High Structural Diversity Research Articles

Semiautomated glycoproteomics data analysis workflow for maximized glycopeptide identification and reliable quantification.

Glycoproteomic data are often very complex, reflecting the high structural diversity of peptide and glycan portions. The use of glycopeptide-centered glycoproteomics by mass spectrometry is rapidly evolving in many research areas, leading to a demand in reliable data analysis tools. In recent years, several bioinformatic tools were developed to facilitate and improve both the identification and quantification of glycopeptides. Here, a selection of these tools was combined and evaluated with the aim of establishing a robust glycopeptide detection and quantification workflow targeting enriched glycoproteins. For this purpose, a tryptic digest from affinity-purified immunoglobulins G and A was analyzed on a nano-reversed-phase liquid chromatography–tandem mass spectrometry platform with a high-resolution mass analyzer and higher-energy collisional dissociation fragmentation. Initial glycopeptide identification based on MS/MS data was aided by the Byonic software. Additional MS1-based glycopeptide identification relying on accurate mass and retention time differences using GlycopeptideGraphMS considerably expanded the set of confidently annotated glycopeptides. For glycopeptide quantification, the performance of LaCyTools was compared to Skyline, and GlycopeptideGraphMS. All quantification packages resulted in comparable glycosylation profiles but featured differences in terms of robustness and data quality control. Partial cysteine oxidation was identified as an unexpectedly abundant peptide modification and impaired the automated processing of several IgA glycopeptides. Finally, this study presents a semiautomated workflow for reliable glycoproteomic data analysis by the combination of software packages for MS/MS- and MS1-based glycopeptide identification as well as the integration of analyte quality control and quantification.

Polycyclic Quinone and Its Dithiin Derivative As Cathode Materials for Sustainable Aqueous Zn-Organic Secondary Batteries

Aqueous Zinc-ion (Zn-ion) batteries are considered as attractive energy storage devices for large scale applications owing to their intrinsic safety, low cost and robustness1. However, their implementation is held back by sluggish diffusion kinetics of Zn2+ into inorganic host materials. Therefore, the focus is on redox active organic materials particularly quinone derivatives. These materials show moderate coulombic repulsions to the Zn2+ diffusion by having big tunnels in the crystal lattice2. Yet, very few organic materials have been reported for aqueous Zn-ion batteries. In the contextual importance of exploring new organic materials that can reversibly host Zn2+. Herein, we have explored highly conjugated pentacene-5,7,12,14-tetraone (PT) as cathode material for aqueous ZIBs for the first time. The versatile features such as strong π-stacking, high theoretical capacity (i.e. 317 mAh g-1 for 4e- transfer), structural diversity, inherent insolubility and non-defamation upon electrochemical process unlike simple quinones make PT a promising candidate to study. Moreover, we used filter paper as a separator instead of nafion membrane and ZnSO4 as supporting electrolyte salt which makes this battery more environmentally friendly and cost effective. In order to improve the rate capability and cycling stability, PT was incorporated in the mesoporous nanonetwork of CMK-3 carbon. In addition, the discharge voltage of the cell was enhanced by introducing sulfur atoms in the PT skeleton. Figure 1

Peptide-Mimicking Poly(2-oxazoline)s Displaying Potent Antimicrobial Properties.

Poly(2-oxazoline)s have excellent biocompatibility and have been used as FDA-approved indirect food additives. The inert property of the hydrophilic poly(2-oxazoline)s suggests them as promising substitutes for poly(ethylene glycol) (PEG) in various applications such as anti-biofouling agents. It was recently reported that poly(2-oxazoline)s themselves have antimicrobial properties as synthetic mimics of host defense peptides. These studies revealed the bioactive properties of poly(2-oxazoline)s as a new class of functional peptide mimics, by mimicking host defense peptides to display potent and selective antimicrobial activities against methicillin-resistant Staphylococcus aureus both in vitro and in vivo, without concerns about antimicrobial resistance. The high structural diversity, facile synthesis, and potent and tunable antimicrobial properties underscore the great potential of poly(2-oxazoline)s as a class of novel antimicrobial agents in dealing with drug-resistant microbial infections and antimicrobial resistance.

Evidence of drought memory in Dipteryx alata indicates differential acclimation of plants to savanna conditions

The remarkable phytogeographic characteristics of the Brazilian savanna (Cerrado) resulted in a vegetation domain composed of plants with high structural and functional diversity to tolerate climate extremes. Here we used a key Cerrado species (Dipteryx alata) to evaluate if species of this domain present a mechanism of stress memory, responding more quickly and efficiently when exposed to recurrent drought episodes. The exposure of D. alata seedlings to drought resulted in several changes, mainly in physiological and biochemical traits, and these changes differed substantially when the water deficit was imposed as an isolated event or when the plants were subjected to drought cycles, suggesting the existence of a drought memory mechanism. Plants submitted to recurrent drought events were able to maintain essential processes for plant survival when compared to those submitted to drought for the first time. This differential acclimation to drought was the result of orchestrated changes in several metabolic pathways, involving differential carbon allocation for defense responses and the reprogramming and coordination of primary, secondary and antioxidant metabolism. The stress memory in D. alata is probably linked the evolutionary history of the species and reflects the environment in which it evolved.

ZIF-8 derived nitrogen-doped carbon composites boost the rate performance of organic cathodes for sodium ion batteries

Biomass derived organic materials have gained a worthy potential for electrode materials of sodium-ion batteries (SIBs) due to their high specific capacity, renewability, lower cost, and structural diversity. However, high solubility and poor electronic conductivity are the key obstacles in development of traditional organic electrodes. Herein, the composite material PI@NC is prepared using 3,4,9,10-perylenetetracarboxylic dianhydride ethylene diamine and nitrogen-doped carbon matrix through in-situ polymerization. The formation of NC conductive scaffolds establishes the efficient pathways in electrodes for electronic conduction. As per expectations, PI@NC as a cathode material boosts the rate performance of SIBs. Specifically, the as-prepared composites offer outstanding redox behavior with superior rate capacities of 91 mAh g−1 at a higher current density of 10 A g−1 for sodium storage. Moreover, in order to show the potential application values of electrode materials, a full battery is successfully fabricated based on our PI@NC cathode and commercial disodium terephthalate (NaTP) anode.

Stand Structural Diversity and Species with Leaf Nitrogen Conservation Drive Aboveground Carbon Storage in Tropical Old-Growth Forests

Tropical old-growth forests are essential for global carbon regulation. Although there is increasing evidence that species and functional diversity, stand structural diversity, functional compositions, and elevation play roles in ecosystem functioning, the relative strengths of these drivers and the underlying mechanisms (mass-ratio hypothesis or niche complementarity hypothesis) are not clear. Aboveground carbon storage, species diversity, stand structural diversity, community-weighted mean (CWM), and functional diversity (FDvar) of 12 leaf traits were analyzed using data from 56 old-growth forest communities in the Dawei Mountain area of Southwest China. Multiple regression models were used to test the relative importance of the predictor variables and the structural equation model was used to explore the direct and indirect influences on aboveground carbon storage. High structural diversity moderately enhanced aboveground carbon storage. CWM leaf nitrogen concentration in young leaves weakly affected aboveground carbon storage. Our final multiple regression model showed that aboveground carbon storage is mostly affected by diameter at breast height (DBH) diversity, followed by FDvar of dry matter concentration in mature leaves and CWM nitrogen concentration in young leaves. The structural equation model indicated that elevation negatively affects aboveground carbon storage via diameter at breast height (DBH) diversity. Our results suggest that niche complementarity effects moderately drive aboveground carbon storage in tropical old-growth forests, but do not fully support the importance of the mass-ratio hypothesis.

Chiral Cobalt(II) Complex Catalyzed Asymmetric [2,3]-Sigmatropic Rearrangement of Allylic Selenides with α-Diazo Pyrazoleamides

Organoselenium compounds, due to their high structural diversity, special function, and biological activities, have drawn attention in synthetic chemistry. Herein, a novel example of chiral N,N′-di...

Fiber Composites of Metal–Organic Frameworks

The high chemical and structural diversity of metal–organic frameworks (MOFs), which are porous crystalline materials, has attracted significant academic and industrial interest. However, the poor ...

Putative SARS-CoV-2 Mpro Inhibitors from an In-House Library of Natural and Nature-Inspired Products: A Virtual Screening and Molecular Docking Study.

A novel coronavirus (severe acute respiratory syndrome coronavirus 2, SARS-CoV-2) has been the cause of a recent global pandemic. The highly contagious nature of this life-threatening virus makes it imperative to find therapies to counteract its diffusion. The main protease (Mpro) of SARS-CoV-2 is a promising drug target due to its indispensable role in viral replication inside the host. Using a combined two-steps approach of virtual screening and molecular docking techniques, we have screened an in-house collection of small molecules, mainly composed of natural and nature-inspired compounds. The molecules were selected with high structural diversity to cover a wide range of chemical space into the enzyme pockets. Virtual screening experiments were performed using the blind docking mode of the AutoDock Vina software. Virtual screening allowed the selection of structurally heterogeneous compounds capable of interacting effectively with the enzymatic site of SARS-CoV-2 Mpro. The compounds showing the best interaction with the protein were re-scored by molecular docking as implemented in AutoDock, while the stability of the complexes was tested by molecular dynamics. The most promising candidates revealed a good ability to fit into the protein binding pocket and to reach the catalytic dyad. There is a high probability that at least one of the selected scaffolds could be promising for further research

Structural Characterization of Dissolved Organic Matter at the Chemical Formula Level Using TIMS-FT-ICR MS/MS.

TIMS-FT-ICR MS is an important alternative to study the isomeric diversity and elemental composition of complex mixtures. While the chemical structure of many compounds in the dissolved organic matter (DOM) remains largely unknown, the high structural diversity has been described at the molecular level using chemical formulas. In this study, we further push the boundaries of TIMS-FT-ICR MS by performing chemical formula-based ion mobility and tandem MS analysis for the structural characterization of DOM. The workflow described is capable to mobility select (R ∼ 100) and isolate molecular ion signals (Δm/z = 0.036) in the ICR cell, using single-shot ejections after broadband ejections and MS/MS based on sustained off-resonance irradiation collision-induced dissociation (SORI-CID). The workflow results are compared to alternative TIMS-q-FT-ICR MS/MS experiments with quadrupole isolation at nominal mass (∼1 Da). The technology is demonstrated with isomeric and isobaric mixtures (e.g., 4-methoxy-1-naphthoic acid, 2-methoxy-1-naphthoic acid, decanedioic acid) and applied to the characterization of DOM. The application of this new methodology to the analysis of a DOM is illustrated by the isolation of the molecular ion [C18H18O10-H]- in the presence of other isobars at nominal mass 393. Five IMS bands were assigned to the heterogeneous ion mobility profile of [C18H18O10-H]-, and candidate structures from the PubChem database were screened based on their ion mobility and the MS/MS matching score. This approach overcomes traditional challenges associated with the similarity of fragmentation patterns of DOM samples (e.g., common neutral losses of H2O, CO2, and CH2-H2O) by narrowing down the isomeric candidate structures using the mobility domain.

Detection of simple and complex de novo mutations with multiple reference sequences.

The characterization of de novo mutations in regions of high sequence and structural diversity from whole-genome sequencing data remains highly challenging. Complex structural variants tend to arise in regions of high repetitiveness and low complexity, challenging both de novo assembly, in which short reads do not capture the long-range context required for resolution, and mapping approaches, in which improper alignment of reads to a reference genome that is highly diverged from that of the sample can lead to false or partial calls. Long-read technologies can potentially solve such problems but are currently unfeasible to use at scale. Here we present Corticall, a graph-based method that combines the advantages of multiple technologies and prior data sources to detect arbitrary classes of genetic variant. We construct multisample, colored de Bruijn graphs from short-read data for all samples, align long-read–derived haplotypes and multiple reference data sources to restore graph connectivity information, and call variants using graph path-finding algorithms and a model for simultaneous alignment and recombination. We validate and evaluate the approach using extensive simulations and use it to characterize the rate and spectrum of de novo mutation events in 119 progeny from four Plasmodium falciparum experimental crosses, using long-read data on the parents to inform reconstructions of the progeny and to detect several known and novel nonallelic homologous recombination events.

Chain engineering-tailored microstructures and lithium storage performance of hydrothermally-synthesized linear polyimides

Polyimides with high capacity, fast kinetics, abundant resource, and structural diversity offer an exhilarating opportunity for developing sustainable rechargeable batteries. Herein, a series of 1,4,5,8-naphthalenetetracarboxylic dianhydride (NTCDA)-based polyimides were successfully crafted through a facile and eco-friendly hydrothermal synthesis route. The microstructure and lithium storage performance of polyimides were tailored by regulating diamine linkers between NTCDA units. Interestingly, the moderate increased length of flexible diamine units with ethylenediamine and diaminobutane can stabilize the polymer skeleton. This leads to the formation of honeycomb-like porous structures with a sufficient exposure of active carbonyl groups, thereby achieving a large capacity and high rate capability. Therefore, polyimides derived from ethylenediamine and diaminobutane show larger reversible capacities (123 and 113.5 mA h/g at 50 mA/g, respectively) and better rate capabilities with capacity retentions of up to 50% when the current increased from 50 to 2000 mA/g. This work would provide new insights into macromolecular engineering of polymers for advanced electrode materials.

Hydroperoxylated vs Dihydroxylated Lipids: Differentiation of Isomeric Cardiolipin Oxidation Products by Multidimensional Separation Techniques.

In recent years, cardiolipin (CL) oxidation products were recognized as potential markers for mitochondrial dysfunction in conjunction with age related diseases. The analysis of oxidized CL requires powerful analysis techniques due to high structural diversity. In addition, low concentrations of partly labile compounds pose a special challenge, supplemented by the occurrence of isomeric compounds, e.g., hydroperoxylated vs dihydroxylated products. Therefore, we present a hyphenated method based on liquid chromatography coupled to trapped ion mobility spectrometry (TIMS) for separation and tandem mass spectrometry (MS/MS) for structural characterization. This enables comprehensive analysis of an artificially oxidized CL extract of bovine heart. Isomeric oxidation products could be differentiated by mobility-resolved MS/MS fragmentation experiments. Our developed method could help to better understand the physiological role of oxidized CL.

Acaricidal Activity of Artemisia nilagirica Leaves Against Rhipicephalus (Boophilus) annulatus Ticks

Since time immemorial, human beings have used various parts of plants in either prevention or treatment of ailments. Plants are rich sources of secondary metabolites such as alkaloids, steroids, terpenoids, flavonoids, and phenolic compounds with a high structural diversity. Many plants/herbs with specific biological activities such as antitumor, antioxidant, anti-inflammatory, antifungal, sedative, and acaricidal activity have been reported. Artemisia nilagirica (C. B. Clarke) Pamp. (Compositae) is a plant traditionally used for insect control in the southern part of India. Previous studies have demonstrated the activity of Artemisia species against pests. The present study thus evaluates the acaricidal activity of crude ethanolic extract of A.nilagirica leaves and its fractions against Rhipicephalus (Boophilus) annulatus. Ticks are ectoparasites that transmit several protozoal, viral, and rickettsial diseases. In south India, R. (B.) annulatus is the commonly observed tick species. Control of these acarine parasites that adversely affect milk and meat production is a tough task. Chemical acaricides such as organophosphates, synthetic pyrethroids, amitraz, and ivermectin are commonly used in tick control. The high cost, environmental hazards, and development of acaricidal resistance are some of the drawbacks of these chemical acaricides. Plant-based formulations are one of the promising approaches for the control of ectoparasites. Previously, extracts from various medicinal/aromatic plants were reported for acaricidal activity from our laboratory, such as Tetrastigma leucostaphylum (Dennst.) Alston, Chassalia curviflora (Wall.) Thwaites, Jatropha curcas L., and Ageratum conyzoides Hieron. Biochemical quantification, fluorescence analysis, and primary phytochemical analysis are already reported for the ethanolic extract and its fractions of areal parts of A.nilagirica. Phytochemical characterization of ethanolic extract of A.nilagirica from Kerala, India was shown to have the presence of terpenoids, flavonoids, steroids, saponins, fixed oils and fats, tannins, and glycosides.

Ion-exchange purification and structural characterization of five sulfated fucoidans from brown algae.

Fucoidans are a diverse class of sulfated polysaccharides integral to the cell wall of brown algae, and due to their various bioactivities, they are potential drugs. Standardized work with fucoidans is required for structure–function studies, but remains challenging since available fucoidan preparations are often contaminated with other algal compounds. Additionally, fucoidans are structurally diverse depending on species and season, urging the need for standardized purification protocols. Here, we use ion-exchange chromatography to purify different fucoidans and found a high structural diversity between fucoidans. Ion-exchange chromatography efficiently removes the polysaccharides alginate and laminarin and other contaminants such as proteins and phlorotannins across a broad range of fucoidans from major brown algal orders including Ectocarpales, Laminariales and Fucales. By monomer composition, linkage analysis and NMR characterization, we identified galacturonic acid, glucuronic acid and O-acetylation as new structural features of certain fucoidans and provided a novel structure of fucoidan from Durvillaea potatorum with α-1,3-linked fucose backbone and β-1,6 and β-1,3 galactose branches. This study emphasizes the use of standardized ion-exchange chromatography to obtain defined fucoidans for subsequent molecular studies.

Nitrogen-Doped Hierarchical Porous Carbon-Promoted Adsorption of Anthraquinone for Long-Life Organic Batteries.

Organic quinone molecules are attractive electrochemical energy storage devices because of their high abundance, multielectron reactions, and structural diversity compared with transition metal-oxide electrode materials. However, they have problems like poor cycle stability and low rate performance on account of the inherent low conductivity and high solubility in the electrolyte. Solving these two key problems at the same time can be challenging. Herein, we demonstrate that using a nitrogen-doped hierarchical porous carbon (NC) with mixed microporous/low-range mesoporous can greatly alleviate the shuttle effect caused by the dissolution of organic molecules in the electrolyte through physical binding and chemisorption, thereby improving the electrochemical performances. Lithium-ion batteries based on the anthraquinone (AQ) electrode exhibit dramatic capacity decay (5.7% capacity retention at 0.2 C after 1000 cycles) and poor rate performance (14.2 mA h g-1 at 2 C). However, the lithium-ion battery based on the NC@AQ cathode shows excellent cycle stability (60.5% capacity retention at 0.2 C after 1000 cycles, 82.8% capacity retention at 0.5 C after 1000 cycles), superior rate capability (152.9 mA h g-1 at 2 C), and outstanding energy efficiency (98% at 0.2 C). Our work offers a new approach to realize the next-generation organic batteries for long life and high rate performance.

Identification of Novel Bioactive Compound Derived from Rheum officinalis against Campylobacter jejuni NCTC11168

Gastric diseases are increasing with the infection of Campylobacter jejuni. Late stages of infection lead to peptic ulcer and gastric carcinoma. C. jejuni infects people within different stages of their life, especially childhood, causing severe diarrhea; it infects around two-thirds of the world population. Due to bacterial resistance against standard antibiotic, a new strategy is needed to impede Campylobacter infections. Plants provide highly varied structures with antimicrobial use which are unlikely to be synthesized in laboratories. A special feature of higher plants is their ability to produce a great number of organic chemicals of high structural diversity, the so-called secondary metabolites. Twenty plants were screened to detect their antibacterial activities. Screening results showed that Rheum officinalis was the most efficient against C. jejuni. Fractionation pattern was obtained by column chromatography, while the purity test was done by thin-layer chromatography (TLC). The chemical composition of bioactive compound was characterized using GC-MS, nuclear magnetic resonance, and infrared analysis. Minimal inhibitory concentration (MIC) of the purified compound was 31.25 µg/ml. Cytotoxicity assay on Vero cells was evaluated to be 497 µg/ml. Furthermore, the purified bioactive compound activated human lymphocytes in vitro. The data presented here show that Rheum officinalis could potentially be used in modern applications aimed at the treatment or prevention of foodborne diseases.

Remarkable Potential of Zerumbone to Generate a Library with Six Natural Product-like Skeletons by Natural Material-Related Diversity-Oriented Synthesis

Diversity-oriented synthesis (DOS) is an effective strategy for the quick creation of diverse and high three-dimensional compounds from simple starting materials. The selection of a starting material is the key to constructing useful, chemically diverse compound libraries for the development of new drugs. Here, we report a novel, general, and facile strategy for the creation of diverse compounds with high structural diversity from readily available natural products, such as zerumbone, as the synthetic starting material. Zerumbone is the major component of the essential oil from wild ginger, Zingiber zerumbet Smith. It is noteworthy that zerumbone has a powerful latent reactivity, partly because of its three double bonds, two conjugated and one isolated, and a double conjugated carbonyl group in an 11-membered ring structure. In fact, zerumbone has been shown to be a successful example of natural material-related DOS (NMRDOS). We will report that zerumbone can be converted in one chemical step from four zerumbone derivatives into rare and markedly different scaffolds by transannulation.

Synthesis of C2 Hybrid Amide‐Based PTC Catalysts and Their Comparison with Saturated Analogues

AbstractWe investigated the synthesis and catalytic efficiency of four new C2 hybrid PTC catalysts and their saturated analogues with reduced double bond. These eight novel hybrid catalysts can be straightforwardly synthesized with good yields and high structural design diversity (with various linkers). The catalytic efficiency of our catalysts was systematically investigated using a glycine imine alkylation reaction, carried out under PTC conditions. It was found that saturated catalysts show both higher reaction yield (up to 98%) and enantioselectivity (up to 94% ee).

Estrutura fitossociológica do manguezal da Lagoa do Roteiro, Alagoas, Nordeste do Brasil

Este estudo teve como objetivo caracterizar a estrutura do manguezal da Lagoa do Roteiro no estado de Alagoas, através de parâmetros fitossociológicos. Para isso, foram traçados seis transectos, cada um dividido em três parcelas de 400 m², distanciadas 10 metros entre si. Para a verificação dos fatores abióticos foram utilizados termômetro (temperatura) e refratômetro (salinidade). Foram coletadas ainda três amostras de sedimento, a uma profundidade de 20 cm, para a análise da granulometria e matéria orgânica. Foram mensuradas 449 árvores, apresentando árvores de Rhizophora mangle, Laguncularia racemosa e Avicennia schaueriana. A densidade média da vegetação arbórea foi de 624 ind.ha-1, sendo a espécie Rhizophora mangle a que apresentou os maiores índices fitossociológicos, com valor de importância de 220,59%. Os valores dos parâmetros fitossociológicos apresentaram grande amplitude nas parcelas analisadas, ocorrendo desde plântulas até árvores adultas. Os valores de temperatura não apresentaram diferenças significativas entre as médias das parcelas franja, intermediária e interior, porém a salinidade se destacou, apresentando um aumento em relação ao interior do bosque. Houve predominância de sedimento areno-lodoso no manguezal estudado. Dessa maneira, a análise fitossociológica revelou elevada diversidade estrutural, em um ambiente onde os fatores abióticos contribuem para o estabelecimento das espécies arbóreas, e uma elevada contribuição da espécie Rhizophora mangle em todos os parâmetros fitossociológicos avaliados no ecossistema.