Unnatural Amino Acids for Biological Spectroscopy and Microscopy

Due to advances in methods for site-specific incorporation of unnatural amino acids (UAAs) into proteins, a large number of UAAs with tailored chemical and/or physical properties have been developed and used in a wide array of biological applications. In particular, UAAs with specific spectroscopic characteristics can be used as external reporters to produce additional signals, hence increasing the information content obtainable in protein spectroscopic and/or imaging measurements. In this Review, we summarize the progress in the past two decades in the development of such UAAs and their applications in biological spectroscopy and microscopy, with a focus on UAAs that can be used as site-specific vibrational, fluorescence, electron paramagnetic resonance (EPR), or nuclear magnetic resonance (NMR) probes. Wherever applicable, we also discuss future directions.

UHPLC-PDA-Q-TOF-MS-α-amylase-FLD activity detection system and molecular docking

INTRODUCTION

Traditional and some scientific literature document the antidiabetic effects of the Ziziphi Spinosae Semen (ZSS). However, the bioactive compounds of ZSS responsible for the antidiabetic effects are not well known.

OBJECTIVES

This study aimed to investigate the material basis of the antidiabetic effects of ZSS by inhibiting α-amylase.

METHODOLOGY

An online analysis platform was established and optimized using an ultra-performance liquid chromatography-photo-diode array-quadrupole-time-of-flight-mass spectrometry-α-amylase-fluorescence detector (UHPLC-PDA-Q-TOF-MS-α-amylase-FLD) system to screen α-amylase inhibitors in ZSS rapidly. The inhibitory effect of these compounds was confirmed by molecular docking screening. and the molecular interactions between α-amylase and active compounds were evaluated, which strongly supported the experimental results.

RESULTS

Seventy-eight compounds were identified in the ZSS extract, eleven of which were screened to have significant α-amylase binding activity.

CONCLUSION

This study demonstrated the feasibility of using an established platform to screen for effective components in ZSS, providing a practical method for the rapid screening of potential antidiabetic active ingredients in traditional Chinese medicine.

Approaching Tryptophan-Derived Polynorbornene Fluorescent Chemosensors: Synthesis, Characterization, and Sensing Ability for Biomedical Applications as Biomarkers for Detecting Fe2+ Ions

We present a novel group of tryptophan (Trp)-based fluorescent polymeric probes synthesized via ring-opening metathesis polymerization (ROMP) of Trp-derived norbornene monomers. These probes, in mono- and disubstituted forms, incorporate amide and ester anchoring groups. The quantity of Trp substituents did not affect fluorescence selectivity but influenced quenching percentage. Poly-diamide-Trp, Poly-monoamide-Trp, Poly-diester-Trp, and Poly-monoester-Trp probes displayed selective detection of Fe2+ and Fe3+ ions with fluorescence on-off characteristics. Poly-diamide-Trp and Poly-monoamide-Trp exhibited a limit of detection (LOD) for Fe2+ and Fe3+ ions of 0.86-11.32 μM, while Poly-diester-Trp and Poly-monoester-Trp showed higher LODs (21.8-108.7 μM). These probes exhibited high selectivity over Fe2+, a crucial metal ion in the body known for its redox properties causing oxidative stress and cell damage. Cell cytotoxicity tests in various cell types confirmed biocompatibility. Additionally, Poly-diamide-Trp displayed excellent cell permeability and iron ion detection in EA.hy926 cells, suggesting potential for bioimaging and clinical applications.

Picolinamide-assisted ortho-C-H functionalization of pyrenylglycine derivatives using aryl iodides

Chemical transformations involving the pyrenylglycine motif (an unnatural amino acid) and practical methods toward it are seldom known. This work aimed at developing a method for synthesizing novel pyrenylglycine (pyrene-based glycine) unnatural amino acid derivatives. To realize this, initially, a new pyrenylglycine substrate possessing the picolinamide moiety was assembled via the Ugi multicomponent reaction. The picolinamide moiety linked to amine substrates is a well-known bidentate directing group for accomplishing the site-selective γ-C-H functionalization of amines. Subsequently, it was aimed at using a Pd(II)-catalyzed bidentate directing group-aided γ-C-H arylation strategy for generating a wide range of unprecedented examples of C(2)-H arylated pyrenylglycines. Accordingly, pyrenylglycine possessing the picolinamide moiety was subjected to Pd(II)-catalyzed C(2)-H arylation in the non-K-region to afford a library of C(2)-arylated pyrenylglycines (π-extended pyrenes). Additionally, pyrenylglycine-based small peptides were assembled using C(2)-arylated pyrenylglycines. The X-ray structure of a representative compound was obtained, which corroborated the structure of pyrenylglycine and the regioselectivity of C(2)-H arylation of the pyrene in the non-K-region.

Self-Assembly of a Novel Pentapeptide into Hydrogelated Dendritic Architecture: Synthesis, Properties, Molecular Docking and Prospective Applications

Currently, ultrashort oligopeptides consisting of fewer than eight amino acids represent a cutting-edge frontier in materials science, particularly in the realm of hydrogel formation. By employing solid-phase synthesis with the Fmoc/tBu approach, a novel pentapeptide, FEYNF-NH2, was designed, inspired by a previously studied sequence chosen from hen egg-white lysozyme (FESNF-NH2). Qualitative peptide analysis was based on reverse-phase high performance liquid chromatography (RP-HPLC), while further purification was accomplished using solid-phase extraction (SPE). Exact molecular ion confirmation was achieved by matrix-assisted laser desorption-ionization mass spectrometry (MALDI-ToF MS) using two different matrices (HCCA and DHB). Additionally, the molecular ion of interest was subjected to tandem mass spectrometry (MS/MS) employing collision-induced dissociation (CID) to confirm the synthesized peptide structure. A combination of research techniques, including Fourier-transform infrared spectroscopy (FTIR), fluorescence analysis, transmission electron microscopy, polarized light microscopy, and Congo red staining assay, were carefully employed to glean valuable insights into the self-assembly phenomena and gelation process of the modified FEYNF-NH2 peptide. Furthermore, molecular docking simulations were conducted to deepen our understanding of the mechanisms underlying the pentapeptide's supramolecular assembly formation and intermolecular interactions. Our study provides potential insights into amyloid research and proposes a novel peptide for advancements in materials science. In this regard, in silico studies were performed to explore the FEYNF peptide's ability to form polyplexes.

Self-Assembled Skin-Penetrating Peptides with Controlled Supramolecular Properties for Enhanced Transdermal Delivery

The use of nanocarriers decorated with penetration-enhancing agents (PEAs) is considered to be a promising approach for efficient transdermal delivery. In this study, we developed short amphiphilic skin-penetrating peptides (17 amino acids) that functioned not only as PEAs but also as building blocks of nanocarriers without the incorporation of additional macromolecules for self-assembly and guest molecule encapsulation. Interestingly, varying only two amino acids in the hydrophobic moiety of the peptides resulted in significantly different self-assembly behavior, thermal stability, protease resistance, and skin-penetration efficiency in a human skin model. The analysis of the peptide secondary structure revealed that such characteristic changes arose due to the sequence variation-mediated conformational change in the hydrophobic block. These findings hold significant promise for the development of simple and effective delivery systems exhibiting controllable supramolecular properties.

Two-photon excitation fluorescence microspectroscopy protocols for examining fluorophores in fossil plants

Fluorescence emission is common in plants. While fluorescence microscopy has been widely used to study living plants, its application in quantifying the fluorescence of fossil plants has been limited. Fossil plant fluorescence, from original fluorophores or formed during fossilization, can offer valuable insights into fluorescence in ancient plants and fossilization processes. In this work, we utilize two-photon fluorescence microspectroscopy to spatially and spectrally resolve the fluorescence emitted by amber-embedded plants, leaf compressions, and silicified wood. The advanced micro-spectroscope utilized, with its pixel-level spectral resolution and line-scan excitation capabilities, allows us to collect comprehensive excitation and emission spectra with high sensitivity and minimal laser damage to the specimens. By applying linear spectral unmixing to the spectrally resolved fluorescence images, we can differentiate between (a) the matrix and (b) the materials that comprise the fossil. Our analysis suggests that the latter correspond to durable tissues such as lignin and cellulose. Additionally, we observe potential signals from chlorophyll derivatives/tannins, although minerals may have contributed to this. This research opens doors to exploring ancient ecosystems and understanding the ecological roles of fluorescence in plants throughout time. Furthermore, the protocols developed herein can also be applied to analyze non-plant fossils and biological specimens.

Recent advances in the peptide-based biosensor designs

Biosensors have rapidly emerged as a high-sensitivity and convenient detection method. Among various types of biosensors, optical and electrochemical are the most commonly used. Conventionally, antibodies have been employed to ensure specific interaction between the transmission material and analytes. However, there has been increasing recognition of peptides as a promising recognition element for biosensor development in recent years. The use of peptides as recognition elements provides high level of specificity, sensitivity, and stability for the detection process. The combination of peptide designs and optical or electrochemical detection methods has significantly improved biosensor efficacy. These advancements present opportunities for developing biosensors with diverse functions that can be used to lay a strong scientific foundation for the development of personalized medicine and various other fields. This paper reviews the recent advancements in the development and application of peptide-based optical and electrochemical biosensors, as well as their prospects as a sensor type.

Mechanism of melanogenesis inhibition by Keggin-type polyoxometalates

Abnormal melanin overproduction can result in hyperpigmentation syndrome in human skin diseases and enzymatic browning of fruits and vegetables. Recently, our group found that Keggin-type polyoxometalates (POMs) can efficiently inhibit tyrosinase activity. However, it remains unclear whether Keggin-type POMs exhibit optimal effects in vivo. Additionally, the inhibitory effect and mechanism of action of POMs on cellular tyrosinase activity and melanogenesis have been rarely reported. Here we demonstrate that our screened and synthesised PMo11Zn and GaMo12 show superior inhibitory effects on melanin formation as well as inhibition of cellular tyrosinase activity compared to other Keggin-type POMs. Intriguingly, we reveal that Keggin-type POMs competitively bind to tyrosinase mainly through more interactions with Cu2+ ions and the amino acid residue is capable of forming van der Waals, cation-π and hydrogen bonds, resulting in a reversible non-covalent complex formation. Our findings provide valuable insights into the design, synthesis and screening of polyoxometalates as multifunctional metallodrugs and food preservatives against hyperpigmentation.

Advances in the design of amino acid and peptide synthesized gold nanoparticles for their applications

The field of therapeutics and diagnostics is advanced by nanotechnology-based approaches including the spatial-temporal release of drugs, targeted delivery, enhanced accumulation of drugs, immunomodulation, antimicrobial action, and high-resolution bioimaging, sensors and detection. Various compositions of nanoparticles (NPs) have been developed for biomedical applications; however, gold NPs (Au NPs) have attracted tremendous attention due to their biocompatibility, easy surface functionalization and quantification. Amino acids and peptides have natural biological activities as such, their activities enhance several folds in combination with NPs. Although peptides are extensively used to produce various functionalities of Au NPs, amino acids have also gained similar interests in producing amino acid-capped Au NPs due to the availability of amine, carboxyl and thiol functional groups. Henceforth, a comprehensive review is needed to timely bridge the synthesis and the applications of amino acid and peptide-capped Au NPs. This review aims to describe the synthesis mechanism of Au NPs using amino acids and peptides along with their applications in antimicrobial, bio/chemo-sensors, bioimaging, cancer therapy, catalysis, and skin regeneration. Moreover, the mechanisms of various activities of amino acid and peptide capped-Au NPs are presented. We believe this review will motivate researchers to better understand the interactions and long-term activities of amino acid and peptide-capped Au NPs for their success in various applications.

Probing the toxic effect of quinoline to catalase and superoxide dismutase by multispectral method

Quinoline is a common nitrogen heterocyclic aromatic hydrocarbon with high water solubility. Studies have shown that quinoline can be teratogenic, carcinogenic and mutagenic. And Hepatocytes are the target cell of quinoline, which contain a large number of mitochondria and are related to cell function and the balance of reactive oxygen species (ROS). However, the research on the effect of quinoline on hepatocyte damage and anti-oxidation system is still unclear. Through the means of multispectral experiments, it is concluded that quinoline can affect the catalase (CAT) and superoxide dismutase (SOD), change their structure and affect their activity. The binding mode and binding site of quinoline to CAT/SOD were analyzed by isothermal calorimetric titration (ITC) and Molecular Operating Environment (MOE). In molecular docking simulation, the binding site of quinoline-CAT system is close to the active site, and affect the microenvironment of Tyr 357. This may be the reason why quinoline affects CAT activity and synchronous fluorescence (Δλ = 15 nm). This study demonstrated that quinoline has a great effect on CAT, which may affect the intracellular ROS balance and become a potential way to cause hepatocyte damage.

Investigating the role of double mutations R12C/P20R, and R12C/R69C on structure, chaperone-like activity, and amyloidogenic properties of human αB-crystallin

α-crystallin is a structurally essential small heat shock protein (sHSP) with a chaperone-like activity which maintains transparency of the lenticular tissues during a period of time that is as long as human life. α-crystallin is a multimeric protein consisting of αA and αB subunits, with 57 % homology. The CRYAB gene on chromosome 11 encodes human αB-crystallin (αB-Cry), which contains 175 amino acid residues. In the current study, the cataractogenic mutations R12C, P20R, R69C, and double mutations R12C/P20R and R12C/P20R were embedded into the human CRYAB gene. Following successful expression in the prokaryotic system and purification, a number of spectroscopic techniques, gel electrophoresis, dynamic light scattering (DLS), and transmission electron microscopy (TEM) were applied to assess the role of these mutations on the structure, amyloidogenicity, and biological function of human αB-Cry. The created mutations caused significant changes in the structure, and oligomeric state of human αB-Cry. These mutations, particularly R12C, R12C/P20R, and R12C/R69C, dramatically enhanced the tendency of this protein for the amyloid fibril formation and reduced its chaperone-like activity. Since double mutations R12C/P20R and R12C/P20R were able to intensely change the protein's structure and chaperone function, it can be suggested that they may play a destructive role in a cumulative manner. Our findings indicated that the simultaneous presence of two pathogenic mutations may have a cumulative destructive impacts on the structure and function of human αB-Cry and this observation is likely related to the disease severity of the mutated proteins.

Investigation of the binding behavior of bioactive 7-methoxyflavone to human serum albumin by coupling multi-spectroscopic with computational approaches

The natural flavonoids with bioactivity as secondary plant metabolites are mostly found in fruits, vegetables, tea and herbs, the distribution and bioavailability of which in vivo depends on the interaction and successive binding with carrier proteins in the systemic circulation. In this paper, the binding behavior of bioactive 7-methoxyflavone (7-MF) with human serum albumin (HSA) was studied with the aid of the combination of multi-spectroscopic methods, molecular docking and molecular dynamic simulation. The results of multi-spectroscopic experiments revealed that 7-MF interacted with HSA predominantly via fluorescence static quenching and the microenvironment around the fluorophore Trp residues in HSA became more hydrophilicity with the binding of 7-MF. Thermodynamic analysis demonstrated that hydrogen bonds and van der Waals forces played a dominant role in stabilizing the HSA-7-MF complex. Moreover, the docking experiment and molecular dynamic simulation further confirmed that 7-MF could enter the active cavity of HSA and caused more stable conformation and change of secondary structure of HSA through forming hydrogen bond. The exploration of the mechanism of 7-MF binding to HSA lights a new avenue to understand the stability, transport and distribution of 7-MF and 7-MF may hold great potential to be extended as a promising alternative of dietary supplements or pharmaceutical agents.

Comprehensive study upon physicochemical properties of bio-ZnO NCs

In this study, for the first time, the comparison of commercially available chemical ZnO NCs and bio-ZnO NCs produced extracellularly by two different probiotic isolates (Latilactobacillus curvatus MEVP1 [OM736187] and Limosilactobacillus fermentum MEVP2 [OM736188]) were performed. All types of ZnO formulations were characterized by comprehensive interdisciplinary approach including various instrumental techniques in order to obtain nanocomposites with suitable properties for further applications, i.e. biomedical. Based on the X- ray diffraction analysis results, all tested nanoparticles exhibited the wurtzite structure with an average crystalline size distribution of 21.1 nm (CHEM_ZnO NCs), 13.2 nm (1C_ZnO NCs) and 12.9 nm (4a_ZnO NCs). The microscopy approach with use of broad range of detectors (SE, BF, HAADF) revealed the core-shell structure of bio-ZnO NCs, compared to the chemical one. The nanoparticles core of 1C and 4a_ZnO NCs are coated by the specific organic deposit coming from the metabolites produced by two probiotic strains, L. fermentum and L. curvatus. Vibrational infrared spectroscopy, photoluminescence (PL) and mass spectrometry (LDI-TOF-MS) have been used to monitor the ZnO NCs surface chemistry and allowed for better description of bio-NCs organic coating composition (amino acids residues). The characterized ZnO formulations were then assessed for their photocatalytic properties against methylene blue (MB). Both types of bio-ZnO NCs exhibited good photocatalytic activity, however, the effect of CHEM_ZnO NCs was more potent than bio-ZnO NCs. Finally, the colloidal stability of the tested nanoparticles were investigated based on the zeta potential (ZP) and hydrodynamic diameter measurements in dependence of the nanocomposites concentration and investigation time. During the biosynthesis of nano-ZnO, the increment of pH from 5.7 to around 8 were observed which suggested possible contribution of zinc aquacomplexes and carboxyl-rich compounds resulted in conversion of zinc tetrahydroxy ion complex to ZnO NCs. Overall results in present study suggest that used accessible source such us probiotic strains, L. fermentum and L. curvatus, for extracellular bio-ZnO NCs synthesis are of high interest. What is important, no significant differences between organic deposit (e.g. metabolites) produced by tested strains were noticed-both of them allowed to form the nanoparticles with natural origin coating. In comparison to chemical ZnO NCs, those synthetized via microbiological route are promising material with further biological potential once have shown high stability during 7 days.

The photophysics of 2-cyanoindole probed by femtosecond spectroscopy

The photophysics of 2-cyanoindole (2-CI) in solution (water, 2,2,2-trifluoroethanol, acetonitrile‚ and tetrahydrofuran) was investigated by steady-state as well as time resolved fluorescence and absorption spectroscopy. The fluorescence quantum yield of 2-cyanoindole is strongly sensitive to the solvent. In water the quantum yield is as low as 4.4 × 10–4. In tetrahydrofuran, it amounts to a yield of 0.057. For 2-CI dissolved in water, a bi-exponential fluorescence decay with time constants of ∼1 ps and ∼8 ps is observed. For short wavelength excitation (266 nm) the initial fluorescence anisotropy is close to zero. For excitation with 310 nm it amounts to 0.2. In water, femtosecond transient absorption reveals that the fluorescence decay is solely due to internal conversion to the ground state. In aprotic solvents, the fluorescence decay takes much longer (acetonitrile: ∼900 ps, tetrahydrofuran: ∼2.6 ns) and intersystem crossing contributes.

Graphical abstract

Influencing factors and characterization methods of nanoparticles regulating amyloid aggregation

Human disorders associated with amyloid aggregation, such as Alzheimer's disease and Parkinson's disease, afflict the lives of millions worldwide. When peptides and proteins in the body are converted to amyloids, which have a tendency to aggregate, the toxic oligomers produced during the aggregation process can trigger a range of diseases. Nanoparticles (NPs) have been found to possess surface effects that can modulate the amyloid aggregation process and they have potential application value in the treatment of diseases related to amyloid aggregation and fibrillary tangles. In this review, we discuss recent progress relating to studies of nanoparticles that regulate amyloid aggregation. The review focuses on the factors influencing this regulation, which are important as guidelines for the future design of NPs for the treatment of amyloid aggregation. We describe the characterization methods that have been utilized so far in such studies. This review provides research information and characterization methods for the rational design of NPs, which should result in therapeutic strategies for amyloid diseases.