PubChem in 2021: new data content and improved web interfaces

Kim, Sunghwan; Chen, Jie; Cheng, Tiejun; Gindulytė, Asta; He, Jia; He, Siqian; Li, Qingliang; Shoemaker, Benjamin A.; Thiessen, Paul A.; Yu, Bo; Zaslavsky, Leonid; Zhang, Jian; Bolton, Evan

doi:10.1093/nar/gkaa971

Cited by 2,678 publications

(2,080 citation statements)

References 57 publications

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“…S1). Isoprene and other common isoprenoids emitted by plants such as alpha-pinene (a monoterpene) have minimal water-solubility (Kim et al, 2020;Martins et al, 2017), so interference by liquid water is negligible. While some PIDs offer an optional on-board correction for humidity and temperature (toggle in the software; RAE Systems Inc., 2013a), this should be disabled as the correction is small relative to the magnitude of sensitivities, and introduces unaccountable noise into the pseudo-raw data.…”

Section: Methods 2 Detecting Leaf Volatiles By Photoionizationmentioning

confidence: 99%

A new field instrument for leaf volatiles reveals an unexpected vertical profile of isoprenoid emission capacities in a tropical forest

Taylor

Wisniewski

Alves

et al. 2021

Preprint

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Both plant physiology and atmospheric chemistry are substantially altered by the emission of volatile isoprenoids (VI), such as isoprene and monoterpenes, from plant leaves. Yet, since gaining scientific attention in the 1950's, empirical research on leaf VI has been largely confined to laboratory experiments and atmospheric observations. Here, we introduce a new field instrument designed to bridge the scales from leaf to atmosphere, by enabling precision VI detection in real time from plants in their natural ecological setting. With a field campaign in the Brazilian Amazon, we reveal an unexpected distribution of leaf emission capacities (EC) across the vertical axis of the forest canopy, with EC peaking in the mid-canopy instead of the sun-exposed canopy surface, and high emissions occurring in understory specialist species. Compared to the simple interpretation that VI protect leaves from heat stress at the hot canopy surface, our results encourage a more nuanced view of the adaptive role of VI in plants. We infer that forest emissions to the atmosphere depend on the dynamic microenvironments imposed by canopy structure, and not simply on canopy surface conditions. We provide a new emissions inventory from 51 tropical tree species, revealing moderate consistency in EC within taxonomic groups. Our self-contained, portable instrument provides real-time detection and live measurement feedback with precision and detection limits better than 0.5 nmol m-2leaf s-1. We call the instrument 'PORCO' based on the gas detection method: photoionization of organic compounds. We provide a thorough validation of PORCO and demonstrate its capacity to detect ecologically driven variation in leaf emission rates and thus accelerate a nascent field of science: the ecology and ecophysiology of plant volatiles.

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Section: Methods 2 Detecting Leaf Volatiles By Photoionizationmentioning

confidence: 99%

A new field instrument for leaf volatiles reveals an unexpected vertical profile of isoprenoid emission capacities in a tropical forest

Taylor

Wisniewski

Alves

et al. 2021

Preprint

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“…Three-dimensional structures of the allergen fragrance molecules in .sdf format were obtained from the PubChem database, which includes three databases; substance, compound, and bioassay databases [33,34]. The corresponding CAS numbers for the compounds used in this study were presented in Table 1.…”

Section: Methodsmentioning

confidence: 99%

Allergen fragrance molecules: a potential relief for COVID-19

Aydın¹,

Altınel

Erdoğmuş³

et al. 2021

BMC Complement Med Ther

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Background The latest coronavirus SARS-CoV-2, discovered in China and rapidly spread Worldwide. COVID-19 affected millions of people and killed hundreds of thousands worldwide. There are many ongoing studies investigating drug(s) suitable for preventing and/or treating this pandemic; however, there are no specific drugs or vaccines available to treat or prevent SARS-CoV-2 as of today. Methods Fifty-eight fragrance materials, which are classified as allergen fragrance molecules, were selected and used in this study. Docking simulations were carried out using four functional proteins; the Covid19 Main Protase (MPro), Receptor binding domain (RBD) of spike protein, Nucleocapsid, and host Bromodomain protein (BRD2), as target macromolecules. Three different software, AutoDock, AutoDock Vina (Vina), and Molegro Virtual Docker (MVD), running a total of four different docking protocol with optimized energy functions were used. Results were compared with the five molecules reported in the literature as potential drugs against COVID-19. Virtual screening was carried out using Vina, molecules satisfying our cut-off (− 6.5 kcal/mol) binding affinity was confirmed by MVD. Selected molecules were analyzed using the flexible docking protocol of Vina and AutoDock default settings. Results Ten out of 58 allergen fragrance molecules were selected for further docking studies. MPro and BRD2 are potential targets for the tested allergen fragrance molecules, while RBD and Nucleocapsid showed weak binding energies. According to AutoDock results, three molecules, Benzyl Cinnamate, Dihydroambrettolide, and Galaxolide, had good binding affinities to BRD2. While Dihydroambrettolide and Galaxolide showed the potential to bind to MPro, Sclareol and Vertofix had the best calculated binding affinities to this target. When the flexible docking results analyzed, all the molecules tested had better calculated binding affinities as expected. Benzyl Benzoate and Benzyl Salicylate showed good binding affinities to BRD2. In the case of MPro, Sclareol had the lowest binding affinity among all the tested allergen fragrance molecules. Conclusion Allergen fragrance molecules are readily available, cost-efficient, and shown to be safe for human use. Results showed that several of these molecules had comparable binding affinities as the potential drug molecules reported in the literature to target proteins. Thus, these allergen molecules at correct doses could have significant health benefits.

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“…Docking simulations were performed using the docking module of MOE. The structures of chemical compounds were downloaded from the PubChem database [45] and were rigidly docked after minimization. Each complex was further minimized and evaluated for the resulting ligand interactions, and their energetic components were calculated.…”

Section: Pharmacophore Elucidationmentioning

confidence: 99%

A Holistic Evolutionary and 3D Pharmacophore Modelling Study Provides Insights into the Metabolism, Function, and Substrate Selectivity of the Human Monocarboxylate Transporter 4 (hMCT4)

Papakonstantinou

Vlachakis

Thireou

et al. 2021

IJMS

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Monocarboxylate transporters (MCTs) are of great research interest for their role in cancer cell metabolism and their potential ability to transport pharmacologically relevant compounds across the membrane. Each member of the MCT family could potentially provide novel therapeutic approaches to various diseases. The major differences among MCTs are related to each of their specific metabolic roles, their relative substrate and inhibitor affinities, the regulation of their expression, their intracellular localization, and their tissue distribution. MCT4 is the main mediator for the efflux of L-lactate produced in the cell. Thus, MCT4 maintains the glycolytic phenotype of the cancer cell by supplying the molecular resources for tumor cell proliferation and promotes the acidification of the extracellular microenvironment from the co-transport of protons. A promising therapeutic strategy in anti-cancer drug design is the selective inhibition of MCT4 for the glycolytic suppression of solid tumors. A small number of studies indicate molecules for dual inhibition of MCT1 and MCT4; however, no selective inhibitor with high-affinity for MCT4 has been identified. In this study, we attempt to approach the structural characteristics of MCT4 through an in silico pipeline for molecular modelling and pharmacophore elucidation towards the identification of specific inhibitors as a novel anti-cancer strategy.

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PubChem in 2021: new data content and improved web interfaces

Cited by 2,678 publications

References 57 publications

A new field instrument for leaf volatiles reveals an unexpected vertical profile of isoprenoid emission capacities in a tropical forest

A new field instrument for leaf volatiles reveals an unexpected vertical profile of isoprenoid emission capacities in a tropical forest

Allergen fragrance molecules: a potential relief for COVID-19

A Holistic Evolutionary and 3D Pharmacophore Modelling Study Provides Insights into the Metabolism, Function, and Substrate Selectivity of the Human Monocarboxylate Transporter 4 (hMCT4)

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