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Abstract from conference

NAPRALERT is a database on natural products, including data on ethnobotany, chemistry, pharmacology, toxicology, and clinical trials from literature dating back to the 19th century. Established in 1975 by Norman R. Farnsworth, it became a web accessible resource in 2005 but soon became stagnant while literature grew exponentially. After a complete rewrite of the platform, the focus is now on connecting this resource to the rest of the existing databases and expanding its usability. The creation of a Pharmacognosy/Natural Product ontology will foster better understanding of this domain, its linking potential with other resources and the ability to automatize literature annotation and entry efficiently.

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.

Composite-based, tooth colored dental restorations, in spite of their aesthetic appeal, are limited by a short life span. Every subsequent restoration results in the loss of healthy dental tissue. Thus, a bio-mimetic approach has been developed to enhance the mechanical strength of dentin using plant-derived proanthocyanidins (PACs). From a panel of eight active plants, grape seed extract showed the highest dentin biomodification potential, a 15-fold enhancement of dentin stiffness measured in MPa. Fractions with varying degrees of polymerization (DP) were obtained using solvent partitioning and centrifugal partition chromatography (CPC). Oligomeric PACs (OPACs, DP 2 – 7) surfaced as the most promising dentin biomodifiers compared to the constituent monomers and polymers (Dp ≥8). OPACs with DP 3 to 4 showed the most efficacious dentin-PAC interaction as evaluated by bio-mechanical tests. While one arm of the separation focused on the development of a highly active custom-made tri- and tetra-meric OPAC enriched mixture (GSE3+4), OPACs were also purified as single chemical entities. OPACs with predominantly 4β→8/6 B-type interflavan linkages (IFLs) along with one having a unique 2→8 IFL were isolated. Structural characterization employed 1D and 2D NMR at low temperature (255K) to overcome line-broadening due to atropisomerism. The presence of gallate ester moieties is a characteristic feature of grape seed PACs and the biological evaluation also highlighted the enhanced effect of galloylated OPACs on dentin biomodification. Grape seeds are thus, a viable source of novel restorative dental biomaterials and highlight a novel application of plant-based natural products in the biomedical field.

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 1H 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 1H spectra encode a wealth of information about bonds and molecular geometry that may be fully mined by 1H iterative full spin analysis (HiFSA). Fully characterized 1D 1H 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.

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.

The ability of certain oligomeric proanthocyanidins (OPACs) to enhance the biomechanical properties of dentin involves collagen cross-linking of the 1.3–4.5 nm wide space via protein–polyphenol interactions. A systematic interdisciplinary search for the bioactive principles of pine bark has yielded the trimeric PAC, ent-epicatechin-(4β→8)-epicatechin-(2β→O→7,4β→8)-catechin (3), representing the hitherto most potent single chemical entity capable of enhancing dentin stiffness. Building the case from two congeneric PAC dimers, a detailed structural analysis decoded the stereochemistry, spatial arrangement, and chemical properties of three dentin biomodifiers. Quantum-mechanics-driven 1H iterative full spin analysis (QM-HiFSA) of NMR spectra distinguished previously unrecognized details such as higher order J coupling and provided valuable information about 3D structure. Detection and quantification of H/D-exchange effects by QM-HiFSA identified C-8 and C-6 as (re)active sites, explain preferences in biosynthetic linkage, and suggest their involvement in dentin cross-linking activity. Mapping of these molecular properties underscored the significance of high δ precision in both 1H and 13C NMR spectroscopy. Occurring at low- to subppb levels, these newly characterized chemical shift differences in ppb are small but diagnostic measures of dynamic processes inherent to the OPAC pharmacophores and can help augment our understanding of nanometer-scale intermolecular interactions in biomodified dentin macromolecules.

1D NMR spectra contain a wealth of vital structural information that can enhance the description of bioactive molecules. The present study demonstrates how quantum-mechanics driven 1H iterative Full Spin Analysis (QM-HiFSA) is capable of distinguishing spectral detail that cannot be interpreted manually or visually, but provides important information of the 3D structure and bonding (re-)activity of the molecules. This approach is established by analyzing 1D NMR spectra of oligomeric proanthocyanidins (OPACs), which exhibit high dentin bioactivity, and were isolated from the inner bark of pine. The higher order coupling and proton-deuterium exchange effects observed in these complex molecules were fully explained and quantified by QM-HiFSA. Dimeric and trimer OPACs provide evidence that high δ precision is applicable to 13C, in addition to 1H 1D NMR spectra, requiring reporting to the ppb level and below. Both the nano chemical shifts (ppb) and the associated nano substituent chemical shifts (s.c.s.) are significant properties of the 1H and 13C NMR spectra and enable recognition of structural properties that are relevant to better understanding of the intermolecular interactions between the OPAC pharmacophores and dentin micromolecules triggering enhanced tissue mechanics.

A recent article by Baell(1) on the problems experienced by medicinal chemists with pan-assay interference compounds (PAINS) and Shoichet’s work(2) on the impact of aggregation occurring in high throughput screening libraries, prompts a consideration of how these and other similar problems are experienced by pharmacognosists with promiscuous invalid metabolites as panaceas (PIMPs). Contrary to the classical definition of secondary metabolites as being species specific (or near specific), several natural products, particularly in the more extensively investigated plant kingdom, are common across species, genera, and even families (e.g. β-sitosterol). In the course of bioactivity-guided fractionation, PIMPs have shown up as major components in active fractions of a wide variety of pharmacological assays, i.e., they have been designated as panaceas. As in the case of PAINS, these assay results are almost invariably invalid and lead enthusiastic young scientists down a garden path. Why does this happen and how can it be avoided? Interestingly, the advances in modern methods of structure determination have exacerbated this problem, because it is possible to determine the structure of a compound when it is quite impure, and residual complexity is characteristic of chromatographic fractionation. That these residuals are often the source of the bioactivity is also frequently overlooked. Classic examples where this has occurred and ways to avoid it will be outlined.

Proanthocyanidins (PACs) are secondary plant metabolites that mediate nonenzymatic collagen cross-linking and enhance the properties of collagen based tissue, such as dentin. The extent and nature of cross-linking is influenced by the composition and specific chemical structure of the bioactive compounds present in certain PAC-rich extracts. This study investigated the effect of the molecular weight and stereochemistry of polyphenol compounds on two important properties of dentin, biomechanics, and biostability. For that, purified phenols, a phenolic acid, and some of its derivatives were selected: PAC dimers (A1, A2, B1, and B2) and a trimer (C1), gallic acid (Ga), its esters methyl-gallate (MGa) and propyl-gallate (PGa), and a pentagalloyl ester of glucose (PGG). Synergism was assessed by combining the most active PAC and gallic acid derivative. Mechanical properties of dentin organic matrix were determined by the modulus of elasticity obtained in a flexural test. Biostability was evaluated by the resistance to collagenase degradation. PACs significantly enhanced dentin mechanical properties and decreased collagen digestion. Among the gallic acid derivatives, only PGG had a significant enhancing effect. The lack of observed C1:PGG synergy indicates that both compounds have similar mechanisms of interaction with the dentin matrix. These findings reveal that the molecular weight of polyphenols have a determinant effect on their interaction with type I collagen and modulates the mechanism of cross-linking at the molecular, intermolecular, and inter-microfibrillar levels.