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.

Binding interactions of hydrophobically-modified flavonols with β-glucosidase: fluorescence spectroscopy and molecular modelling study

Natural flavonoids are capable of inhibiting glucosidase activity, so they can be used for treating diabetes mellitus and hypertension. However, molecular-level details of their interactions with glucosidase enzymes remain poorly understood. This paper describes the synthesis and spectral characterization of a series of fluorescent flavonols and their interaction with the β-glucosidase enzyme. To tune flavonol-enzyme interaction modes and affinity, we introduced different polar halogen-containing groups or bulky aromatic/alkyl substituents in the peripheral 2-aryl ring of a flavonol moiety. Using fluorescence spectroscopy methods in combination with molecular docking and molecular dynamics simulations, we examined the binding affinity and identified probe binding patterns, which are critical for steric blockage of the key catalytic residues of the enzyme. Using a fluorescent assay, we demonstrated that the binding of flavonol 2e to β-glucosidase decreased its enzymatic activity up to 3.5 times. In addition, our molecular docking and all-atom molecular dynamics simulations suggest that the probe binding is driven by hydrophobic interactions with aromatic Trp and Tyr residues within the catalytic glycone binding pockets of β-glucosidase. Our study provides a new insight into structure-property relations for flavonol-protein interactions, which govern their enzyme binding, and outlines a framework for a rational design of new flavonol-based potent inhibitors for β-glucosidases.

Total syntheses of pongaflavone and its natural analogues

The efficient total synthesis of anti-tumor natural product pongaflavone (1) was described starting from commercially available 2,4-dihydroxyacetophenone (9) via seven steps and in 16% overall yield. Its two natural analogues pongachromene (2) and 7,8-(2",2"-dimethylpyrano)-5,3',4'-trihydroxy-3-methoxyflavone (3) were also synthesized following the similar procedure with the yields of 11% and 18%, respectively. Their preliminary anti-tumor activities were evaluated by the inhibition effect on A549 cells. The result showed that this kind of natural products exhibited different levels of anti-tumor activity. Among them, pongachromene (2) displayed the best anti-tumor activity.

Intramolecular dual hydrogen bonded fluorescent "turn-on" probe for Al3+ and HSO4- ions: Applications in real water samples and molecular keypad lock

Dual hydrogen bonded Schiff base containing unsymmetrical double proton transfer sites, one with imine bond (CN) and hydroxyl group (OH), and the other with benzimidazole and hydroxyl groups has been successfully synthesized. Probe 1 displayed intramolecular charge transfer and acts as a potential sensor for Al³⁺ and HSO₄^- ions. Probe 1 displayed two absorption peaks at 325 nm and 340 nm and an emission band at 435 nm upon excitation at 340 nm. Probe 1 behaves as a fluorescence "turn-on" chemosensor for both Al³⁺ and HSO₄^- ions in H₂O-CH₃OH solvent system. The proposed method allows the determination of Al³⁺ and HSO₄^- ions up to 39 nM and 23 nM at emission wavelength 385 nm and 390 nm, respectively. The binding behavior of probe 1 towards these ions is determined by the Job's plot method and ¹H NMR titrations. Probe 1 is used to construct a molecular keypad lock where the absorbance channel can be opened only in the presence of the correct sequence. Further, it is used for the quantitative determination of HSO₄^- ion in different real-field water samples.

Discovery of Flavone Derivatives Containing Carboxamide Fragments as Novel Antiviral Agents

Plant virus diseases seriously affect the yield and quality of agricultural products, and their prevention and control are difficult. It is urgent to develop new and efficient antiviral agents. In this work, a series of flavone derivatives containing carboxamide fragments were designed, synthesized, and systematically evaluated for their antiviral activities against tobacco mosaic virus (TMV) on the basis of a structural-diversity-derivation strategy. All the target compounds were characterized by 1H-NMR, 13C-NMR, and HRMS techniques. Most of these derivatives displayed excellent in vivo antiviral activities against TMV, especially 4m (inactivation inhibitory effect, 58%; curative inhibitory effect, 57%; and protection inhibitory effect, 59%), which displayed similar activity to ningnanmycin (inactivation inhibitory effect, 61%; curative inhibitory effect, 57%; and protection inhibitory effect, 58%) at 500 μg mL-1; thus, it emerged as a new lead compound for antiviral research against TMV. Antiviral mechanism research by molecular docking demonstrated that compounds 4m, 5a, and 6b could interact with TMV CP and disturb virus assembly.

Total Syntheses and Anti-inflammatory Evaluations of Pongamosides A-C, Natural Furanoflavonoid Glucosides from Fruit of Pongamia pinnata (L.) Pierre

The syntheses of three natural furanoflavonoid glucosides, including two flavone glucosides, pongamosides A (1) and B (2), and a flavonol glucoside, pongamoside C (3), were achieved for the first time in 9-15 steps from commercially available materials in overall yields ranging from 2.9% to 29%. The synthetic sequence featured a NaH-promoted BK-VK rearrangement and acid-catalyzed intramolecular cyclization to furnish the furanoflavonoid aglycone. Meanwhile, phase-transfer-catalyzed glycosylation and Schmidt's trichloroacetimidate procedure were employed to establish the pivotal O-glycosidic linkage. The anti-inflammatory activities of compounds 1-3, as well as their aglycones 5a, 5b, and 23, were determined against NO production in the LPS-stimulated RAW264.7 cells. The results indicated that the O-glycosylation may reduce the anti-inflammatory activity of furanoflavonoid in vitro.

Effect of number and different types of proton donors on excited-state intramolecular single and double proton transfer in bipyridine derivatives: theoretical insights

Intra-HBs are strengthened upon photoexcitation, confirmed by red-shift in vibrational mode and topology analysis. Number and type of donors result in difference in photophysical properties. Occurrence of ESIPT depends on barrier and reaction energy.

Ratiometric Fluorescent Sensor Array as a Versatile Tool for Bacterial Pathogen Identification and Analysis

Rapid and reliable identification of pathogenic microorganisms is of great importance for human and animal health. Most conventional approaches are time-consuming and require expensive reagents, sophisticated equipment, trained personnel, and special storage and handling conditions. Sensor arrays based on small molecules offer a chemically stable and cost-effective alternative. Here we present a ratiometric fluorescent sensor array based on the derivatives of 2-(4'- N, N-dimethylamino)-3-hydroxyflavone and investigate its ability to provide a dual-channel ratiometric response. We demonstrate that, by using discriminant analysis of the sensor array responses, it is possible to effectively distinguish between eight bacterial species and recognize their Gram status. Thus, multiple parameters can be derived from the same data set. Moreover, the predictive potential of this sensor array is discussed, and its ability to analyze unknown samples beyond the list of species used for the training matrix is demonstrated. The proposed sensor array and analysis strategies open new avenues for the development of advanced ratiometric sensors for multiparametric analysis.