A vibrational circular dichroism approach to the determination of the absolute configurations of flavorous 5-substituted-2(5H)-furanones

Natural Products from Singapore Soil-Derived Streptomycetaceae Family and Evaluation of Their Biological Activities

Natural products have long been used as a source of antimicrobial agents against various microorganisms. Actinobacteria are a group of bacteria best known to produce a wide variety of bioactive secondary metabolites, including many antimicrobial agents. In this study, four actinobacterial strains found in Singapore terrestrial soil were investigated as potential sources of new antimicrobial compounds. Large-scale cultivation, chemical, and biological investigation led to the isolation of a previously undescribed tetronomycin A (1) that demonstrated inhibitory activities against both Gram-positive bacteria Staphylococcus aureus (SA) and methicillin-resistant Staphylococcus aureus (MRSA) (i.e., MIC90 of 2-4 μM and MBC90 of 9-12 μM), and several known antimicrobial compounds, namely nonactin, monactin, dinactin, 4E-deacetylchromomycin A3, chromomycin A2, soyasaponin II, lysolipin I, tetronomycin, and naphthomevalin. Tetronomycin showed a two- to six-fold increase in antibacterial activity (i.e., MIC90 and MBC90 of 1-2 μM) as compared to tetronomycin A (1), indicating the presence of an oxy-methyl group at the C-27 position is important for antibacterial activity.

Chemistry and Biology of Natural Azoxy Compounds

Azoxy compounds belong to a small yet intriguing group of natural products sharing a common functional group with the general structure RN═N⁺(O^-)R. Their intriguing chemical structures, diverse biological activities, and important industrial applications have received attention from researchers in natural product chemistry, total synthesis, and biosynthesis. This review presents current updates about the structural diversity of natural azoxy compounds isolated from different organisms and highlights the enzymes and biological logic involved in their construction. We assume that the identification of key enzymes will provide efficient tools in biocatalysis to generate new azoxy compounds, while genome mining may result in novel natural azoxy compounds of medical and industrial interest.

Chirality: An Important Phenomenon Regarding Biosynthesis, Perception, and Authenticity of Flavor Compounds

Chirality plays an important role in flavor research. This will be outlined using selected examples from the key areas analysis, authenticity assessment, biogenesis, and odor perception. Developments of analytical techniques, in particular the use of chiral stationary phases in capillary gas chromatography, enabled the determination of naturally occurring configurations of chiral volatiles at trace levels. Thus, knowledge of pathways and enzymes involved in the biogenesis of chiral substances was acquired, and enantioselective analysis has become a prominent tool in the authenticity assessment of flavorings. Increasing information is also available on structure-odor relationships of chiral flavor compounds and the influence of their configurations on odor thresholds and odor properties. A substantial extension of these data sets and a further understanding of the role of chirality in the perception of aroma compounds is expected from studies on the enantioselectivity of odorant receptor systems. Developments in these areas will be put into a historical perspective, recent progress will be emphasized, and data gaps will be described.

Novel biotechnological glucosylation of high-impact aroma chemicals, 3(2H)- and 2(5H)-furanones

Glucosyltransferases are versatile biocatalysts to chemically modify small molecules and thus enhance their water solubility and structural stability. Although the genomes of all organisms harbor a multitude of glucosyltransferase genes, their functional characterization is hampered by the lack of high-throughput in-vivo systems to rapidly test the versatility of the encoded proteins. We have developed and applied a high-throughput whole cell biotransformation system to screen a plant glucosyltransferase library. As proof of principle, we identified 25, 24, 15, and 18 biocatalysts transferring D-glucose to sotolone, maple furanone, furaneol and homofuraneol, four highly appreciated flavor compounds, respectively. Although these 3(2H)- and 2(5H)-furanones have extremely low odor thresholds their glucosides were odorless. Upscaling of the biotechnological process yielded titers of 5.3 and 7.2 g/L for the new to nature β-D-glucopyranosides of sotolone and maple furanone, respectively. Consequently, plant glucosyltransferase show stunning catalytic activities, which enable the economical production of novel and unexplored chemicals with exciting new functionalities by whole-cell biotransformation.

Stereochemistry of spongosoritins: beyond optical rotation

A combination of spectroscopic methods reveals the dependence of the chiroptical properties of spongosoritins on achiral structural features.

Configurational Study of an Aporphine Alkaloid from Annona purpurea

Purpureine (1), norpurpureine (2), and 3-hydroxyglaucine (4) were isolated from the leaves of Annona purpurea. A vibrational circular dichroism study for the absolute configuration determination of 1 provides evidence for the mutually dependent atropisomerism, local chirality of the sole stereogenic center, and the geometry of the tetrahedral nitrogen atom in aporphine alkaloids. The observed change in the optical rotation sign between 2 and its hydrochloride 3 might explain why this compound has been reported as dextrorotatory and levorotatory from the same botanical source. Furthermore, 1H and 13C NMR spectra of 1, 2 and 4 were fully assigned for the first time.

Enantiomeric Mixtures in Natural Product Chemistry: Separation and Absolute Configuration Assignment

Chiral natural product molecules are generally assumed to be biosynthesized in an enantiomerically pure or enriched fashion. Nevertheless, a significant amount of racemates or enantiomerically enriched mixtures has been reported from natural sources. This number is estimated to be even larger since the enantiomeric purity of secondary metabolites is rarely checked in the natural product isolation pipeline. This latter fact may have drastic effects on the evaluation of the biological activity of chiral natural products. A second bottleneck is the determination of their absolute configurations. Despite the widespread use of optical rotation and electronic circular dichroism, most of the stereochemical assignments are based on empirical correlations with similar compounds reported in the literature. As an alternative, the combination of vibrational circular dichroism and quantum chemical calculations has emerged as a powerful and reliable tool for both conformational and configurational analysis of natural products, even for those lacking UV-Vis chromophores. In this review, we aim to provide the reader with a critical overview of the occurrence of enantiomeric mixtures of secondary metabolites in nature as well the best practices for their detection, enantioselective separation using liquid chromatography, and determination of absolute configuration by means of vibrational circular dichroism and density functional theory calculations.

Importance and Difficulties in the Use of Chiroptical Methods to Assign the Absolute Configuration of Natural Products: The Case of Phytotoxic Pyrones and Furanones Produced by Diplodia corticola

α-Pyrones and furanones are metabolites produced by Diplodia corticola, a pathogen of cork oak. Previously, the absolute configuration (AC) of diplopyrone was defined by chiroptical methods and Mosher's method. Using X-ray and chiroptical methods, the AC of sapinofuranone C was assigned, while that of the (4S,5S)-enantiomer of sapinofuranone B was established by enantioselective total synthesis. Diplofuranone A and diplobifuranylones A-C ACs are still unassigned. Here electronic and vibrational circular dichroism (ECD and VCD) and optical rotatory dispersion (ORD) spectra are reported and compared with density functional theory computations. The AC of the (4S,5S)-enantiomer of sapinofuranone B and sapinofuranone C is checked for completeness. The AC of diplobifuranylones A-C is assigned as (2S,2'S,5'S,6'S), (2S,2'R,5'S,6'R), and (2S,2'S,5'R,6'R), respectively, with the Mosher's method applied to define the absolute configuration of the carbinol stereogenic carbon. The AC assignment of sapinofuranones is problematic: while diplofuranone A is (4S,9R), sapinofuranones B and C are (4S,5S) according to ORD and VCD, but not to ECD. To eliminate these ambiguities, ECD and VCD spectra of a di-p-bromobenzoate derivative of sapinofuranone C are measured and calculated. For phytotoxicity studies, it is relevant that all six compounds share the S configuration for the stereogenic carbon atom of the lactone moiety.

Crinoids: ancient organisms, modern chemistry

This review summarises known crinoid chemistry from 1877 to the present day, and discusses some of the problems (and potential solutions) with establishing crinoid natural product structures, as well as future directions for crinoid research.

Reinvestigation of the Absolute Configurations of Chiral β-Mercaptoalkanones Using Vibrational Circular Dichroism and 1H NMR Analysis

The absolute configurations of chiral β-mercaptoalkanones were previously assigned on the basis of the ¹H NMR anisotropy method using (S)-2-methoxy-2-(1-naphthyl)propionic acid ((S)-MαNP) as the chiral auxiliary. This study presents a reinvestigation of the configurations of 4-mercapto-2-pentanone 1, 4-mercapto-2-heptanone 2, and 2-mercapto-4-heptanone 3. Enantiomers of 1, 2, and 3 were obtained by lipase-catalyzed hydrolyses of the respective acetylthioalkanones. Upon derivatization with (S)-MαNP, the configurations of the reaction products were deduced based on the order of the HPLC elution of the diastereoisomeric thioesters, assuming that the sector rule previously developed for secondary alcohols is also valid for thiols. In addition, the configurations were experimentally determined by vibrational circular dichroism (VCD) and ¹H NMR analyses after esterification with (R)-hydratropic acid (HTA) and 2-methoxy-2-phenylacetic acid (MPA). The assignments of the configurations using VCD and NMR analyses of HTA- and MPA-thioesters were in agreement. However, they were opposite to those deduced for (S)-MαNP thioesters via the sector rule. Consequently, the formerly assigned configurations of β-mercaptoalkanones deduced via investigation of (S)-MαNP-derivatives have to be revised.

Reassignment of the absolute configuration of plakinidone from the sponge consortium Plakortis halichondrioides-Xestospongia deweerdtae using a combination of synthesis and a chiroptical approach

Recent work by Wu et al. in connection with the first synthesis of the marine natural product plakinidone revealed that the most salient feature of its purported structure, a six-membered perlactone moiety, was in fact a five-membered lactone, i.e. a 3-methyl-4-hydroxy-2(5H)-furanone or tetronic acid ring. With the planar structure of plakinidone confidently revised, we undertook a new investigation to unambiguously establish its absolute configuration. Upon preparing two stable derivatives 1 and 5 from a sample of naturally occurring plakinidone extracted from the sponge association Plakortis halichondriodes-Xetospongia deweerdtae, the absolute configuration was assigned by synthesis and vibrational and electronic circular dichroism (VCD and ECD) measurements in combination with density functional theory calculations at the B3LYP/aug-cc-pVDZ/PCM(CH3CN) level of theory. Our combined efforts and the agreement between the experimental and calculated VCD/ECD spectra of 1 revealed that the absolute configuration of plakinidone was in fact (11S,17R) and not the formerly reported (11S,17S) diastereomer assigned by Wu et al.. Therefore, we propose that natural plakinidone is accurately represented by structure 12.

X-ray Crystallography, DFT Calculations and Molecular Docking of Indole-Arylpiperazine Derivatives as α1A-Adrenoceptor Antagonists

Indole-arylpiperazine derivatives have exhibited good selectivity for the α_1A-adrenoceptor, but the structure-activity-binding mechanism relationship remains unclear. In the current study, three compounds (1, 2 and 3) were investigated through single-crystal X-ray diffraction analysis, density functional theory (DFT) calculations and molecular docking using a homology model of the α_1A receptor. Compounds 1 and 3 form H-bonds networks to stabilize their three-dimensional structures, while C–H···π interactions play a significant role in the packing of 2. Based on DFT-optimized conformations, the HOMO-LUMO energy gaps and molecular electrostatic potential (MEP) were theoretically calculated at the B3LYP/6-311G (d, p) level of theory. Chemical reactivity increases in the order of 3 < 2 < 1, and the maximum positive region of the MEP maps is mainly localized over the NH group. The binding mechanisms of ligand-α_1A-adrenoceptor complexes were illustrated by molecular docking. Binding to Gln177 of the second extracellular loop region via hydrogen bonds is likely to be essential for α_1A-selective antagonists. The present work sheds light on the studies of structure-activity-binding mechanism and aids in the design of α_1A antagonists with high selectivity.

Tyrosyl-DNA Phosphodiesterase I Inhibitors from the Australian Plant Macropteranthes leichhardtii

Mass-directed isolation of the CH2Cl2/MeOH extract from the bark of an Australian plant, Macropteranthes leichhardtii, resulted in the purification of a new phenylpropanoid glucoside, macropteranthol (1), together with four known analogues (2-5). The structure of compound 1 was elucidated by NMR and MS data analyses and quantum chemical calculations. Compounds 3 and 5 showed inhibitory activity against tyrosyl-DNA phosphodiesterase I with IC50 values of ∼1.0 μM.

Structure and Absolute Configuration of Diterpenoids from Hymenaea stigonocarpa

Chemical investigations of the ethanolic extracts from the flowers and leaves of Hymenaea stigonocarpa Mart. ex Hayne afforded one new ent-halimane diterpenoid, 18-hydroxy-ent-halima-1(10),13-(E)-dien-15-oic acid (1), together with five known compounds (2-6). The structural elucidation was performed by means of NMR (COSY, HSQC, HMBC, and NOESY) and MS analyses. Complete (1)H and (13)C NMR data assignments are also reported for labd-13-en-8β-ol-15-oic (2) and labd-7,13-dien-15-oic (3) acids. The absolute configurations of 1 and 2 were established by comparison of experimental and calculated Raman optical activity spectra.

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.

Mechanistic and chiroptical studies on the desulfurization of epidithiodioxopiperazines reveal universal retention of configuration at the bridgehead carbon atoms

The stereochemistry of the desulfurization products of chiral natural and synthetic 3,6-epidithiodiketopiperazines (ETPs) is specified inconsistently in the literature. Qualitative mechanisms have been put forward to explain apparently divergent stereochemical pathways, but the quantitative feasibility of such mechanistic pathways has not been assessed. We report a computational study revealing that desulfurization of ETPs should occur universally with retention of configuration. While the majority of stereochemically assigned and reassigned cases fit this model, until now desulfurization of the synthetic gliotoxin analogue shown has remained assigned as proceeding via inversion of configuration. Through detailed chiroptical studies comparing experimentally obtained optical rotation values, electronic circular dichroism spectra, and vibrational circular dichroism spectra to their computationally simulated counterparts as well as chemical derivatization studies, we have unambiguously demonstrated that contrary to its current assignment in the literature, the desulfurization of this synthetic ETP also proceeds with retention of configuration.

Plakortolide stereochemistry revisited: the checkered history of plakortolides e and I

The relative configuration of the plakortolide metabolite (4) isolated from a Madagascan Plakortis sp. and named (+)-plakortolide I is revised following reassignment of the ¹³C signals for C-7 and C-16, thereby establishing that the metabolite isolated was likely (+)-plakortolide E (3). We propose that the name "plakortolide I" should be retained for the plakortolide metabolite 5 first isolated by the Faulkner group; its enantiomer 4 can then be named ent-plakortolide I in line with the description of Barnych and Vatèle. The spectroscopic data for MPA esters prepared from synthetic samples of seco derivatives of plakortolide E (3) and ent-plakortolide I (4) were compared with those of MPA esters of seco derivatives from naturally isolated plakortolides L (1) and K (2) and of seco-plakortolide E (6a). Likewise, the spectroscopic data for MTPA esters derived from 3 and 4 were compared with data for the MTPA esters derived from 5. These various comparisons established that the sign of the specific rotation associated with the natural isolates is an unreliable indicator of absolute configuration and verify that the absolute configurations of plakortolides L (1), K (2), E (3), and I (5) are (3S, 4S, 6S), (3R, 4R, 6S), (3R, 4R, 6R), and (3S, 4S, 6R), respectively.

Absolute configuration of podophyllotoxin related lignans from Bursera fagaroides using vibrational circular dichroism

The ethanol extract from the dried exudate of Bursera fagaroides (Burseraceae) showed significant cytotoxic activity in the HT-29 (human colon adenocarcinoma) test system. The extract provided four podophyllotoxin related lignans, identified as (7'R,8R,8'R)-(-)-deoxypodophyllotoxin (3), (7'R,8R,8'R)-(-)-morelensin (4), (8R,8'R)-(-)-yatein (5), and (8R,8'R)-(-)-5'-desmethoxyyatein (6), whose spectroscopic and chiroptical properties were compared with those of (7R,7'R,8R,8'R)-(-)-podophyllotoxin (1) and its acetyl derivative (2). Their absolute configurations were assigned by comparison of the vibrational circular dichroism spectra of 1 and 3 with those obtained by density functional theory calculations.