VCD to determine absolute configuration of natural product molecules: secolignans from Peperomia blanda

VCD Analysis of Axial Chirality in Synthetic Stereoisomeric Biaryl-Type bis-Isochroman Heterodimers with Isolated Blocks of Central and Axial Chirality

Optically active heterodimeric 5,5'-linked bis-isochromans, containing a stereogenic ortho-trisubstituted biaryl axis and up to four chirality centers, were synthesized stereoselectively by using a Suzuki-Miyaura biaryl coupling reaction of optically active isochroman and 1-arylpropan-2-ol derivatives, providing the first access to synthetic biaryl-type isochroman dimers. Enantiomeric pairs and stereoisomers up to seven derivatives were prepared with four different substitution patterns, which enabled us to test how OR, ECD, and VCD measurements and DFT calculations can be used to determine parallel central and axial chirality elements in three isolated blocks of chirality. In contrast to natural penicisteckins A-D and related biaryls, the ECD spectra and OR data of (aS) and (aR) atropodiastereomers did not reflect the opposite axial chirality, but they were characteristic of the central chirality. The atropodiastereomers showed consistently near-mirror-image VCD curves, allowing the determination of axial chirality with the aid of DFT calculation or by comparison of characteristic VCD transitions.

Acyclic Triterpenoids from Alpinia katsumadai Seeds with Proprotein Convertase Subtilisin/Kexin Type 9 Expression and Secretion Inhibitory Activity

Cholesterol is one of the primary causes of cardiovascular disease. Investigating and developing potential drugs to effectively treat hypercholesterolemia are therefore of critical importance. Proprotein convertase subtilisin/kexin type 9 (PCSK9) inhibitors have been developed to lower the levels of low-density lipoprotein cholesterol in patients with hypercholesterolemia. In this study, we aimed to identify compounds that inhibit the PCSK9 mRNA expression and secretion. The bioassay-guided investigation of Alpinia katsumadai seeds utilizing a PCSK9 mRNA expression monitoring assay yielded the isolation and identification of seven new compounds. Among these were three acyclic triterpenoids (1-3), an acyclic sesquiterpenoid (5), one arylpentanoid (6), and two diarylheptanoids (7 and 8), alongside 10 known compounds. The structures of these compounds were determined using nuclear magnetic resonance (NMR) spectroscopy, vibrational circular dichroism (VCD), and electronic circular dichroism (ECD). The absolute configurations of compounds 1 and 2 were identified by comparing the calculated and experimental VCD data as the ECD method was unable to distinguish the diastereomers. All the isolated compounds were evaluated for their regulatory effects on the low-density lipoprotein receptor (LDLR) and PCSK9 mRNA expression, as well as PCSK9 secretion. Of the tested compounds, two of the acyclic triterpenoids (1 and 2) demonstrated potent effects in downregulating PCSK9 at both the mRNA and protein levels, compared with the positive control (berberine chloride). Additionally, compound 1 inhibited PCSK9 secretion to a level comparable to that of berberine chloride. This study identifies compounds that inhibit PCSK9 mRNA expression and secretion, offering significant contributions to the development of novel drugs for the effective treatment of hypercholesterolemia..

Fatty Acids Reverse the Supramolecular Chirality of Insulin Fibrils

Long-chain unsaturated and polyunsaturated fatty acids (LCUFAs and LCPUFAs, respectively) are the essential components of phospholipids and sphingolipids, major building blocks of plasma and organelle membranes. These molecules are also involved in cell signaling and energy metabolism. Hence, both LCUFAs and LCPUFAs are broadly used as food supplements. However, the role of these fatty acids (FAs) in the self-assembly of misfolded proteins remains unclear. In this study, we investigated the effect of LCUFAs and LCPUFAs, as well as their saturated analogue, on insulin aggregation. Using vibrational circular dichroism, we found that all analyzed FAs reversed the supramolecular chirality of insulin fibrils. Molecular dynamics simulations showed that strong hydrophobic interactions were formed between the long aliphatic tails of FAs and hydrophobic amino acid residues of insulin. We infer that such insulin:FA complexes had different self-assembly mechanisms compared to that of insulin alone, which resulted in the observed reversal of the supramolecular chirality of the amyloid fibrils.

Approaches to Configuration Determinations of Flexible Marine Natural Products: Advances and Prospects

Flexible marine natural products (MNPs), such as eribulin and bryostatin, play an important role in the development of modern marine drugs. However, due to the multiple chiral centers and geometrical uncertainty of flexible systems, configuration determinations of flexible MNPs face great challenges, which, in turn, have led to obstacles in druggability research. To resolve this issue, the comprehensive use of multiple methods is necessary. Additionally, configuration assignment methods, such as X-ray single-crystal diffraction (crystalline derivatives, crystallization chaperones, and crystalline sponges), NMR-based methods (JBCA and Mosher's method), circular dichroism-based methods (ECCD and ICD), quantum computational chemistry-based methods (NMR calculations, ECD calculations, and VCD calculations), and chemical transformation-based methods should be summarized. This paper reviews the basic principles, characteristics, and applicability of the methods mentioned above as well as application examples to broaden the research and applications of these methods and to provide a reference for the configuration determinations of flexible MNPs.

Deuterium labelling to extract local stereochemical information by VCD spectroscopy in the C-D stretching region: a case study of sugars

Stereochemical elucidation of molecules with multiple chiral centers is difficult. Even with VCD spectroscopy, excluding all but one diastereomeric structural candidate is challenging because the stereochemical inversion of one chiral center among many centers does not always result in noticeable differences in their VCD spectra. This work demonstrates that the introduction of a suitable VCD chromophore with absorption in the 2300-1900 cm^-1 region can be used for extracting local stereochemical information and for the stereochemical assignment of the C-1 position of various sugars as a case study. Through studies on a series of epimeric pairs of monosaccharides and their derivatives, we found that the introduction of one -OCD₃ group to each C-1 position produced almost mirror-image VCD patterns in the 2300-1900 cm^-1 region depending on the C-1 stereochemistry irrespective of the other molecular moieties. This work also shows that comparison of the observed VCD signals and the calculated ones enables the stereochemical assignment of a chiral center in the vicinity of the chromophore. This study provides a proof of concept that the use of a VCD chromophore in the 2300-1900 cm^-1 region enables the analysis of selected stereochemistry of suitable molecular systems. Further studies on this concept should lead to the development of a method useful for the structural elucidation of other types of complex molecules.

Direct deposition GC/IR techniques in natural product identification

Covering: up to the end of 2019 The application of coupled gas chromatography/direct deposition Fourier transform infrared (GC/DD-FTIR) spectroscopy in the field of volatile natural product identification yields orthogonal information to GC/MS analysis about functional groups and C-C double bonds. This underused method facilitates structure elucidation of trace compounds and can be combined with modern DFT-calculation to further improve the usefulness of the obtained results.

Structural Characterization of a Cyclodextrin/l-menthol Inclusion Complex in the Solid-state by Solid-state NMR and Vibrational Circular Dichroism

Hydrophobic and volatile flavor molecules can be encapsulated inside cyclodextrins (CyDs). Inclusion complexes are frequently used in solid or dispersed states in preserved food and cosmetics. In this study, the solid-state structures of spray-dried inclusion complexes of l-menthol in α-CyD and β-CyD were analyzed using ¹³C solid-state NMR and vibrational circular dichroism (VCD). The NMR signals of l-menthol and CyDs were identified in the physical mixture and the l-menthol inclusion complex of α- and β-CyD. The NMR signal of the isopropyl-methyl group of menthol in the α-CyD inclusion complex exhibited a large low-field shift, which suggested a steric hindrance between menthol and α-CyD. VCD exhibited specific changes in the intensity of bands corresponding to C-C vibrations in α-CyD and O-C stretching vibrations in l-menthol. Our results indicated that l-menthol specifically fitted the narrow space within α-CyD. The combined solid-state NMR and VCD analysis provided structural insights into the flavor inclusion complex in the solid-state.

Theory and algorithms for chiroptical properties and spectroscopies of aqueous systems

Chiroptical properties and spectroscopies are valuable tools to study chiral molecules and assign absolute configurations. The spectra that result from chiroptical measurements may be very rich and complex, and hide much of their information content. For this reason, the interplay between experiments and calculations is especially useful, provided that all relevant physico-chemical interactions that are present in the experimental sample are accurately modelled. The inherent difficulty associated to the calculation of chiral signals of systems in aqueous solutions requires the development of specific tools, able to account for the peculiarities of water-solute interactions, and especially its ability to form hydrogen bonds. In this perspective we discuss a multiscale approach, which we have developed and challenged to model the most used chiroptical techniques.

Sensitivity of VCD spectroscopy for small structural and stereochemical changes of macrolide antibiotics

We report the application of VCD spectroscopy for the characterization of clarithromycin and erythromycin. We show that the VCD spectra of these large macrolides are distinctly different and that spectra calculations reproduce the experimentally observed VCD signatures. In addition, computed VCD spectra of different epimers indicate that they should also be distinguishable from the correct structure of clarithromycin.

The chemical constituents with cytotoxicity from Urtica fissa seed

Phytochemical investigation of Urtica fissa seed led to the isolation of a new secolignan (1) and a new glycoalkaloid (2), together with 16 known compounds (3-18). The subsequent active evaluation indicated that two lignans (1, 12), two ceramides (3, 4), and the glycoalkaloid (2) possessed the significant cytotoxicity. They could obviously inhibit the proliferation of tumor cells HeLa and CCRF-CEM cells, with IC₅₀ values as low as 1.5 μM.

New lignans from Urticae Fissae Herba

Two new lignans named neourticol A (1) and neourticol B (2), together with seven known compounds (3-9), were isolated from Urticae Fissae Herba, a folk medicine for rheumatism arthritis in China. The active evaluation results showed that 1 and 2 possessed the potent anti-complement and anti-inflammatory activities.

Crude leaf extracts of Piperaceae species downmodulate inflammatory responses by human monocytes

In this study, we aimed to evaluate the immunomodulatory effects of crude leaf extracts from Piper gaudichaudianum Kunth, P. arboreum Aub., P. umbellata L., P. fuligineum Kunth, and Peperomia obtusifolia A. Dietr. on an in vitro model of inflammatory response. The crude extracts were previously obtained by maceration of the leaves. The half-maximal inhibitory concentration was determined by the MTT assay using human peripheral blood mononuclear cells. Human monocytes were simultaneously challenged with each crude extract and lipopolysaccharide (LPS), the major component of the outer membrane of Gram-negative bacteria, to induce a strong inflammatory response. After 24 h of incubation, cell-free supernatants were used for evaluating the mediators involved in inflammation: H₂O₂, TNF-α, IL-8, IL-6, IL-1β, IL-10, IL-12, FGF-b, and TGF-β1. We also compared the results with the effects of ketoprofen, a well-known anti-inflammatory drug. The P. gaudichaudianum crude extract downmodulated the production of H₂O₂, IL-1β, IL-6, IL-8, and TGF-β1 by LPS-stimulated monocytes; P. arboreum, IL-1β, IL-6, IL-8, and TNF-α; P. umbellata and P. fuligineum, H₂O₂, IL-1β, IL-6, IL-8, IL-10, and TNF-α; and P. obtusifolia, H₂O₂, IL-6, IL-8, IL-10, and TNF-α. In general, the crude leaf extracts amplified the anti-inflammatory response when compared with ketoprofen, particularly reducing the production of IL-8, a mediator involved in neutrophil recruitment during tissue damage. Thus, the crude leaf extracts of P. gaudichaudianum, P. arboreum, P. umbellata, P. fuligineum, and Peperomia obtusifolia elicited an anti-inflammatory response against LPS-challenged monocytes. These findings show the anti-inflammatory properties of these crude leaf extracts and offer new perspectives for their use in the treatment of inflammatory diseases.

Chirality Induction from a Chiral Guest to the Hydrogen-Bonding Network of Its Hexameric Resorcinarene Host Capsule

The hexameric capsule of resorcin[4]arene 1 is capable of encapsulating tertiary amines, which has recently been used in the application of [(1)₆ (H₂ O)₈ ] as (co-)catalyst in various asymmetric reactions. However, not much is known about the highly asymmetric but conformationally very dynamic structure of the capsule after uptake of chiral molecules. Therefore, in this contribution, we utilize electronic circular dichroism and vibrational circular dichroism spectroscopy to investigate how several chiral guest molecules affect the structural preferences of the capsule [(1)₆ (H₂ O)₈ ]. In particular, we show that one small chiral amine encapsulated in [(1)₆ (H₂ O)₈ ] is sufficient to control and dictate the stereochemical preferences of the entire capsule. Furthermore, neither strong π-π interactions nor a significant steric bulk are required for this induction. The observation of such a chiral imprint of the guest's stereochemistry onto its host molecule is expected to have implications also for other supramolecular capsules.

Analysis of Configuration and Conformation of Furanose Ring in Carbohydrate and Nucleoside by Vibrational Circular Dichroism

A reliable and convenient method for determining the configuration and conformation of the furanose ring in carbohydrates and nucleosides by vibrational circular dichroism (VCD) spectroscopy is described. Diastereomeric pairs of several furanose monosaccharides and nucleosides were prepared, and their VCD spectra were analyzed. The results revealed that VCD spectroscopy elucidates the equibrated state of the furanose ring puckers, which is often difficult to study by other techniques.

Assignment of absolute configurations of highly flexible linear diterpenes from the brown alga Bifurcaria bifurcata by VCD spectroscopy

Correct assignment of the stereogenic centers of highly flexible linear diterpenes (LDs) is challenging. Herein we report the first application of VCD spectroscopy for the absolute configuration determination of LDs of algal origin and provide experimental and computational procedures, such as a fragmentation approach, which will facilitate the use of VCD spectroscopy for configuration assignments of LDs.

Natural compounds isolated from Brazilian plants are potent inhibitors of hepatitis C virus replication in vitro

Compounds extracted from plants can provide an alternative approach to new therapies. They present characteristics such as high chemical diversity, lower cost of production and milder or inexistent side effects compared with conventional treatment. The Brazilian flora represents a vast, largely untapped, resource of potential antiviral compounds. In this study, we investigate the antiviral effects of a panel of natural compounds isolated from Brazilian plants species on hepatitis C virus (HCV) genome replication. To do this we used firefly luciferase-based HCV sub-genomic replicons of genotypes 2a (JFH-1), 1b and 3a and the compounds were assessed for their effects on both HCV replication and cellular toxicity. Initial screening of compounds was performed using the maximum non-toxic concentration and 4 compounds that exhibited a useful therapeutic index (favourable ratio of cytotoxicity to antiviral potency) were selected for extra analysis. The compounds APS (EC50=2.3μM), a natural alkaloid isolated from Maytrenus ilicifolia, and the lignans 3(∗)43 (EC50=4.0μM), 3(∗)20 (EC50=8.2μM) and 5(∗)362 (EC50=38.9μM) from Peperomia blanda dramatically inhibited HCV replication as judged by reductions in luciferase activity and HCV protein expression in both the subgenomic and infectious systems. We further show that these compounds are active against a daclatasvir resistance mutant subgenomic replicon. Consistent with inhibition of genome replication, production of infectious JFH-1 virus was significantly reduced by all 4 compounds. These data are the first description of Brazilian natural compounds possessing anti-HCV activity and further analyses are being performed in order to investigate the mode of action of those compounds.

Recent advances in the use of vibrational chiroptical spectroscopic methods for stereochemical characterization of natural products

A comprehensive look into application of vibrational optical activity methods for conformational and configurational assignments in natural product molecules over the last 15 years is provided.

Cytotoxic non-aromatic B-ring flavanones from Piper carniconnectivum C. DC

The EtOAc extract from the leaves of Piper carniconnectivum C. DC. was subjected to chromatographic separation to afford two non-aromatic B-ring flavanone compounds: 5-hydroxy-2-(1'-hydroxy-4'-oxo-cyclohex-2'-en-1'-yl)-6,7-dimethoxy-2,3-dihydro-4H-chromen-4-one (1) and 5-hydroxy-2-(1',2'-dihydroxy-4'-oxo-cyclohexyl)-6,7-dimethoxy-2,3-dihydro-4H-chromen-4-one (2). The absolute configuration of (+)-1 was unambiguously determined as 2S,1'R by electronic circular dichroism (ECD) spectroscopy and comparison to simulated spectra that were calculated using time-dependent density functional theory (TDDFT). This methodology allowed the assignment of the absolute configuration of (+)-2 also as 2S,1'R, except for the stereogenic center at C-2', which was assigned as R because of the evidence drawn from high resolution NMR experiments. The cytotoxic activity of both compounds and 3 (hydrogenated B-ring derivative of 1) was evaluated on twelve human leukemia cell lines, and the IC50 values (<10 μM) indicated the activity of 1 against seven cell lines.

Two rare-class tricyclic diterpenes with antitubercular activity from the Caribbean sponge Svenzea flava. Application of vibrational circular dichroism spectroscopy for determining absolute configuration

Two new natural products, 3 and 4, and their predecessor 7-isocyanoisoneoamphilecta-1(14),15-diene (2), of the rare isoneoamphilectane class of marine diterpenes, along with the known amphilectane diterpenes 6-8, were isolated from the n-hexane extract of the marine sponge Svenzea flava collected at Great Inagua Island, Bahamas. The molecular structures of compounds 3 and 4 were established by spectroscopic (1D/2D NMR, IR, UV, HRMS) methods and confirmed by a series of chemical correlation studies. In a first ever case study of the assignment of the absolute configuration of a molecule based on the isoneoamphilectane carbon skeleton, the absolute configuration of compound 5 was established as 3S,4R,7S,8S,11R,12S,13R by application of vibrational circular dichroism (VCD). In vitro anti-TB screenings revealed that metabolites 2-4 and, in particular, semisynthetic analogue 5, are strong growth inhibitors of Mycobacterium tuberculosis H37Rv.

COX-2 inhibitory activity of homoisoflavanones and xanthones from the bulbs of the Southern African Ledebouria socialis and Ledebouria ovatifolia (Hyacinthaceae: Hyacinthoideae)

The bulbs of Ledebouria socialis (Hyacinthaceae) yielded the benzocyclobutene homoisoflavonoid, (R)-2',5-dihydroxy-3',4',7-trimethoxyspiro{2H-1-benzopyran-3-(4H)-9-bicyclo[4.2.0]octa[1,3,5]triene}-4-one, socialinone (1). Ledebouria ovatifolia yielded (2ε,3R)-2,5-dihydroxy-7-methoxyspiro[2H-1-benzopyran-3(4H), 5'(6'H)-cyclobuta[f][1,3]benzodioxol]-4-one (2) and the homoisoflavanone, (E)-3-(3',4'-dihydroxybenzylidene)-5,7-dihydroxychroman-4-one, ovatifolionone (5), the dihydrochalcone, 4,4'-dihydroxy-2',6'-dimethoxydihydrochalcone (3), and xanthone, 1,6-dihydroxy-2,3,5-trimethoxy-8-methyl-9H-xanthen-9-one (4) along with 21 known compounds. Structures were determined using spectroscopic techniques. The anti-inflammatory activities of the homoisoflavonoids and xanthones isolated were evaluated against cyclooxygenase-1 and -2 isoenzymes. (R)-3-(3',4'-Dihydroxybenzyl)-7-hydroxy-5-methoxychroman-4-one (7), (E)-3-(3',4'-dihydroxybenzylidene)-7-hydroxy-5-methoxychroman-4-one (10), 1,3,6-trihydroxy-2-methoxy-8-methylxanthen-9-one (6) and ovatifolionone acetate (5Ac) exhibited significant activity against cyclooxygenase-2 at <10μM.

3-Ishwarone, a rare ishwarane sesquiterpene from Peperomia scandens Ruiz & Pavon: structural elucidation through a joint experimental and theoretical study

3-Ishwarone, (1), a sesquiterpene with a rare ishwarane skeleton, was isolated from Peperomia scandens Ruiz & Pavon (Piperaceae). Its structure was unambiguously determined by 1D- and 2D-NMR and infrared analyses, as well as by comparative theoretical studies which involved calculations of 13C-NMR chemical shifts, using the Density Functional Theory (DFT) with the mPW1PW91 hybrid functional and Pople's 6-31G(d) basis set, and of vibrational frequencies, using the B3LYP hybrid functional and triple ζ Dunning's correlation consistent basis set (cc-pVTZ), of (1) and three of its possible diastereomers, compounds 2-4.