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Covering: up to 2018With contributions from the global natural product (NP) research community, and continuing the Raw Data Initiative, this review collects a comprehensive demonstration of the immense scientific value of disseminating raw nuclear magnetic resonance (NMR) data, independently of, and in parallel with, classical publishing outlets. A comprehensive compilation of historic to present-day cases as well as contemporary and future applications show that addressing the urgent need for a repository of publicly accessible raw NMR data has the potential to transform natural products (NPs) and associated fields of chemical and biomedical research. The call for advancing open sharing mechanisms for raw data is intended to enhance the transparency of experimental protocols, augment the reproducibility of reported outcomes, including biological studies, become a regular component of responsible research, and thereby enrich the integrity of NP research and related fields.

Correction for 'The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research' by James B. McAlpine et al., Nat. Prod. Rep., 2018, DOI: .

The revision of the structure of the sesquiterpene aquatolide from a bicyclo[2.2.0]hexane to a bicyclo[2.1.1]hexane structure using compelling NMR data, X-ray crystallography, and the recent confirmation via full synthesis exemplify that the achievement of "structural correctness" depends on the completeness of the experimental evidence. Archived FIDs and newly acquired aquatolide spectra demonstrate that archiving and rigorous interpretation of 1D (1)H NMR data may enhance the reproducibility of (bio)chemical research and curb the growing trend of structural misassignments. Despite being the most accessible NMR experiment, 1D (1)H spectra encode a wealth of information about bonds and molecular geometry that may be fully mined by (1)H iterative full spin analysis (HiFSA). Fully characterized 1D (1)H spectra are unideterminant for a given structure. The corresponding FIDs may be readily submitted with publications and collected in databases. Proton NMR spectra are indispensable for structural characterization even in conjunction with 2D data. Quantum interaction and linkage tables (QuILTs) are introduced for a more intuitive visualization of 1D J-coupling relationships, NOESY correlations, and heteronuclear experiments. Overall, this study represents a significant contribution to best practices in NMR-based structural analysis and dereplication.

Flavan‐3‐ol monomers are the building blocks of proanthocyanidins (PACs), natural compounds from plants shown to mediate specific biologic activities on dentin. While the stereochemistry of the terminal flavan‐3‐ols, catechin (C) versus epicatechin (EC), impacts the biomechanical properties of the dentin matrix treated with oligomeric PACs, structure–activity relationships driving this bioactivity remain elusive. To gain insights into the modulatory role of the terminal monomers, two highly congruent trimeric PACs from Pinus massoniana only differing in the stereochemistry of the terminal unit (Trimer‐C vs. Trimer‐EC) were prepared to evaluate their chemical characteristics as well as their effects on the viscoelasticity and biostability of biomodified dentin matrices via infrared spectroscopy and multi‐scale dynamic mechanical analyses. The subtle alteration of C versus EC as terminal monomers lead to distinct immediate PAC‐trimer biomodulation of the dentin matrix. Nano‐ and micro‐dynamic mechanical analyses revealed that Trimer‐EC increased the complex moduli (0.51 GPa) of dentin matrix more strongly than Trimer‐C (0.26 GPa) at the nanoscale length (p < 0.001), whereas the reverse was found at the microscale length (p <.001). The damping capacity (tan δ) of dentin matrix decreased by 70% after PAC treatment at the nano‐length scale, while increased values were found at the micro‐length scale (~0.24) compared to the control (0.18 ; p <.001). An increase in amide band intensities and a decrease of complex moduli was observed after storage in simulated body fluid for both Trimer‐C and Trimer‐EC modified dentin. The stereochemical configuration of the terminal monomeric units, C and EC, did not impact the chemo‐mechanical stability of dentin matrix. [ABSTRACT FROM AUTHOR]

Grape seed extract contains a complex mixture of proanthocyanidins (PACs), a class of plant biopolymers that can be used as a biomaterial to improve reparative and preventive dental therapies. Co-polymerization of PACs with type I collagen mechanically reinforces the dentin extracellular matrix. This study assessed the biocompatibility of PACs from grape seed extract on dental pulp stem cells (DPSCs) in a model simulating leaching through dentin to the pulp cavity. The aim was to determine the type of PACs (galloylated vs. non-galloylated) within grape seed extract that are most compatible with dental pulp tissue. Human demineralized dentin was treated with selectively-enriched dimeric PACs prepared from grape seed extract using liquid-liquid chromatography. DPSCs were cultured within a 2D matrix and exposed to PAC-treated dentin extracellular matrix. Cell proliferation was measured using the MTS assay and expression of odontoblastic genes was analyzed by qRT-PCR. Categorization of PACs leaching from dentin was performed using HPLC-MS. Enriched dimeric fractions containing galloylated PACs increased the expression of certain odontoblastic genes in DPSCs, including Runt-related transcription factor 2 (RUNX2), vascular endothelial growth factor (VEGF), bone morphogenetic protein 2 (BMP2), basic fibroblast growth factor (FGF2), dentin sialophosphoprotein (DSPP) and collagen, type I, alpha 1 (COLI). Galloylated dimeric PACs also exhibited minor effects on DPSC proliferation, resulting in a decrease compared to control after 5 days of treatment. The non-galloylated dimer fraction had no effect on these genes or on DPSC proliferation. Galloylated PACs are biocompatible with DPSCs and may even exert a beneficial effect on cells within dental pulp tissue. The observed increase in odontoblastic genes induced by galloylated PACs together with a decrease in DPSC proliferation is suggestive of a shift toward cell differentiation. This data supports the use of dimeric PACs as a safe biomaterial, with galloylated dimeric PACs exhibiting potential benefits to odontoblasts supporting dentin regeneration. [ABSTRACT FROM AUTHOR]

Plant‐derived proanthocyanidins (PACs) mediate physicochemical modifications to the dentin extracellular matrix (ECM). The structure–activity relationships of PACs remain largely unknown, mostly due to the varied complex composition of crude extracts, as well as the challenges of purification and mechanistic assessment. To assess the role of galloylated PACs as significant contributors to high yet unstable biomodification activity to the dentin ECM, we removed the galloyl moieties (de‐galloylation) via enzymatic hydrolysis from three galloyl‐rich PAC‐containing extracts (Camellia sinensis, Vitis vinifera, and Hamamelis virginiana). The biomechanical and biological properties of dentin were assessed upon treatment with these extracts vs. their de‐galloylated counterparts. An increase in the complex modulus of the dentin matrix was found with all extracts, however, the crude extract was significantly higher when compared to the de‐galloylated version. Exhibiting the highest content of galloylated PACs among the investigated plants, Camellia sinensis crude extract also exhibited the biggest relapse in mechanical properties after one‐month incubation. De‐galloylation did not modify the damping capacity of dentin ECM. Moreover, PAC‐mediated protection against proteolytic degradation was unaffected by de‐galloylation. The de‐galloylation experiments confirmed that gallic acid in galloylated rich‐PAC extracts drive stronger yet significantly less sustained mechanical effects in dentin ECM. [ABSTRACT FROM AUTHOR]

Quantitative correlations between the contents of the flavonolignans silychristin A and silybins A/B provide biosynthetic clues that support a pathway in which one mesomeric form of a taxifolin radical is undergoing an oxidative coupling with a coniferyl alcohol radical. The flavonolignan content and patterns reported in the literature for 53 samples, representing populations of the Silybum marianum plant growing in different parts of the world, were subject to a meta-analysis. Linear regression analyses were carried out on these data sets, and a mathematical model was derived that predicts the content of silychristin A relative to the metabolomic pattern of its congeners. The validity of the model was verified by applying it to test samples. This approach could potentially become a tool to enhance the understanding of both the relative composition of the silymarin complex and the biosynthetic pathways that underlie its formation. [ABSTRACT FROM AUTHOR]

The notion of data transparency is gaining a strong awareness among the scientific community. The availability of raw data is actually regarded as a fundamental way to advance science by promoting both integrity and reproducibility of research outcomes. Particularly, in the field of natural product and chemical research, NMR spectroscopy is a fundamental tool for structural elucidation and quantification (qNMR). As such, the accessibility of original NMR data, i.e., Free Induction Decays (FIDs), fosters transparency in chemical research and optimizes both peer review and reproducibility of reports by offering the fundamental tools to perform efficient structural verification. Although original NMR data are known to contain a wealth of information, they are rarely accessible along with published data. This viewpoint discusses the relevance of the availability of original NMR data as part of good research practices not only to promote structural correctness, but also to enhance traceability and reproducibility of both chemical and biological results. [ABSTRACT FROM AUTHOR]

High-throughput biology has contributed a wealth of data on chemicals, including natural products (NPs). Recently, attention was drawn to certain, predominantly synthetic, compounds that are responsible for disproportionate percentages of hits but are false actives. Spurious bioassay interference led to their designation as pan-assay interference compounds (PAINS). NPs lack comparable scrutiny, which this study aims to rectify. Systematic mining of 80+ years of the phytochemistry and biology literature, using the NAPRALERT database, revealed that only 39 compounds represent the NPs most reported by occurrence, activity, and distinct activity. Over 50% are not explained by phenomena known for synthetic libraries, and all had manifold ascribed bioactivities, designating them as invalid metabolic panaceas (IMPs). Cumulative distributions of -200,000 NPs uncovered that NP research follows power-law characteristics typical for behavioral phenomena. Projection into occurrence-bioactivity-effort space produces the hyperbolic black hole of NPs, where IMPs populate the high-effort base. [ABSTRACT FROM AUTHOR]