Progression of Absolute Configuration Determination in Natural Product Chemistry Using Optical Rotation (Dispersion), Matrix Determinant and Electronic Circular Dichroism Methods

Absolute Configuration of Oxabornyl Polyenes Prugosenes A1-A3 and Structural Revision of Prugosene A2

Oxabornyl polyenes represent a unique group of polyketides characterized by a central polyene core flanked by a conserved oxabornyl moiety and a structurally diverse oxygen heterocyclic ring. They are widely distributed in fungi and possess a variety of biological activities. Due to the significant spatial separation between the two stereogenic ring systems, it is difficult to establish their overall relative configurations. Here, we isolated three oxabornyl polyenes, prugosenes A1-A3 (1-3), from Talaromyces sp. JNU18266-01. Although these compounds were first reported from Penicillium rugulosum, their overall relative and absolute configurations remained unassigned. By employing ozonolysis in combination with ECD calculations, we were able to establish their absolute configurations, and additionally obtained seven new chemical derivatives (4-10). Notably, through NMR data analysis and quantum chemical calculations, we achieved the structural revision of prugosene A2. Furthermore, prugosenes A1-A3 exhibited potent antiviral activity against the respiratory syncytial virus, with compound 1 displaying an IC50 value of 6.3 μM. Our study thus provides a valuable reference for absolute configuration assignment of oxabornyl polyene compounds.

A green bio-organic catalyst (taurine) promoted one-pot synthesis of (R/S)-2-thioxo-3,4-dihydropyrimidine(TDHPM)-5-carboxanilides: chiral investigations using circular dichroism and validation by computational approaches

Owing to the massive importance of dihydropyrimidine (DHPMs) scaffolds in the pharmaceutical industry and other areas, we developed an effective and sustainable one-pot reaction protocol for the synthesis of (R/S)-2-thioxo-DHPM-5-carboxanilides via the Biginelli-type cyclo-condensation reaction of aryl aldehydes, thiourea and various acetoacetanilide derivatives in ethanol at 100 °C. In this protocol, taurine was used as a green and reusable bio-organic catalyst. Twenty-three novel derivatives of (R/S)-TDHPM-5-carboxanilides and their structures were confirmed by various spectroscopy techniques. The aforementioned compounds were synthesized via the formation of one asymmetric centre, one new C-C bond, and two new C-N bonds in the final product. All the newly synthesized compounds were obtained in their racemic form with up to 99% yield. In addition, the separation of the racemic mixture of all the newly synthesized compounds was carried out by chiral HPLC (Prep LC), which provided up to 99.99% purity. The absolute configuration of all the enantiomerically pure isomers was determined using a circular dichroism study and validated by a computational approach. With up to 99% yield of 4d, this one-pot synthetic approach can also be useful for large-scale industrial production. One of the separated isomers (4R)-(+)-4S developed as a single crystal, and it was found that this crystal structure was orthorhombic.

Absolute Stereochemistry Determination of Bioactive Marine-Derived Cyclopeptides by Liquid Chromatography Methods: An Update Review (2018-2022)

Cyclopeptides are considered as one of the most important classes of compounds derived from marine sources, due to their structural diversity and a myriad of their biological and pharmacological activities. Since marine-derived cyclopeptides consist of different amino acids, many of which are non-proteinogenic, they possess various stereogenic centers. In this respect, the structure elucidation of new molecular scaffolds obtained from natural sources, including marine-derived cyclopeptides, can become a very challenging task. The determination of the absolute configurations of the amino acid residues is accomplished, in most cases, by performing acidic hydrolysis, followed by analyses by liquid chromatography (LC). In a continuation with the authors' previous publication, and to analyze the current trends, the present review covers recently published works (from January 2018 to November 2022) regarding new cyclopeptides from marine organisms, with a special focus on their biological/pharmacological activities and the absolute stereochemical assignment of the amino acid residues. Ninety-one unreported marine-derived cyclopeptides were identified during this period, most of which displayed anticancer or antimicrobial activities. Marfey's method, which involves LC, was found to be the most frequently used for this purpose.

Amplification of the chiroptical response of UV-transparent amines and alcohols by N-phthalimide derivatization enabling absolute configuration determination through ECD computational analysis

The stereoselective transformation of chiral UV-transparent amines and alcohols to phthalimides has proved to be a simple and efficient method to enhance the chiroptical response of these substrates allowing their reliable absolute configuration determination by computational analysis of ECD spectra. Such a transformation also leads to a significant reduction in the molecular conformational flexibility thus simplifying the conformational analysis required by the computational treatment. The method described herein thus allows the absolute configuration assignment to these challenging substrates to be much easier and reliable.

New bioactive cyclopeptide alkaloids with rare terminal unit from the root bark of Ziziphus cambodiana

Six new 14-membered ring cyclopeptide alkaloids, cambodines A–F (1–6), and two known compounds, frangufoline (7) and lotusanine B (8), were isolated from the root bark extract of Ziziphus cambodiana Pierre. Their structures and configurations were established based on 1D and 2D NMR, HRMS, ECD, and X-ray crystallographic data. Compounds 1 and 3 are rare 5(14)-type cyclopeptide alkaloids that possess an imidazolidin-4-one ring in the terminal unit. The cyclopeptides were tested for their in vitro antiplasmodial, antitubercular, and cytotoxic effects against three cancer cell lines. Compound 3 showed significant antiplasmodial activity against the malarial parasite Plasmodium falciparum, with an IC₅₀ value of 6.09 μM.

Six new 14-membered ring cyclopeptide alkaloids, cambodines A–F (1–6), and two known compounds, frangufoline (7) and lotusanine B (8), were isolated from the root bark extract of Ziziphus cambodiana Pierre.

Antibacterial Indole Alkaloids with Complex Heterocycles from Voacanga africana

Voacafricines A and B, two unique monoterpenoid indole alkaloids each bearing five fused heterocycles, were obtained from the fruits of Voacanga africana. Their structures were elucidated by extensive spectroscopic methods and computational studies. A plausible biogenetic pathway was proposed from a common precursor, 19- epi-voacristine. Both compounds exhibited potent activity against Staphylococcus aureus and Salmonella typhi, and their activities were superior to those of the well-known antibacterial drugs berberine and fibrauretine.

Beyond optical rotation: what's left is not always right in total synthesis

This work describes the application of vibrational (VCD) and electronic (ECD) circular dichroism spectroscopy to solve the longstanding debate around the absolute configuration of (+)-frondosin B (1). The absolute configuration of (+)-1 could confidently be assigned as (R) using these spectroscopic techniques. The discrepancy in the optical rotation (OR) values obtained in previous studies can be attributed to an undetected minor impurity (ca. 7%) that arose unexpectedly in a key step late in the synthesis. Additionally, the conditions used in the final step of the previous reports for demethylation to form the natural product proceeded with significant loss of enantiopurity. The large OR measured for the impurity at its observed level, when compared to the small rotation for the less enantiopure natural product 1, led to a measured OR value for the synthetic material that had the opposite sign of the natural product.

Diastereo- and enantioselective construction of biologically important pyrrolo[1,2-a]indole scaffolds via catalytic asymmetric [3 + 2] cyclodimerizations of 3-alkyl-2-vinylindoles

A catalytic asymmetric [3 + 2] cyclodimerization of 3-alkyl-2-vinylindoles has been established, which efficiently constructed a pyrrolo[1,2-a]indole scaffold in a diastereo- and enantioselective fashion.

Antifungal Monoterpene Derivatives from the Plant Endophytic Fungus Pestalotiopsis foedan

A new monoterpene lactone, (1R,4R,5R,8S)-8-hydroxy-4,8-dimethyl-2-oxabicyclo[3.3.1]nonan-3-one (1), along with one related known compound, (2R)-2-[(1R)-4-methylcyclohex-3-en-1-yl]propanoic acid (2), were isolated from the liquid culture of the plant endophytic fungus Pestalotiopsis foedan obtained from the branch of Bruguiera sexangula. The structure and absolute configuration of 1 were determined on the basis of extensive analysis of NMR spectra combined with computational methods via calculation of the optical rotation (OR) and ¹³ C-NMR. Both compounds exhibited strong antifungal activities against Botrytis cinerea and Phytophthora nicotianae with MIC values of 3.1 and 6.3 μg/ml, respectively, which are comparable to those of the known antifungal drug ketoconazole. Compound 2 also showed modest antifungal activity against Candida albicans with a MIC value of 50 μg/ml.

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.

Reinvestigation of the stereochemistry of the C-glycosidic ellagitannins, vescalagin and castalagin

The stereochemistry of the C-glycosidic ellagitannins, vescalagin and castalagin, has been reinvestigated using computational methods. DFT calculations of their (1)H and (13)C NMR spectra, as well as TDDFT calculations of the ECD spectra of their des-hexahydroxydiphenoyl analogues, revealed that the structure of the triphenoyl moiety of vescalagin and castalagin should be revised.

Peniphenones A-D from the mangrove fungus Penicillium dipodomyicola HN4-3A as inhibitors of Mycobacterium tuberculosis phosphatase MptpB

A pair of unusual benzannulated 6,6-spiroketal enantiomers [(-)-1 and (+)-1] and three new biogenetically related compounds (2-4), together with two known related analogues (5 and 6), have been isolated from a mangrove fungus, Penicillium dipodomyicola HN4-3A. Their structures were elucidated on the basis of spectroscopic analysis (1D and 2D NMR data) and X-ray crystallography. The absolute configurations of enantiomers (-)-1 and (+)-1 were determined using quantum chemical calculations of the electronic circular dichroic (ECD) spectra. Compounds 2 and 3 exhibited strong inhibitory activity against Mycobacterium tuberculosis protein tyrosine phosphatase B (MptpB) with IC50 values of 0.16±0.02 and 1.37±0.05 μM, respectively.

Xylariterpenoids A–D, four new sesquiterpenoids from the Xylariaceae fungus

Four new sesquiterpenoids, sesquiterpenoids A–D (1–4), were isolated from solid cultures of the Xylariaceae fungus (no. 63-19-7-3).

Determination of the absolute configuration of natural products

Structural elucidation of natural products is always one of the most important tasks for natural product researchers in related fields. Particularly, the absolute configuration (AC), being a great challenge for natural product chemists, has attracted much attention. During the past few decades, many techniques and approaches have been developed to determine the AC of natural products, including direct (or absolute) methods, e.g. X-ray diffraction (XRD), electronic and vibrational circular dichroism (ECD and VCD), and Raman optical activity (ROA), as well as indirect (or relative) methods using a reference or a derivatizing agent with known AC, e.g. CD with empirical rules and nuclear magnetic resonance (NMR) utilizing anisotropic effects of chiral derivatizing agents. However, none of the currently applied techniques is capable of dominating AC determination, since they each have their respective limitations corresponding to the different structural features. This mini review summarizes most of the techniques and methods which are commonly used in AC assignment of natural products, or have potential application prospects, and briefly describes their principles, advantages and limitations.

Three pairs of variecolortide enantiomers from Eurotium sp. with caspase-3 inhibitory activity

7-O-methylvariecolortide A (1), variecolortide B (2), and variecolortide C (3), the rare variecolortides existing in racemic manner, were isolated from an endolichenic fungal strain Eurotium sp. (No. 17-11-8-1). With the chiral HPLC technology, (-)-(S)-7-O-methylvariecolortide A (1a), (+)-(R)-7-O-methylvariecolortide A (1b), (-)-(S)-variecolortide B (2a), (+)-(R)-variecolortide B (2b), (-)-(S)-variecolortide C (3a), and (+)-(R)-variecolortide C (3b) were successfully separated and obtained. Their absolute configurations were firstly assigned by ECD experiment and ECD calculation. According to the relation of isolated compounds, a plausible biosynthetic pathway for variecolortides was proposed. In caspase-3 enzymatic assay, compounds 1-3 showed inhibitory activity, with IC50 values of 1.7, 0.8 and 15.7 μM, respectively.

Transition polarizability model of induced resonance Raman optical activity

Induced resonance Raman optical activity (IRROA) proved to be a very sensitive method to detect molecular chirality. It is exhibited, for example, by complexes of lanthanides with chiral alcohols or ketones. So far, the phenomenon has not been understood at a quantitative level. To elucidate its mechanisms and to correctly relate the spectra to the structure, a transition polarizability model (TPM) is developed and applied to a camphor-europium complex. The model well reproduces the high ROA/Raman intensity ratio of the IRROA observed experimentally. The results additionally indicate a fundamental role of the nonchiral fod ligand in the Eu(fod)3 compound for the chirality enhancement. The TPM model thus serves as a guidance for both experimental and theoretical studies to come.

Determination of absolute configuration and conformation of a cyclic dipeptide by NMR and chiral spectroscopic methods

Increasing precision of contemporary computational methods makes spectroscopies such as vibrational (VCD) and electronic (ECD) circular dichroism attractive for determination of absolute configurations (AC) of organic compounds. This is, however, difficult for polar, flexible molecules with multiple chiral centers. Typically, a combination of several methods provides the best picture of molecular behavior. As a test case, all possible stereoisomers with known AC (RS, SR, SS, and RR) of the cyclic dipeptide cyclo(Arg-Trp) (CAT) were synthesized, and the performances of the ECD, infrared (IR), VCD, Raman, Raman optical activity (ROA), and nuclear magnetic resonance (NMR) techniques for AC determination were investigated. The spectra were interpreted with the aid of density functional theory (DFT) calculations. Folded geometries stabilized by van der Waals and electrostatic interactions between the diketopiperazine (DKP) ring and the indole group are predicted to be preferred for CAT, with more pronounced folding due to Arg-Trp stacking in the case of SS/RR-CAT. The RS/SR isomers prefer a twist-boat puckering of the DKP ring, which is relatively independent of the orientation of the side chains. Calculated conformer-averaged VCD and ECD spectra explain most of the experimentally observed bands and allow for AC determination of the tryptophan side-chain, whereas the stereochemical configuration of the arginine side-chain is visible only in VCD. NMR studies provide characteristic long-range (2)J(C,H) and (3)J(C,H) coupling constants, and nuclear Overhauser effect (NOE) correlations, which in combination with either ECD or VCD also allow for complete AC determination of CAT.

Sesquiterpenoids from Incarvillea arguta: absolute configuration and biological evaluation

Diincarvilones A-D (1-4), incarvilone A (5), and a known compound, argutosine B (6), were isolated from Incarvillea arguta. The structures, including the absolute configurations of the new compounds, were determined by NMR spectroscopy, X-ray diffraction analysis, CD spectroscopy, and a variety of computational methods. The biological properties of these substances, including effects on intracellular Ca(2+) influx, nitric oxide (NO) production, and human cancer cells, were evaluated. The results showed that at the concentration of 10 μM (in HBSS buffer) diincarvilones A and B cause a persistent increase in cytoplasmic calcium levels in A549 cells.