A Sample-Centric and Knowledge-Driven Computational Framework for Natural Products Drug Discovery.

The ENPKG framework organizes large heterogeneous metabolomics data sets as a knowledge graph, offering exciting opportunities for drug discovery and chemodiversity characterization.

Comparative metabolomic study of fungal foliar endophytes and their long-lived host : a model for exploring the chemodiversity of host-microbe interactions.

Introduction: In contrast to the dynamics observed in plant/pathogen interactions, endophytic fungi have the capacity to establish enduring associations within their hosts, leading to the development of a mutually beneficial relationship that relies on specialized chemical interactions. Research indicates that the presence of endophytic fungi has the ability to significantly modify the chemical makeup of the host organism. Our hypothesis proposes the existence of a reciprocal exchange of chemical signals between plants and fungi, facilitated by specialized chemical processes that could potentially manifest within the tissues of the host.

Metabolomics in Ecology and Bioactive Natural Products Discovery: Challenges and Prospects for a Comprehensive Study of the Specialised Metabolome.

Metabolomics is playing an increasingly prominent role in chemical ecology and in the discovery of bioactive natural products (NPs). The identification of metabolites is a common/central objective in both research fields. NPs have significant biological properties and play roles in multiple chemical-ecological interactions.

A fine-tuned defense at the pea root caps: Involvement of border cells and arabinogalactan proteins against soilborne diseases.

Plants have to cope with a myriad of soilborne pathogens that affect crop production and food security. The complex interactions between the root system and microorganisms are determinant for the whole plant health. However, the knowledge regarding root defense responses is limited as compared to the aerial parts of the plant.

Open and reusable annotated mass spectrometry dataset of a chemodiverse collection of 1,600 plant extracts.

As privileged structures, natural products often display potent biological activities. However, the discovery of novel bioactive scaffolds is often hampered by the chemical complexity of the biological matrices they are found in. Large natural extract collections are thus extremely valuable for their chemical novelty potential but also complicated to exploit in the frame of drug-discovery projects.

: A computational tool to discover structural novelty in natural extracts libraries.

Collections of natural extracts hold potential for the discovery of novel natural products with original modes of action. The prioritization of extracts from collections remains challenging due to the lack of a workflow that combines multiple-source information to facilitate the data interpretation. Results from different analytical techniques and literature reports need to be organized, processed, and interpreted to enable optimal decision-making for extracts prioritization.

MEMO: Mass Spectrometry-Based Sample Vectorization to Explore Chemodiverse Datasets.

In natural products research, chemodiverse extracts coming from multiple organisms are explored for novel bioactive molecules, sometimes over extended periods. Samples are usually analyzed by liquid chromatography coupled with fragmentation mass spectrometry to acquire informative mass spectral ensembles. Such data is then exploited to establish relationships among analytes or samples (e.

The LOTUS initiative for open knowledge management in natural products research.

Contemporary bioinformatic and chemoinformatic capabilities hold promise to reshape knowledge management, analysis and interpretation of data in natural products research. Currently, reliance on a disparate set of non-standardized, insular, and specialized databases presents a series of challenges for data access, both within the discipline and for integration and interoperability between related fields. The fundamental elements of exchange are referenced structure-organism pairs that establish relationships between distinct molecular structures and the living organisms from which they were identified.

Ascorbic acid 2-glucoside: An ascorbic acid pro-drug with longer-term antioxidant efficacy in skin.

Objective: Deleterious effects of pollutants and ultraviolet radiation on the skin can be attenuated using formulations containing antioxidants. However, these have disadvantages, including chemical instability, photodegradation, poor bioavailability or biological activity. Here, two commercial formulations were evaluated: one optimized to stabilize and deliver ascorbic acid (AA) at 15% and the other containing a glucoside form of AA, namely ascorbic acid 2-glucoside (AA2G), at 1.

Root cap-derived cells and mucilage: a protective network at the root tip.

Root cap-derived cells and mucilage provide the first line of defense of the plant against soil microbial pathogens. These cells form a mucilaginous root extracellular trap (RET), which also harbors a range of molecules including exDNA and defensive peptides and proteins much like the neutrophil extracellular trap (NET) of mammalians. Plant RETs resemble mucus structures found in mammalian systems and are rich in arabinogalactan proteins that have similarities to highly glycosylated human mucins.

A Mass Spectrometry Based Metabolite Profiling Workflow for Selecting Abundant Specific Markers and Their Structurally Related Multi-Component Signatures in Traditional Chinese Medicine Multi-Herb Formulae.

In Traditional Chinese Medicine (TCM), herbal preparations often consist of a mixture of herbs. Their quality control is challenging because every single herb contains hundreds of components (secondary metabolites). A typical 10 herb TCM formula was selected to develop an innovative strategy for its comprehensive chemical characterization and to study the specific contribution of each herb to the formula in an exploratory manner.

Correction: Haddad, J.G., et al. , an Indigenous Medicinal Plant from Mascarene Islands, Is a Potent Inhibitor of Zika and Dengue Virus Infection in Human Cells 2019, , 2382.

The author wishes to make the following correction to this paper [...

an Indigenous Medicinal Plant from Mascarene Islands, Is a Potent Inhibitor of Zika and Dengue Virus Infection in Human Cells.

Zika virus (ZIKV) and Dengue virus (DENV) are mosquito-borne viruses of the genus that could cause congenital microcephaly and hemorrhage, respectively, in humans, and thus present a risk to global public health. A preventive vaccine against ZIKV remains unavailable, and no specific antiviral drugs against ZIKV and DENV are licensed. Medicinal plants may be a source of natural antiviral drugs which mostly target viral entry.

The Flavonoid Isoquercitrin Precludes Initiation of Zika Virus Infection in Human Cells.

The medical importance of Zika virus (ZIKV) was fully highlighted during the recent epidemics in South Pacific islands and Americas due to ZIKV association with severe damage to fetal brain development and neurological complications in adult patients. A worldwide research effort has been undertaken to identify effective compounds to prevent or treat ZIKV infection. Fruits and vegetables may be sources of compounds with medicinal properties.

Neurodegenerative disease-associated mutants of a human mitochondrial aminoacyl-tRNA synthetase present individual molecular signatures.

Mutations in human mitochondrial aminoacyl-tRNA synthetases are associated with a variety of neurodegenerative disorders. The effects of these mutations on the structure and function of the enzymes remain to be established. Here, we investigate six mutants of the aspartyl-tRNA synthetase correlated with leukoencephalopathies.

Online comprehensive two-dimensional ion chromatography × capillary electrophoresis.

A comprehensively coupled online two-dimensional ion chromatography-capillary electrophoresis (IC × CE) system for quantitative analysis of inorganic anions and organic acids in water is introduced. The system employs an in-house built sequential injection-capillary electrophoresis instrument and a nonfocusing modulation interface comprising a tee-piece and a six-port two-position injection valve that allows comprehensive sampling of the IC effluent. High field strength (+2 kV/cm) enables rapid second-dimension separations in which each peak eluted from the first-dimension separation column is analyzed at least three times in the second dimension.

Micellar electrokinetic chromatography of organic and peroxide-based explosives.

CE methods have been developed for the analysis of organic and peroxide-based explosives. These methods have been developed for deployment on portable, in-field instrumentation for rapid screening. Both classes of compounds are neutral and were separated using micellar electrokinetic chromatography (MEKC).

Polymeric microchip for the simultaneous determination of anions and cations by hydrodynamic injection using a dual-channel sequential injection microchip electrophoresis system.

A dual-channel sequential injection microchip capillary electrophoresis system with pressure-driven injection is demonstrated for simultaneous separations of anions and cations from a single sample. The poly(methyl methacrylate) (PMMA) microchips feature integral in-plane contactless conductivity detection electrodes. A novel, hydrodynamic "split-injection" method utilizes background electrolyte (BGE) sheathing to gate the sample flows, while control over the injection volume is achieved by balancing hydrodynamic resistances using external hydrodynamic resistors.

Released selective pressure on a structural domain gives new insights on the functional relaxation of mitochondrial aspartyl-tRNA synthetase.

Mammalian mitochondrial aminoacyl-tRNA synthetases are nuclear-encoded enzymes that are essential for mitochondrial protein synthesis. Due to an endosymbiotic origin of the mitochondria, many of them share structural domains with homologous bacterial enzymes of same specificity. This is also the case for human mitochondrial aspartyl-tRNA synthetase (AspRS) that shares the so-called bacterial insertion domain with bacterial homologs.

In-plane alloy electrodes for capacitively coupled contactless conductivity detection in poly(methylmethacrylate) electrophoretic chips.

A simple method for producing PMMA electrophoresis microchips with in-plane electrodes for capacitively coupled contactless conductivity detection is presented. One PMMA plate (channel plate) is embossed with the microfluidic and electrode channels and lamination bonded to a blank PMMA cover plate of equal dimensions. To incorporate the electrodes, the bonded chip is heated to 80 °C, above the melting point of the alloy (≈ 70 °C) and below the glass transition temperature of the PMMA (≈ 105 °C), and the molten alloy drawn into the electrode channels with a syringe before being allowed to cool and harden.

On-line simultaneous and rapid separation of anions and cations from a single sample using dual-capillary sequential injection-capillary electrophoresis.

A novel capillary electrophoresis (CE) approach has been developed for the simultaneous rapid separation and identification of common environmental inorganic anions and cations from a single sample injection. The method utilised a sequential injection-capillary electrophoresis instrument (SI-CE) with capacitively-coupled contactless conductivity detection (C(4)D) constructed in-house from commercial-off-the-shelf components. Oppositely charged analytes from a single sample plug were simultaneously injected electrokinetically onto two separate capillaries for independent separation and detection.

Tuneable nanochannel formation for sample-in/answer-out devices.

Control of the dielectric breakdown of PDMS was achieved by limiting the current during the breakdown process. This enabled tuning of the nanochannel pore size and hence their permeability for molecules of different molecular weights. This method enabled the analysis of the drug quinine from whole blood in 3 min using a simple, disposable microfluidic device.

Thermodynamic properties distinguish human mitochondrial aspartyl-tRNA synthetase from bacterial homolog with same 3D architecture.

In the mammalian mitochondrial translation apparatus, the proteins and their partner RNAs are coded by two genomes. The proteins are nuclear-encoded and resemble their homologs, whereas the RNAs coming from the rapidly evolving mitochondrial genome have lost critical structural information. This raises the question of molecular adaptation of these proteins to their peculiar partner RNAs.