Identification of Bioactive Compounds of Asparagus officinalis L.: Permutation Test Allows Differentiation among “Triguero” and Hybrid Green Varieties

In this study, we determined the phytochemical profile of the Spanish “triguero” asparagus landrace “verde-morado” (Asparagus officinalis L.), a wild traditional landrace, and the improved “triguero” HT-801, together with two commercial green asparagus varieties. For comparison, we used reverse-phase high-performance liquid chromatography coupled with diode array electrospray time-of-flight mass spectrometry (RP-HPLC-DAD-ESI-TOF/MS) followed by a permutation test applied using a resampling methodology valid under a relaxed set of assumptions, such as i.i.d. errors (not necessarily normal) that are exchangeable under the null hypothesis. As a result, we postulate that “triguero” varieties (the improved HT-801 followed by its parent “verde-morado”) have a significantly different phytochemical profile from that of the other two commercial hybrid green varieties. In particular, we found compounds specific to the “triguero” varieties, such as feruloylhexosylhexose isomers, or isorhamnetin-3-O-glucoside, which was found only in the “triguero” variety HT-801. Although studies relating the phytochemical content of “triguero” asparagus varieties to its health-promoting effects are required, this characteristic phytochemical profile can be used for differentiating and revalorizating these asparagus cultivars.     

Target-driven DNA association to initiate cyclic assembly of hairpins for biosensing and logic gate operation

A target-driven DNA association was designed to initiate cyclic assembly of hairpins, which led to an enzyme-free amplification strategy for detection of a nucleic acid or aptamer substrate and flexible construction of logic gates. The cyclic system contained two ssDNA (S1 and S2) and two hairpins (H1 and H2). These ssDNA could co-recognize the target to produce an S1–target–S2 structure, which brought their toehold and branch-migration domains into close proximity to initiate the cyclic assembly of hairpins. The assembly product further induced the dissociation of a double-stranded probe DNA (Q:F) via toehold-mediated strand displacement to switch the fluorescence signal. This method could detect DNA and ATP as model analytes down to 21.6 pM and 38 nM, respectively. By designing different DNA input strands, the “AND”, “INHIBIT” and “NAND” logic gates could be activated to achieve the output signal. The proposed biosensing and logic gate operation platform showed potential applications in disease diagnosis.     

Chemical sensing in two dimensional porous covalent organic nanosheets

Two new imide-based crystalline, porous, and chemically stable covalent organic frameworks (COFs) (TpBDH and TfpBDH) have been successfully synthesized employing solvothermal crystallization route. Furthermore, thin layered covalent organic nanosheets (CONs) were derived from these bulk COFs by the simple liquid phase exfoliation method. These 2D CONs showcase increased luminescence intensity compared to their bulk counterparts (COFs). Notably, TfpBDH-CONs showcase good selectivity and prominent, direct visual detection towards different nitroaromatic analytes over TpBDH-CONs. Quite interestingly, TfpBDH-CONs exhibit a superior “turn-on” detection capability for 2,4,6-trinitrophenol (TNP) in the solid state, but conversely, they also show a “turn-off” detection in the dispersion state. These findings describe a new approach towards developing an efficient, promising fluorescence chemosensor material for both visual and spectroscopic detection of nitroaromatic compounds with very low [10^–5 (M)] analyte concentrations.     

Switch From Pauli‐Lowering to LUMO‐Lowering Catalysis in Brønsted Acid‐Catalyzed Aza‐Diels‐Alder Reactions

Brønsted acid‐catalyzed inverse‐electron demand (IED) aza‐Diels‐Alder reactions between 2‐aza‐dienes and ethylene were studied using quantum chemical calculations. The computed activation energy systematically decreases as the basic sites of the diene progressively become protonated. Our activation strain and Kohn‐Sham molecular orbital analyses traced the origin of this enhanced reactivity to i) “Pauli‐lowering catalysis” for mono‐protonated 2‐aza‐dienes due to the induction of an asynchronous, but still concerted, reaction pathway that reduces the Pauli repulsion between the reactants; and ii) “LUMO‐lowering catalysis” for multi‐protonated 2‐aza‐dienes due to their highly stabilized LUMO(s) and more concerted synchronous reaction path that facilitates more efficient orbital overlaps in IED interactions. In all, we illustrate how the novel concept of “Pauli‐lowering catalysis” can be overruled by the traditional concept of “LUMO‐lowering catalysis” when the degree of LUMO stabilization is extreme as in the case of multi‐protonated 2‐aza‐dienes.     

Fluorine teams up with water to restore inhibitor activity to mutant BPTI

Introducing fluorine into molecules has a wide range of effects on their physicochemical properties, often desirable but in most cases unpredictable. The fluorine atom imparts the C–F bond with low polarizability and high polarity, and significantly affects the behavior of neighboring functional groups, in a covalent or noncovalent manner. Here, we report that fluorine, present in the form of a single fluoroalkyl amino acid side chain in the P1 position of the well-characterized serine-protease inhibitor BPTI, can fully restore inhibitor activity to a mutant that contains the corresponding hydrocarbon side chain at the same site. High resolution crystal structures were obtained for four BPTI variants in complex with bovine β-trypsin, revealing changes in the stoichiometry and dynamics of water molecules in the S1 subsite. These results demonstrate that the introduction of fluorine into a protein environment can result in “chemical complementation” that has a significantly favorable impact on protein–protein interactions.     

Protein ubiquitination and formation of polyubiquitin chains without ATP,E1 and E2 enzymes

Studying protein ubiquitination is difficult due to the complexity of the E1–E2–E3 ubiquitination cascade. Here we report the discovery that C-terminal ubiquitin thioesters can undergo direct transthiolation with the catalytic cysteine of the model HECT E3 ubiquitin ligase Rsp5 to form a catalytically active Rsp5∼ubiquitin thioester (Rsp5∼Ub). The resulting Rsp5∼Ub undergoes efficient autoubiquitination, ubiquitinates protein substrates, and synthesizes polyubiquitin chains with native Ub isopeptide linkage specificity. Since the developed chemical system bypasses the need for ATP, E1 and E2 enzymes while maintaining the native HECT E3 mechanism, we named it “Bypassing System” (ByS). Importantly, ByS provides direct evidence that E2 enzymes are dispensable for K63 specific isopeptide bond formation between ubiquitin molecules by Rsp5 in vitro. Additionally, six other E3 enzymes including Nedd4-1, Nedd4-2, Itch, and Wwp1 HECT ligases, along with Parkin and HHARI RBR ligases processed Ub thioesters under ByS reaction conditions. These findings provide general mechanistic insights on protein ubiquitination, and offer new strategies for assay development to discover pharmacological modulators of E3 enzymes.     

Extending N-heterocyclic carbene ligands into the third dimension: a new type of hybrid phosphazane/NHC system

A simple, “click” synthetic approach to a new type of hybrid phosph(III)azane/NHC system is described. The presence of the phosphazane P₂N₂ ring unit, with P atoms flanking the NCN fragment and with this ring perpendicular to the binding site of the NHC, provides unique opportunities for modifying the electronic and steric character of these carbenes.     

Transition-metal-free controlled polymerization for poly(p-aryleneethynylene)s

A transition-metal-free controlled polymerization for the attainment of poly(p-aryleneethynylene)s is developed. The polymerization of 1-pentafluorophenyl-4-[(trimethylsilyl)ethynyl]benzene with a catalytic amount of fluoride anions proceeds in a chain-growth-like manner to afford polymers with controlled molecular weights and low polydispersity indexes. The mechanism involves a pentacoordinated fluorosilicate as a key intermediate. The anionic “living” nature of this process is applied to block copolymerization and also surface-terminated polymerization.     

A “Double-Locked” and Enzyme/pH-Activated Theranostic Agent for Accurate Tumor Imaging and Therapy

Theranostic agents for concurrent cancer therapy and diagnosis have begun attracting attention as a promising modality. However, accurate imaging and identification remains a great challenge for theranostic agents. Here, we designed and synthesized a novel theranostic agent H6M based on the “double-locked” strategy by introducing an electron-withdrawing nitro group into 1-position of a pH-responsive 3-amino-β-carboline and further covalently linking the hydroxamic acid group, a zinc-binding group (ZBG), to the 3-position of β-carboline to obtain histone deacetylase (HDAC) inhibitory effect for combined HDAC-targeted therapy. We found that H6M can be specifically reduced under overexpressed nitroreductase (NTR) to produce H6AQ, which emits bright fluorescence at low pH. Notably, H6M demonstrated a selective fluorescence imaging via successive reactions with NTR (first “key”) and pH (second “key”), and precisely identified tumor margins with a high S/N ratio to guide tumor resection. Finally, H6M exerted robust HDAC1/cancer cell inhibitory activities compared with a known HDAC inhibitor SAHA. Therefore, the NTR/pH-activated theranostic agent provided a novel tool for precise diagnosis and efficient tumor therapy.     

Metal oxidation states in biological water splitting

A central question in biological water splitting concerns the oxidation states of the manganese ions that comprise the oxygen-evolving complex of photosystem II. Understanding the nature and order of oxidation events that occur during the catalytic cycle of five S_i states (i = 0–4) is of fundamental importance both for the natural system and for artificial water oxidation catalysts. Despite the widespread adoption of the so-called “high-valent scheme”—where, for example, the Mn oxidation states in the S₂ state are assigned as III, IV, IV, IV—the competing “low-valent scheme” that differs by a total of two metal unpaired electrons (i.e. III, III, III, IV in the S₂ state) is favored by several recent studies for the biological catalyst. The question of the correct oxidation state assignment is addressed here by a detailed computational comparison of the two schemes using a common structural platform and theoretical approach. Models based on crystallographic constraints were constructed for all conceivable oxidation state assignments in the four (semi)stable S states of the oxygen evolving complex, sampling various protonation levels and patterns to ensure comprehensive coverage. The models are evaluated with respect to their geometric, energetic, electronic, and spectroscopic properties against available experimental EXAFS, XFEL-XRD, EPR, ENDOR and Mn K pre-edge XANES data. New 2.5 K ⁵⁵Mn ENDOR data of the S₂ state are also reported. Our results conclusively show that the entire S state phenomenology can only be accommodated within the high-valent scheme by adopting a single motif and protonation pattern that progresses smoothly from S₀ (III, III, III, IV) to S₃ (IV, IV, IV, IV), satisfying all experimental constraints and reproducing all observables. By contrast, it was impossible to construct a consistent cycle based on the low-valent scheme for all S states. Instead, the low-valent models developed here may provide new insight into the over-reduced S states and the states involved in the assembly of the catalytically active water oxidizing cluster.     

GC-MS Metabolic Profile and α-Glucosidase-, α-Amylase-, Lipase-, and Acetylcholinesterase-Inhibitory Activities of Eight Peach Varieties

The inhibition of certain digestive enzymes by target food matrices represents a new approach in the treatment of socially significant diseases. Proving the ability of fruits to inhibit such enzymes can support the inclusion of specific varieties in the daily diets of patients with diabetes, obesity, Alzheimer’s disease, etc., providing them with much more than just valuable micro- and macromolecules. The current study aimed atidentifying and comparing the GC-MS metabolic profiles of eight peach varieties (“Filina”, “Ufo 4, “Gergana”, “Laskava”, “July Lady”, “Flat Queen”, “Evmolpiya”, and “Morsiani 90”) grown in Bulgaria (local and introduced) and to evaluate the inhibitory potential of their extracts towards α-glucosidase, α-amylase, lipase, and acetylcholinesterase. In order to confirm samples’ differences or similarities, principal component analysis (PCA) and hierarchical cluster analysis (HCA) were also applied to the identified metabolites. The results provide important insights into the metabolomic profiles of the eight peach varieties and represent a first attempt to characterize the peels of the peach varieties with respect to α-glucosidase-, α-amylase-, lipase-, and acetylcholinesterase-inhibitory activities. All of the studied peach extracts displayed inhibitory activity towards α-glucosidase (IC₅₀: 125–757 mg/mL) and acetylcholinesterase (IC₅₀: 60–739 mg/mL), but none of them affected α-amylase activity. Five of the eight varieties showed inhibitory activity towards porcine pancreatic lipase (IC₅₀: 24–167 mg/mL). The obtained results validate the usefulness of peaches and nectarines as valuable sources of natural agents beneficial for human health, although further detailed investigation should be performed in order to thoroughly identify the enzyme inhibitors responsible for each activity.     

Phytochemical Content and Antioxidant Activity of Malus domestica Borkh Peel Extracts

Apple is an important dietary source of carotenoids and phenolic compounds, and its regular consumption is associated with several health benefits. The aim of this study was to evaluate the phytochemical composition of fresh peels of four red-skinned (“Champion”, “Generos”, “Idared”, “Florina”) and two yellow-skinned (“Golden Delicious”, “Reinette Simirenko”) apple varieties. Antioxidant activity of apple peel extracts was determined by ferric reducing antioxidant power (FRAP) and ABTS radical scavenging capacity assays. Total carotenoid and polyphenolic contents were determined spectrophotometrically, while the profile of individual carotenoids and anthocyanins (in red-skinned varieties) was analyzed using high-performance liquid chromatography coupled to a photodiode array detector (HPLC-PDA). Carotenoid composition was specific for each variety, and total carotenoid content was slightly higher in yellow-skinned apple peels compared to red-skinned varieties. In contrast, total phenolic content was higher in the peels of red-skinned cultivars. Anthocyanin profile was predominated by cyanidin-3-O-galactoside. Antioxidant potential followed the trend of the total polyphenolic content, being highest in “Florina”, as measured by both FRAP and ABTS assays. Our results demonstrated apple peels have high phytochemical content with diverse compositions, and their regular consumption can be an excellent source of antioxidants.     

Design,preparation, and selection of DNA-encoded dynamic libraries

We report a method for the preparation and selection of DNA-encoded dynamic libraries (DEDLs). The library is composed of two sets of DNA-linked small molecules that are under dynamic exchange through DNA hybridization. Addition of the protein target shifted the equilibrium, favouring the assembly of high affinity bivalent binders. Notably, we introduced a novel locking mechanism to stop the dynamic exchange and “freeze” the equilibrium, thereby enabling downstream hit isolation and decoding by PCR amplification and DNA sequencing. Our DEDL approach has circumvented the limitation of library size and realized the analysis and selection of large dynamic libraries. In addition, this method also eliminates the requirement for modified and immobilized target proteins.     

Microwave-Assisted Extraction of Phenolic Compounds from Spent Coffee Grounds. Process Optimization Applying Design of Experiments

In this study, sustainable technology microwave-assisted extraction (MAE) in association with green solvents was applied to recover phenolic compounds from spent coffee grounds (SCGs). A design of experiments (DOE) was used for process optimization. Initially, a 2⁴⁻¹ two level Fractional Factorial Design was used and ratios “solvent to solute” and “ethanol to water” were identified as the significant experimental factors. Consequently, Central Composite Design (CCD) was applied to analyze the effects of the significant variables on the response yield, total polyphenols content (TPC), and antioxidant activity (AA) by the DPPH assay method, and quadratic surfaces to optimize those responses were generated. The values of the significant factors of 16.7 (solvent/solute) and 68.9% (ethanol/water) were optimized simultaneously the yield (%) at 6.98 ± 0.27, TPC (mg GAE/g) at 117.7 ± 6.1, and AA (µmol TE/g) at 143.8 ± 8.6 and were in excellent agreement with those predicted from the CCD model. The variations of the compositions of the lipids, caffeine, pentacyclic diterpenes, and FAME as a function of the dominant factor % ethanol in the solvent mixture were analyzed by applying NMR and GC-FID, and the results obtained confirmed their determinative significance.     

Improving the Cellular Selectivity of a Membrane-Disrupting Antimicrobial Agent by Monomer Control and by Taming

Antimicrobial resistance represents a significant world-wide health threat that is looming. To meet this challenge, new classes of antimicrobial agents and the redesign of existing ones will be required. This review summarizes some of the studies that have been carried out in my own laboratories involving membrane-disrupting agents. A major discovery that we made, using a Triton X-100 as a prototypical membrane-disrupting molecule and cholesterol-rich liposomes as model systems, was that membrane disruption can occur by two distinct processes, depending on the state of aggregation of the attacking agent. Specifically, we found that monomers induced leakage, while attack by aggregates resulted in a catastrophic rupture of the membrane. This discovery led us to design of a series of derivatives of the clinically important antifungal agent, Amphotericin B, where we demonstrated the feasibility of separating antifungal from hemolytic activity by decreasing the molecule’s tendency to aggregate, i.e., by controlling its monomer concentration. Using an entirely different approach (i.e., a “taming” strategy), we found that by covalently attaching one or more facial amphiphiles (“floats”) to Amphotericin B, its aggregate forms were much less active in lysing red blood cells while maintaining high antifungal activity. The possibility of applying such “monomer control” and “taming” strategies to other membrane-disrupting antimicrobial agents is briefly discussed.     

Plasmonic giant quantum dots: hybrid nanostructures for truly simultaneous optical imaging,photothermal effect and thermometry

Hybrid semiconductor–metal nanoscale constructs are of both fundamental and practical interest. Semiconductor nanocrystals are active emitters of photons when stimulated optically, while the interaction of light with nanosized metal objects results in scattering and ohmic damping due to absorption. In a combined structure, the properties of both components can be realized together. At the same time, metal–semiconductor coupling may intervene to modify absorption and/or emission processes taking place in the semiconductor, resulting in a range of effects from photoluminescence quenching to enhancement. We show here that photostable ‘giant’ quantum dots when placed at the center of an ultrathin gold shell retain their key optical property of bright and blinking-free photoluminescence, while the metal shell imparts efficient photothermal transduction. The latter is despite the highly compact total particle size (40–60 nm “inorganic” diameter and <100 nm hydrodynamic diameter) and the very thin nature of the optically transparent Au shell. Importantly, the sensitivity of the quantum dot emission to local temperature provides a novel internal thermometer for recording temperature during infrared irradiation-induced photothermal heating.     

A two-dimensional molecular beacon for mRNA-activated intelligent cancer theranostics

Ideal theranostics should possess directly correlated imaging and therapy modalities that could be simultaneously activated in the disease site to generate high imaging contrast and therapeutic efficacy with minimal side effects. However, so far it still remains challenging to engineer all these characteristics into a single theranostic probe. Herein, we report a new type of photosensitizer (PS)-derived “two-dimensional” molecular beacon (TMB) that could be specifically activated within tumor cells to exhibit both high imaging contrast and therapeutic efficacy that outperforms conventional photosensitizers for cancer theranostics. The TMB is constructed by integrating a photosensitizer (chlorin e6 (Ce6)), a quantum dot (QD), and a dark quencher (BHQ3) into a hairpin DNA molecule to generate multiple synergistic FRET modes. The imaging modality and therapy modality, which are mediated by FRET between the QD and BHQ3 and FRET between the QD and Ce6 respectively, are interconnected within the TMB and could be simultaneously activated by tumor mRNA molecules. We show that highly effective cancer imaging and therapy could be achieved for cancer cell lines and xenografted tumor models. The reported TMB represents an unprecedented theranostic platform for intelligent cancer theranostics.