluation

A novel FRET-based sensor has been designed and developed through the conjugation of naphthyl and rhodamine via propylamine spacer, Naph-Rh. The naphthyl moiety serves as a FRET donor due to its emission spectrum overlapping with the rhodamine B absorption band. Naph-Rh exhibited a selectivity for sensing Fe³⁺ over other metal ions with a visual color change and fluorescent enhancement. The ratio of the Naph-Rh and Fe³⁺ was determined to be 1:1 based on Job's plot analysis with a detection limit of 83 nM. The probe exhibited a linear response to Fe³⁺ in the range of 0-120 μM. Furthermore, the density functional theory (DFT) calculations of Naph-Rh were carried out to rationalize the design and portray the plausible Fe³⁺ sensing mechanism.

Concomitant binding of two fluorescent probes at site-I of human serum albumin: The protein acting as a scaffold enabling fluorescence resonance energy transfer

Human serum albumin (HSA) is the primary drug carrier in the blood plasma. Here, I aimed to show that two ligands can be accommodated simultaneously in the binding site-I of HSA. To do so, I studied the interaction inside the protein among site-I ligands of HSA via fluorescence resonance energy transfer (FRET), synchronous fluorescence, red edge excitation shift (REES), and induced circular dichroism (ICD). Warfarin (WAR), coumarin-153 (C153), 6-(p-toluidino)-2-naphthalenesulfonic acid sodium salt (TNS), dansylglycine (DGY), and 4-(dicyanomethylene)-2-methyl-6-(4-dimethylaminostyryl)-4H-pyran (DCM) were enrolled in the investigation. I found that WAR can transfer energy to C153 only in the presence of the protein. In addition, the presence of WAR at site-I altered the protein microenvironment felt by C153. The alteration was detected by measuring the synchronous fluorescence, REES, and ICD in C153. The findings were validated by measuring the energy transfer from TNS to DCM and the alteration in synchronous fluorescence and REES. FRET was not observed using WAR as donor and DGY as acceptor. The result is consistent, as DGY is a site-II ligand at a higher WAR distance. In all studied cases, the effects were only observed in the presence of HSA. In conclusion, the protein acted as a scaffold approximating the ligands. These findings prove that more than one ligand can simultaneously be complex at site-I of HSA.

Ratiometric fluorescence resonance energy transfer for reliable and sensitive detection of intracellular telomerase RNA via strand displacement reaction amplification

Human telomerase RNA (hTR) is one essential component of telomerase and is overexpressed in tumor cells. Therefore, the reliable and sensitive detection of hTR is essential for the early cancer diagnosis. Herein, to avoid the false positive signals caused by co-existing components in the cell, a ratiometric fluorescence resonance energy transfer (FRET) strategy was developed to achieve reliable detection of intracellular hTR. Manganese dioxide nanosheets (MnO₂NS) with good biocompatibility carry two fluorophore-labelled hairpin DNA probes into the cancer cell and then release the probes via decomposition of MnO₂NS by intracellular L-glutathione reduced (GSH). Then, hTR triggered the cyclic strand displacement reaction (SDR) between two hairpin DNA probes to continuously form DNA duplexes, which made two fluorophores close to each other and led to an effective FRET. Fluorescence imaging demonstrated a higher expression level of hTR in HeLa cells than that in normal HL-7702 cells. The high specificity of hairpin DNA probes and SDR make it easy to discriminate the single-base mutation. Therefore, it provides a highly sensitive, simple and reliable method for the extracellular and intracellular detection of hTR.

Bio-physical and Computational Studies on Serum Albumin / Target Protein Binding of a Potential Anti-Cancer Agent

The successful evolution of an effective drug depends on its pharmacokinetics, efficiency and safety and these in turn depend on the drug-target/drug-carrier protein binding. This work, deals with the interaction of a pyridine derivative, 2-hydroxy-5-(4-methoxyphenyl)-6-phenylpyridine 3-carbonitrile (HDN) with serum albumins at physiological conditions utilizing the steady state and time-resolved fluorescence techniques by probing the emission behavior of Trp in BSA and HSA. In-silico studies revealed a combined static and dynamic quenching mechanism for the interactions. The binding studies suggests a spontaneous binding between HDN and the albumins with a moderate binding affinity (Kb ∼ 10-5 M-1) with a single class of binding site. The FRET mediated emission from HDN indicates preferential binding of HDN in subdomain IIA of the albumins with Trp residue in close proximity. Circular dichroism results indicate HDN induced conformational changes for BSA and HSA, but the α-helical secondary structure was well preserved even up to a concentration of 10 µM HDN. Moderate binding affinity of HDN with BSA and HSA and the unaltered secondary structure of proteins on binding propose the potential application of HDN as an efficient drug. The application of docking method on the affinity of HDN towards the proposed target/receptor is discussed.

CeO2 quantum dots for highly selective and ultrasensitive fluorescence detection of 4-nitrophenol via the fluorescence resonance energy transfer mechanism

A rapid and simple fluorescence probe based on CeO₂ quantum dots (QDs) was developed for highly selective and ultrasensitive direct determination of 4-nitrophenol (4-NP). CeO₂ QDs were prepared using the sol-gelmethod with the precursor of Ce(NO₃)₃·6H₂O as a cerium source. The products were characterized through high-resolution electron microscopy, X-ray diffraction, X-ray photoelectron spectroscopy, and Raman spectroscopy. The fluorescent probe based on CeO₂ QDs exhibited a broad linear response to the concentration of 4-NP in the range of 0.005-75.00 μM and provided a low detection limit of 1.50 nM. The fluorescence of CeO₂ QDs was quenched by 4-NP through the fluorescence resonance energy transfer mechanism owing to the well overlaps between the fluorescence emission spectrum of CeO₂ QDs with the ultraviolet absorption spectrum of 4-NP. This result was confirmed by the time-resolved fluorescence spectra and the evaluation of the interaction distance between CeO₂ QDs and 4-NP. The prepared CeO₂ QDs are successfully applied to the determination of 4-NP in real water samples, where the spiked recoveries range from 98.2% to 102.4%.

Upconversion nanoparticles-based FRET system for sensitive detection of Staphylococcus aureus

Staphylococcus aureus (S. aureus) is a pathogenic bacterium that seriously endangers food safety. Herein, a rapid, sensitive and specific aptasensor based on upconversion fluorescence resonance energy transfer (FRET) was developed for S. aureus detection in food. Aptamer-functionalized gold nanoparticles (AuNPs-aptamers) were bonded to cDNA-modified upconversion nanoparticles (UCNPs-cDNA) by complementary pairing, resulting in fluorescence quenching. After adding S. aureus into the system, the aptamers preferentially combined with S. aureus, dissociated UCNPs-cDNA from AuNPs-aptamers, and the fluorescence was recovered. Under optimized conditions, there was a significant linear correlation between fluorescence intensity and S. aureus concentration over the range 47-4.7 × 10⁷ CFU/mL (R² = 0.9904) with a detection limit of 10.7 CFU/mL. Furthermore, the precision and accuracy of the developed biosensor were validated using standard plate count method, yielding no significant differences. The proposed method has potential application for rapid and sensitive quantification of S. aureus in food.

Rapid and sensitive detection of diazinon in food based on the FRET between rare-earth doped upconversion nanoparticles and graphene oxide

Diazinon is a typical phosphorothionate, which is widely used to prevent and control harmful organisms that endanger the agriculture productions. However, it is among the most toxic substances and can cause damage to the environment, food and human health even in very low concentrations. Hence, ultra-sensitive screening methods are urgently required for the detection of this extensively used pesticide. In this study, a rapid and sensitive fluorescence resonance energy transfer (FRET) method was developed for low concentration detection of diazinon in food. The aptamer-modified upconversion nanoparticles (Apt-UCNPs) were synthesized and conjugated with graphene oxide (GO) through π-π interaction. Due to the FRET between UCNPs and GO, the fluorescence was quenched. When diazinon was added, the aptamer preferentially bound with it, caused the separation of GO, and resulted in the enhancement of fluorescent signal. Under the optimal conditions, a wide linear detection range from 0.05 to 500 ng/mL was achieved, with a limit of detection (LOD) of 0.023 ng/mL. The proposed method was successfully applied to measure diazinon in real samples. Results showed that the proposed nanosensor offers an efficient, specific and simple approach for the detection of diazinon in food and has a high potential for food safety and quality control.

Donor-Pyrene-Acceptor Distance-Dependent Intramolecular Charge-Transfer Process: A State-Specific Solvation Preferred to the Linear-Response Approach

Photoinduced intramolecular charge-transfer (ICT) molecules are important in various applications such as a probe for single-molecule spectroscopy, cell imaging, laser dyes, biomarkers, solar cells, in photosynthesis, etc. Here, we report a new set of substituted pyrene dye molecules, N,N-dimethylamino nitrilo pyrene and its higher analogues, containing pull-push donor (D)-chromophore (π)-acceptor (A) functional groups with enhanced photophysical characteristics like oscillator strength, light-harvesting, and ICT properties. The excited-state ICT process has been established by quantum chemical calculations using the density functional theory method in vacuo and in solvents of different polarity and hydrogen-bonding ability using linear-response (LR) and state-specific (SS) solvation approaches with gradually increasing the D-A distance. The studied molecules show solvent polarity-dependent larger Stokes' shifts (3609-9016 cm^-1, in acetonitrile), higher excited-state dipole moments (11.7-16.8 Debye, in acetonitrile), higher possibilities of highest occupied molecular orbital (HOMO)-lowest unoccupied molecular orbital (LUMO) electronic transitions, etc., which support the occurrence of the excited-state ICT process. Here, we demonstrate how to increase the efficiency of the ICT process and also tune the ICT fluorescence maximum. We find that with a variation of the D-A distance, studied molecules show a noticeable effect on the spectroscopic and molecular properties such as the position of absorption and fluorescence band maxima, Stokes' shift, dipole moment, light-harvesting, and ICT properties. We also show that the SS solvation approach is more supportive than the LR method to the ICT process.

Design and Biological Evaluation of Novel Imidazolyl Flavonoids as Potent and Selective Protein Tyrosine Phosphatase Inhibitors

BACKGROUND

Protein tyrosine phosphatases 1B are considered to be a desirable validated target for therapeutic development of type II diabetes and obesity.

METHODS

A new series of imidazolyl flavonoids as potential protein tyrosine phosphatase inhibitors were synthesized and evaluated.

RESULTS

Bioactive results indicated that some synthesized compounds exhibited potent protein phosphatase 1B (PTP1B) inhibitory activities at the micromolar range. Especially, compound 8b showed the best inhibitory activity (IC50=1.0 µM) with 15-fold selectivity for PTP1B over the closely related T-cell protein tyrosine phosphatase (TCPTP). Cell viability assays indicated that 8b is cell permeable with lower cytotoxicity. Molecular modeling and dynamics studies revealed the reason for selectivity of PTP1B over TCPTP. Quantum chemical studies were carried out on these compounds to understand the structural features essential for activity.

CONCLUSION

Compound 8b should be a potential selective PTP1B inhibitor.

Identification of novel imidazole flavonoids as potent and selective inhibitors of protein tyrosine phosphatase

A series of imidazole flavonoids as new type of protein tyrosine phosphatase inhibitors were synthesized and characterized. Most of them gave potent protein phosphatase 1B (PTP1B) inhibitory activities. Especially, compound 11a could effectively inhibit PTP1B with an IC₅₀ value of 0.63 μM accompanied with high selectivity ratio (9.5-fold) over T-cell protein tyrosine phosphatase (TCPTP). This compound is cell permeable with relatively low cytotoxicity. The high binding affinity and selectivity was disclosed by molecular modeling and dynamics studies. The structural features essential for activity were confirmed by quantum chemical studies.

Selective binding of pyrene in subdomain IB of human serum albumin: Combining energy transfer spectroscopy and molecular modelling to understand protein binding flexibility

The ability of human serum albumin (HSA) to bind medium-sized hydrophobic molecules is important for the distribution, metabolism, and efficacy of many drugs. Herein, the interaction between pyrene, a hydrophobic fluorescent probe, and HSA was thoroughly investigated using steady-state and time-resolved fluorescence techniques, ligand docking, and molecular dynamics (MD) simulations. A slight quenching of the fluorescence signal from Trp214 (the sole tryptophan residue in the protein) in the presence of pyrene was used to determine the ligand binding site in the protein, using Förster's resonance energy transfer (FRET) theory. The estimated FRET apparent distance between pyrene and Trp214 was 27Å, which was closely reproduced by the docking analysis (29Å) and MD simulation (32Å). The highest affinity site for pyrene was found to be in subdomain IB from the docking results. The calculated equilibrium structure of the complex using MD simulation shows that the ligand is largely stabilized by hydrophobic interaction with Phe165, Phe127, and the nonpolar moieties of Tyr138 and Tyr161. The fluorescence vibronic peak ratio I₁/I₃ of bound pyrene inside HSA indicates the presence of polar effect in the local environment of pyrene which is less than that of free pyrene in buffer. This was clarified by the MD simulation results in which an average of 5.7 water molecules were found within 0.5nm of pyrene in the binding site. Comparing the fluorescence signals and lifetimes of pyrene inside HSA to that free in buffer, the high tendency of pyrene to form dimer was almost completely suppressed inside HSA, indicating a high selectivity of the binding pocket toward pyrene monomer. The current results emphasize the ability of HSA, as a major carrier of several drugs and ligands in blood, to bind hydrophobic molecules in cavities other than subdomain IIA which is known to bind most hydrophobic drugs. This ability stems from the nature of the amino acids forming the binding sites of the protein that can easily adapt their shape to accommodate a variety of molecular structures.

Dual-sensor fluorescent probes of surfactant-induced unfolding of human serum albumin

Two extrinsic fluorescent probes, 3-(dimethylamino)-8,9,10,11-tetrahydro-7H-cyclohepta[a]naphthalen-7-one (1) and 7-(dimethylamino)-2,3-dihydrophenanthren-4(1H)-one (2), are used to probe the unfolding of human serum albumin by sodium dodecyl sulfate (SDS). These probes respond separately to the polarity and H-bond-donating ability of their surroundings. Competitive binding experiments show that fluorophore 1 binds to site I (domain IIA) and 2 binds to site II (domain IIIA). The local acidity of 1 in site I is out of the sensing range of 1, whereas the local acidity of 2 in site II is calculated to be nearly zero on Catalan's solvent acidity index. Both probes show that the first two equivalents of bound SDS result in a decrease in the local polarity of the binding sites. Each subsequent equivalent of SDS gives rise to a dramatic increase in polarity until HSA is saturated with seven molecules of SDS at the end of the specific binding domain. Compound 2 experiences an increase of acidity of 0.10 on Catalan's solvent acidity index through seven equivalents of SDS, but the local acidity for 1 is still out of range. The increase in acidity experienced by 2 is greater than the increase in polarity. This result is consistent with greater exposure of the carbonyl group in 2, but not the bulk of 2, to the aqueous solvent in site II of the SDS-saturated HSA complex.

Binding of a potential anti-hepatoma drug cis,cis,trans-[Pt(NH3)2Cl2(O2CCH2CH2COOH)-(OCONHC16H33)] with serum albumin – thermodynamic and conformational investigations

A potential anti-cancer compound with high activity was synthesized and its binding properties with human serum albumin were tested.

Binding properties of food colorant allura red with human serum albumin in vitro

Allura red (AR) is a widely used colorant in food industry, but may have a potential security risk. In this study, the properties of interaction between AR and human serum albumin (HSA) in vitro were determined by fluorescence, UV-Vis absorption and circular dichroism (CD) spectroscopy combining with multivariate curve resolution-alternating least squares (MCR-ALS) chemometrics and molecular modeling approaches. An expanded UV-Vis data matrix was resolved by MCR-ALS method, and the concentration profiles and pure spectra for the three reaction components (AR, HSA, and AR-HSA complex) of the system were then successfully obtained to evaluate the progress interaction of AR with HSA. The calculated thermodynamic parameters indicated that hydrogen binding and hydrophobic interactions played major roles in the binding process, and the interaction induced a decrease in the protein surface hydrophobicity. The competitive experiments revealed that AR mainly located in Sudlow's site I of HSA, and this result was further supported by molecular modeling studies. Analysis of CD spectra found that the addition of AR induced the conformational changes of HSA. This study have provided new insight into the mechanism of interaction between AR and HSA.

Proton transfer assisted charge transfer phenomena in photochromic Schiff bases and effect of -NEt2 groups to the anil Schiff bases

Photochromic Schiff bases 5-diethylamino-2-[(4-diethylamino-benzylidene)-hydrazonomethyl]-phenol (DDBHP) and N,N'-bis(4-N,N-diethylaminosalisalidene) hydrazine (DEASH) with both the proton and charge transfer moieties have been synthesized, and their photophysical properties such as excited state intramolecular charge transfer (ICT) and proton transfer (ESIPT) processes have been reported on the basis of steady-state and time-resolved spectral measurement in various solvents. The ground-state six-membered intramolecular hydrogen bonding network at the proton transfer site accelerates the ESIPT process for these compounds. Both the compounds show large Stokes-shifted emission bands for proton transfer and charge transfer processes. The hydrogen bonding solvents play a crucial role in these photophysical processes. Excited-state dipole moment of DDBHP and DEASH calculated by the solvatochromic method supports the polar character of the charge transfer excited state. Introduction of -NEt(2) groups to the reported salicylaldehyde azine (SAA) Schiff base results an increase in fluorescence lifetime from femtosecond to picosecond time scale for the proton transfer process.