Determination of the absolute configuration of natural products

New Techniques of Structure Elucidation for Sesquiterpenes

The most significant new techniques that have been used in the twenty-first century for the structure elucidation of sesquiterpenes and some derivatives are reviewed in this chapter. A distinctive feature of these methodologies is the combination of accurate experimental measurements with theoretical data obtained by molecular modeling calculations that allow to visualize, understand, and quantify many structural characteristics. This has been the case for NMR spectroscopy, which has expanded its potential for solving complex structural problems by means of comparison with quantum mechanical molecular models. Ab initio and density functional theory calculations of chemical shifts, coupling constants, and residual chemical shift anisotropies have played important roles in the solution of many structures of sesquiterpenes. The assignments of their absolute configurations by evaluation of calculated and experimental chiroptical properties as electronic and vibrational circular dichroism are also reviewed. This chapter also includes the use of X-ray diffraction analysis with emphasis on calculations of the Flack and Hooft parameters, which are applicable to all molecules that crystallize in non-centrosymmetric space groups. The accurate molecular models of sesquiterpenes, validated by concordance with their experimental properties, are nowadays essential for the interpretation of the effects of these natural products on biological systems.

A Novel Antioxidant Protects Against Contrast Medium-Induced Acute Kidney Injury in Rats

Many studies proposed that oxidative stress and apoptosis are key mechanisms in the pathogenesis of contrast-induced acute kidney injury (CI-AKI). Xylose-pyrogallol conjugate (XP) is an original effective antioxidant that showed decent antioxidant and anti-apoptosis effect before. Thus the therapeutic effect and mechanism of XP in preventing CI-AKI in the short and long term were investigated in this research. Renal function and histological grade were evaluated to determine the severity of renal injury. Kidney samples were then collected for the measurement of oxidative stress markers and the detection of apoptosis. Transmission electron microscopy (TEM) and western blot of mitochondrial protein were utilized for the analysis of the mitochondrial conditions. The results demonstrated that the CI-AKI rats caused a significant decrease in renal function accompanied by a remarkable increase in Malondialdehyde (MDA), bax, caspase-3, cytochrome c (Cyt C) level, TdT-mediated dUTP nick end labeling (TUNEL) positive apoptotic cells, and damaged mitochondria, while a decline in antioxidase activities and mitochondrial superoxide dismutase 2 (SOD2) expression compared with the control rats. However, when XP (50 or 100 or 200 mg/kg/day) was given orally for consecutive 7 days before CI-AKI modeling, XP (200 mg/kg) showed a better capability to restore renal dysfunction, histopathological appearance, the level of apoptosis, mitochondrial damage, oxidative stress, and fibrosis generation without interference in computed tomographic imaging. Our study indicated that antioxidant XP played a nephroprotective role probably via antiapoptotic and antioxidant mechanisms. Besides, XP may regulate the mitochondria pathway via decreasing the ratio of bax/bcl-2, inhibiting caspase-3 expression, cytochrome c release, and superoxide dismutase 2 activity. Overall, XP as a high-efficient antioxidant may have the potentials to prevent CI-AKI.

Drophiobiolins A and B, Bioactive Ophiobolan Sestertepenoids Produced by Dreschslera gigantea

Two new bioactive ophiobolan sestertepenoids, named drophiobiolins A and B (1 and 2) were isolated from Drechslera gigantea, a fungus proposed as a mycoherbicide for biocontrol of Digitaria sanguinalis. They were isolated together with ophiobolin A, the main metabolite, 6-epi-ophiobolin A, 3-anhydro-6-epi-ophiobolin A, and ophiobolin I. Drophiobolins A and B were characterized by NMR, HRESIMS, and chemical methods as 7-hydroxy-7-(6-hydroxy-6-methylheptan-2-yl)-1,9a-dimethyl-3-oxo-3,3a,6,6a,7,8,9,9a,10,10a-decahydrodicyclopenta [a,d][8]annulene-4-carbaldehyde and 6-(hydroxymethyl)-3',9,10a-trimethyl-5'-(2-methylprop-1-en-1-yl)-3a,4,4',5',10,10a-hexahydro-1H,3'H-spiro[dicyclopenta[a,d] [8]annulene-3,2'-furan]-5,7(2H,9aH)-dione. The relative configuration of drophiobolins A and B, which did not afford crystals suitable for X-ray analysis, was determined by NOESY experiments, while the absolute configuration was assigned by comparison of their experimental and TDDFT calculated electronic circular dichroism (ECD) spectra. The phytotoxic activity of drophiobolins A and B was tested by leaf-puncture assay on cultivated (Lycopersicon esculentum L.), as well as on host (Digitaria sanguinalis L.) and nonhost (Chenopodium album L.) weed plants, compared to that of ophiobolin A. Both of the newly identified ophiobolins showed significant phytotoxicity. Drophiobolins A and B exhibited cytotoxicity against Hela B cells with an IC₅₀ value of 10 μM. However, they had a lesser or no effect against Hacat, H1299, and A431 cells when compared to that of ophiobolin A.

Absolute Configuration Assignment to Chiral Natural Products by Biphenyl Chiroptical Probes: The Case of the Phytotoxins Colletochlorin A and Agropyrenol

The application of flexible biphenyls as chiroptical probes for the absolute configuration assignment to chiral natural products is described. The method is straightforward and reliable and can be applied to conformationally mobile and ECD silent compounds, not treatable by computational analysis of chiroptical data. By this approach, the (6'R) absolute configuration of the phytotoxin colletochlorin A (1) was confirmed, while the absolute configuration of the phytotoxin agropyrenol (2), previously assigned by the NMR Mosher method, was revised and assigned as (3'S,4'S). Moreover, with the biphenyl method the configurational assignment can be obtained simply by the sign of a diagnostic Cotton effect at 250 nm in the ECD spectrum, thus allowing application without the need of advanced knowledge of chiroptical spectroscopy and computational protocols.

Meliacarpinin-Type Limonoids from the Bark of Melia toosendan

Three new meliacarpinin-type limonoids, toosendanes A⁻C (1⁻3), along with three, known meliacarpinins (4⁻6) were isolated from the bark of Melia toosendan. Their structures, along with their absolute configurations, were elucidated, based on detailed analyses. These included HRESIMS and 1D/2D-NMR, modified Mosher's method, and electronic circular dichroism (ECD). Limonoids 2 and 3 showed moderate inhibitory activity on LPS-activated, RAW 264.7 macrophages.

Cytotoxic Serrulatane-Type Diterpenoids from the Gorgonian Euplexaura sp. and Their Absolute Configurations by Vibrational Circular Dichroism

Vibrational circular dichroism (VCD) method has become robust and reliable alternative for the stereochemical characterization of natural products. In this paper, three new serrulatane-type diterpenoids, euplexaurenes A-C (1-3), and a known metabolite, anthogorgiene P (4), were obtained from the South China Sea gorgonian Euplexaura sp. GXWZ-05. The absolute configuration of C-11 in 1-4, which was difficult to be determined by common means due to the high conformational flexibility of the eight-carbon aliphatic chain attached at C-4, was determined by VCD method, suggesting a new horizon to define the absolute configurations of natural products possessing chains. Compounds 1-4 were found to show selective cytotoxic activities against human laryngeal carcinoma (Hep-2) cell line with the IC50 values of 1.95, 7.80, 13.6 and 5.85 μM, respectively.

Vibrational Circular Dichroism: Recent Advances for the Assignment of the Absolute Configuration of Natural Products

Vibrational circular dichroism (VCD) emerged during the last decade as a reliable tool for the absolute configuration (AC) determination of organic compounds. The principles, instrumentation, and methodology applied prior to early 2013 were recently reviewed by us. Since VCD is a very dynamic field, the aim of this review is to update VCD advances for the AC assignment of terpenoids, aromatic compounds, alkaloids, and other natural products for the 2013–2014 period, when VCD was applied to the AC assignment of some 70 natural products. In addition, although discovered in 2012, a brief introduction to the VCD exciton coupling approach and its applications in natural products AC assignment is presented.

Cycloelatanene A and B: absolute configuration determination and structural revision by the crystalline sponge method

The crystalline sponge method revealed the absolute configuration of cycloelatanene A and B.

Cycloelatanene A and B are marine natural products first reported a few years ago. Their relative structures had been elucidated by an extensive NMR study and found to be epimers. However, their absolute configurations had not been established because they were isolated in only minute quantities as oily compounds. In this study, the complete structures of cycloelatanene A and B, including absolute configurations, were determined by the crystalline sponge method. The structure analysis confirmed the unique tricyclic structure involving a spiro[5.5]undecene skeleton. One stereogenic centre at C4 was revised as a result of this analysis. Since it only took 1–2 weeks to complete the experiments using the crystalline sponge method (guest-soaking followed by crystallographic analysis), this method is now highly recommended as a first port of call to achieve complete natural product structure elucidation.

Vibrational Circular Dichroism: Recent Advances for the Assignment of the Absolute Configuration of Natural Products

Vibrational circular dichroism (VCD) emerged during the last decade as a reliable tool for the absolute configuration (AC) determination of organic compounds. The principles, instrumentation, and methodology applied prior to early 2013 were recently reviewed by us. Since VCD is a very dynamic field, the aim of this review is to update VCD advances for the AC assignment of terpenoids, aromatic compounds, alkaloids, and other natural products for the 2013-2014 period, when VCD was applied to the AC assignment of some 70 natural products. In addition, although discovered in 2012, a brief introduction to the VCD exciton coupling approach and its applications in natural products AC assignment is presented.